Geographical genetics and the conservation of forest trees

Marco  Pautasso

Trees are key ecosystem engineers. Many analyses of the genetic diversity of forest trees over substantial parts of their distributional ranges are appearing. These studies are of relevance for forest and landscape management, the inventory of botanical genetic resources and the conservation biology of rare, endemic, relictual, and endangered tree species. This review focuses on (i) recent investigations of the influence of human disturbances, (ii) comparative analyses of closely related and hybridizing species, (iii) reconstructions of refugia and of the spread of tree populations during the postglacial, (iv) studies of both range-wide and range-edge genetic patterns, and (v) assessments of the role of tree genetic diversity in the face of future climate warming. There is a need to include more tropical and austral trees in genetic analyses, as most studies have dealt with the relatively species-poor Palaearctic and Nearctic regions. Further studies are also needed on the role of tree genetic diversity in variations in phenology, resistance to insect defoliators and fungal pathogens, reactions to increased CO2 and ozone concentrations, growth, mortality rates and other traits. Most macroecological and scaling patterns of species richness still need to be studied for genetic diversity. Open research questions in this rapidly evolving field involve invasion biology, island biogeography, and urban ecology. There is a need for more knowledge transfer from the many studies of tree genetic diversity to the day-to-day management of trees and forests.

ARTICLE IN PRESS Perspectives in Plant Ecology, Evolution and Systematics Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 www.elsevier.de/ppees Geographical genetics and the conservation of forest trees Marco Pautasso Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK Received 28 May 2008; received in revised form 7 November 2008; accepted 23 January 2009 Abstract Trees are key ecosystem engineers. Many analyses of the genetic diversity of forest trees over substantial parts of their distributional ranges are appearing. These studies are of relevance for forest and landscape management, the inventory of botanical genetic resources and the conservation biology of rare, endemic, relictual, and endangered tree species. This review focuses on (i) recent investigations of the inﬂuence of human disturbances, (ii) comparative analyses of closely related and hybridizing species, (iii) reconstructions of refugia and of the spread of tree populations during the postglacial, (iv) studies of both range-wide and range-edge genetic patterns, and (v) assessments of the role of tree genetic diversity in the face of future climate warming. There is a need to include more tropical and austral trees in genetic analyses, as most studies have dealt with the relatively species-poor Palaearctic and Nearctic regions. Further studies are also needed on the role of tree genetic diversity in variations in phenology, resistance to insect defoliators and fungal pathogens, reactions to increased CO2 and ozone concentrations, growth, mortality rates and other traits. Most macroecological and scaling patterns of species richness still need to be studied for genetic diversity. Open research questions in this rapidly evolving ﬁeld involve invasion biology, island biogeography, and urban ecology. There is a need for more knowledge transfer from the many studies of tree genetic diversity to the day-to-day management of trees and forests. r 2009 Rübel Foundation, ETH Zürich. Published by Elsevier GmbH. All rights reserved. Keywords: Dendrology; Evolutionary history; Global change; Isolation by distance; Plant biodiversity; Scale extent and grain Contents Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Inﬂuences of forest management/exploitation . . . . . . Inﬂuence of fragmentation . . . . . . . . . . . . . . . . . . . Rare, endemic, relictual, and threatened tree species . Comparative analyses of related tree species. . . . . . . Tracking tree species spread and divergence . . . . . . . Range-wide vs. range-edge studies. . . . . . . . . . . . . . Climate change and gene conservation in trees . . . . . Conclusions and future directions . . . . . . . . . . . . . . Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tel.: +44 20 759 42533. E-mail address: m.pautasso@ic.ac.uk. 1433-8319/$ - see front matter r 2009 Rübel Foundation, ETH Zürich. Published by Elsevier GmbH. All rights reserved. doi:10.1016/j.ppees.2009.01.003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158 159 160 162 163 165 167 169 171 173 173 ARTICLE IN PRESS 158 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Introduction Trees are living constituents of many terrestrial and coastal ecosystems, from impenetrable rain forests to open woodlands, from mangrove to riparian, lowland, and subalpine forests. They are characterized by great size and longevity, as well as by high reproductive output and recruit mortality (Petit and Hampe, 2006). Woody species such as trees are ecosystem engineers and landscape modulators as they create resource niches and patches for a whole suite of other organisms dependent on the development, structural support, decay, and renewal of trees (e.g. Wright and Jones, 2006; Lonsdale et al., 2008; Shachak et al., 2008). The spatial variation in tree genetic diversity, in turn, determines the adaptability of tree populations to environmental change and is thus essential for the long-term sustainability of forest ecosystems (e.g. Giannini et al., 1991; Rehfeldt et al., 2002; Bilgen and Kaya, 2007; Savolainen et al., 2007). The importance of the conservation of tree genetic diversity has been long recognized (e.g. Ledig, 1992; Kremer, 1994; Müller-Starck, 1995b; Geburek, 1997; Rajora and Mosseler, 2001; Wang and Szmidt, 2001), but only recently have tools to characterise DNA variation of these long-lived species across increasing parts of their distributional ranges become widely used. For example, the genetic variation of different oak species has been investigated in the USA (e.g. Manos and Fairbrothers, 1987; Schnabel and Hamrick, 1990; Howard et al., 1997; Williams et al., 2001; Craft et al., 2002) and in Western and Northern Europe for many Table 1. years now (e.g. Aas, 1993; Petit et al., 1993a, b, 1997, 2002a, b, 2004b; Zanetto and Kremer, 1995; Aas et al., 1997; Ferris et al., 1998; Manos et al., 1999; Muir et al., 2000; König et al., 2002; Kremer et al., 2002b; Deguilloux et al., 2004), but only recently have such comparative analyses been extended to oaks of other regions (e.g. Croatia: Franjic et al., 2006; Israel (and Jordan): Schiller et al., 2003, 2004, 2006; Japan: Okaura et al., 2007; Korea: Chung and Chung, 2004; Mexico: Alfonso-Corrado et al., 2004; Poland: Dering et al., 2008; Romania: Curtu et al., 2007a,b ; the Russian Far East: Potenko et al., 2007; Slovakia: Gömöry and Schmidtová, 2007; Taiwan: Shih et al., 2006). The spread of molecular tools to researchers throughout the world has resulted in an increasing number of studies on the genetic variation of trees. A number of reviews of this and related topics have appeared (Table 1), but new studies are accumulating and there is thus a need for an update. For deﬁnitions of key terms such as genetic diversity and the different methods to measure it, the reader is referred, e.g., to Newton et al. (1999), Manel et al. (2003), and González-Martı́nez et al. (2006). This review underlines the relevance of recent genetic analyses of tree diversity for forest and landscape management (Perry, 1998; Sork and Smouse, 2006; Lexer et al., 2007), for the sustainability of botanical genetic resources (Hamrick et al., 2006; Hosius et al., 2006; Geburek and Konrad, 2008; Newton, 2008) and for the conservation of biodiversity in the face of future climate warming (Botkin et al., 2007; Pertoldi et al., 2007; Reusch and Wood, 2007). The focus is on selected genetic studies of natural vs. Selected recent reviews related to the genetic diversity of plant and trees. Main focus Main region Reference Climate change Postglacial history Postglacial history Postglacial history, seed and pollen ﬂow, hybridization Molecular phylogeography and conservation Sustainable forest management Inbreeding and genetic diversity Postglacial history Tree invasions Oak hybridizations Chloroplast, mitochondrial and nuclear diversity Silvicultural regimes Global environmental change Habitat loss and degradation Genomics and adaptive evolution Comparative phylogeography Genetic landscape connectivity Gene ﬂow and local adaptation Forest fragmentation Past climatic changes Tropics North America, Europe, Japan Europe Europe, Japan Worldwide Switzerland – Europe Worldwide Europe Worldwide Worldwide North and Central America, Europe Neotropics Worldwide Eastern North America Worldwide Worldwide Worldwide Worldwide Bawa and Dayanandan (1998) Comes and Kadereit (1998) Taberlet et al. (1998) Ennos et al. (1999) Newton et al. (1999) Finkeldey (2001) Charlesworth (2003) Petit et al. (2003) Petit et al. (2004a) Petit et al. (2004b) Petit et al. (2005) Finkeldey and Ziehe (2004) Hamrick (2004) Lowe et al. (2005) González-Martı́nez et al. (2006) Soltis et al. (2006) Sork and Smouse (2006) Savolainen et al. (2007) Kramer et al. (2008a) Petit et al. (2008) ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 managed/exploited tree populations, (2) the effects of forest fragmentation, and (3) rare, endemic, relictual, and threatened species. The review moves then on to discuss (4) comparative analyses of closely related and hybridizing species, (5) reconstructions of refugia and of the spread of tree populations during the last postglacial, and (6) studies investigating genetic diversity throughout the distributional range of tree species but also at the margin of their range. Preliminary conclusions involve (7) the relevance of these studies for efforts to safeguard tree species from global change and (8) open research questions in this rapidly developing research area. Influences of forest management/exploitation Human inﬂuences on the environment are now pervasive (e.g. Rosen and Dincer, 1997; Lubchenco 1998; Fenberg and Roy, 2008) and thus deserve to be treated from the very beginning of this review. Studies of tree genetic diversity can provide evidence for the longterm inﬂuence of forest management and/or exploitation on tree populations (e.g. Ledig, 1992; Bradshaw, 2004; Lefèvre, 2004). Much recent evidence of post-logging loss of tree genetic diversity has been obtained for tropical species. Examples include Swietenia macrophylla (André et al., 2008) and Hymenaea courbaril (de Lacerda et al., 2008) in the Brazilian Amazon, Prunus africana in the Kakamega forest, Kenya (Farwig et al., 2008) and Scaphium macropodum in Malaysia (Lee et al., 2002). Some studies fail to report signiﬁcant genetic effects of selective logging of tropical tree species (e.g. Cespedes et al., 2003 (Swietenia macrophylla); Cloutier et al., 2007 (Carapa guianensis); Silva et al., 2008 (Bagassa guianensis)). However, modelling suggests that, over a sufﬁciently long term, logging scenarios are likely to result in loss of alleles and genotypes for many tropical tree species currently harvested (Lowe et al., 2005; Degen et al., 2006; Sebbenn et al., 2008). For extra-tropical forests, evidence of the genetic impacts of forest management is mixed (Schaberg et al., 2008). Impacts on Eucalyptus consideniana and Eucalyptus sieberi in Victoria, Australia, vary with the regeneration system and the DNA marker used for E. consideniana and with the measure of genetic diversity for E. sieberi (Glaubitz et al., 2003a, b). No signiﬁcant differences are found in Europe for allelic richness, number of rare alleles and heterozygosity in managed and relatively little managed stands of Fagus sylvatica (Buiteveld et al., 2007; but see Starke, 1993). A similar result is obtained for coppice vs. open woodland of Quercus pyrenaica in Central Spain (Valbuena-Carabaña et al., 2008; but see Mattioni et al., 2008 for the role of management on shaping genetic diversity of Castanea sativa throughout Europe). A reduction in genetic 159 diversity with management is reported for Tsuga heterophylla but not for Abies amabilis in coastal montane forests of Western North America (El-Kassaby et al., 2003). No signiﬁcant differences in size of clones of Populus tremula are established between old-growth and managed forests in Finland (Suvanto and LatvaKarjanmaa, 2005) and no signiﬁcant differences in the mean proportion of polymorphic fragments and estimated heterozygosity are recovered for Pinus brutia in the Mediterranean region of Turkey (Lise et al., 2007). Given the notorious publication bias against negative results, this evidence against genetic effects of forest management is paradoxical. However, there is also some clear evidence for temperate tree species that harvesting can lead to reduction in genetic diversity. In two old-growth eastern white pine (Pinus strobus) stands in Ontario, reduction in the number of trees by 75% leads to a reduction in the total and mean number of alleles by 25%, a loss which predominantly affects rare alleles (Rajora et al., 2000). An old-growth stand of the same species in Wisconsin shows a stronger spatial genetic structure than other ﬁve sites with different forest management strategies (Marquardt et al., 2007). A reduction in allelic richness is observed in a logged vs. old-growth forest of Acer saccharum in the Great Smoky Mountains, USA (Baucom et al., 2005), in one logged vs. four un-logged stand(s) of Quercus tiaoloshanica on Hainan Island, China (Zheng et al., 2005), and in ﬁve plantations of Quercus rubra compared to ﬁve old-growth populations in Southern New England, USA (Gerwein and Kesseli, 2006). In the latter study, the size of the old-growth stands is positively correlated with the levels of genetic diversity. In the strongly fragmented Scottish landscape, larger woodland remnants of Fraxinus excelsior are mainly pollen donors, whilst smaller remnants are mainly pollen recipients (Bacles and Ennos, 2008). Similarly, genetic diversity is found to be positively correlated with the size of fragmented populations of Quercus robur in Finland (Vakkari et al., 2006). But populations in smaller fragments have a higher differentiation amongst them than that among large populations. As opposed to the ﬁndings for Quercus spp. in Finland and New England, in 26 Swiss populations of Sorbus torminalis molecular variance (assessed with biparentally and maternally inherited markers) is not correlated with population size (Angelone et al., 2007). This could be explained by relatively recent (during the last century) fragmentation of the different stands, so that the deleterious effects of isolation following the darkening of Swiss forests have not yet had the time to affect the genetic diversity of this pioneer tree species (Fig. 1). However, there is evidence for isolation by distance in 22 populations of S. torminalis in a study of a neighbouring region of comparable size in ARTICLE IN PRESS 160 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Fig. 1. Geographical distribution of 10 cpDNA haplotypes identiﬁed in Swiss Sorbus torminalis populations (from Angelone et al., 2007). Shading of the small pie charts corresponds to haplotype proportions within populations, whereas the shading of the large pie chart gives the relative frequencies of haplotypes across all populations. With kind permission of Wiley–Blackwell. North-Western Italy (Belletti et al., 2008). The implication for forest management of these studies is that rare populations of such light-demanding tree species need to be connected by landscape corridors (Hoebee et al., 2007), as already naturally happens for English yew (Taxus baccata), in Northern Switzerland, where a combination of wind-borne pollen and occasional long-distance seed dispersal avoids isolation by distance (Hilﬁker et al., 2004). A different policy suggestion comes from a study of Prunus avium in two ancient woodlands in Kent, Britain, with different management regimes. As for Sorbus and Taxus, seeds of P. avium are dispersed by birds. The relatively high levels of genetic diversity observed in the non-managed stand lead to a ‘do-nothing’ recommendation, especially following winter storms, which appear to enable the co-existence of different clonal groups under a disrupted canopy layer (Vaughan et al., 2007). Similar conclusions can be drawn from a long-term study of the effects of thinning on the genetic structure of a Tsuga canadensis forest in Maine, USA (Hawley et al., 2005). Removal of ‘inferior’ phenotypes, a long tradition also in Europe, results in the loss of rare alleles, which could diminish the potential of populations to withstand environmental change. Influence of fragmentation In some cases, mixed results of studies on the impacts of logging may be due to the similarity in the patches suitable for regeneration in logged and naturally regenerated forests (Oddou-Muratorio et al., 2004; Ally and Ritland, 2007). In other cases, absences of genetic differences can be due to the absence of a perfect control, as most woods, not only in Europe, are not entirely pristine and there is a long history of human interventions (e.g. Cottrell et al., 2003). This issue may apply also to habitat fragmentation, whose detrimental inﬂuence is often invoked to explain loss of genetic diversity. Habitat fragmentation ultimately affects genetic diversity due to the alteration in the landscape features, which in turn leads to reduced gene dispersal (Hanaoka et al., 2007; Born et al., 2008a; OddouMuratorio and Klein, 2008). Loss of genetic variation through random genetic drift and increased selﬁng can then cause the local extinction of small populations (Honnay and Jacquemyn, 2007). However, this is still a contentious issue. In some cases, small population size may be a consequence of evolutionary processes (e.g. apomixis in Sorbus; e.g. Robertson et al., 2004), may be due to a naturally patchy woodland habitat (e.g. for Euclea schimperi in monsoonal fog oases in Southern Arabia; Meister et al., 2007), or may lead to evolutionary adaptations (e.g. Cupressus dupreziana; Pichot et al., 2008). Population extinction can theoretically be directly caused by genetic drift and the associated loss of genetic diversity, but in many cases genetic drift might lag behind demography. Whether demographic processes or genetic effects are more likely to cause the (regional) extinction of tree species would need more attention. There are many examples of tree species showing genetic depauperation as a consequence of habitat fragmentation and/or exploitation. Cedrus libani populations from Lebanon show severe cases of genetic drift, and this is thought to be a consequence of the long periods of intense exploitation and population ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 fragmentation (Fady et al., 2008). The low genetic variability of some populations of Pilgerodendron uviferum, an endemic conifer of Southern Chile and Argentina, is probably related to the history of human exploitation (Allnutt et al., 2003). Similarly, for Picea asperata in Sichuan and Gansu, China, high levels of genetic differentiation amongst tree populations, which suggest restricted gene ﬂow, could be explained by habitat fragmentation caused by human land-use (Wang et al., 2005). A similar explanation of the high genetic differentiation among populations (low levels of gene ﬂow possibly due to the isolation following human fragmentation) may apply to Lumnitzera littorea, an endangered mangrove species found in tropical Asia and Australia (Su et al., 2007). As is the case for logging, some indicators may not be signiﬁcantly different in continuous vs. fragmented forest plots (e.g. the number of alleles per hectare in the tropical tree Symphonia globulifera), but other measures may be different (e.g. inbreeding in the same species; Aldrich et al., 1998). A similar result is reported for Samanea saman in dry forests of Costa Rica (Cascante et al., 2002), whilst the opposite (lower allelic richness but same levels of inbreeding in an isolated fragment vs. contiguous forest) is documented for Carapa guianensis (Dayanandan et al., 1999). In some cases, as with Syzygium nervosum in Australian rain forests, high levels of homozygosity and the absence of a correlation of forest patch size with genetic diversity may be explained by self-compatibility, i.e. by the lack of negative effects of inbreeding depression (Shapcott, 1998). Similar levels of genetic diversity in fragmented vs. non-fragmented populations may be explained by differences in the scale of sampling for the two populations (as suggested for Sorbus aucuparia in fragments in Scotland vs. continuous forests in Europe; Bacles et al., 2004). An additional confounding factor can be the nature of the landscape matrix and the amount of scattered forest remnants in proximity to fragmented populations (as pointed out in a study of Terminalia amazonia in Belize; Pither et al., 2003). There is also an issue in the temporal scale of studies: inbreeding effects may be immediate, but it may take a few generations for the impacts of forest fragmentation on tree genetic diversity to become manifest (Pye and Gadek, 2004; Lowe et al., 2005; Mathiasen et al., 2007; Williams et al., 2007). A similar lag between pattern and process can be obtained by sampling adult trees in forest fragments: the samples may still represent a formerly contiguous population without signs of subpopulation structure. Given that fragmentation is concurrent with the loss of subpopulations, its genetic effects may be difﬁcult to distinguish from those of sheer habitat loss (as pointed out in a study of the endangered tree species Manilkara huberi in the Amazon; Azevedo et al., 2007; see also 161 Yaacobi et al., 2007). Small fragments may show (i) a lower within-population genetic diversity (e.g. in Caesalpinia echinata in coastal Brazil; Cardoso et al., 2005), (ii) a lower allelic richness (e.g. in Pithecellobium elegans in coastal Costa Rica (Hall et al., 1996), in Quercus humboldtii in montane Colombia (Fernández and Sork, 2007), as well as in Myricaria floribunda in the Atlantic forests of Brazil (Franceschinelli et al., 2007)), or (iii) a loss of low-frequency alleles (e.g. in Swietenia humilis in Honduras; White et al., 1999) but this can be expected from the positive relationship between genetic diversity and area (Zhou et al., 2008). In spite of all these methodological problems, tropical trees are particularly threatened by forest fragmentation because of their generally higher rarity, i.e. lower density, than extra-tropical tree species. In Bursera simaruba, in Puerto Rico, population size of fragments rather than isolation distance seems to limit recruitment (Dunphy and Hamrick, 2007). For Dipteryx panamensis in Costa Rica, increasingly isolated trees show less frequent pollen dispersal (Hanson et al., 2008). Pollen dispersal between fragments, particularly in the case of wind-pollinated trees, can contribute in lessening the genetic impacts of fragmentation. A study of Araucaria angustifolia in two forest fragments nearly 2 km from each other in Southern Brazil reports restricted seed dispersal but effective pollen ﬂow between the two populations (Bittencourt and Sebbenn, 2007). In some cases, however, it does not seem to be pollen ﬂow which maintains genetic diversity, but random mating of a high proportion of the local parent trees, as suggested for the pioneer tree Aucoumea klaineana in Central Africa (Born et al., 2008b). There is also evidence of the genetic effects of fragmentation for extra-tropical species. Although the genetic diversities of adult trees of a fragmented vs. continuous population of Magnolia obovata in Japan do not differ, the saplings of the former have signiﬁcantly lower genetic diversity than the saplings of the latter and than the adult trees of both (Isagi et al., 2007). Further work is needed to know whether these preliminary results are conﬁrmed using replicate treatments. In spite of the wind pollination, the regeneration of Fagus sylvatica is surprisingly found to suffer from genetic bottlenecks in fragmented stands compared to continuous, old-growth forests in Catalonia, Spain (Jump and Peñuelas, 2006). Signiﬁcant population differentiation, a symptom of restricted gene ﬂow, is also pointed out for the wind-pollinated tree-like shrub Juniperus communis at the larger scale of Ireland (Provan et al., 2008). That woodland fragmentation may result in non-random mating of tree populations is also suggested in Ireland by a country-wide study of Quercus petraea and Q. robur using morphological and molecular analyses (Kelleher et al., 2005). Absence of genetic differences between Quercus crispula trees in a semi-fragmented vs. a ARTICLE IN PRESS 162 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 neighbouring forest in the Chichibu Mountains, Japan, may be due to the partial fragmentation of the study system (Ohsawa et al., 2006). In a landscape fragmented by agriculture in Ontario, in spite of a higher selﬁng rate in medium vs. large fragments of Picea glauca, there are no signiﬁcant differences in the genetic diversity of the seeds compared to the parent population (O’Connell et al., 2006). These examples show that habitat fragmentation is not only posing a threat to tree species because it will make more difﬁcult migration to track climate change, but also because it has negatively affected their genetic diversity, i.e. the intrinsic capacity of tree species to respond to new environmental conditions. From the point of view of tree species and their genetic diversity, it is thus more than important to maintain landscape connectivity by preserving and creating woodland corridors. This is true also for tropical landscapes (Vieira and de Carvalho, 2008). Rare, endemic, relictual, and threatened tree species Genetic analyses of remnant forest fragments are particularly important for rare, endemic, relictual, and threatened tree species. Many threatened tree species are located in the (sub)tropics, and there are thus several studies from those latitudes. Recurring issues involving this kind of tree species are human disturbance and the need to preserve the structure of the regional gene pool, the interactions between overexploitation, habitat deterioration and low levels of diversity, and the question of whether population decline is due to genetic depauperation or to demographic processes only. In South America, remnant populations in the Brazilian Atlantic forest of Dalbergia nigra, an endangered tree which has been intensely exploited for centuries, have relatively high diversity, which does not correlate with fragment size but is inﬂuenced negatively by the degree of human disturbance (Ribeiro et al., 2005). In the same region, ﬁve remnants of the endangered C. echinata show a correlation of genetic and geographic distance (Cardoso et al., 1998). The implication for managers is that population separation and thus the regional gene pools need to be maintained. Similar ﬁndings and recommendations for conservation are given in a study in Central Brazil of the endangered dioecious Myracrodruon urundeuva (Reis and Grattapaglia, 2004). In the Peruvian Amazon, high genetic diversity is observed in nine Cedrela odorata populations, a species threatened by unsustainable logging and deforestation, thus suggesting the need to preserve tree populations in each of the major watersheds (de la Torre et al., 2008). In Costa Rica, two ecotypes of C. odorata are identiﬁed, with higher diversity in populations from dry forests compared to those in wet regions (Cavers et al., 2003a). In the same country, the dry forest endemic Lonchocarpus costaricensis shows range-wide and local spatial genetic structure in cpDNA and AFLP diversity, respectively, suggesting that the extreme fragmentation has not yet affected the genetic diversity of the species (Navarro et al., 2005). In Guatemala and Southern Mexico, genetic analysis of the threatened Pinus chiapensis suggests a high degree of differentiation amongst populations, which implies that populations throughout the range should be preserved (Newton et al., 2002). In Eastern Mexico, the only three extant populations of the narrow endemic Antirhea aromatica display high genetic variability and are thus all irreplaceable (González-Astorga and Castillo-Campos, 2004). Similar ﬁndings and conclusions are drawn from a study of the three remaining populations of the arborescent cycad Dioon angustifolium in North-Eastern Mexico (González-Astorga et al., 2005). In the Hawaiian Islands, two rare and declining endemic species (Colubrina oppositifolia and Alphitonia ponderosa) have genetic diversity levels which are thought to be similar to those previous to disturbance (habitat destruction and competition of invasive species), but the lack of recruitment makes these species of conservation concern (Kwon and Morden, 2002). In New Caledonia, a hotspot of endemic conifer species with high levels of habitat destruction, evidence for inbreeding and loss of rare alleles is found in the juvenile cohort of the endangered Araucaria nemorosa but not in the adult cohort of the same species and in both cohorts of the common and widespread Araucaria columnaris (Kettle et al., 2007). In four sites in Yunnan, China, and a remaining site in Thailand, Trigonobalanus doichangensis is threatened by habitat deterioration and low levels of genetic diversity (Sun et al., 2006b). In Yunnan, similar low levels of genetic diversity are found for Pinus squamata, one of the most endangered conifers in the world, possibly a consequence of strong bottlenecks during the evolutionary history and of current unsustainable logging (Zhang et al., 2005). In Africa, Benin, the genetic diversity of Adansonia digitata in different regions correlates with morphological features such as tree height and number of main branches (Assogbadjo et al., 2006). A study of the endangered medicinal species Prunus africana in various African mountains documents signiﬁcant genetic variation within Cameroon and Madagascar, thus suggesting that in these cases conservation should take into account differences amongst populations at the national level (Dawson and Powell, 1999). In Ethiopia, a genetic study of 12 populations of the endangered dioecious Hagenia abyssinica suggests that human disturbance has not yet had the time to affect genetic parameters; the study also ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 identiﬁes sites suitable for conservation (Feyissa et al., 2007). In Madagascar, populations at ﬁve locations of the critically endangered palm Beccariophoenix madagascariensis reveal considerable within-population genetic diversity in spite of the small size of the populations, suggesting that inbreeding has not yet jeopardized reproductive viability (Shapcott et al., 2007). Many extra-tropical studies of endemic/endangered trees have dealt with species of the genus Abies. In South China, both current genetic drift due to small populations and the range contraction and fragmentation during the glaciations may have contributed to the current low levels of genetic variation in the highly endangered, endemic Abies ziyuanensis, which is restricted to island-like mountains (Tang et al., 2008). In the Santa Lucia Mountains, California, Abies bracteata similarly shows absence of correlation between genetic and geographic distance, but has a low differentiation in spite of the fragmented range (Ledig et al., 2006). In Sicily, Italy, the narrow endemic Abies nebrodensis is restricted to a single population of 30 adult individuals, but these and the juveniles present considerable levels of genetic variation, with no correlation with physical distance (Conte et al., 2004). Whether the low levels of genetic variation in Abies alba might have been related to the species decline observed in Europe in the 1980s is a question posed, e.g., by Bergmann et al. (1990). Decline of a tree species, and its associated lack of recruitment and absence of small size classes, can lead to a negative feedback due to the self-reinforcing genetic bottleneck (e.g. Aldrich et al., 2005; Hirayama et al., 2007). The implication for conservation is again that meta-population structure needs to be preserved so as to ensure genetic ﬂow between subpopulations, as pointed out, e.g., for the threatened endemic Magnolia stellata in Japan (Ueno et al., 2005; Setsuko et al., 2007) and for Taxus baccata in Switzerland (Hilﬁker et al., 2004). Population decline is a particular problem for endemic species with a restricted range, such as Quercus lobata in California, where habitat loss is unfortunately concurrent with areas of distinctive genetic history (Grivet et al., 2008). But population decline can also be troublesome for widespread species. For example, in spite of the partial resistance to chestnut blight, the widespread distributional range and the high levels of genetic diversity, Castanea pumila is deemed to be an endangered species (Fu and Dane, 2003). Also C. sequinii, a widespread yet endemic tree species in China (Ying et al., 2007), and Changiostyrax dolichocarpa, a once widespread but now critically endangered tree in central China (Yao et al., 2007), need a conservation plan for their genetic resources. Such plans are made easier when endemic, endangered tree species still have high levels of genetic diversity, as happens, e.g., for Nothofagus alessandrii in central Chile 163 (Torres-Dı́az et al., 2007), but are urgent when such threatened species combine a restricted range with a low genetic variability, as is the case, e.g., for Dendropanax morbifera in Korea (Kim et al., 2006). Other endangered species which show contrasting patterns of genetic diversity and geographical distribution are Picea omorika in Serbia, a relictual, highly restricted and genetically depauperate endemic (Nasri et al., 2008), Araucaria araucana in Southern South America, with a larger geographic range and higher genetic diversity but of concern due to the current human pressure (Bekessy et al., 2002), and Wollemia nobilis, the recently discovered relict in South Australia, previously only known from the fossil record (Peakall et al., 2003). Compared with the related Araucaria cunninghamii and Agathis robusta, W. nobilis has extremely low genetic variation, which probably contributes to its susceptibility to exotic fungal pathogens outside of its natural environment. Although at ﬁrst sight similar problems (e.g. unsustainable logging, lack of recruitment, small populations, habitat degradation) are affecting rare and threatened tree species in different continents, whether the conservation problems of these species are the same regardless of the region in which they occur is still debatable and would need standardized, comparative analyses of different declining species from various regions. Comparative analyses of related tree species Not only can genetic analyses provide insights into the conservation biology of rare, endemic, relictual, and threatened tree species, they can also inform conservation decisions by comparing patterns amongst closely related taxa. Comparative studies of a rare, endangered species and of an abundant and closely related species can help determine the conservation measures to be taken for the threatened taxon. In South-Western Australia, the extremely rare and critically endangered Acacia sciophanes shows lower allelic richness, observed heterozygosity and gene diversity than the common and widespread sister species Acacia anfractuosa (Coates et al., 2006). In the same region, genetic analyses have provided insights in the Acacia acuminata complex, which includes three taxa originating from the fragmentation caused by climatic instability in the Pleistocene (Byrne et al., 2002). Again for Acacia species, an analysis from Argentina suggests that Acacia aroma and Acacia macracantha are not two distinct species (Casiva et al., 2004). On the contrary, absence of conspeciﬁcity with the endangered Picea chihuahuana is reported for Picea martinezii, so that the latter species needs independent conservation initiatives (Jaramillo-Correa et al., 2006). ARTICLE IN PRESS 164 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Further comparative analyses involve: Zelkova abelicea (Crete) and Zelkova sicula (Sicily), relict species which show genetic differentiation due to the geographic isolation (Fineschi et al., 2002), Alnus cordata (wet mountain forests) and Alnus glutinosa (riparian habitats) in Corsica and Southern Italy (King and Ferris, 2000), Alnus maritima (rare) and Alnus serrulata (widespread) in Oklahoma and Georgia (Gibson et al., 2008), F. excelsior and Fraxinus angustifolia in France (Fernandez-Manjarres et al., 2006), Cryptomeria japonica, Taxodium distichum, and Chamaecyparis obtusa in Japan (Kado et al., 2006, 2008). Multi-species studies of the genetic variation and phylogeography of trees deal with, e.g., the genus Abies in Guatemala and Southern Mexico (Jaramillo-Correa et al., 2008), Eurasian Larix spp. (Semerikov and Lascoux, 2003; Khatab et al., 2008), species of the genus Castanopsis in Japan (Yamada et al., 2006), three endemic Castanea species in China (Lang and Huang, 1999), and deciduous Quercus spp. of North-Western Italy (Belletti et al., 2005). Oaks are particularly amenable to genetic comparative studies and are traditionally investigated (see ‘Introduction’). These tree species are important in tree genetics because of the common introgression amongst species and the resulting potential reticulate evolution (e.g. Aas, 1993; Müller, 1999; Muir et al., 2001; Kremer et al., 2002a; Muir and Schlotterer, 2005; de Casas et al., 2007; Tovar-Sanchez et al., 2008). Further insights in the differentiation of oak species are provided by a small-scale morphological and molecular study of Q. petraea or Q. robur, where micro-site selection appears to foster taxon-speciﬁc spatial aggregation which in turn promotes species separation (Gugerli et al., 2007), thereby conﬁrming previous ﬁndings of Aas (1993). It would be interesting to know whether this result holds over most of the overlapping range of the two species. For Quercus affinis and Quercus laurina at 39 locations across their distributional ranges in Mexico, the haplotype distribution follows a mosaic pattern, with contrasting populations often situated at small distance from each other (González-Rodrı́guez et al., 2004). Other studies of oak species which are clearly distinguished can provide knowledge about the degree of genetic differentiation within and amongst populations. For example, a study of Quercus suber and Quercus ilex populations in Portugal distinguishes a higher degree of polymorphism in the latter species. For Q. suber in that region, most genetic variation (96%) is found within rather than among populations (Coelho et al., 2006). This contrasts with a comparative analysis of genetic variation in Betula pubescens and Betula pendula in Russia and Western Europe (Maliouchenko et al., 2007). In this case, there is a roughly 50–50 division of genetic variation within and amongst populations. It could be that the scale of analysis has a non-negligible inﬂuence on how much genetic variance is found within vs. amongst tree populations (Aguinagalde et al., 2005). Molecular marker sets are becoming important tools whenever species or taxa are difﬁcult to distinguish based on their morphology. Apart from oaks, an example is provided by a study of a number of different Populus taxa in Switzerland (Holderegger et al., 2005), which resulted in the likely identiﬁcation of many individuals of Populus nigra, a rare and endangered species not only because of the declining habitat (riparian forests), but also because of the hybridization with exotic Populus taxa (Cottrell et al., 2005; Pospiskova and Salkova, 2006; Smulders et al., 2008; Ziegenhagen et al., 2008). A similar situation applies to Pinus mugo ssp. uncinata, which has become rare or extinct in many parts of Europe, again not only because of the decreasing primary habitat (peat bogs), but also because of the hybridization with Pinus sylvestris and the associated genetic erosion, as shown by a study in Poland (Wachowiak et al., 2005). Less evidence for such hybridization is available from the Tatra Mountains, in Poland, for P. sylvestris and P. mugo (Wachowiak et al., 2006; see also Wachowiak and Prus-Glowacki, 2008), whilst a study in the Alps conﬁrms the conspeciﬁcity of P. mugo ssp. uncinata and ssp. mugo (Monteleone et al., 2006). The latter study, however, makes use of the less reliable RAPD markers and so would need to be conﬁrmed by further analyses. Further application of comparative genetic studies can be found in suture zones of hybridizing species, whenever these are parapatric (as is not the case, e.g., for the sympatric Tilia species in Europe (e.g. Fromm and Hattemer, 2003) and for the deciduous Nothofagus antarctica and the evergreen Nothofagus dombeyi in South America (Stecconi et al., 2004)). For example, a study of inter- and intra-speciﬁc genetic diversity in a hybrid zone between Salix sericea and Salix eriocephala in New York State suggests both historic introgression and current hybridization (Hardig et al., 2000). At the contact zone between the allopatric ranges of Picea mariana and Picea rubens in North-Eastern America there is a higher diversity due to rare mitotypes intermediate between the commonly observed ones for the two species (Jaramillo-Correa and Bousquet, 2005). The same approach can be useful for suture zones of natural hybrids (e.g. Thomas et al., 2008; van Loo et al., 2008) and in clades of the same species, e.g., originating from different glacial refugia, as shown in Bavaria and Austria for Abies alba (Breitenbach-Dorfer et al., 1997), in Norway for Ulmus glabra (Myking and Yakovlev, 2006) and in the Kanto District, Japan, for Fagus crenata (Kobashi et al., 2006). Such studies are providing increasing information about the recent evolutionary history of tree species. ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Tracking tree species spread and divergence Large-scale studies of genetic diversity can provide insights about the geographical origin of species. An analysis throughout the species range suggests that Quercus suber originated from the Middle-East or the central Mediterranean and then spread westward during the Tertiary (Lumaret et al., 2005). At a larger scale, sequence analysis of paternally inherited chloroplast regions and of a maternally inherited mitochondrial intron, combined with other lines of evidence including fossils, suggest that the genus Picea originated in North America, and spread repeatedly from America to Asia via the Bering land bridge. Europe is believed to be the tip of this westward colonization of the Northern hemisphere (Ran et al., 2006). Similarly westward, but with a different origin, appears to have been the migration route of the genus Castanea. Based on chloroplast DNA sequence information from extant species, this genus seems to have originated in Asia, and then to have spread to North America via Europe (Lang et al., 2006, 2007). Given that newly founded populations tend to lose genetic diversity, this migration pattern might contribute to explain the lower chestnut blight resistance of Castanea species from North America and Europe. In this and similar studies, higher levels of genetic diversity are found in the centres of origin or refugia of a species. Examples of this pattern include from America Pinus monticola (Steinhoff et al., 1983), from Europe Fagus sylvatica (Demesure et al., 1996) and species of the genus Quercus (Dumolin-Lapègue et al., 1997), and from Asia Cunninghamia lanceolata (Chung et al., 2004) and Pinus tabulaeformis (Chen et al., 2008) in China and Chamaecyparis obtusa in Japan (Tsumura et al., 2007). The assumption is that intra-speciﬁc diversity declines in newly colonized regions due to bottlenecks during founder events (e.g. Hewitt, 1996). This assumption is often used when reconstructing the recolonization of tree species following glacial events. For example, the ﬁnding that populations of Picea abies from Austria tend to be monomorphic in the West of the country, whereas they are slightly to highly polymorphic in Central and Eastern Austria, may be explained by the westward recolonization of the Austrian Alps from glacial refugia located in the Dinaric Alps or the Carpathians (Maghuly et al., 2007; see also Gugerli et al., 2001). A similar explanation is invoked for the weak, but statistically signiﬁcant northward trend of diminishing allelic richness in Juglans nigra in the central hardwood region of the USA (Victory et al., 2006). The relatively low genetic diversity of Aextoxicon punctatum, the only taxon of the family Aextoxicaceae and an endemic of temperate Western South America, is interpreted as a consequence of the repeated impacts of glacial cycles on the geographic range of this species 165 (Núñez-Ávila and Armesto, 2006). Similarly, the depleted gene pool of F. sylvatica compared to its vicariant species in the Middle-East (Fagus orientalis) is probably a consequence of the more severe impact of the Pleistocene glaciations on F. sylvatica (Gömöry et al., 2007). However, it is also possible that high levels of genetic diversity are found in newly colonized regions due to several founder events (Petit et al., 2003; a similar explanation may apply at the assemblage level to explain why some regions have higher b-diversity than others; Dick et al., 2003a). This is suggested to explain the high levels of diversity observed for Picea abies in some populations of the Maritime Alps, which may follow from the combined inﬂuence of various gene pools of origin (Scotti et al., 2000; Meloni et al., 2007). A similar argument is made for the weak phylogeographic structure of 19 populations of Castanopsis hystrix in China, which are attributed to its migration from numerous and scattered refugias (Li et al., 2007). Multiple refugias are also proposed for Poulsenia armata in central America (Aide and Rivera, 1998) and for Araucaria araucana in Chile (Ruiz et al., 2007). Moreover, recently founded populations at the edge of the range may be more differentiated than older populations at the centre of the range in a transient way due to (i) chance (as suggested, e.g., for Quercus rubra; Magni et al., 2005), (ii) clonal growth and its associated longer generation times and higher mutation rates (as shown by Sorbus torminalis on islands of the Baltic Sea (Rasmussen and Kollmann, 2008), or (iii) recent divergence: Cedrus brevifolia, an endemic from Cyprus, shows the highest levels of diversity in a comparison of species of the genus Cedrus, and this suggests a recent divergence rather than a relictual, declining population (Dagher-Kharrat et al., 2007). In some cases there may be an absence of genetic differentiation between peripheral and core tree populations, but the former may lack some rare alleles due to recent bottlenecks, as is the case for the endemic Picea alcoquiana in Japan (Aizawa et al., 2008). In other cases, peripheral and core populations may be difﬁcult to distinguish, as with the range disjunction of Pinus balfouriana in the Klamath Mountains and the Sierra Nevada, California (Eckert et al., 2008). Given all these exceptions to the rule that core populations show higher levels of genetic diversity than peripheral populations, when postglacial migration routes need to be inferred, a combination of independent lines of evidence should be considered (Magri et al., 2006; Ruiz et al., 2007). This necessity is shown by a study of the putative postglacial migration of Abies alba in the South-Western Alps (Muller et al., 2007). The available palaeoecological data are not consistent with previous assertions of the existence of A. alba refugia in Southern France, as this tree species appears to have ARTICLE IN PRESS 166 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 rapidly migrated northwards from the Apennine refugia in spite of the constraint posed by the aridity of the inner Alpine valleys. For the same species, it is postulated that it might have survived in a number of refugia but might have migrated from only some of them (Konnert and Bergmann, 1995). For Nothofagus nervosa, an endemic of South American temperate forests, pollen records indicate long-distance dispersal from refugia located far away from the current occurrence of the species in Southern latitudes. However, chloroplast DNA markers provide evidence for the persistence of the species in cryptic refugia at Southern latitudes (Marchelli and Gallo, 2006). In some cases combinations of different scenarios may apply for the same species. For Larix sibirica, the similarity in haplotype frequencies of tree populations from Northern and Southern Siberia is suggestive of multiple reintroductions, but the genetic speciﬁcity of individual northern populations speaks for a founder effect (Semerikov et al., 2007). For Picea mariana in Quebec, Canada, whilst the presence of a single mitotype variant in subarctic populations is consistent with a travelling wave of recolonization, there is also evidence for long-distance dispersal events and for pollen exchange among populations (Gamache et al., 2003). In other cases, different scenarios may tend to pertain to groups of trees with different traits (e.g. range and seed size), as suggested by meta-analytical studies (Svenning and Skov, 2007a, b; Bhagwat and Willis, 2008). For North American species, the lack of mountain ranges parallel to the equator is thought to have allowed a lower number of tree species extinctions in spite of the magnitude of the Laurentide ice sheet (for white oaks in Europe vs. California, see Grivet et al., 2006). However, recent molecular studies suggest a fairly well structured pattern in genetic variation of several tree species in relation to dividing features such as the Appalachians (Soltis et al., 2006). Such a discontinuity appears to be consistent amongst various tree species (e.g. P. mariana (Jaramillo-Correa et al., 2004) and Pinus banksiana (Godbout et al., 2005), but see for Acer rubrum Gugger et al. (2008)). Also in North-East Asia, which was mainly free of ice sheets during the Quaternary, genetic differentiation between tree populations can be detected due to range expansion and contraction in a topographically structured region (presence of islands, land bridges, mountain ranges). An example is provided by a study of mitochondrial haplotypes of Picea jezoensis throughout its distributional range (Amur Region, China, Japan, Kamchatka and South Korea; Aizawa et al., 2007). In Europe, mountain ranges parallel to the equator posed a signiﬁcant obstacle both to retreating and recolonizing (tree) species. The general lack of the haplotypes of the Spanish populations of Populus nigra elsewhere in Europe is believed to be a consequence of the barrier posed by the Pyrenees (Cottrell et al., 2005). For Alnus glutinosa, most of Central and Northern Europe is believed to have been colonized from a refuge in the Carpathians (King and Ferris, 1998). Quercus species are thought to have taken 2–3 millennia to cross or circumvent the Alps at the end of the last glaciation (Mátyás and Sperisen, 2001; Finkeldey and Mátyás, 2003). Similar orders of magnitude are reported for the recolonization of F. sylvatica (Magri, 2008), A. alba and P. abies (Burga and Hussendörfer, 2001). With the possible exception of Salix species (Palmé et al., 2003a), geographic barriers to migration appear to have operated for many other European tree species. Examples include Betula pendula (Palmé et al., 2003b), Corylus avellana (Palmé and Vendramin, 2002), F. excelsior (Heuertz et al., 2004b), Ilex aquifolium (Rendell and Ennos, 2003) and P. sylvestris (Soranzo et al., 2000; Naydenov et al., 2007; Pyhäjärvi et al., 2008). Of course, mountain ranges may have constituted natural dispersal barriers also in other continents, as shown by the strong landscape effects of the Hengduan and Dabashan mountains in a phylogeographic study of Taxus wallichiana in China and Vietnam (Gao et al., 2007; Fig. 2). Topography is believed to have played a role also in the formation of refuges and in the postglacial recolonization of Picea likiangensis in Tibet and Quinghai (Peng et al., 2007) and in the genetic differentiation of populations of Pinus koraiensis in Korea, China, and the Russian Far East (Kim et al., 2005) and of Olea europaea ssp. laperrinei in the central Saharan mountains (Besnard et al., 2007). In other cases, geographical barriers appear to have been overcome surprisingly easily, as shown by the lack of isolation to pollen ﬂow in Picea crassifolia in regions separated by the Tengger desert (Tibet; Meng et al., 2007) and by the evidence of inter-continental dispersal for the lowland tropical rainforest tree Ceiba pentandra (Dick et al., 2007). A strong geographical structure in the distribution of haplotypes can be found also in the absence of major mountain ranges parallel to the equator, as, e.g., for Eucalyptus globulus in Southern Australia (Freeman et al., 2001). In some cases mountains might not have posed a barrier to recolonization, as refuges were already located beyond them. Recent studies in Europe and North America suggest the existence of previously unrecognized northern refugia (McLachlan et al., 2005; Bhagwat and Willis, 2008; Varga, 2008). For example, Pinus contorta appears to have had a glacial refuge off the coast of British Columbia (Godbout et al., 2008). Low density refuges of Fagus grandifolia and Acer rubrum at short distance from the Laurentide ice sheet are also reported (McLachlan et al., 2005). This development makes it likely that previous estimations of postglacial ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 167 Fig. 2. The distribution of the 19 chloroplast haplotypes found in 50 populations of Taxus wallichiana in China and adjacent regions (from Gao et al., 2007). Red lines represent major ﬂoristic boundaries, green lines show minor boundaries. The inset in the top left corner shows an enlarged view of the Hengduan Mountain and East Himalayan regions. Codes: D, Sino-Japanese Forest subkingdom; D8, North China region; D9, East China region; D10, Central China; D11, South China mountain region; D12, Yunnan. Guizhou and Guangxi limestone mountain and hill region: E, Sino-Himalayan forest subkingdom; E13, Yunnan Plateau region; E14, Hengduan mountain region; E15, East Himalayan region; G, Malesian subkingdom; G19, North Taiwan region; G22, Tonkin Bay region. DS, Dabashan Mountain; HD, Hengduan Mountain; MSD, Mekong-Salween Divide; QL, Qinling Mountain; SB, Sichuan Basin. A, Anhui; C, Chongqing; Fj, Fujian; Gd, Guangdong; Gs, Gansu; Gx, Guangxi; Gz, Guizhou; He, Henan; Hn, Hunan; Hu, Hubei; Jx, Jiangxi; S, Sichuan; Sx, Shaanxi; Sa, Shanxi; Y, Yunnan; Zj, Zhejiang; T, Taiwan; V, Vietnam; M, Myanmar. With kind permission of Wiley–Blackwell. migration rates may have been excessive and current tree distributions may be even more dispersal limited than models making recolonization start from refuges located far away would suggest. Genetic analyses can also help in distinguishing wild populations from those introduced by man. For Ginkgo biloba, the famous living fossil, an analysis of eight potential refugial populations suggests that the tree population of Tianmu Mountain, previously considered to be natural, is likely to have been transplanted by monks, due to the presence of only one common haplotype (Shen et al., 2005). This analysis makes it likely that G. biloba refugia were located in SouthWestern China only, but there is now evidence for the existence of a refuge also on the West Tianmu Mountains in East China (Gong et al., 2008). Reasons to believe that humans inﬂuenced the distribution of tree genetic diversity are also present in the Netherlands for oaks (Buiteveld and Koelewijn, 2006), in Southern Germany for Fraxinus excelsior (Hebel et al., 2006), and throughout its range in the Mediterranean for Pinus pinea, a species with surprisingly low genetic diversity (Vendramin et al., 2008; Fig. 3). Together with the evidence for current anthropic impacts on tree genetic diversity, these studies remind us that the inﬂuence of man should not be overlooked when studying tree recolonization routes after glaciations. Range-wide vs. range-edge studies Many studies of the geographical structure of the genetic diversity of tree species report isolation by distance, i.e. a positive relationship between ARTICLE IN PRESS 168 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Fig. 3. Chloroplast DNA variation in Pinus pinea populations across its range (from Vendramin et al., 2008). Only four haplotypes were identiﬁed when surveying 13 microsatellites: H1: yellow, H2: red, H3: green, H4: black. With kind permission of The Society for the Study of Evolution. geographical and genetic distances. This pattern applies for example for Larix lyallii and L. occidentalis in Western North America (Khasa et al., 2006) and to Swietenia macrophylla in Central America (Novick et al., 2003). For Pinus contorta throughout its distributional range (Western Canada and USA), isolation by distance is found up to a distance of 1000 km, but no association between genetic and geographic distance is manifest beyond that range (Marshall et al., 2002). For Betula maximowicziana, a long-lived pioneer of Japanese cool temperate forests, isolation by distance is detected amongst the 23 populations analyzed throughout its distributional range, but not within regions (Tsuda and Ide, 2005). A weak isolation by distance is evident for Dalbergia monticola, an endangered tree species in Madagascar (Andrianoelina et al., 2006), for Cedrus atlantica in Morocco (Terrab et al., 2006) and for Pinus taeda in Arkansas, Mississippi and Oklahoma (Xu et al., 2008). No correlation between geographic and genetic distance amongst populations is instead apparent for Abies nordmanniana populations throughout its restricted range in the Caucasian region (Hansen et al., 2005), A. nephrolepis populations in Korea mountains (Woo et al., 2008), Castanopsis carlesii in Taiwan (Cheng et al., 2005), Pinus echinata in Arkansas, Mississippi and Oklahoma (Xu et al., 2008), Quercus macrobata in Illinois (Craft and Ashley, 2007), Acer pseudoplatanus in North-Western Italy (Belletti et al., 2007) and Alnus glutinosa in Poland (Mejnartowicz, 2008). These examples could suggest that the presence or absence of isolation by distance may be related to the scale of the study, but any inﬂuence of study scale on the presence of isolation by distance may be masked by an expanding, stable or retreating distributional range (Hampe and Petit, 2005; Troupin et al., 2006) and by the variation in life history traits of various tree species. For example, Hippophae rhamnoides ssp. sinensis, an endemic to China, shows no association between genetic and geographic distance, probably because of the wind pollination and the long-distance bird dispersal of seeds (Sun et al., 2006a). High genetic differentiation amongst populations is often associated with heavy seeds (e.g. species of the family Fagaceae, e.g. Shanjani et al., 2004). Isolation by distance can also be inﬂuenced by the presence of multiple glacial refugia, as for example in Europe for Fraxinus excelsior (Heuertz et al., 2004b) and Pinus nigra (Afzal-Raﬁi and Dodd, 2007). Range-wide molecular studies of genetic variation in tree species are becoming more frequent. In the tropics, however, such analyses are still rare (e.g. Vitellaria paradoxa in sub-saharan Africa; Fontaine et al., 2004). In Europe, recent examples include range-wide genetic analyses of P. abies (Vendramin et al., 2000; Collignon et al., 2002; Acheré et al., 2005; Heuertz et al., 2006b; Tollefsrud et al., 2008), white oaks (Quercus spp., Petit et al., 2002b), Pinus pinaster (Burban and Petit, 2003), Corylus avellana (a North-South transect; Persson et al., 2004), Carpinus betulus (Grivet and Petit, 2003; Coart et al., 2005), Fraxinus ornus, F. angustifolia, and F. excelsior (Heuertz et al., 2006a), Hippophaë rhamnoides (together with Asia Minor; Bartish et al., 2006), and Pinus pinea (Vendramin et al., 2008). These comprehensive analyses can provide indications as to which regions should be the focus of protection given their outstanding diversity. For example, hotspots of ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 genetic diversity have been identiﬁed for P. pinaster in central and South-Eastern Spain (Bucci et al., 2007). But this does not mean that areas of low haplotypic diversity (in this case Morocco and Western Iberia) should be disregarded, as they may still harbour unusual genotypes which could be better adapted to local conditions in spite of the overall lower diversity of these tree populations. Similarly, Apennine populations of P. sylvestris at the Southern edge of the distributional range show lower genetic variability in comparison to Alpine populations, possibly as a consequence of the progressive isolation from the early Holocene onwards and of the postglacial migrational routes (Cheddadi et al., 2006; Pyhäjärvi et al., 2008). However, Apennine Scots pine remnants are regarded as worthy of conservation given their speciﬁc genetic constitution (Labra et al., 2006). Genetic diversity can be higher at one edge of the range compared to another, as reported at the eastern edge and in the Appalachian interior vs. the western edge of the geographic range for Tsuga canadensis in the SouthEastern USA (Potter et al., 2008). Hence, generalizations about the importance of range margins for a certain species should be made with caution. Moreover, given that within-population estimates of gene diversity using different traits are often not correlated (for P. pinaster, González-Martı́nez et al., 2004), it is not advisable to base conservation strategies of tree species genetic resources on a limited number of populations, even if these show high diversity relative to other populations (Lara-Gomez et al., 2005). This all the more so given that different markers can (but do not need to, see e.g. Fineschi et al., 2005; Xia et al., 2008) provide different answers to research questions of geographical genetics of tree populations, as shown by studies of P. mariana in subarctic Quebec (Gamache et al., 2003), Fraxinus excelsior in Europe (Heuertz et al., 2004a), P. sylvestris and P. heldreichii in Bulgaria (Naydenov et al., 2005a, b) and Quercus semiserrata in Thailand (Pakkad et al., 2008). Peripheral (i.e., at the edge of the distributional range) populations may be growing in suboptimal environments compared to core populations, but may have evolved adaptations to future adverse climatic or edaphic conditions (Ritland et al., 2005). For a more thorough understanding of the evolution of forest tree distributional ranges, and for providing the required scientiﬁc background for conservation decisions, comparative studies between neutral and non-neutral (adaptive) variation at the core and at the edges of tree species ranges are needed (Bridle and Vines, 2007). Peripheral populations and their adaptations are often at risk due to the usually low numbers of individuals (e.g. Avicennia marina, a mangrove in South-East Asia; Arnaud-Haond et al., 2006). Range-edge populations may thus need to be protected with larger nature 169 reserves than populations at the core of the range, as suggested for Picea sitchensis (Gapare and Aitken, 2005). Current Pinus canariensis populations are believed to be the remnants of larger populations severely reduced by changes in climate and by human impacts following European colonization in the XV century (Vaxevanidou et al., 2006). However, P. canariensis still shows variability in genetic diversity amongst different populations and this is important for its conservation planning. A similar situation is likely to apply to many other relictual and peripheral tree populations. Fagus grandifolia ssp. mexicana is a threatened subspecies with only about ten remaining populations of limited extent (less than 1 km2 each) in the Sierra Madre Oriental. These populations, however, still have high genetic variation, which needs to be preserved to provide the basis for a future enlargement of the population (Rowden et al., 2004). In other cases, low population size of endangered tree species unfortunately coincides with low genetic diversity, although there may still be genetic differentiation amongst populations, as for Cathaya argyrophylla, an endangered conifer restricted to subtropical mountains in China (Wang and Ge, 2006). Although genetic differentiation among tree populations can already be observed within relatively small geographic areas (e.g. Bulgaria for P. nigra; Naydenov et al., 2006), range-wide molecular studies are key for a more comprehensive picture about postglacial recolonization and for forecasting the fate of tree species and populations during the next climatic changes. Climate change and gene conservation in trees Knowledge about the degree to which past climate vagaries affected the distribution and genetic diversity of tree species is a necessary condition to predict the dynamics of the same species under future climate change (e.g. Liesebach, 2002; de Heredia et al., 2007). The recent ﬁnding that Picea glauca apparently survived the last glaciation in a refuge in Alaska makes the recolonization of Alaska from areas south of the Laurentide Ice Sheet unlikely (Anderson et al., 2006). This would imply that postglacial migration rates of this species have been largely overestimated. If such previously unrecognized glacial refuges were to be a common feature in many regions (Stewart and Lister, 2001), the capacity of tree species to migrate following future climate warming might be lower than previously believed. Given (i) the many bottlenecks documented during past climate change, (ii) the pervasiveness of climatic changes (in the Southern Hemisphere from Southern South America (e.g. Marchelli and Gallo, 2006) to the Brazilian Cerrado (Ramos et al., 2007) and Australia (Taylor et al., 2005)), and (iii) the rapidity of ARTICLE IN PRESS 170 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 the forecasted warming, future global change may have a substantial impact on the genetic resources of forest trees (e.g. Bawa and Dayanandan, 1998). Genetic variation, in turn, can play a key role in adaptation to a changing environment (e.g. Lande and Shannon, 1996; Schaberg et al., 2008) and is thus important in the potential ability of tree species to withstand future global change. However, whilst recent past climate ﬂuctuations challenged the survival of many tree species because of the generally glacial conditions, future climate is predicted to change towards warmer temperatures. It is true that at the end of the glacial maximum tree species also had to migrate away from the tropics and the lowlands. We know that throughout much of the Tertiary, the Arctic was covered by forests (Abbott et al., 2000). However, such an up- and/or pole-wards migration is an unprecedented event at the end of an interglacial. An example is the recent spread of the frostsensitive Juglans regia up an alpine valley of Tyrol, Austria, which is well correlated with the increasingly warmer local climate after 1970 (Loacker et al., 2007). There are many other reports of treeline advancement (but few investigations of the genetic patterns in this expansion; e.g. Truong et al., 2007), although in some cases the relative contribution of climate warming and land/grazing abandonment is not clear (Camarero and Gutierrez, 2007; Gehrig-Fasel et al., 2007). In this context, the rear end of range shifts (i.e. the northern end of ranges in austral tree species – and vice versa for the boreal hemisphere) assumes a key importance to determine whether genetic or rather demographic processes will govern the persistence of peripheral populations under conditions warmer than the physiological limits of the tree species. Climate warming has also consequences for a potentially increased activity of tree pathogens at the treeline (and range edge), which could exert a negative effect on such altitudinal/ latitudinal range expansions/retreats (Tomback and Resler, 2007). The literature about whether altitudinal gradients in genetic diversity of tree species are the rule or the exception is controversial (see review in Ohsawa and Ide, 2008). Four patterns are reported: (i) lower genetic diversity at lower and higher altitudes than at intermediate ones (e.g. for Quercus crispula in the Chichibu Mountains, Japan; Ohsawa et al., 2007), (ii) no variation in genetic diversity with altitude (e.g. P. abies in Switzerland; Müller-Starck, 1995a; Sequoia sempervirens in California; Rogers, 2000; Q. aquifolioides in the Wolong Natural Reserve, China; Zhang et al., 2006), (iii) higher diversity at higher altitude (e.g. F. sylvatica at mount Vogelsberg in Germany; Sander et al., 2000, this result would need to be conﬁrmed using replicate gradients), and (iv) higher diversity at lower altitude (e.g. Nothofagus pumilio in the Southern Andes; Premoli, 2003). This variability in ﬁndings implies that the evolutionary potential of mountain tree species to withstand future warming will tend to vary between regions and species. In many cases, the warm conditions of the current interglacial have resulted in tree species migrating upwards and in part sheltering at high elevation in mountains (Lozano-Garcia et al., 2005; Strong and Hills, 2005). Examples include: P. sylvestris in the Meseta plains in Spain (Robledo-Arnuncio et al., 2005), Pinus cembra in the Alps and Eastern Carpathians (combined with anthropogenic pressure: Belokon et al., 2005), and F. crenata in South-Western Japan (Okaura and Harada, 2002). Further warming could make many of these situations precarious, and it will be of little help knowing with increasing detail thanks to state-of-the-art molecular studies that these tree species were able to withstand repeated glaciation events by retreating to lower altitudes and/or latitudes. In other cases, as with Eucalyptus grandis in Eastern Australia, a trend towards aridity is thought to have resulted in a retreat towards valley bottoms. The drier climate of the Pleistocene may have contributed to the range split of E. grandis, which is thought to have happened relatively recently, as only a weak population structure was detected between the subtropical range core and the disjuncted tropical populations (Jones et al., 2006). The consequences of future changes in precipitation and aridity patterns for the conservation of tree species and of their genetic diversity are still largely unexplored. In some cases, tree species may still be recovering from the most recent Pleistocene glacial period. An example is Pinus resinosa in Canada, which showed high levels of differentiation amongst the populations studied probably due to inbreeding following population bottlenecks (Fowler and Morris, 1977; Boys et al., 2005) and may thus be ill-adapted to withstand future global change. However, it is also possible that rear-edge populations may have already purged their genetic load through different glacial–interglacial cycles and might be now adapted to climate change conditions (Hampe and Petit, 2005), although the speed of the forecasted warming is probably unprecedented. Germplasm collections need in such cases to consider individuals from as many populations as possible. On the contrary, whenever much higher levels of genetic diversity are observed within rather than amongst tree populations, it is recommended to collect propagation material from a large number of individuals of a small number of populations (e.g. for a study of seven populations of Betula alnoides from Guangxi, China; Zeng et al., 2003). But suppose the genetic survey had missed some rare alleles from unsampled populations which would have been invaluable in withstanding future unprecedented climatic conditions? This is a problem also because the ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 majority of the studies examine neutral genetic markers, and these do not provide adequate information about adaptive genetic variability (at the level of phenotypes). Moreover, many genetic studies draw their conclusions from surprisingly low numbers of sampled populations. There is evidence that standard population sampling protocols may fail to capture within-population allelic richness and expected heterozygosity of tree populations at the margin of their distributional range, when these show high within-population genetic structure (which is usually the case for tree species, in particular when assessing nuclear markers; Furnier and Adams, 1986), as shown by a study of Picea sitchensis (Gapare et al., 2007). Conclusions and future directions There is now a substantial body of research on natural patterns of and anthropic effects on the genetic diversity of threatened and unthreatened tree species. Much knowledge is available on recolonization processes following glaciations, at different scales of analysis and parts of distributional ranges. Many of these studies provide information with which to gauge the degree to which future climate change may imperil tree species and their genetic resources. It is important that the available knowledge be widely disseminated to scientists and managers involved in the conservation of forest ecosystems and tree species. The rest of this review outlines some outstanding research questions. Most studies of tree genetic diversity analyze one or a few related species. Given the differences amongst independent studies in, e.g., number of locations sampled, proportion of the distributional range considered, choice of molecular markers, and other factors (e.g. Ohsawa and Ide, 2008), it is often difﬁcult to compare and quantitatively synthesize results from different publications. One time-consuming, yet potentially feasible solution would be to extend studies of intra-speciﬁc tree genetic diversity to a number of species often found together in particular forest types (Petit et al., 2003). This approach is similar to the one used in comparative analyses of closely related tree species. For example, genetic variation was surveyed for 34 species in deciduous broad-leaved forests in Japan (Iwasaki et al., 2006), for 30 species of Fagaceae in forests of Northern Thailand (Chokchaichamnankit et al., 2008), and for multiple stone oak species (genus Lithocarpus) in South-East Asia (Cannon and Manos, 2003). This approach is often unavoidable for rain forest species which are difﬁcult to identify in the ﬁeld outside of their period of reproduction, as pointed out by a genetic study of Carapa spp. individuals from French Guiana (Duminil et al., 2006). 171 Even for single species, there is a need for an increased collaboration between conservation biologists, biometeorologists, dendrologists, ecophysiologists, evolutionary, forest, landscape and urban ecologists, geneticists, palaeoecologists, pathologists, and phylogeographers (Sork and Smouse, 2006; Paoletti et al., 2007; Wehenkel et al., 2007; Belmonte et al., 2008; Kettle et al., 2008; Kramer et al., 2008b; Morris et al., 2008; Petit et al., 2008; Reich and Oleksyn, 2008; Riddle et al., 2008; Rossetto, 2008; Whitham et al., 2008). Tree genetic diversity is a key interdisciplinary ingredient for sustainable ecosystem management (Christensen et al., 1996). For instance, studies of DNA variation should ideally be matched to studies in variation of ecologically important traits from provenance trials (e.g. Karhu et al., 1996; Zelener et al., 2005; O’Brien et al., 2007; Tripiana et al., 2007). This could help in investigating whether the susceptibility of forested landscapes to tree fungal pathogens and insect defoliators is decreased not just by increased tree species diversity, but also if the species constituting forest patches show a higher genetic diversity (Hertel and Zaspel, 1996; Chen et al., 2001; Holdenrieder et al., 2004; Pautasso et al., 2005; Jactel and Brockerhoff, 2007). Research in this direction is particularly needed for white pine blister rust (caused by Cronartium ribicola; e.g. Kinloch et al., 2004; Sniezko, 2006; Richardson et al., 2008). For the emerging tree and shrub dieback known as Sudden Oak Death in the West Coast of the USA (Hansen, 2008), the main host Umbellularia californica appears to show substantial variation both in genetic diversity and in susceptibility to the pathogen Phytophthora ramorum, but disease expression is mostly driven by environmental variability (Anacker et al., 2007). Tree genetic diversity may be an important factor to be considered in studies of the reaction of tree populations (in terms of photosynthesis, growth, and mortality rates) to increased levels of N supply in soil, CO2, ozone, and other air pollutants (e.g. Taylor, 1994; Paludan-Muller et al., 1999; Spinnler et al., 2003; Longauer et al., 2004; Major et al., 2007). However, researchers should not be tempted to interpret results of selectively neutral molecular markers exclusively in the light of adaptation (Neale and Ingvarsson, 2008). Neutral molecular markers are useful to identify evolutionary afﬁnities and lineages, but can be problematic when trying to establish adaptive population differentiation in phenological traits. Although there have been studies on the genetic impacts of habitat degradation, loss and fragmentation for tropical angiosperms (e.g. Hewitt, 2000; Dick et al., 2003b; Lowe et al., 2005; Aguilar et al., 2006), there are still relatively few genetic studies of tropical tree species compared to the amount of information available from North America, Europe and temperate Asia and South America (Fig. 4). This is unfortunate, given the notoriously high tree diversity of the tropics ARTICLE IN PRESS 172 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 nearctic neotropical palearctic ethiopian oriental australasian Fig. 4. Geographical distribution of the studies on the genetic diversity of forest trees mentioned in this review. (e.g. Denslow, 1987; Gentry, 1992; Parmentier et al., 2007) and the presence of many endangered tree species from tropical and subtropical latitudes (e.g. Gillespie et al., 2000; Butaud et al., 2005; Adekunle, 2006). A greater research output from the tropics is not only important because the bulk of biodiversity is located there, but also because such studies would enable to investigate in a more comprehensive way latitudinal gradients in intra-population tree genetic diversity. Also in this case, it is difﬁcult to quantitatively summarize results if such studies encompass a different range of latitudes (e.g. Podocarpus parlatorei in the subtropical nearctic (Quiroga and Premoli, 2007), Austrocedrus chilensis in Argentina (Pastorino et al., 2004), Fraxinus mandschurica in North-East China (Hu et al., 2008), S. torminalis in Poland (Bednorz et al., 2006), P. abies (Collignon et al., 2002), Corylus avellana (Persson et al., 2004) and Populus tremula (Hall et al., 2007) in Europe). There is a vast literature documenting positive species richness-area, -time, and -energy relationships, but the study of such patterns for genetic diversity is still in its infancy (e.g. Jansson and Davies, 2008). There is also scope for more research on tree genetic diversity using geostatistic tools (e.g. Le Corre et al., 1998). For example, do haplotype frequencies and other measures of genetic diversity correlate with environmental parameters such as (i) mean annual rainfall and number of dry months, as studied for Cedrela odorata in Mesoamerica (Cavers et al., 2003b), (ii) cool-season temperatures and summer drought, as investigated for Pseudotsuga menziesii in Oregon and Washington (St Clair et al., 2005), (iii) a temperature–humidity gradient, as documented for all remnant populations of Cedrus libani (Semaan and Dodd, 2008), and (iv) latitude and moisture index, as shown for Eucalyptus camaldulensis in Australia (Butcher et al., 2009)? Are levels of tree genetic diversity higher in protected areas than outside them and are protected area networks chosen well from the point of view of tree genetic diversity (Hamann et al., 2004; Lipow et al., 2004; Avise, 2008; Soares et al., 2008)? Many studies of tree genetic diversity have been carried out on islands, either independently or in comparison with the mainland of continents. Examples include Pinus radiata in California (Rogers et al., 2006), Santalum austrocaledonicum in New Caledonia (Bottin et al., 2005), Eucalyptus perriniana in South-Eastern Australia and Tasmania (Rathbone et al., 2007), Eucalyptus urophylla in Indonesia (Payn et al., 2007, 2008), P. luchuensis in China, Taiwan, and the Ryukyu Archipelago (Chiang et al., 2006), P. canariensis on Canary Island (Navascués and Emerson, 2007), and P. abies in islands of Northern Sweden (Wang et al., 2003). Nevertheless, given that islands are often fragile and species-rich ecosystems (Kreft et al., 2008), the island biogeography of tree genetic diversity certainly deserves more attention. Similarly, many interesting research questions are arising from local to regional studies of patterns in gene ﬂow of tree species. For example, how consistent are different genetic markers in studies of the spatial genetic structure formed by pollination patterns (e.g. Jump and Peñuelas, 2007)? A study of Eucalyptus wandoo in South-Western Australia reveals substantial pollen dispersal amongst remnant tree patches of this insectpollinated species (Byrne et al., 2008), but there is a need to assess from more systems whether isolated forest patches may still be able to guarantee gene ﬂow (Bacles et al., 2004, 2005; Kramer et al., 2008a). For P. sitchensis on the Paciﬁc Coast of North America, range-edge populations have a higher selﬁng rate than central populations due to their isolation (Mimura and Aitken, 2007). Similar investigations of patterns in inbreeding frequencies and gene ﬂow in different parts of the range are needed for tropical tree species (Hardy et al., 2006). Studies of genetic population structure of tree species which use hydrochory for dispersal in ﬂoodplain forests (e.g. C. guianensis in the Amazon basin; Cloutier et al., 2005) may make proﬁtable use of recent theoretical advances on dendritic networks (Grant et al., 2007). A rarely investigated question is the role of nurse logs for the spatial structuring of the genetic diversity of new tree generations (Lian et al., 2008). Although there have been several studies limited to single countries (e.g. Fraxinus excelsior for Bulgary (Heuertz et al., 2001), France (Morand et al., 2002), Italy (Ferrazzini et al., 2007), and Germany (Rüdinger et al., 2008)), many recent studies of the genetic diversity of trees aim understandably to cover most of the distributional range of the species of interest. However, a national study can sometimes be appropriate, while a large sampling range may just reﬂect bad resource allocation (if not adequate for the questions asked). For the species which have already been studied throughout their range, it can make sense to narrow down the extent of the analysis by making use of the tools of landscape genetics to investigate, e.g., landscape patterns in genetic connectivity (e.g. Sork and Smouse, 2006; Holderegger and Wagner, 2008). Restricting some future analyses to ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 parts of the range would enable a scale-dependent perspective (e.g. Raspé et al., 2000; Rivera-Ocasio et al., 2006; Voigt et al., 2009). For example, the correlation of the species richness of various taxa and of human population has been suggested to be scale-dependent, as over local scales high numbers of people cause species impoverishment, whilst at a large scale species-rich regions tend to be densely populated (e.g. Luck, 2007; Pautasso, 2007; McKinney, 2008). Is there a genetic diversity–people correlation, which form does this correlation take at different levels of urbanization and human impacts, and is this correlation scale-dependent? These are all outstanding questions which deserve investigation. Other potential research questions include: can the genetic diversity of tree species contribute in predicting their potential invasion status? Arboreta and botanical gardens can play a key role in this research area given their expertise, living and germplasm collections (e.g. Yang and Yeh, 1992; Pautasso and Parmentier, 2007; Dawson et al., 2008). Are old-growth forests reservoirs of tree genetic diversity (Mosseler et al., 2003; Takahashi et al., 2008) and is there an inﬂuence of past land-use on tree genetic diversity as is manifest for plant species richness (Hermy and Verheyen, 2007) and snag density (Wisdom and Bate, 2008)? Can the genetic diversity of trees be predicted from sets of environmental variables (e.g. Garnier-Géré and Ades, 2001; Gram and Sork, 2001), as it is possible to do for tree species occurrences and richness (e.g. Guisan et al., 2007; Nightingale et al., 2008)? Also in this case a word of caution is needed, as the use of neutral genetic markers may inform little on the adaptation potential of tree populations. Is there any relationship/tradeoff between species and genetic diversity (e.g. Hosius et al., 2001; Gregorius et al., 2003; Vellend, 2005; Vellend and Geber, 2005; Wehenkel et al., 2006), and what are the consequences for ecosystem function (Scherer-Lorenzen et al., 2007; Hughes et al., 2008)? Is there a biodiversity surrogate also for tree genetic diversity, and can tree genetic diversity be used as an indicator for other levels of biodiversity, as is the case for vascular plant species richness (e.g. Rodrigues and Brooks, 2007)? Given the multiple ways in which tree genetic diversity can play a functional role from local ecosystems to continents, this diversity can be investigated with a variety of research questions, approaches, and scales. Acknowledgements Many thanks to G. Aas, L. Ambrosino, P. Belletti, L. Denzler, C. Ferrari, D. Fontaneto, K. Gaston, M. Hermy, K. Hilﬁker, O. Holdenrieder, M. Jeger, D. Lonsdale, G. Müller-Starck, I. Parmentier, L. Paul, P. Rotach, M. Sieber, J.-P. Sorg, P. Weisberg, and 173 M. Zotti for insights and discussion. Special thanks to O. Holdenrieder, H. Jones, T. Matoni, and three anonymous reviewers for helpful comments on a previous draft. References Aas, G., 1993. Taxonomical impact of morphological variation in Quercus robur and Q. petraea – a contribution to the hybrid controversy. Ann. Sci. For. 50, S107–S113. Aas, G., Müller, B., Holdenrieder, O., Sieber, M., 1997. Are pedunculate oak and sessile oak two separate species? Allg. Forstz. Waldwirtsch. Umweltvors. 52, 960–962. Abbott, R.J., Smith, L.C., Milne, R.I., Crawford, R.M.M., Wolff, K., Balfour, J., 2000. Molecular analysis of plant migration and refugia in the Arctic. Science 289, 1343–1346. Acheré, V., Favre, J.M., Besnard, G., Jeandroz, S., 2005. Genomic organization of molecular differentiation in Norway spruce (Picea abies). Mol. Ecol. 14, 3191–3201. Adekunle, V.A.J., 2006. Conservation of tree species diversity in tropical rainforest ecosystem of South-West Nigeria. J. Trop. Sci. 18, 91–101. Afzal-Raﬁi, Z., Dodd, R.S., 2007. Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in western Europe. Mol. Ecol. 16, 723–736. Aguilar, R., Ashworth, L., Galetto, L., Aizen, M.A., 2006. Plant reproductive susceptibility to habitat fragmentation: review and synthesis through a meta-analysis. Ecol. Lett. 9, 968–980. Aguinagalde, I., Hampe, A., Mohanty, A., Martin, J.P., Duminil, J., Petit, R.J., 2005. Effects of life-history traits and species distribution on genetic structure at maternally inherited markers in European trees and shrubs. J. Biogeogr. 32, 329–339. Aide, T.M., Rivera, E., 1998. Geographic patterns of genetic diversity in Poulsenia armata (Moraceae): implications for the theory of Pleistocene refugia and the importance of riparian forest. J. Biogeogr. 25, 695–705. Aizawa, M., Yoshimaru, H., Saito, H., Katsuki, T., Kawahara, T., Kitamura, K., Shi, F., Kaji, M., 2007. Phylogeography of a northeast Asian spruce, Picea jezoensis, inferred from genetic variation observed in organelle DNA markers. Mol. Ecol. 16, 3393–3405. Aizawa, M., Yoshimaru, H., Katsuki, T., Kaji, M., 2008. Imprint of post-glacial history in a narrowly distributed endemic spruce, Picea alcoquiana, in central Japan observed in nuclear microsatellites and organelle DNA markers. J. Biogeogr. 35, 1295–1307. Aldrich, P.R., Glaubitz, J.C., Parker, G.R., Rhodes Jr., O.E., Michler, C.H., 2005. Genetic structure inside a declining red oak community in old-growth forest. J. Heredity 96, 627–634. Aldrich, P.R., Hamrick, J.L., Chavarriaga, P., Kochert, G., 1998. Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera. Mol. Ecol. 7, 933–944. Alfonso-Corrado, C., Esteban-Jiménez, R., Clark-Tapia, R., Pinero, D., Campos, J.E., Mendoza, A., 2004. Clonal and ARTICLE IN PRESS 174 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 genetic structure of two Mexican oaks: Quercus eduardii and Quercus potosina (Fagaceae). Evol. Ecol. 18, 585–599. Allnutt, T.R., Newton, A.C., Premoli, A., Lara, A., 2003. Genetic variation in the threatened South American conifer Pilgerodendron uviferum (Cupressaceae), detected using RAPD markers. Biol. Conserv. 114, 245–253. Ally, D., Ritland, K., 2007. A case study: looking at the effects of fragmentation on genetic structure in different life history stages of old-growth mountain hemlock (Tsuga mertensiana). J. Heredity 98, 73–78. Anacker, B.L., Rank, N.E., Hueberli, D., Garbelotto, M., Gordon, S., Harnik, T., Whitkus, R., Meentemeyer, R., 2007. Susceptibility to Phytophthora ramorum in a key infectious host: landscape variation in host genotype, host phenotype, and environmental factors. New Phytol. 177, 756–766. Anderson, L.L., Hu, F.S., Nelson, D.M., Petit, R.J., Paige, K.N., 2006. Ice-age endurance: DNA evidence of a white spruce refugium in Alaska. Proc. Natl. Acad. Sci. USA 103, 12447–12450. André, T., Lemes, M.R., Grogan, J., Gribel, R., 2008. Postlogging loss of genetic diversity in a mahogany (Swietenia macrophylla King, Meliaceae) population in Brazilian Amazonia. For. Ecol. Manage. 255, 340–345. Andrianoelina, O., Rakotondraoelina, H., Ramamonjisoa, L., Maley, J., Danthu, P., Bouvet, J.-M., 2006. Genetic diversity of Dalbergia monticola (Fabaceae) an endangered tree species in the fragmented oriental forest of Madagascar. Biodiv. Conserv. 15, 1109–1128. Angelone, S., Hilﬁker, K., Holderegger, R., Bergamini, A., Hoebee, S.E., 2007. Regional population dynamics deﬁne the local genetic structure in Sorbus torminalis. Mol. Ecol. 16, 1291–1301. Arnaud-Haond, S., Teixeira, S., Massa, S.I., Billot, C., Saenger, P., Coupland, G., Duarte, C.M., Serrão, E.A., 2006. Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations. Mol. Ecol. 15, 3515–3525. Assogbadjo, A.E., Kyndt, T., Sinsin, B., Gheysen, G., Van Damme, P., 2006. Patterns of genetic and morphometric diversity in baobab (Adansonia digitata) populations across different climatic zones of Benin (West Africa). Ann. Bot. 97, 819–930. Avise, J.C., 2008. Three ambitious (and rather unorthodox) assignments for the ﬁeld of biodiversity genetics. Proc. Natl. Acad. Sci. USA 105, 11564–11570. Azevedo, V.C.R., Kanashiro, M., Ciampi, A.Y., Grattapaglia, D., 2007. Genetic structure and mating system of Manilkara huberi (Ducke) A. Chev., a heavily logged Amazonian timber species. J. Heredity 98, 646–654. Bacles, C.F.E., Ennos, R.A., 2008. Paternity analysis of pollen-mediated gene ﬂow for Fraxinus excelsior L. in a chronically fragmented landscape. Heredity 101, 368–380. Bacles, C.F.E., Lowe, A.J., Ennos, R.A., 2004. Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape. Mol. Ecol. 13, 573–584. Bacles, C.F.E., Burczyk, J., Lowe, A.J., Ennos, R.A., 2005. Historical and contemporary mating patterns in remnant populations of the forest tree Fraxinus excelsior L. Evolution 59, 979–990. Bartish, I.V., Kadereit, J.W., Comes, H.P., 2006. Late Quaternary history of Hippophaë rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation. Mol. Ecol. 15, 4065–4083. Baucom, R.S., Estill, J.C., Cruzan, M.B., 2005. The effect of deforestation on the genetic diversity and structure in Acer saccharum (Marsh): evidence for the loss and restructuring of genetic variation in a natural system. Conserv. Genet. 6, 39–50. Bawa, K.S., Dayanandan, S., 1998. Global climate change and tropical forest genetic resources. Clim. Change 39, 473–485. Bednorz, L., Myczko, L., Kosinski, P., 2006. Genetic variability and structure of the wild service tree (Sorbus torminalis (L.) crantz) in Poland. Silvae Genet. 55, 197–202. Bekessy, S.A., Allnutt, T.R., Premoli, A.C., Lara, A., Ennos, R.A., Burgman, M.A., Cortes, M., Newton, A.C., 2002. Genetic variation in the vulnerable and endemic Monkey Puzzle tree, detected using RAPDs. Heredity 88, 243–249. Belletti, P., Leonardi, S., Monteleone, I., Piovani, P., 2005. Allozyme variation in different species of deciduous oaks from north-western Italy. Silvae Genet. 54, 9–16. Belletti, P., Monteleone, I., Ferrazzini, D., 2007. Genetic variability at allozyme markers in sycamore (Acer pseudoplatanus) populations from northwestern Italy. Can. J. For. Res. 37, 395–403. Belletti, P., Monteleone, I., Ferrazzini, P., 2008. A population genetic study in a scattered forest species, wild service tree [Sorbus torminalis (L.) Crantz], using RAPD markers. Eur. J. For. Res. 127, 103–114. Belmonte, J., Alarcon, M., Avila, A., Scialabba, E., Pino, D., 2008. Long-range transport of beech (Fagus sylvatica L.) pollen to Catalonia (north-eastern Spain). Int. J. Biomet. 52, 675–687. Belokon, M.M., Belokon, Y.S., Politov, D.V., Altukhov, Y.P., 2005. Allozyme polymorphism of Swiss stone pine Pinus cembra L. in mountain populations of the Alps and the Eastern Carpathians. Russ. J. Genet. 41, 1268–1280. Bergmann, F., Gregorius, H.R., Larsen, J.B., 1990. Levels of genetic variation in European silver ﬁr (Abies alba). Are they related to the species’ decline? Genetica 82, 1–10. Besnard, G., Christin, P.A., Baali-Cherif, D., Bouguedoura, N., Anthelme, F., 2007. Spatial genetic structure in the Laperrine’s olive (Olea europaea subsp. laperrinei), a longliving tree from the central Saharan mountains. Heredity 99, 649–657. Bhagwat, S.A., Willis, K.J., 2008. Species persistence in northerly glacial refugia of Europe: a matter of chance or biogeographical traits? J. Biogeogr. 35, 464–482. Bilgen, B.B., Kaya, N., 2007. Allozyme variations in six natural populations of Scots pine (Pinus sylvestris) in Turkey. Biologia 62, 697–703. Bittencourt, J.V.M., Sebbenn, A.M., 2007. Patterns of pollen and seed dispersal in a small, fragmented population of the wind-pollinated tree Araucaria angustifolia in southern Brazil. Heredity 99, 580–591. Born, C., Hardy, O.J., Chevalier, M.-H., Ossari, S., Attéké, C., Wickings, J., Hoassaert-McKey, M., 2008a. Small-scale ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 spatial genetic structure in the Central African rainforest tree species Aucoumea klaineana: a stepwise approach to infer the impact of limited gene dispersal, population history and habitat fragmentation. Mol. Ecol. 17, 2041–2050. Born, C., Kyellberg, F., Chevallier, M.H., Vignes, H., Dikangadissi, J.T., Sanguie, J., Wickings, E.J., HossaertMcKey, M., 2008b. Colonization processes and the maintenance of genetic diversity: insights from a pioneer rainforest tree, Aucoumea klaineana. Proc. R. Soc. London B 275, 2171–2179. Botkin, D.B., Saxe, H., Araújo, M.B., et al., 2007. Forecasting the effects of global warming on biodiversity. Bioscience 57, 227–236. Bottin, L., Verhaegen, D., Tassin, J., Olivieri, I., Vaillant, A., Bouvet, J.M., 2005. Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago. Mol. Ecol. 14, 1979–1989. Boys, J., Cherry, M., Dayanandan, S., 2005. Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae). Am. J. Bot. 92, 833–841. Bradshaw, R.H.W., 2004. Past anthropogenic inﬂuence on European forests and some possible genetic consequences. For. Ecol. Manage. 197, 203–212. Breitenbach-Dorfer, M., Konnert, M., Pinsker, W., Starlinger, F., Geburek, T., 1997. The contact zone between two migration routes of silver ﬁr, Abies alba (Pinaceae), revealed by allozyme studies. Plant Syst. Evol. 206, 259–272. Bridle, J.R., Vines, T.H., 2007. Limits to evolution at range margins: when and why does adaptation fail? Trends Ecol. Evol. 22, 140–147. Bucci, G., González-Martı́nez, S.C., Le Provost, G., Plomion, C., Ribeiro, M.M., Sebastiani, F., Alia, R., Vendramin, G.G., 2007. Range-wide phylogeography and gene zones in Pinus pinaster Ait. revealed by chloroplast microsatellite markers. Mol. Ecol. 16, 2137–2153. Buiteveld, J., Koelewijn, H.P., 2006. CpDNA haplotype variation reveals strong human inﬂuence on oak stands of the Veluwe forest in the Netherlands. For. Ecol. Manage. 228, 160–167. Buiteveld, J., Vendramin, G.G., Leonardi, S., Kamer, K., Geburek, T., 2007. Genetic diversity and differentiation in European beech (Fagus sylvatica L.) stands varying in management history. For. Ecol. Manage. 247, 98–106. Burban, C., Petit, R.J., 2003. Phylogeography of maritime pine inferred with organelle markers having contrasted inheritance. Mol. Ecol. 12, 1487–1495. Burga, C.A., Hussendörfer, E., 2001. Vegetation history of Abies alba Mill. (silver ﬁr) in Switzerland-pollen analytical and genetic surveys related to aspects of vegetation history of Picea abies (L.) H. Karsten (Norway spruce). Veg. Hist. Archeobot. 10, 151–159. Butaud, J.-F., Rives, F., Verhaegen, D., Bouvet, J.-M., 2005. Phylogeography of Eastern Polynesian sandalwood (Santalum insulare), an endangered tree species from the Paciﬁc: a study based on chloroplast microsatellites. J. Biogeogr. 32, 1763–1774. Butcher, P.A., McDonald, M.W., Bell, J.C., 2009. Congruence between environmental parameters, morphology and genetic structure in Australia’s most widely distributed 175 eucalypt, Eucalyptus camaldulensis. Tree Genet. Genomes 5,189–210. Byrne, M., Elliott, C.P., Yates, C.J., Coates, D.J., 2008. Maintenance of high pollen dispersal in Eucalyptus wandoo, a dominant tree of the fragmented agricultural region in Western Australia. Conserv. Genet. 9, 97–105. Byrne, M., MacDonald, B., Coates, D., 2002. Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia. J. Evol. Biol. 15, 576–587. Camarero, J.J., Gutierrez, E., 2007. Response of Pinus uncinata recruitment to climate warming and changes in grazing pressure in an isolated population of the Iberian system (NE Spain). Arct. Antarct. Alp. Res. 39, 210–217. Cannon, C.H., Manos, P.S., 2003. Phylogeography of the Southeast Asian stone oaks (Lithocarpus). J. Biogeogr. 30, 211–226. Cardoso, S.R.S., Provan, J., Lira, C.F., Pereira, L.O.R., Ferreira, P.C.G., Cardoso, M.A., 2005. High levels of genetic structuring as a result of population fragmentation in the tropical tree species Caesalpinia echinata Lam. Biodiv. Conserv. 14, 1047–1057. Cardoso, M.A., Provan, J., Powell, W., Ferreira, P.C.B., De Oliveira, D.E., 1998. High genetic differentiation among remnant populations of the endangered Caesalpinia echinata Lam. (Leguminosae–Caesalpinioideae). Mol. Ecol. 7, 601–608. Cascante, A., Quesada, M., Lobo, J.J., Fuchs, E.A., 2002. Effects of dry tropical forest fragmentation on the reproductive success and genetic structure of the tree Samanea saman. Conserv. Biol. 16, 137–147. Casiva, P.V., Vilardiu, J.C., Cialdella, A.M., Saldman, B.O., 2004. Mating system and population structure of Acacia aroma and A. macracantha (Fabaceae). Am. J. Bot. 91, 58–64. Cavers, S., Navarro, C., Lowe, A.J., 2003a. A combination of molecular markers identiﬁes evolutionarily signiﬁcant units in Cedrela odorata L. (Meliaceae) in Costa Rica. Conserv. Genet. 4, 571–580. Cavers, S., Navarro, C., Lowe, A.J., 2003b. Chloroplast DNA phylogeography reveals colonization history of a neotropical tree, Cedrela odorata L., in Mesoamerica. Mol. Ecol. 12, 1451–1460. Cespedes, M., Gutierrez, M.V., Holbrook, N.M., Rocha, O.J., 2003. Restoration of genetic diversity in the dry forest tree Swietenia macrophylla (Meliaceae) after pasture abandonment in Costa Rica. Mol. Ecol. 12, 3201–3212. Charlesworth, D., 2003. Effects of inbreeding on the genetic diversity of populations. Phil. Trans. R. Soc. London B 358, 1051–1070. Cheddadi, R., Vendramin, G.G., Litt, T., Francois, L., Kageyama, M., Lorentz, S., Laurent, J.M., de Beaulieu, J.L., Sadori, L., Jost, A., Lunt, D., 2006. Imprints of glacial refugia in the modern genetic diversity of Pinus sylvestris. Glob. Ecol. Biogeogr. 15, 271–282. Chen, K.M., Abbott, R.J., Milne, R.I., Tian, X.M., Liu, J.Q., 2008. Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China. Mol. Ecol. 17, 4276–4288. ARTICLE IN PRESS 176 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Chen, Z., Kolb, T.E., Clancy, K.M., Hipkins, V.D., DeWald, L.E., 2001. Allozyme variation in interior Douglas-ﬁr: association with growth and resistance to western spruce budworm herbivory. Can. J. For. Res. 31, 1691–1700. Cheng, Y.-P., Hwang, S.-Y., Lin, T.-P., 2005. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae). Mol. Ecol. 14, 2075–2085. Chiang, Y.-C., Hung, K.-H., Schaal, B.A., Ge, X.-J., Hsu, T.-W., Chiang, T.-Y., 2006. Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex. Mol. Ecol. 15, 765–779. Chokchaichamnankit, P., Chulalaksananukul, W., Phengklai, C., Anamthawat-Jonsson, K., 2008. Species and genetic diversity of Fagaceae in northern Thailand based on ISSR markers. J. Trop. For. Sci. 20, 8–18. Christensen, N.L., Bartuska, A.M., Brown, J.H., Carpenter, S., D’Antonio, C., Francis, R., Franklin, J.F., MacMahon, J.A., Noss, R.F., Parsons, D.J., Peterson, C.H., Turner, M.G., Woodmansee, R.G., 1996. The report of the ecological society of America committee on the scientiﬁc basis for ecosystem management. Ecol. Appl. 6, 665–691. Chung, M.Y., Chung, M.G., 2004. Spatial genetic structure in populations of Quercus mongolica var. grosseserrata (Fagaceae) from southern Korea. Can. J. Bot. 82, 1402–1408. Chung, J.D., Lin, T.P., Tan, Y.C., Lin, M.Y., Hwang, S.Y., 2004. Genetic diversity and biogeography of Cunninghamia konishii (Cupressaceae), an island species in Taiwan: a comparison with Cunninghamia lanceolata, a mainland species in China. Mol. Phylogenet. Evol. 33, 791–801. Cloutier, D., Povoa, J.S.R., Procopio, L.C., Leao, N.V.M., Wadt, L.H.O., Ciampi, A.Y., Schoen, D.J., 2005. Chloroplast DNA Variation of Carapa guianensis in the Amazon basin. Silvae Genet. 54, 270–274. Cloutier, D., Kanashiro, M., Ciampi, A.Y., Schoen, D.J., 2007. Impact of selective logging on inbreeding and gene dispersal in an Amazonian tree population of Carapa guianensis Aubl. Mol. Ecol. 16, 797–809. Coart, E., Van Glabeke, S., Petit, R.J., Van Bockstaele, E., Roldán-Ruiz, I., 2005. Range wide versus local patterns of genetic diversity in hornbeam (Carpinus betulus L.). Conserv. Genet. 6, 259–273. Coates, D.J., Tischler, G., McComb, J.A., 2006. Genetic variation and the mating system in the rare Acacia sciophanes compared with its common sister species Acacia anfractuosa (Mimosaceae). Conserv. Genet. 7, 931–944. Coelho, A.C., Lima, M.B., Neves, D., Cravador, A., 2006. Genetic diversity of two evergreen oaks [Quercus suber (L.) and Quercus ilex subsp. rotundifolia (Lam.)] in Portugal using AFLP markers. Silvae Genet. 55, 105–118. Collignon, A.M., Van de Sype, H., Favre, J.M., 2002. Geographical variation in random ampliﬁed polymorphic DNA and quantitative traits in Norway spruce. Can. J. For. Res. 32, 266–282. Comes, H.P., Kadereit, J.W., 1998. The effect of Quaternary climatic changes on plant distribution and evolution. Trends Plant Sci. 3, 432–438. Conte, L., Cotti, C., Schicchi, R., Raimondo, F.M., Cristofolini, G., 2004. Detection of ephemeral genetic sub-structure in the narrow endemic Abies nebrodensis (Lojac.) Mattei (Pinaceae) using RAPD markers. Plant Biosystems 138, 279–289. Cottrell, J.E., Munro, R.C., Tabbener, H.E., Milner, A.D., Forrest, G.I., Lowe, A.J., 2003. Comparison of ﬁne-scale genetic structure using nuclear microsatellites within two British oakwoods differing in population history. For. Ecol. Manage. 176, 287–303. Cottrell, J.E., Krystufek, V., Tabbener, H.E., Milner, A.D., Connolly, T., Sing, L., Fluch, S., Burg, K., Lefèvre, F., Achard, P., Bordács, S., Gebhardt, K., Vornam, B., Smulders, M.J.M., Van den Broeck, A.H., Van Slycken, J., Storme, V., Boerjan, W., Castiglione, S., Fossati, T., Alba, N., Agúndez, D., Maestro, C., Notivol, E., Bovenschen, J., van Dam, B.C., 2005. Postglacial migration of Populus nigra L.: lessons learnt from chloroplast DNA. For. Ecol. Manage. 106, 71–90. Craft, K.J., Ashley, M.V., 2007. Landscape genetic structure of bur oak (Quercus macrocarpa) savannas in Illinois. For. Ecol. Manage. 239, 13–20. Craft, K.J., Ahsley, M.V., Koenig, W.D., 2002. Limited hybridization between Quercus lobata and Quercus douglasii (Fagaceae) in a mixed stand in central coastal California. Am. J. Bot. 89, 1792–1798. Curtu, A.L., Gailing, O., Finkeldey, R., 2007a. Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community. BMC Evol. Biol. 7, 218. Curtu, A.L., Gailing, O., Leinemann, L., Finkeldey, R., 2007b. Genetic variation and differentiation within a natural community of ﬁve oak species (Quercus spp.). Plant Biol. 9, 116–126. Dagher-Kharrat, M.B., Mariette, S., Lefevre, F., Fady, B., de March, G.G., Plomion, C., Savoure, A., 2007. Geographical diversity and genetic relationships among Cedrus species estimated by AFLP. Tree Genet. Genomes 3, 275–285. Dawson, I.K., Powell, W., 1999. Genetic variation in the Afromontane tree Prunus africana, an endangered medicinal species. Mol. Ecol. 8, 151–156. Dawson, W., Mndolwa, A.S., Burslem, D.F.R.P., Hulme, P.E., 2008. Assessing the risks of plant invasions arising from collections in tropical botanical gardens. Biodiv. Conserv. 17, 1979–1995. Dayanandan, S., Dole, J., Bawa, K., Kesseli, R., 1999. Population structure delineated with microsatellite markers in fragmented populations of a tropical tree, Carapa guianensis (Meliaceae). Mol. Ecol. 8, 1585–1592. de Casas, R.R., Cano, E., Balaguer, L., Perez-Corona, E., Manrique, E., Garcia-Verdugo, C., Vargas, P., 2007. Taxonomic identity of Quercus coccifera L. in the Iberian Peninsula is maintained in spite of widespread hybridisation, as revealed by morphological, ISSR and ITS sequence data. Flora 202, 488–499. de Heredia, U.L., Carrion, J.S., Jimenez, P., Collada, C., Gil, L., 2007. Molecular and palaeoecological evidence for multiple glacial refugia for evergreen oaks on the Iberian Peninsula. J. Biogeogr. 34, 1505–1517. de Lacerda, A.E.B., Kanashiro, M., Sebbenn, A.M., 2008. Effects of reduced impact logging on genetic diversity and spatial genetic structure of a Hymenaea courbaril ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 population in the Brazilian Amazon Forest. For. Ecol. Manage. 255, 1034–1043. de la Torre, A., López, C., Yglesias, E., Cornelius, J.P., 2008. Genetic (AFLP) diversity of nine Cedrela odorata populations in Madre de Dios, southern Peruvian Amazon. For. Ecol. Manage. 255, 334–339. Degen, B., Blanc, L., Caron, H., Maggia, L., Kremer, A., Gourlet-Fleury, S., 2006. Impact of selective logging on genetic composition and demographic structure of four tropical tree species. Biol. Conserv. 131, 386–401. Deguilloux, M.F., Pemonge, M.H., Petit, R.J., 2004. Use of chloroplast microsatellites to differentiate oak populations. Ann. For. Sci. 61, 825–830. Demesure, B., Comps, B., Petit, R.J., 1996. Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution 50, 2515–2520. Denslow, J.S., 1987. Tropical rain forest gaps and tree species diversity. Ann. Rev. Ecol. Syst. 18, 431–451. Dering, M., Lewandowski, A., Ufnalski, K., Kedzierska, A., 2008. How far to the east was the migration of white oaks from the Iberian refugium? Silva Fenn. 42, 327–335. Dick, C.W., Abdul-Salim, K., Bermingham, E., 2003a. Molecular systematic analysis reveals cryptic tertiary diversiﬁcation of a widespread tropical rain forest tree. Am. Nat. 162, 691–703. Dick, C.W., Etchelecu, G., Austerlitz, F., 2003b. Pollen dispersal of tropical trees (Dinizia excelsa: Fabaceae) by native insects and African honeybees in pristine and fragmented Amazonian rainforest. Mol. Ecol. 12, 753–764. Dick, C.W., Bermingham, E., Lemes, M.R., Gribel, R., 2007. Extreme long-distance dispersal of the lowland tropical rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics. Mol. Ecol. 16, 3039–3049. Duminil, J., Caron, H., Scotti, I., Cazal, S.-O., Petit, R.J., 2006. Blind population genetics survey of tropical rainforest trees. Mol. Ecol. 15, 3505–3513. Dumolin-Lapègue, S., Demesure, B., Fineschi, S., Le Corre, V., Petit, R.J., 1997. Phylogenetic structure of white oaks throughout the European continent. Genetics 146, 1475–1487. Dunphy, B.K., Hamrick, J.L., 2007. Estimation of gene ﬂow into fragmented populations of Bursera simaruba (Burseraceae) in the dry-forest life zone of Puerto Rico. Am. J. Bot. 94, 1786–1794. Eckert, A.J., Tearse, B.R., Hall, B.D., 2008. A phylogeographical analysis of the range disjunction for foxtail pine (Pinus balfouriana, Pinaceae): the role of Pleistocene glaciation. Mol. Ecol. 17, 1983–1997. El-Kassaby, Y.A., Dunsworth, B.G., Krakowski, J., 2003. Genetic evaluation of alternative silvicultural systems in coastal montane forests: western hemlock and amabilis ﬁr. Theor. Appl. Genet. 107, 598–610. Ennos, R.A., Sinclair, W.T., Hu, X.S., Langdon, A., 1999. Using organelle markers to elucidate the history, ecology and evolution of plant populations. In: Hollingsworth, P.M., Bateman, R.M., Gornall, R.J. (Eds.), Molecular Systematics and Plant Evolution of Plant Populations. Taylor & Francis, London, pp. 1–19. Fady, B., Lefevre, F., Vendramin, G.G., Ambert, A., Regnier, C., Bariteau, M., 2008. Genetic consequences of past 177 climate and human impact on eastern Mediterranean Cedrus libani forests. Implications for their conservation. Conserv. Genet. 9, 85–96. Farwig, N., Braun, C., Böhning-Gaese, K., 2008. Human disturbance reduces genetic diversity of an endangered tropical tree, Prunus africana (Rosaceae). Conserv. Genet. 9, 317–326. Fenberg, P.B., Roy, K., 2008. Ecological and evolutionary consequences of size-selective harvesting: how much do we know? Mol. Ecol. 17, 209–220. Fernández, J.F.M., Sork, V.L., 2007. Genetic variation in fragmented forest stands of the Andean oak Quercus humboldtii Bonpl. (Fagaceae). Biotropica 39, 72–78. Fernandez-Manjarres, J.F., Gerard, P.R., Dufour, J., Raquin, C., Frascaria-Lacoste, N., 2006. Differential patterns of morphological and molecular hybridization between Fraxinus excelsior L. and Fraxinus angustifolia Vahl (Oleaceae) in eastern and western France. Mol. Ecol. 15, 3245–3257. Ferrazzini, D., Monteleone, I., Belletti, P., 2007. Genetic variability and divergence among Italian populations of common ash (Fraxinus excelsior L.). Ann. For. Sci. 64, 159–168. Ferris, C., King, R.A., Vainola, R., Hewitt, G.M., 1998. Chloroplast DNA recognizes three refugial sources of European oaks and suggests independent eastern and western immigrations to Finland. Heredity 80, 584–593. Feyissa, T., Nybom, H., Bartish, I.V., Welander, M., 2007. Analysis of genetic diversity in the endangered tropical tree species Hagenia abyssinica using ISSR markers. Gen. Res. Crop Evol. 54, 947–958. Fineschi, S., Anzidei, M., Cafasso, D., Cozzolino, S., Garfı́, G., Pastorelli, R., Salvini, D., Taurchini, D., Vendramin, G.G., 2002. Molecular markers reveal a strong genetic differentiation between two European relic tree species: Zelkova abelicea (Lam.) Boissier and Z. sicula Di Pasquale, Garfı̀ & Quézel (Ulmaceae). Conserv. Genet. 3, 145–153. Fineschi, S., Cozzolino, S., Migliaccio, M., Musacchio, A., Innocenti, M., Vendramin, G.G., 2005. Sicily represents the Italian reservoir of chloroplast DNA diversity of Quercus ilex L. (Fagaceae). Ann. For. Sci. 62, 79–84. Finkeldey, R., 2001. Forschung zur Vielfalt, vielfältige Forschung: Ziele und Wege der Forstgenetik. Schw. Z. Forstw. 152, 162–168. Finkeldey, R., Ziehe, M., 2004. Genetic implications of silvicultural regimes. For. Ecol. Manage. 197, 231–244. Finkeldey, R., Mátyás, G., 2003. Genetic variation of oaks (Quercus spp.) in Switzerland. 3. Lack of impact of postglacial recolonization history on nuclear gene loci. Theor. Appl. Genet. 106, 346–352. Fontaine, C., Lovett, P.N., Sanou, H., Maley, J., Bouvet, J.-M., 2004. Genetic diversity of the shea tree (Vitellaria paradoxa C. F. Gaertn), detected by RAPD and chloroplast microsatellite markers. Heredity 93, 639–648. Fowler, D.P., Morris, R.W., 1977. Genetic diversity in red pine: evidence for low genic heterozygosity. Can. J. For. Res. 7, 343–347. Franceschinelli, E.V., Vasconcelos, G.M.P., Landau, E.C., Ono, K.Y., Santos, F.A.M., 2007. The genetic diversity of Myrciaria floribunda (Myrtaceae) in Atlantic Forest fragments of different sizes. J. Trop. Ecol. 23, 361–367. ARTICLE IN PRESS 178 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Franjic, J., Liber, Z., Skvorc, Z., Idzojtic, M., Sostaric, R., Stancic, Z., 2006. Morphological and molecular differentiation of the Croatian populations of Quercus pubescens Willd. (Fagaceae). Acta Soc. Bot. Pol. 75, 123–130. Freeman, J.S., Jackson, H.D., Steane, D.A., McKinnon, G.E., Dutkowski, G.W., Potts, B.M., Vaillancourt, R.E., 2001. Chloroplast DNA phylogeography of Eucalyptus globulus. Aust. J. Bot. 49, 585–596. Fromm, M., Hattemer, H.H., 2003. Inheritance of allozymes and hybridization in two European Tilia species. Heredity 91, 337–344. Fu, Y., Dane, F., 2003. Allozyme variation in endangered Castanea pumila var. pumila. Ann. Bot. 92, 223–230. Furnier, G.R., Adams, W.T., 1986. Geographic patterns of allozyme variation in Jeffrey pine. Am. J. Bot. 73, 1009–1015. Gamache, I., Jaramillo-Correa, J.P., Payette, S., Bousquet, J., 2003. Diverging patterns of mitochondrial and nuclear DNA diversity in subarctic black spruce: imprint of a founder effect associated with postglacial colonization. Mol. Ecol. 12, 891–901. Gao, L.M., Möller, M., Zhang, X.M., Hollingsworth, M.L., Liu, J., Mill, R.R., Gibby, M., Li, D.-Z., 2007. High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Mol. Ecol. 16, 4684–4698. Gapare, W.J., Aitken, S.N., 2005. Strong spatial genetic structure in peripheral but not core populations of Sitka spruce [Picea sitchensis (Bong.) Carr.]. Mol. Ecol. 14, 2659–2667. Gapare, W.J., Yanchuk, A.D., Aitken, S.N., 2007. Optimal sampling strategies for capture of genetic diversity differ between core and peripheral populations of Picea sitchensis (Bong.) Carr. Conserv. Genet. 9, 411–418. Garnier-Géré, P.H., Ades, P.K., 2001. Environmental surrogates for predicting and conserving adaptive genetic variability in tree species. Conserv. Biol. 15, 1632–1644. Geburek, T., 1997. Isozymes and DNA markers in gene conservation of forest trees. Biodiv. Conserv. 6, 1639–1654. Geburek, T., Konrad, H., 2008. Why the conservation of forest genetic resources has not worked. Conserv. Biol. 22, 267–274. Gehrig-Fasel, J., Guisan, A., Zimmermann, N.E., 2007. Tree line shifts in the Swiss Alps: climate change or land abandonment? J. Veg. Sci. 18, 571–582. Gentry, A.H., 1992. Tropical forest biodiversity – distributional patterns and their conservational signiﬁcance. Oikos 63, 19–28. Gerwein, J.B., Kesseli, R.V., 2006. Genetic diversity and population structure of Quercus rubra (Fagaceae) in oldgrowth and secondary forests in southern New England. Rhodora 108, 1–18. Giannini, R., Morgante, M., Vendramin, G.G., 1991. Allozyme variation in Italian populations of Picea abies (L.) Karst. Silvae Genet. 40, 160–166. Gibson, J.P., Rice, S.A., Stucke, C.M., 2008. Comparison of population genetic diversity between a rare narrowly distributed species and a common widespread species of Alnus (Betulaceae). Am. J. Bot. 95, 588–596. Gillespie, T.W., Grijalva, A., Farris, C.N., 2000. Diversity, composition, and structure of tropical dry forests in Central America. Plant Ecol. 147, 37–47. Glaubitz, J.C., Murrell, J.C., Moran, G.F., 2003a. Effects of native forest regeneration practices on genetic diversity in Eucalyptus consideniana. Theor. Appl. Genet. 107, 422–431. Glaubitz, J.C., Wu, H.X., Moran, G.F., 2003b. Impacts of silviculture on genetic diversity in the native forest species Eucalyptus sieberi. Conserv. Genet. 4, 275–287. Godbout, J., Jaramillo-Correa, J.P., Beaulieu, J., Bousquet, J., 2005. A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer. Mol. Ecol. 14, 3497–3512. Godbout, J., Fazekas, A., Newton, C.H., Yeh, F.C., Bousquet, J., 2008. Glacial vicariance in the Paciﬁc Northwest: evidence from a lodgepole pine mitochondrial DNA minisatellite for multiple genetically distinct and widely separated refugia. Mol. Ecol. 17, 2463–2475. Gömöry, D., Schmidtová, J., 2007. Extent of nuclear genome sharing among white oak species (Quercus L. subgen. Lepidobalanus (Endl.) Oerst.) in Slovakia estimated by allozymes. Plant Syst. Evol. 266, 253–264. Gömöry, D., Paule, L., Visny, J., 2007. Patterns of allozyme variation in western Eurasian Fagus. Bot. J. Linn. Soc. 154, 165–174. Gong, W., Chen, C., Dobes, C., Fu, C.X., Koch, M.A., 2008. Phylogeography of a living fossil: Pleistocene glaciations forced Ginkgo biloba L. (Ginkgoaceae) into two refuge areas in China with limited subsequent postglacial expansion. Mol. Phylogen. Evol. 48, 1094–1105. González-Astorga, J., Castillo-Campos, G., 2004. Genetic variability of the narrow endemic tree Antirhea aromatica Castillo-Campos & Lorence, (Rubiaceae, Guettardeae) in a tropical forest of Mexico. Ann. Bot. 93, 521–528. González-Astorga, J., Vovides, A.P., Cruz-Angon, A., Octavio-Aguilar, P., Iglesias, C., 2005. Allozyme variation in the three extant populations of the narrowly endemic cycad Dioon angustifolium Miq. (Zamiaceae) from North-eastern Mexico. Ann. Bot. 95, 999–1007. González-Martı́nez, S.C., Mariette, S., Ribeiro, M.M., Burban, C., Rafﬁn, A., Chambel, M.R., Ribeiro, C.A.M., Aguiar, A., Plomion, C., Alia, R., Gil, L., Vendramin, G.G., Kremer, A., 2004. Genetic resources in maritime pine (Pinus pinaster Aiton): molecular and quantitative measures of genetic variation and differentiation among maternal lineages. For. Ecol. Manage. 197, 103–115. González-Martı́nez, S.C., Krutovsky, K.V., Neale, D.B., 2006. Forest-tree population genomics and adaptive evolution. New Phytol. 170, 227–238. González-Rodrı́guez, A., Bain, J.F., Golden, J.L., Oyama, K., 2004. Chloroplast DNA variation in the Quercus affinis–Q. laurina complex in Mexico: geographical structure and associations with nuclear and morphological variation. Mol. Ecol. 13, 3467–3476. Gram, W.K., Sork, V.L., 2001. Association between environmental and genetic heterogeneity in forest tree populations. Ecology 82, 2012–2021. ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Grant, E.H.C., Lowe, W.H., Fagan, W.F., 2007. Living in the branches: population dynamics and ecological processes in dendritic networks. Ecol. Lett. 10, 165–175. Gregorius, H.R., Bergmann, F., Wehenkel, C., 2003. Analysis of biodiversity across levels of biological organization: a problem of deﬁning traits. Perspect. Plant Ecol. Evol Syst. 5, 209–218. Grivet, D., Petit, R.J., 2003. Chloroplast DNA phylogeography of the hornbeam in Europe: evidence for a bottleneck at the outset of postglacial colonization. Conserv. Genet. 4, 47–56. Grivet, D., Sork, V.L., Westfall, R.D., Davis, F.W., 2008. Conserving the evolutionary potential of California valley oak (Quercus lobata Née): a multivariate genetic approach to conservation planning. Mol. Ecol. 17, 139–156. Grivet, D., Deguilloux, M.-F., Petit, R.J., Sork, V.L., 2006. Contrasting patterns of historical colonization in white oaks (Quercus spp.) in California and Europe. Mol. Ecol. 15, 4085–4093. Gugerli, F., Sperisen, C., Buchler, U., Magni, F., Geburek, T., Jeandroz, S., Senn, J., 2001. Haplotype variation in a mitochondrial tandem repeat of Norway spruce (Picea abies) populations suggests a serious founder effect during postglacial re-colonization of the western Alps. Mol. Ecol. 10, 1255–1263. Gugerli, F., Walser, J.-C., Dounavi, K., Holderegger, R., Finkeldey, R., 2007. Coincidence of small-scale spatial discontinuities in leaf morphology and nuclear microsatellite variation of Quercus petraea and Q. robur in a mixed forest. Ann. Bot. 99, 713–722. Gugger, P.F., McLachlan, J.S., Manos, P.S., Clark, J.S., 2008. Inferring long-distance dispersal and topographic barriers during post-glacial colonization from the genetic structure of red maple (Acer rubrum L.) in New England. J. Biogeogr. 35, 1665–1673. Guisan, A., Zimmermann, N.E., Elith, J., Graham, C.H., Phillips, S., Peterson, A.T., 2007. What matters for predicting the occurrences of trees: techniques, data, or species’ characteristics? Ecol. Monogr. 77, 615–630. Hall, D., Luquez, V., Garcia, V.M., Onge, K.R., Jansson, S., Ingvarsson, P.K., 2007. Adaptive population differentiation in phenology across a latitudinal gradient in European aspen (Populus tremula, L.): a comparison of neutral markers, candidate genes and phenotypic traits. Evolution 61, 2849–2860. Hall, P., Walker, S., Bawa, K., 1996. Effect of forest fragmentation on genetic diversity and mating system in a tropical tree, Pithecellobium elegans. Conserv. Biol. 10, 757–768. Hamann, A., Aitken, S.N., Yanchuk, A.D., 2004. Cataloguing in situ protection of genetic resources for major commercial forest trees in British Columbia. For. Ecol. Manage. 197, 295–305. Hampe, A., Petit, R., 2005. Conserving biodiversity under climate change: the rear edge matters. Ecol. Lett. 8, 461–467. Hamrick, J.L., 2004. Response of forest trees to global environmental changes. For. Ecol. Manage. 197, 323–335. 179 Hamrick, J.L., Godt, M.J.W., Gonzales, E., 2006. Conservation of genetic diversity in old-growth forest communities of the southeastern United States. Appl. Veg. Sci. 9, 51–57. Hanaoka, S., Yuzurihara, J., Asuka, Y., Tomaru, N., Tsumura, Y., Kakubari, Y., Mukai, Y., 2007. Pollenmediated gene ﬂow in a small, fragmented natural population of Fagus crenata. Can. J. Bot. 85, 404–413. Hansen, E.M., 2008. Alien forest pathogens: Phytophthora species are changing world forests. Bor. Environ. Res. 13, 33–41. Hansen, O.K., Kjaer, E.D., Vendramin, G.G., 2005. Chloroplast microsatellite variation in Abies nordmanniana and simulation of causes for low differentiation among populations. Tree Genet. Genomes 1, 116–123. Hanson, T.R., Brunsﬁeld, S.J., Finegan, B., Waits, L.P., 2008. Pollen dispersal and genetic structure of the tropical tree Dipteryx panamensis in a fragmented Costa Rican landscape. Mol. Ecol. 17, 2060–2073. Hardig, T.M., Brunsﬁeld, S.J., Fritz, R.S., Morgan, M., Orians, C.M., 2000. Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone. Mol. Ecol. 9, 9–24. Hardy, O.J., Maggia, L., Bandou, E., Breyne, P., Caron, H., Chevallier, M.-H., Doligez, A., Dutech, C., Kremer, A., Latouche-Halle, C., Troispoux, V., Veron, V., Degen, B., 2006. Fine-scale genetic structure and gene dispersal inferences in 10 neotropical tree species. Mol. Ecol. 15, 559–571. Hawley, G.J., Schaberg, P.G., DeHayes, D.H., Brissette, J.C., 2005. Silviculture alters the genetic structure of an eastern hemlock forest in Maine, USA. Can. J. For. Res. 35, 143–150. Hebel, I., Haas, R., Dounavi, A., 2006. Genetic variation of common ash (Fraxinus excelsior L.) populations from provenance regions in Southern Germany by using nuclear and chloroplast microsatellites. Silvae Genet. 55, 38–44. Hermy, M., Verheyen, K., 2007. Legacies of the past in the present-day forest biodiversity: a review of past land-use effects on forest plant species composition and diversity. Ecol. Res. 22, 361–371. Hertel, H., Zaspel, I., 1996. Investigations on vitality and genetic structure in oak stands. Ann. Sci. For. 53, 761–773. Heuertz, M., Hausman, J.-F., Tsvetkov, I., Frascaria-Lacoste, N., Vekemans, X., 2001. Assessment of genetic structure within and among Bulgarian populations of the common ash (Fraxinus excelsior L.). Mol. Ecol. 10, 1615–1623. Heuertz, M., Fineschi, S., Anzidei, M., Pastorelli, R., Salvini, D., Paule, L., Frascaria-Lacoste, N., Hardy, O.J., Vekemans, X., Vendramin, G.G., 2004a. Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol. Ecol. 13, 3437–3452. Heuertz, M., Hausman, J.F., Hardy, O.J., Vendramin, G.G., Frascaria-Lacoste, N., Vekemans, X., 2004b. Nuclear microsatellites reveal contrasting patterns of genetic structure between western and southeastern European populations of the common ash (Fraxinus excelsior L.). Evolution 58, 976–988. Heuertz, M., Carnevale, S., Fineschi, S., Sebastiani, F., Hausman, J.F., Paule, L., Vendramin, G.G., 2006a. ARTICLE IN PRESS 180 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Chloroplast DNA phylogeography of European ashes, Fraxinus sp. (Oleaceae): roles of hybridization and life history traits. Mol. Ecol. 15, 2131–2140. Heuertz, M., De Paoli, E., Källman, T., Larsson, H., Jurman, I., Morgante, M., Lascoux, M., Gyllenstrand, N., 2006b. Multilocus patterns of nucleotide diversity, linkage disequilbrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174, 2095–2105. Hewitt, G.M., 1996. Some genetic consequences of ice age, and their role in divergence and speciation. Biol. J. Linn. Soc. 58, 247–276. Hewitt, G.M., 2000. The genetic legacy of the quaternary ice ages. Nature 405, 907–913. Hilﬁker, K., Holderegger, R., Rotach, P., Gugerli, F., 2004. Dynamics of genetic variation in Taxus baccata: local versus regional perspectives. Can. J. Bot. 82, 219–227. Hirayama, K., Ishida, K., Setsuko, S., Tomaru, N., 2007. Reduced seed production, inbreeding, and pollen shortage in a small population of a threatened tree, Magnolia stellata. Biol. Conserv. 136, 315–323. Hoebee, S.E., Arnold, U., Düggelin, C., Gugerli, F., Brodbeck, S., Rotach, P., Holderegger, R., 2007. Mating patterns and contemporary gene ﬂow by pollen in a large continuous and a small isolated population of the scattered forest tree Sorbus torminalis. Heredity 99, 47–55. Holdenrieder, O., Pautasso, M., Weisberg, P.J., Lonsdale, D., 2004. Tree diseases and landscape processes: the challenge of landscape pathology. Trends Ecol. Evol. 19, 446–452. Holderegger, R., Wagner, H.H., 2008. Landscape genetics. BioScience 58, 199–207. Holderegger, R., Angelone, S., Brodbeck, S., Csencsics, D., Gugerli, F., Hoebee, S.E., Finkeldey, R., 2005. Application of genetic markers to the discrimination of European Black Poplar (Populus nigra) from American Black Poplar (P. deltoides) and Hybrid Poplars (P.x canadensis) in Switzerland. Trees 19, 742–747. Honnay, O., Jacquemyn, H., 2007. Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation. Conserv. Biol. 21, 823–831. Hosius, B., Leinemann, L., Bergmann, F., Maurer, W., Tabel, U., Eder, W., 2001. Species diversity and genetic diversity – is there any relationship? Allg. Forst- Jagdz. 172, 87–91. Hosius, B., Leinemann, L., Konnert, M., Bergmann, F., 2006. Genetic aspects of forestry in the Central Europe. Eur. J. For. Res. 125, 407–417. Howard, D.J., Preszler, R.W., Williams, J., Fenchel, S., Boecklen, W.J., 1997. How discrete are oak species? Insights from a hybrid zone between Quercus grisea and Quercus gambelii. Evolution 51, 747–755. Hu, L.J., Uchiyama, K., Shen, H.L., Saito, Y., Tsuda, Y., Ide, Y., 2008. Nuclear DNA microsatellites reveal genetic variation but a lack of phylogeographical structure in an endangered species, Fraxinus mandshurica, across northeast China. Ann. Bot. 102, 195–205. Hughes, A.R., Inouye, B.D., Johnson, M.T.J., Underwood, N., Vellend, M., 2008. Ecological consequences of genetic diversity. Ecol. Lett. 11, 609–623. Isagi, Y., Tateno, R., Matsuki, Y., Hirao, A., Watanabe, S., Shibata, M., 2007. Genetic and reproductive consequences of forest fragmentation for populations of Magnolia obovata. Ecol. Res. 22, 382–389. Iwasaki, T., Aoki, K., Seo, A., Murakami, N., 2006. Intraspeciﬁc sequence variation of chloroplast DNA among the component species of deciduous broad-leaved forests in Japan. J. Plant Res. 119, 539–552. Jactel, H., Brockerhoff, E.G., 2007. Tree diversity reduces herbivory by forest insects. Ecol. Lett. 10, 835–848. Jansson, R., Davies, T.J., 2008. Global variation in diversiﬁcation rates of ﬂowering plants: energy vs. climate change. Ecol. Lett. 11, 173–183. Jaramillo-Correa, J.P., Bousquet, J., 2005. Mitochondrial genome recombination in the zone of contact between two hybridizing conifers. Genetics 171, 1951–1962. Jaramillo-Correa, J.P., Beaulieu, J., Bousquet, J., 2004. Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Mol. Ecol. 13, 2735–2747. Jaramillo-Correa, J.P., Beaulieu, J., Ledig, F.T., Bousquet, J., 2006. Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer. Mol. Ecol. 15, 2787–2800. Jaramillo-Correa, J.P., Aguirre-Planter, E., Khasa, D.P., Eguiarte, L.E., Piñero, D., Furnier, G.R., Bousquet, J., 2008. Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala. Mol. Ecol. 17, 2476–2490. Jones, M.E., Shepherd, M., Henry, R.J., Delves, A., 2006. Chloroplast DNA variation and population structure in the widespread forest tree, Eucalyptus grandis. Conserv. Genet. 7, 691–703. Jump, A.S., Peñuelas, J., 2006. Genetic effects of chronic habitat fragmentation in a wind-pollinated tree. Proc. Natl. Acad. Sci. USA 103, 8096–8100. Jump, A.S., Peñuelas, J., 2007. Extensive spatial genetic structure revealed by AFLP but not SSR molecular markers in the wind-pollinated tree, Fagus sylvatica. Mol. Ecol. 16, 925–936. Kado, T., Matsumoto, A., Ujino-Ihara, T., Tsumura, Y., 2008. Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato). Tree Genet. Genomes 4, 133–141. Kado, T., Ushio, Y., Yoshimaru, H., Tsumura, Y., Tachida, H., 2006. Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato). Genes Genet. Syst. 81, 103–113. Karhu, A., Hurme, P., Karjalainen, M., Karvonen, P., Kärkkäinen, K., Neale, D., Savolainen, O., 1996. Do molecular markers reﬂect patterns of differentiation in adaptive traits of conifers? Theor. Appl. Genet. 93, 215–221. Kelleher, C.T., Hodkinson, T.R., Douglas, G.C., Kelly, D.L., 2005. Species distinction in Irish populations of Quercus petraea and Q. robur: morphological versus molecular analyses. Ann. Bot. 96, 1237–1246. ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Kettle, C.J., Hollingsworth, P.M., Jaffre, T., Moran, B., Ennos, R.A., 2007. Identifying the early genetic consequences of habitat degradation in a highly threatened tropical conifer, Araucaria nemorosa Laubenfels. Mol. Ecol. 16, 3581–3591. Kettle, C.J., Ennos, R.A., Jaffre, T., Gardner, M., Hollingsworth, P.M., 2008. Cryptic genetic bottlenecks during restoration of an endangered tropical conifer. Biol. Conserv. 141, 1953–1961. Khasa, D.P., Jaramillo-Correa, J.P., Jaquish, B., Bousquet, J., 2006. Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns. Mol. Ecol. 15, 3907–3918. Khatab, I.A., Ishiyama, H., Inomata, N., Wang, X.-R., Szmidt, A.E., 2008. Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes. Genes Genet. Syst. 83, 55–66. Kim, S.H., Jang, Y.S., Han, J.G., Chung, H.G., Lee, S.W., Cho, K.J., 2006. Genetic variation and population structure of Dendropanax morbifera Lev. (Araliaceae) in Korea. Silvae Genet. 55, 7–13. Kim, Z.S., Hwang, J.W., Lee, S.W., Yang, C., Gorovy, P.G., 2005. Genetic variation of Korean pine (Pinus koraiensis Sieb. Et Zucc.) at allozyme and RAPD markers in Korea, China and Russia. Silvae Genet. 54, 235–246. King, R.A., Ferris, C., 1998. Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Mol. Ecol. 7, 1151–1161. King, R.A., Ferris, C., 2000. Chloroplast DNA and nuclear DNA variation in the sympatric alder species, Alnus cordata (Lois.) Duby and A. glutinosa (L.) Gaertn. Biol. J. Linn. Soc. 70, 147–160. Kinloch, B.B., Sniezko, R.A., Dupper, G.E., 2004. Virulence gene distribution and dynamics of the white pine blister rust pathogen in western North America. Phytopathology 94, 751–758. Kobashi, S., Fujii, N., Nojima, A., Hori, N., 2006. Distribution of chloroplast DNA haplotypes in the contact zone of Fagus crenata in the southwest of Kanto District, Japan. J. Plant Res. 119, 265–269. König, A.O., Ziegenhagen, B., van Dam, B.C., Csaikl, U.M., Coart, E., Degen, B., Burg, K., de Vries, S.M.G., Petit, R.J., 2002. Chloroplast DNA variation of oaks in western Central Europe and genetic consequences of human inﬂuences. For. Ecol. Manage. 156, 147–166. Konnert, M., Bergmann, F., 1995. The geographical distribution of genetic variation of silver ﬁr (Abies alba, Pinaceae) in relation to its migration history. Plant Syst. Evol. 196, 19–30. Kramer, A.T., Ison, J.L., Ashley, M.V., Howe, H.F., 2008a. The paradox of forest fragmentation genetics. Conserv. Biol. 22, 878–885. Kramer, K., Buiteveld, J., Forstreuter, M., Geburek, T., Leonardi, S., Menozzi, P., Povillon, F., Schelhaas, M., du Cros, E.T., Vendramin, G.G., van der Werf, D.C., 2008b. Bridging the gap between ecophysiological and genetic knowledge to assess the adaptive potential of European beech. Ecol. Model. 216, 333–353. 181 Kreft, H., Jetz, W., Mutke, J., Kier, G., Barthlott, W., 2008. Global diversity of island ﬂoras from a macroecological perspective. Ecol. Lett. 11, 116–127. Kremer, A., 1994. Genetic diversity and phenotypic variability of forest trees. Genet. Select. Evol. 26, S105–S123. Kremer, A., Dupouey, J.L., Deans, J.D., Cottrell, J., Csaikl, U., Finkeldey, R., Espinel, S., Jensen, J., Kleinschmit, J., Van Dam, B., Ducousso, A., Forrest, I., de Heredia, U.L., Lowe, A.J., Tutkova, M., Munro, R.C., Steinhoff, S., Badeau, V., 2002a. Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands. Ann. For. Sci. 59, 777–787. Kremer, A., Kleinschmit, J., Cottrell, J., Cundall, E.P., Deans, J.D., Ducousso, A., Konig, A.O., Lowe, A.J., Munro, R.C., Petit, R.J., Stephan, B.R., 2002b. Is there a correlation between chloroplastic and nuclear divergence, or what are the roles of history and selection on genetic diversity in European oaks? For. Ecol. Manage. 156, 75–87. Kwon, J.A., Morden, C.W., 2002. Population genetic structure of two rare tree species (Colubrina oppositifolia and Alphitonia ponderosa, Rhamnaceae) from Hawaiian dry and mesic forests using random ampliﬁed polymorphic DNA markers. Mol. Ecol. 11, 991–1001. Labra, M., Grassi, F., Sgorbati, S., Ferrari, C., 2006. Distribution of genetic variability in southern populations of Scots pine (Pinus sylvestris L.) from the Alps to the Apennines. Flora 201, 468–476. Lande, R., Shannon, S., 1996. The role of genetic variation in adaptation and population persistence in a changing environment. Evolution 50, 434–437. Lang, P., Huang, H.W., 1999. Genetic diversity and geographic variation in natural populations of the endemic Castanea species in China. Acta Bot. Sin. 41, 651–657. Lang, P., Dane, F., Kubisiak, T.L., 2006. Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data. Tree Genet. Genomes 2, 132–139. Lang, P., Dane, F., Kubisiak, T.L., Huang, H., 2007. Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America. Mol. Phylog. Evol. 43, 49–59. Lara-Gomez, G., Gailing, O., Finkeldey, R., 2005. Untersuchung der genetischen Variation in isolierten Populationen der Ahornart Acer skutchii Rehd. Allg. Forst- Jagdz. 176, 97–103. Le Corre, V., Roussel, G., Zanetto, A., Kremer, A., 1998. Geographical structure of gene diversity in Quercus petraea (Matt.) Liebl. III. Patterns of variation identiﬁed by geostatistical analyses. Heredity 80, 464–473. Ledig, F.T., 1992. Human impacts on genetic diversity in forest ecosystems. Oikos 63, 87–108. Ledig, F.T., Hodgskiss, P.D., Johnson, D.R., 2006. Genetic diversity and seed production in Santa Lucia ﬁr (Abies bracteata), a relict of the Miocene Broadleaved Evergreen Forest. Conserv. Genet. 7, 383–398. Lee, C.-T., Wickneswari, R., Mahani, M.C., Zakri, A.H., 2002. Effect of selective logging on the genetic diversity of Scaphium macropodum. Biol. Conserv. 104, 107–118. ARTICLE IN PRESS 182 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Lefèvre, F., 2004. Human impacts on forest genetic resources in the temperate zone: an updated review. For. Ecol. Manage. 197, 257–271. Lexer, C., Van Loo, M., Barbará, T., 2007. Towards forest community and ecosystem genomics. New Phytol. 173, 673–676. Li, J., Ge, X.J., Cao, H.L., Ye, W.H., 2007. Chloroplast DNA diversity in Castanopsis hystrix populations in south China. For. Ecol. Manage. 243, 94–101. Lian, C., Goto, S., Kubo, T., Takahashi, Y., Nakagawa, M., Hogetsu, T., 2008. Nuclear and chloroplast microsatellite analysis of Abies sachalinensis regeneration on fallen logs in a subboreal forest in Hokkaido, Japan. Mol. Ecol. 17, 2948–2962. Liesebach, M., 2002. On the adaptability of Norway spruce (Picea abies (L.) Karst.) to the projected change of climate in Germany. Forstw. Centrblt. 121, 130–144. Lipow, S.R., Vance-Borland, K., St Clair, J.B., Henderson, J., McCain, C., 2004. Gap analysis of conserved genetic resources for forest trees. Conserv. Biol. 18, 412–423. Lise, Y., Kaya, Z., Isik, F., Sabuncu, R., Kandemir, I., Önde, S., 2007. The impact of over-exploitation on the genetic structure of Turkish red pine (Pinus brutia Ten.) populations determined by RAPD markers. Silva Fenn. 41, 211–220. Loacker, K., Koﬂer, W., Pagitz, K., Oberhuber, W., 2007. Spread of walnut (Juglans regia L.) in an Alpine valley is correlated with climate warming. Flora 202, 70–78. Longauer, R., Gomory, D., Paule, L., Blada, I., Popescu, F., Mankovska, B., Muller-Starck, G., Schubert, R., Percy, K., Szaro, R.C., Karnosky, D.F., 2004. Genetic effects of air pollution on forest tree species on the Carpathian mountains. Environ. Pollut. 130, 85–92. Lonsdale, D., Pautasso, M., Holdenrieder, O., 2008. Wooddecaying fungi in the forest: conservation needs and management options. Eur. J. For. Res. 127, 1–22. Lowe, A.J., Boshier, D., Ward, M., Bacles, C.F.E., Navarro, C., 2005. Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees. Heredity 95, 255–273. Lozano-Garcia, S., Sosa-Najera, S., Sugiura, Y., Caballero, M., 2005. 23,000 yr of vegetation history of the Upper Lerma, a tropical high-altitude basin in Central Mexico. Quat. Res. 64, 70–82. Lubchenco, J., 1998. Entering the century of the environment: a new social contract for science. Science 279, 491–497. Luck, G.W., 2007. A review of the relationships between human population density and biodiversity. Biol. Rev. 82, 607–645. Lumaret, R., Tryphon-Dionnet, M., Michaud, H., Sanuy, A., Ipotesi, I., Born, C., Mir, C., 2005. Phylogeographical variation of chloroplast DNA in cork oak (Quercus suber). Ann. Bot. 96, 853–861. Maghuly, F., Nittinger, F., Pinsker, W., Praznik, W., Fluch, S., 2007. Differentiation among Austrian populations of Norway spruce [Picea abies (L.) Karst.] assayed by mitochondrial DNA markers. Tree Genet. Genomes 3, 199–206. Magni, C.R., Ducousso, A., Caron, H., Petit, R.J., Kremer, A., 2005. Chloroplast DNA variation of Quercus rubra L. in North America and comparison with other Fagaceae. Mol. Ecol. 14, 513–524. Magri, D., 2008. Patterns of post-glacial spread and the extent of glacial refugia of European beech (Fagus sylvatica). J. Biogeogr. 35, 450–463. Magri, D., Vendramin, G.G., Comps, B., Dupanloup, I., Geburek, T., Gömöry, D., Latałowa, M., Litt, T., Paule, L., Roure, J.M., Tantau, I., van der Knaap, W.O., Petit, R.J., de Beaulieu, J.-L., 2006. A new scenario for the Quaternary history of European beech populations: palaeobotanical evidence and genetic consequences. New Phytol. 171, 199–221. Major, J.E., Barsi, D.C., Mosseler, A., Campbell, M., 2007. Genetic variation and control of chloroplast pigment concentrations in Picea rubens, Picea mariana and their hybrids. I. Ambient and elevated [CO2] environments. Tree Physiol. 27, 353–364. Maliouchenko, O., Palme, A.E., Buonamici, A., Vendramin, G.G., Lascoux, M., 2007. Comparative phylogeography and population structure of European Betula species, with particular focus on B. pendula and B. pubescens. J. Biogeogr. 34, 1601–1610. Manel, S., Schwartz, M.K., Luikart, G., Taberlet, P., 2003. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol. Evol. 18, 189–197. Manos, P.S., Fairbrothers, D.E., 1987. Allozyme variation in populations of 6 northeastern American red oaks (Fagaceae, Quercus subg. Erythrobalanus). Syst. Bot. 12, 365–373. Manos, P.S., Doyle, J.J., Nixon, K.C., 1999. Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae). Mol. Phylog. Evol. 12, 333–349. Marchelli, P., Gallo, L., 2006. Multiple ice-age refugia in a southern beech of South America as evidenced by chloroplast DNA markers. Conserv. Genet. 7, 591–603. Marquardt, P.E., Echt, C.S., Epperson, B.K., Pubanz, D.M., 2007. Genetic structure, diversity, and inbreeding of eastern white pine under different management conditions. Can. J. For. Res. 37, 2652–2662. Marshall, H.D., Newton, C., Ritland, K., 2002. Chloroplast phylogeography and evolution of highly polymorphic microsatellites in lodgepole pine (Pinus contorta). Theor. Appl. Genet. 104, 367–378. Mathiasen, P., Rovere, A.E., Premoli, A.C., 2007. Genetic structure and early effects of inbreeding in fragmented temperate forests of a self-incompatible tree, Embothrium coccineum. Conserv. Biol. 21, 232–240. Mattioni, C., Cherubini, M., Micheli, E., Villani, F., Bucci, G., 2008. Role of domestication in shaping Castanea sativa genetic variation in Europe. Tree Genet. Genomes 4, 563–574. Mátyás, G., Sperisen, C., 2001. Chloroplast DNA polymorphisms provide evidence for postglacial re-colonisation of oaks (Quercus spp.) across the Swiss Alps. Theor. Appl. Genet. 102, 12–20. McKinney, M.L., 2008. Effects of urbanization on species richness: a review of plants and animals. Urban Ecosyst. 11, 161–176. ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 McLachlan, J.S., Clark, J.S., Manos, P.S., 2005. Molecular indicators of tree migration capacity under rapid climate change. Ecology 86, 2088–2098. Meister, J., Kilian, N., Oberprieler, C., 2007. Genetic structure of Euclea schimperi (Ebenaceae) populations in monsoonal fog oases of the southern Arabian Peninsula. Nord. J. Bot. 25, 217–226. Mejnartowicz, L., 2008. Genetic variation within and among naturally regenerating populations of alder (Alnus glutinosa). Acta Soc. Bot. Pol. 77, 105–110. Meloni, M., Perini, D., Binelli, G., 2007. The distribution of genetic variation in Norway spruce (Picea abies Karst.) populations in the western Alps. J. Biogeogr. 34, 929–938. Meng, L., Yang, R., Abbott, R.J., Miehe, G., Hu, T., Liu, J., 2007. Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai–Tibetan Plateau and adjacent highlands. Mol. Ecol. 16, 4128–4137. Mimura, M., Aitken, S.N., 2007. Increased selﬁng and decreased effective pollen donor number in peripheral relative to central populations in Picea sitchensis (Pinaceae). Am. J. Bot. 94, 991–998. Monteleone, I., Ferrazzini, D., Belletti, P., 2006. Effectiveness of neutral RAPD markers to detect genetic divergence between the subspecies uncinata and mugo of Pinus mugo Turra. Silva Fenn. 40, 391–406. Morand, M.-E., Brachet, S., Rossignol, P., Dufour, J., Frascaria-Lacoste, N., 2002. A generalized heterozygote deﬁciency assessed with microsatellites in French common ash populations. Mol. Ecol. 11, 377–385. Morris, A.B., Ickert-Bond, S.M., Brunson, D.B., Soltis, D.E., Soltis, P.S., 2008. Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae). Mol. Ecol. 17, 3889–3900. Mosseler, A., Major, J.E., Rajora, O.P., 2003. Old-growth red spruce forests as reservoirs of genetic diversity and reproductive ﬁtness. Theor. Appl. Genet. 106, 931–937. Muir, G., Fleming, C.C., Schlotterer, C., 2000. Species status of hybridizing oaks. Nature 405, 1016. Muir, G., Fleming, C.C., Schlotterer, C., 2001. Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Mol. Biol. Evol. 18, 112–119. Muir, G., Schlotterer, C., 2005. Evidence for shared ancestral polymorphism rather than recurrent gene ﬂow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.). Mol. Ecol. 14, 549–561. Müller, B., 1999. Variation und hybridisierung von Quercus pubescens. Diss. Naturwiss. ETH Zürich, CH, Nr. 13025, /http://e-collection.ethbib.ethz.ch/view/eth:22996S. Müller-Starck, G., 1995a. Genetic variation in high elevated populations of Norway spruce (Picea abies (L.) Karst.) in Switzerland. Silvae Genet. 44, 356–362. Müller-Starck, G., 1995b. Protection of genetic variability in forest trees. For. Genet. 2, 121–124. Muller, S.D., Nakagawa, T., de Beaulieu, J.-L., Court-Picon, M., Carcaillet, C., Miramont, C., Roiron, P., Boutterin, C., Ali, A.A., Bruneton, H., 2007. Post-glacial migration of silver ﬁr (Abies alba Mill.) in the south-western Alps. J. Biogeogr. 34, 876–899. 183 Myking, T., Yakovlev, I., 2006. Variation in leaf morphology and chloroplast DNA in Ulmus glabra in the northern suture zone: effects of distinct glacial refugia. Scand. J. For. Res. 21, 99–107. Nasri, N., Bojovic, S., Vendramin, G.G., Fady, B., 2008. Population genetic structure of the relict Serbian spruce, Picea omorika, inferred from plastid DNA. Plant Syst. Evol. 271, 1–7. Navarro, C., Cavers, S., Colpaert, N., Hernandez, G., Breyne, P., Lowe, A.J., 2005. Chloroplast and total genomic diversity in the endemic Costa Rican tree Lonchocarpus costaricensis (J. D. Smith) Pittier (Papilionaceae). Silvae Genet. 54, 293–300. Navascués, M., Emerson, B.C., 2007. Natural recovery of genetic diversity by gene ﬂow in reforested areas of the endemic Canary Island pine, Pinus canariensis. For. Ecol. Manage. 244, 122–128. Naydenov, K.D., Tremblay, F.M., Alexandrov, A., Fenton, N.J., 2005a. Structure of Pinus sylvestris L. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: provenance tests. Biochem. Syst. Ecol. 33, 1226–1245. Naydenov, K.D., Tremblay, F.M., Bergeron, Y., Alexandrov, A., Fenton, N., 2005b. Dissimilar patterns of Pinus heldreichii Christ. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis. Biochem. Syst. Ecol. 33, 133–148. Naydenov, K.D., Tremblay, F.M., Fenton, N.J., Alexandrov, A., 2006. Structure of Pinus nigra Arn. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: provenance tests. Biochem. Syst. Ecol. 34, 562–574. Naydenov, K., Senneville, S., Beaulieu, J., Tremblay, F., Bousquet, J., 2007. Glacial vicariance in Eurasia: mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor. BMC Evol. Biol. 7, 233. Neale, D.B., Ingvarsson, P.K., 2008. Population, quantitative and comparative genomics of adaptation in forest trees. Curr. Opin. Plant Biol. 11, 149–155. Newton, A.C., 2008. Conservation of tree species through sustainable use: how can it be achieved in practice? Oryx 42, 195–205. Newton, A.C., Allnutt, T.R., Dvorak, W.S., Del Castillo, R.F., Ennos, R.A., 2002. Patterns of genetic variation in Pinus chiapensis, a threatened Mexican pine, detected by RAPD and mitochondrial DNA RFLP markers. Heredity 89, 191–198. Newton, A.C., Allnutt, T.R., Gillies, A.C.M., Lowe, A.J., Ennos, A.R., 1999. Molecular phylogeography, intraspeciﬁc variation and the conservation of tree species. Trends Ecol. Evol. 14, 140–145. Nightingale, J.M., Fan, W., Coops, N.C., Waring, R.H., 2008. Predicting tree diversity across the United States as a function of modeled gross primary production. Ecol. Appl. 18, 93–103. Novick, R.R., Dick, C.W., Lemes, M.R., Navarro, C., Caccone, A., Bermingham, E., 2003. Genetic structure of Mesoamerican populations of Big-leaf mahogany ARTICLE IN PRESS 184 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 (Swietenia macrophylla) inferred from microsatellite analysis. Mol. Ecol. 12, 2885–2893. Núñez-Ávila, M.C., Armesto, J.J., 2006. Relict islands of the temperate rainforest tree Aextoxicon punctatum (Aextoxicaceae) in semi-arid Chile: genetic diversity and biogeographic history. Aust. J. Bot. 54, 733–743. O’Brien, E.K., Mazanec, R.A., Krauss, S.L., 2007. Provenance variation of ecologically important traits of forest trees: implications for restoration. J. Appl. Ecol. 44, 583–593. O’Connell, L.M., Mosseler, A., Rajora, O.P., 2006. Impacts of forest fragmentation on the mating system and genetic diversity of white spruce (Picea glauca) at the landscape level. Heredity 97, 418–426. Oddou-Muratorio, S., Demesure-Musch, B., Pélissier, R., Gouyon, P.-H., 2004. Impacts of gene ﬂow and logging history on the local genetic structure of a scattered tree species, Sorbus torminalis L. Crantz. Mol. Ecol. 13, 3689–3702. Oddou-Muratorio, S., Klein, E.K., 2008. Comparing direct vs. indirect estimates of gene ﬂow within a population of a scattered tree species. Mol. Ecol. 17, 2743–2754. Ohsawa, T., Tsuda, Y., Saito, Y., Sawada, H., Ide, Y., 2006. Genetic diversity and gene ﬂow of Quercus crispula in a semi-fragmented forest together with neighbouring forests. Silvae Genet. 55, 4–5. Ohsawa, T., Tsuda, Y., Saito, Y., Sawada, H., Yde, Y., 2007. Altitudinal genetic diversity and differentiation of Quercus crispula in the Chichibu Mountains, Central Japan. Int. J. Plant Sci. 168, 333–340. Ohsawa, T., Ide, Y., 2008. Global patterns of genetic variation in plant species along vertical and horizontal gradients on mountains. Glob. Ecol. Biogeogr. 17, 152–163. Okaura, T., Harada, K., 2002. Phylogeographical structure revealed by chloroplast DNA variation in Japanese Beech (Fagus crenata Blume). Heredity 88, 322–329. Okaura, T., Quang, N.D., Ubukata, M., Harada, K., 2007. Spatial genetic structure in populations of Quercus mongolica var. grosseserrata (Fagaceae) from southern Korea. Genes Genet. Syst. 82, 465–477. Pakkad, G., Ueno, S., Yoshimaru, H., 2008. Genetic diversity and differentiation of Quercus semiserrata Roxb. in northern Thailand revealed by nuclear and chloroplast microsatellite markers. For. Ecol. Manage. 255, 1067–1077. Palmé, A.E., Vendramin, G.G., 2002. Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, Corylus avellana. Mol. Ecol. 11, 1769–1779. Palmé, A.E., Semerikov, V., Lascoux, M., 2003a. Absence of geographical structure of chloroplast DNA variation in sallow, Salix caprea L. Heredity 91, 465–474. Palmé, A.E., Su, Q., Rautenberg, A., Manni, F., Lascoux, M., 2003b. Postglacial recolonization and cpDNA variation of silver birch, Betula pendula. Mol. Ecol. 12, 201–212. Paludan-Muller, G., Saxe, H., Leverenz, J.W., 1999. Responses to ozone in 12 provenances of European beech (Fagus sylvatica): genotypic variation and chamber effects on photosynthesis and dry-matter partitioning. New Phytol. 144, 261–273. Paoletti, E., Bytnerowicz, A., Andersen, C., Augustaitis, A., Ferretti, M., Grulke, N., Gunthardt-Goerg, M.S., Innes, J., Johnson, D., Karnosky, D., Luangjame, J., Matyssek, R., McNulty, S., Muller-Starck, G., Musselman, R., Percy, K., 2007. Impacts of air pollution and climate change on forest ecosystems-emerging research needs. Sci. World J. 7, 1–8. Parmentier, I., Malhi, Y., Senterre, B., et al., 2007. The odd man out? Might climate explain the lower tree alphadiversity of African rain forests relative to Amazonian rain forests? J. Ecol. 95, 1058–1071. Pastorino, M.J., Gallo, L.A., Hattemer, H.H., 2004. Genetic variation in natural populations of Austrocedrus chilensis, a cypress of the Andean-Patagonian forest. Biochem. Syst. Ecol. 32, 993–1008. Pautasso, M., 2007. Scale dependence of the correlation between human population presence and vertebrate and plant species richness. Ecol. Lett. 10, 16–24. Pautasso, M., Parmentier, I., 2007. Are the living collections of the world’s botanical gardens following species-richness patterns observed in natural ecosystems? Bot. Helv. 117, 15–28. Pautasso, M., Holdenrieder, O., Stenlid, J., 2005. Susceptibility to fungal pathogens of forests differing in tree diversity. In: Scherer-Lorenzen, M., Koerner, Ch., Schulze, E.D. (Eds.), Forest Diversity and Function: Temperate and Boreal Systems. Springer, Berlin, pp. 263–289. Payn, K.G., Dvorak, W.S., Myburg, A.A., 2007. Chloroplast DNA phylogeography reveals the island colonisation route of Eucalyptus urophylla (Myrtaceae). Aust. J. Bot. 55, 673–683. Payn, K.G., Dvorak, W.S., Janse, B.J.H., Myburg, A.A., 2008. Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla, endemic to seven islands in eastern Indonesia. Tree Genet. Genomes 4, 519–530. Peakall, R., Ebert, D., Scott, L.J., Meagher, P.F., Offord, C.A., 2003. Comparative genetic study conﬁrms exceptionally low genetic variation in the ancient and endangered relictual conifer, Wollemia nobilis (Araucariaceae). Mol. Ecol. 12, 2331–2343. Peng, X.-L., Zhao, C.-M., Wu, G.-L., Liu, J.-Q., 2007. Genetic variation and phylogeographic history of Picea likiangensis revealed by RAPD markers. Trees 21, 457–464. Persson, H., Widén, B., Andersson, S., Svensson, L., 2004. Allozyme diversity and genetic structure of marginal and central populations of Corylus avellana L. (Betulaceae) in Europe. Plant Syst. Evol. 244, 157–179. Perry, D.A., 1998. The scientiﬁc basis of forestry. Ann. Rev. Ecol. Syst. 29, 435–466. Pertoldi, C., Bijlsma, R., Loeschcke, V., 2007. Conservation genetics in a globally changing environment: present problems, paradoxes and future challenges. Biodiv. Conserv. 16, 4147–4163. Petit, R.J., Hampe, A., 2006. Some evolutionary consequences of being a tree. Ann. Rev. Ecol. Evol. Syst. 37, 187–214. Petit, R.J., Kremer, A., Wagner, D.B., 1993a. Geographic structure of chloroplast DNA polymorphisms in European oaks. Theor. Appl. Genet. 87, 122–128. Petit, R.J., Wagner, D.B., Kremer, A., 1993b. Ribosomal DNA and chloroplast DNA polymorphisms in a mixed stand of Quercus robur and Q. petraea. Ann. Sci. For. 50, 41s–47s. ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Petit, R.J., Pineau, E., Demesure, B., Bacilieri, R., Ducousso, A., Kremer, A., 1997. Chloroplast DNA footprints of postglacial recolonization by oaks. Proc. Natl. Acad. Sci. USA 94, 9996–10001. Petit, R.J., Brewer, S., Bordacs, S., et al., 2002a. Identiﬁcation of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For. Ecol. Manage. 156, 49–74. Petit, R.J., Csaikl, U.M., Bordacs, S., et al., 2002b. Chloroplast DNA variation in European white oaks-phylogeography and patterns of diversity based on data from over 2600 populations. For. Ecol. Manage. 156, 5–26. Petit, R.J., Aguinagalde, I., de Beaulieu, J.L., et al., 2003. Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300, 1563–1565. Petit, R.J., Bialozyt, R., Garnier-Gere, P., Hampe, A., 2004a. Ecology and genetics of tree invasions: from recent introductions to Quaternary migrations. For. Ecol. Manage. 197, 117–137. Petit, R.J., Bodenes, C., Ducousso, A., Roussel, G., Kremer, A., 2004b. Hybridization as a mechanism of invasion in oaks. New Phytol. 161, 151–164. Petit, R.J., Duminil, J., Fineschi, S., Hampe, A., Salvini, D., Vendramin, G.G., 2005. Comparative organisation of chloroplast, mitochondrial and nuclear diversity in plant populations. Mol. Ecol. 14, 689–701. Petit, R.J., Hu, F.S., Dick, C.W., 2008. Forests of the past: a window to future changes. Science 320, 1450–1452. Pichot, C., Liens, B., Nava, J.L.R., Bachelier, J.B., El maataoui, M., 2008. Cypress surrogate mother produces haploid progeny from alien pollen. Genetics 178, 379–383. Pither, R., Shore, J.S., Kellman, M., 2003. Genetic diversity of the tropical tree Terminalia amazonia (Combretaceae) in naturally fragmented populations. Heredity 91, 307–313. Pospiskova, M., Salkova, I., 2006. Population structure and parentage analysis of black poplar along the Morava River. Can. J. For. Res. 36, 1067–1076. Potenko, V.V., Koren, O.G., Verkholat, V.P., 2007. Genetic variation and differentiation in populations of Japanese emperor oak Quercus dentata Thunb. and Mongolian oak Quercus mongolica Fisch. Ex Ledeb. in the South of the Russian Far East. Russ. J. Genet. 43, 387–395. Potter, K.M., Dvorak, W.S., Crane, B.S., Hipkins, V.D., Jetton, R.M., Whittier, W.A., Rhea, R., 2008. Allozyme variation and recent evolutionary history of eastern hemlock (Tsuga canadensis) in the southeastern United States. New For. 35, 131–145. Premoli, A.C., 2003. Isozyme polymorphisms provide evidence of clinal variation with elevation in Nothofagus pumilio. J. Heredity 94, 218–226. Provan, J., Beatty, G.E., Hunter, A.M., McDonald, R.A., McLaughlin, E., Preston, S.J., Wilson, S., 2008. Restricted gene ﬂow in fragmented populations of a wind-pollinated tree. Conserv. Genet. 9, 1521–1532. Pye, M.G., Gadek, P.A., 2004. Genetic diversity, differentiation and conservation in Araucaria bidwillii (Araucariaceae), Australia’s Bunya pine. Conserv. Genet. 5, 619–629. Pyhäjärvi, T., Salmela, M.J., Savolainen, O., 2008. Colonization routes of Pinus sylvestris inferred from distribution of 185 mitochondrial DNA variation. Tree Genet. Genomes 4, 247–254. Quiroga, M.P., Premoli, A.C., 2007. Genetic patterns in Podocarpus parlatorei reveal the long-term persistence of cold-tolerant elements in the southern Yungas. J. Biogeogr. 34, 447–455. Rajora, O.P., Mosseler, A., 2001. Challenges and opportunities for conservation of forest genetic resources. Euphytica 118, 197–212. Rajora, O.P., Rahman, M.H., Buchert, G.P., Dancik, B.P., 2000. Microsatellite DNA analysis of genetic effects of harvesting in old-growth eastern white pine (Pinus strobus) in Ontario, Canada. Mol. Ecol. 9, 339–348. Ramos, A.C.S., Lemos-Filho, J.P., Ribeiro, R.A., Santos, F.R., Lovato, M.B., 2007. Phylogeography of the tree Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae) and the inﬂuence of quaternary climate change in the Brazilian Cerrado. Ann. Bot. 100, 1219–1228. Ran, J.-H., Wei, X.-X., Wang, X.-Q., 2006. Molecular phylogeny and biogeography of Picea (Pinaceae): implications for phylogeographical studies using cytoplasmic haplotypes. Mol. Phylog. Evol. 41, 405–419. Rasmussen, K.K., Kollmann, J., 2008. Low genetic diversity in small peripheral populations of a rare European tree (Sorbus torminalis) dominated by clonal reproduction. Conserv. Gen. 9, 1533–1539. Raspé, O., Saumitou-Laprade, P., Cuguen, J., Lacquemart, A.-L., 2000. Chloroplast DNA haplotype variation and population differentiation in Sorbus aucuparia L. (Rosaceae: Maloideae). Mol. Ecol. 9, 1113–1122. Rathbone, D.A., McKinnon, G.E., Potts, B.M., Steane, D.A., Vaillancourt, R.E., 2007. Microsatellite and cpDNA variation in island and mainland populations of a regionally rare eucalypt, Eucalyptus perriniana (Myrtaceae). Aust. J. Bot. 55, 513–520. Rehfeldt, G.E., Tschebakova, N.M., Parfenova, Y.I., Wykoff, W.R., Kuzmina, N.A., Milyutin, L.I., 2002. Intraspeciﬁc responses to climate in Pinus sylvestris. Glob. Change Biol. 8, 912–929. Reich, P.B., Oleksyn, J., 2008. Climate warming will reduce growth and survival of Scots pine except in the far north. Ecol. Lett. 11, 588–597. Reis, A.M.M., Grattapaglia, D., 2004. RAPD variation in a germplasm collection of Myracrodruon urundeuva (Anacardiaceae), an endangered tropical tree: recommendations for conservation. Gen. Res. Crop Evol. 51, 529–538. Rendell, S., Ennos, R.A., 2003. Chloroplast DNA diversity of the dioecious European tree Ilex aquifolium L. (English holly). Mol. Ecol. 12, 2681–2688. Reusch, T.B.H., Wood, T.E., 2007. Molecular ecology of global change. Mol. Ecol. 16, 3973–3992. Ribeiro, R.A., Ramos, A.C.S., Filho, J.P.L., Lovato, M.B., 2005. Genetic variation in remnant populations of Dalbergia nigra (Papilionoideae), an endangered tree from the Brazilian Atlantic forest. Ann. Bot. 95, 1171–1177. Richardson, B.A., Klopfenstein, N.B., Zambino, P.J., McDonald, G.I., Geils, B.W., Carris, L.M., 2008. Inﬂuence of host resistance on the genetic structure of the white pine blister rust fungus in the western United States. Phytopathology 98, 413–420. ARTICLE IN PRESS 186 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Riddle, B.R., Dawson, M.N., Hadly, E.A., Hafner, D.J., Hickerson, M.J., Mantooth, S.H., Yoder, A.D., 2008. The role of molecular genetics in sculpting the future of integrative biogeography. Prog. Phys. Geogr. 32, 173–202. Ritland, K., Meagher, L.D., Edwards, D.G.W., El-Kassaby, Y.A., 2005. Isozyme variation and the conservation genetics of Garry oak. Can. J. Bot. 83, 1478–1487. Rivera-Ocasio, E., Mitchell Aide, T., McMillan, W.O., 2006. The inﬂuence of spatial scale on the genetic structure of a widespread tropical wetland tree, Pterocarpus offcinalis (Fabaceae). Conserv. Genet. 7, 251–266. Robertson, A., Newton, A.C., Ennos, R.A., 2004. Breeding systems and continuing evolution in the endemic Sorbus taxa on Arran. Heredity 93, 487–495. Robledo-Arnuncio, J.J., Collada, C., Alia, R., Gil, L., 2005. Genetic structure of montane isolates of Pinus sylvestris L. in a Mediterranean refugial area. J. Biogeogr. 32, 595–605. Rodrigues, A.S.L., Brooks, T.M., 2007. Shortcuts for biodiversity conservation planning: the effectiveness of surrogates. Ann. Rev. Ecol. Evol. Syst. 38, 713–737. Rogers, D.L., 2000. Genotypic diversity and clone size in oldgrowth populations of coast redwood (Sequoia sempervirens). Can. J. Bot. 78, 1408–1419. Rogers, D.L., Matheson, A.C., Vargas-Hernandez, J.J., Guerra-Santos, J.J., 2006. Genetic conservation of insular populations of monterey pine (Pinus radiata D. Don). Biodiv. Conserv. 15, 779–798. Rosen, M.A., Dincer, I., 1997. On exergy and environmental impact. Int. J. Energy Res. 21, 643–654. Rossetto, M., 2008. From populations to communities: understanding changes in rainforest diversity through the integration of molecular, ecological and environmental data. Telopea 12, 47–58. Rowden, A., Robertson, A., Allnutt, T., Heredia, S., WilliamsLinera, G., Newton, A.C., 2004. Conservation genetics of Mexican beech, Fagus grandifolia var. mexicana. Conserv. Genet. 5, 475–484. Rüdinger, M.C.D., Gläser, J., Hebel, I., Dounavi, A., 2008. Genetic structures of common ash (Fraxinus excelsior) populations in Germany at sites differing in water regimes. Can. J. For. Res. 38, 1199–1210. Ruiz, E., Gonzalez, F., Torres-Diaz, C., Fuentes, G., Mardones, M., Stuessy, T., Samuel, R., Becerra, J., Silva, M., 2007. Genetic diversity and differentiation within and among Chilean populations of Araucaria araucana (Araucariaceae) based on allozyme variability. Taxon 56, 1221–1228. Sander, T., König, S., Rothe, G.M., Janssen, A., Weisgerber, H., 2000. Genetic variation of European beech (Fagus sylvatica L.) along an altitudinal transect at mount Vogelsberg in Hesse, Germany. Mol. Ecol. 9, 1349–1361. Savolainen, O., Pyhäjärvi, T., Knürr, T., 2007. Gene ﬂow and local adaptation in trees. Ann. Rev. Ecol. Evol. Syst. 38, 595–619. Schaberg, P.G., DeHayes, D.H., Hawley, G.J., Nijensohn, S.E., 2008. Anthropogenic alterations of genetic diversity within tree populations: implications for forest ecosystem resilience. For. Ecol. Manage. 256, 855–862. Scherer-Lorenzen, M., Schulze, E.-D., Don, A., Schumacher, J., Weller, E., 2007. Exploring the functional signiﬁcance of forest diversity: a new long-term experiment with temperate tree species (BIOTREE). Persp. Plant Ecol. Evol. Syst. 9, 53–70. Schiller, G., Shklar, G., Korol, L., 2003. Genetic diversity assessment by random ampliﬁed polymorphic DNA of oaks in Israel. 1. Tabor oak (Quercus aegilops L. ssp ithaburensis [Decne] Boiss.). Isr. J. Plant Sci. 51, 1–10. Schiller, G., Shklar, G., Korol, L., 2004. Genetic diversity assessment by random ampliﬁed polymorphic DNA of oaks in Israel. 2. Quercus boissieri Reut. Isr. J. Plant Sci. 52, 315–322. Schiller, G., Shklar, G., Ungar, E.D., Al-Omari, A., Zyadin, A.F., Korol, L., 2006. Genetic diversity assessment by random ampliﬁed polymorphic DNA of oaks: 3. Quercus calliprinos Webb. in Israel and Jordan. Isr. J. Plant Sci. 54, 137–148. Schnabel, A., Hamrick, J.L., 1990. Comparative analysis of population genetic structure in Quercus macrocarpa and Quercus gambelii (Fagaceae). Syst. Bot. 15, 240–251. Scotti, I., Vendramin, G.G., Matteotti, L.S., Scarponi, C.M., Sari-Gorla, G., Binelli, G., 2000. Postglacial recolonization routes for Picea abies K. in Italy as suggested by the analysis of sequence-characterized ampliﬁed region (SCAR) markers. Mol. Ecol. 9, 699–708. Sebbenn, A.M., Degen, B., Azevedo, V.C.R., Silva, M.B., de Lacerda, A.E.B., Ciampi, A.Y., Kanashiro, M., Carneiro, F.S., Thompson, I., Loveless, M.D., 2008. Modelling the long-term impacts of selective logging on genetic diversity and demographic structure of four tropical tree species in the Amazon forest. For. Ecol. Manage. 254, 335–349. Semaan, M.T., Dodd, R.S., 2008. Genetic variability and structure of the remnant natural populations of Cedrus libani (Pinaceae) of Lebanon. Tree Genet. Genomes 4, 757–766. Semerikov, V.L., Iroshnikov, A.I., Lascoux, M., 2007. Mitochondrial DNA variation pattern and postglacial history of the Siberian Larch (Larix sibirica Ledeb.). Russ. J. Ecol. 38, 147–154. Semerikov, V.L., Lascoux, M., 2003. Nuclear and cytoplasmic variation within and between Eurasian Larix (Pinaceae) species. Am. J. Bot. 90, 1113–1123. Setsuko, S., Ishida, K., Ueno, S., Tsumura, Y., Tomaru, N., 2007. Population differentiation and gene ﬂow within a metapopulation of a threatened tree, Magnolia stellata (Magnoliaceae). Am. J. Bot. 94, 128–136. Shachak, M., Boeken, B., Groner, E., Kadmon, R., Lubin, Y., Meron, E., Neeman, G., Perevolotsky, A., Shkedy, Y., Ungar, E.D., 2008. Woody species as landscape modulators and their effect on biodiversity patterns. Bioscience 58, 209–221. Shanjani, P.S., Vettori, C., Giannini, R., Khavari-Nejad, R.A., 2004. Intraspeciﬁc variation and geographic patterns of Fagus orientalis Lipsky chloroplast DNA. Silvae Genet. 53, 193–197. Shapcott, A., 1998. Vagile but inbred: patterns of inbreeding and the genetic structure within populations of the monsoon rain forest tree Syzygium nervosum (Myrtaceae) in northern Australia. J. Trop. Ecol. 14, 595–614. ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Shapcott, A., Rakotoarinivo, M., Smith, R.J., Lysakova, G., Fay, M.F., Dransﬁeld, J., 2007. Can we bring Madagascar’s critically endangered palms back from the brink? Genetics, ecology and conservation of the critically endangered palm Beccariophoenix madagascariensis. Bot. J. Linn. Soc. 154, 589–608. Shen, L., Chen, X.-Y., Zhang, X., Li, Y.-Y., Fu, C.-X., Qiu, Y.-X., 2005. Genetic variation of Ginkgo biloba L. (Ginkgoaceae) based on cpDNA PCR-RFLPs: inference of glacial refugia. Heredity 94, 396–401. Shih, F.L., Cheng, Y.P., Hwang, S.Y., Lin, T.P., 2006. Partial concordance between nuclear and organelle DNA in revealing the genetic divergence among Quercus glauca (Fagaceae) populations in Taiwan. Int. J. Plant Sci. 167, 863–872. Silva, M.B., Kanashiro, M., Ciampi, A.Y., Thompson, I., Sebbenn, A.M., 2008. Genetic effects of selective logging and pollen gene ﬂow in a low-density population of the dioecious tropical tree Bagassa guianensis in the Brazilian Amazon. For. Ecol. Manage. 255, 1548–1558. Smulders, M.J.M., Cottrell, J.E., Lefèvre, F., et al., 2008. Structure of the genetic diversity in black poplar (Populus nigra L.) populations across European river systems: consequences for conservation and restoration. For. Ecol. Manage. 255, 1388–1399. Sniezko, R.A., 2006. Resistance breeding against non-native pathogens in forest trees – current successes in North America. Can. J. Plant Path. 28, S270–S279. Soares, T.N., Chaves, L.J., Telles, M.P.D., Diniz-Filho, J.A.F., Resende, L.V., 2008. Landscape conservation genetics of Dipteryx alata (‘‘baru’’ tree: Fabaceae) from Cerrado region of central Brazil. Genetica 132, 9–19. Soltis, D.E., Morris, A.B., McLachlan, J.S., Manos, P.S., Soltis, P.S., 2006. Comparative phylogeography of unglaciated eastern North America. Mol. Ecol. 15, 4261–4293. Soranzo, N., Alia, R., Provan, J., Powell, W., 2000. Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations. Mol. Ecol. 9, 1205–1211. Sork, V.L., Smouse, P.E., 2006. Genetic analysis of landscape connectivity in tree populations. Lands. Ecol. 21, 821–836. Spinnler, D., Egli, P., Koerner, Ch., 2003. Provenance effects and allometry in beech and spruce under elevated CO2 and nitrogen on two different forest soils. Basic Appl. Ecol. 4, 467–478. St Clair, J.B., Mandel, N.L., Vance-Borland, K.W., 2005. Genecology of Douglas ﬁr in Western Oregon and Washington. Ann. Bot. 96, 1199–1214. Starke, R., 1993. Gene markers as decision-making tools in gene conservation. 2. Isoenzymes as gene markers for the declaration of forest resources. Allg. Forst- Jagdz. 164, 181–186. Stecconi, M., Marchelli, P., Puntieri, J., Picca, P., Gallo, L., 2004. Natural hybridization between a deciduous (Nothofagus antarctica, Nothofagaceae) and an evergreen (N. dombeyi) forest tree species: evidence from morphological and isoenzymatic traits. Ann. Bot. 94, 775–786. 187 Steinhoff, R.J., Joyce, D.G., Fins, L., 1983. Isozyme variation in Pinus monticola. Can. J. For. Res. 13, 1122–1132. Stewart, J.R., Lister, A.M., 2001. Cryptic northern refugia and the origins of the modern biota. Trends Ecol. Evol. 16, 608–613. Strong, W.L., Hills, L.V., 2005. Late-glacial and Holocene palaeovegetation zonal reconstruction for central and north-central North America. J. Biogeogr. 32, 1043–1062. Su, G., Huang, Y., Tan, F., Ni, X., Tang, T., Shi, S., 2007. Conservation genetics of Lumnitzera littorea (Combretaceae), an endangered mangrove, from the Indo-West Paciﬁc. Mar. Biol. 150, 321–328. Sun, K., Chen, W., Ma, R., Chen, X., Li, A., Ge, S., 2006a. Genetic variation in Hippophae rhamnoides ssp. sinensis (Elaeagnaceae) revealed by RAPD markers. Biochem. Genet. 44, 186–197. Sun, W., Zhou, Y., Han, C., Zeng, C., Shi, X., Xiang, Q., Coombes, A., 2006b. Status and conservation of Trigobalanus doichangensis (Fagaceae). Biodiv. Conserv. 15, 1303–1318. Suvanto, L.I., Latva-Karjanmaa, T.B., 2005. Clone identiﬁcation and clonal structure of the European aspen (Populus tremula). Mol. Ecol. 14, 2851–2860. Svenning, J.-C., Skov, F., 2007a. Ice age legacies in the geographical distribution of tree species richness in Europe. Glob. Ecol. Biogeogr. 16, 234–245. Svenning, J.-C., Skov, F., 2007b. Could the tree diversity pattern in Europe be generated by postglacial dispersal limitation? Ecol. Lett. 10, 453–460. Taberlet, P., Fumagalli, L., Wust-Saucy, A.G., Cosson, J.F., 1998. Comparative phylogeography and postglacial colonization routes in Europe. Mol. Ecol. 7, 453–464. Takahashi, T., Tani, N., Niiyama, K., Yoshida, S., Taira, H., Tsumura, Y., 2008. Genetic succession and spatial genetic structure in a natural old growth Cryptomeria japonica forest revealed by nuclear and chloroplast microsatellite markers. For. Ecol. Manage. 255, 2820–2828. Tang, S., Dai, W., Li, M., Zhang, Y., Geng, T., Wang, L., Zhong, Y., 2008. Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers. Genetica 133, 21–30. Taylor, G.E., 1994. Role of genotype in the response of loblolly pine to tropospheric ozone – effects at the whole tree, stand, and regional level. J. Environ. Qual. 23, 63–82. Taylor, K.J., Lowe, A.J., Hunter, R.J., Ridgway, T., Gresshoff, P.M., Rossetto, M., 2005. Genetic diversity and regional identity in the Australian remnant Nothofagus moorei. Aust. J. Bot. 53, 437–444. Terrab, A., Paun, O., Talavera, S., Tremetsberger, K., Arista, M., Stuessy, T.F., 2006. Genetic diversity and population structure in natural populations of Moroccan Atlas cedar (Cedrus atlantica; Pinaceae) determined with cpSSR markers. Am. J. Bot. 93, 1274–1280. Thomas, D.T., Ahedor, A.R., Williams, C.F., Depamphilis, C., Crawford, D.J., Xiang, Q.Y., 2008. Genetic analysis of a broad hybrid zone in Aesculus (Sapindaceae): is there evidence of long-distance pollen dispersal? Int. J. Plant Sci. 169, 647–657. Tollefsrud, M.M., Kissling, R., Gugerli, F., Johnsen, O., Skroppa, T., Cheddadi, R., van der Knap, W.O., Latalowa, ARTICLE IN PRESS 188 M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 M., Terhurne-Berson, R., Litt, T., Geburek, T., Brochmann, C., Sperisen, C., 2008. Genetic consequences of glacial survival and postglacial colonization in Norway spruce: combined analysis of mitochondrial DNA and fossil pollen. Mol. Ecol. 17, 4134–4150. Tomback, D.F., Resler, L.M., 2007. Invasive pathogens at alpine treeline: consequences for treeline dynamics. Phys. Geogr. 28, 397–418. Torres-Dı́az, C., Ruiz, E., González, F., Fuentes, G., Cavieres, L.A., 2007. Genetic diversity in Nothofagus alessandrii (Fagacaeae), an endangered endemic tree species of the coastal Maulino forest of central Chile. Ann. Bot. 100, 75–82. Tovar-Sanchez, E., Mussali-Galante, P., Esteban-Jimenez, R., Pinero, D., Arias, D.M., Dorado, O., Oyama, K., 2008. Chloroplast DNA polymorphism reveals geographic structure and introgression in the Quercus crassifolia x Quercus crassipes hybrid complex in Mexico. Botany 86, 228–239. Tripiana, V., Bourgeois, M., Verhaegen, D., Vigneron, P., Bouvet, J.M., 2007. Combining microsatellites, growth, and adaptive traits for managing in situ genetic resources of Eucalyptus urophylla. Can. J. For. Res. 37, 773–785. Troupin, D., Nathan, R., Vendramin, G.G., 2006. Analysis of spatial genetic structure in an expanding Pinus halepensis population reveals development of ﬁne-scale genetic clustering over time. Mol. Ecol. 15, 3617–3630. Truong, C., Palmé, A.E., Felber, F., 2007. Recent invasion of the mountain birch Betula pubescens ssp tortuosa above the treeline due to climate change: genetic and ecological study in northern Sweden. J. Evol. Biol. 20, 369–380. Tsuda, Y., Ide, Y., 2005. Wide-range analysis of genetic structure of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in the cool temperate zone of Japan. Mol. Ecol. 14, 3929–3941. Tsumura, Y., Matsumoto, A., Tani, N., Ujino-Ihara, T., Kado, T., Iwata, H., Uchida, K., 2007. Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation. Heredity 99, 161–172. Ueno, S., Setsuko, S., Kawahara, T., Yoshimaru, H., 2005. Genetic diversity and differentiation of the endangered Japanese endemic tree Magnolia stellata using nuclear and chloroplast microsatellite markers. Conserv. Genet. 6, 563–574. Vakkari, P., Blom, A., Rusanen, M., Raisio, J., Toivonen, H., 2006. Genetic variability of fragmented stands of pedunculate oak (Quercus robur) in Finland. Genetica 127, 231–241. Valbuena-Carabaña, M., González-Martı́nez, S.C., Gil, L., 2008. Coppice forests and genetic diversity: a case study in Quercus pyrenaica Willd. from Central Spain. For. Ecol. Manage. 254, 225–232. van Loo, M., Joseph, J.A., Heinze, B., Fay, M.F., Lexer, C., 2008. Clonality and spatial genetic structure in Populus canescens and its sympatric backcross parent P. alba in a Central European hybrid zone. New Phytol. 177, 506–516. Varga, Z., 2008. Mountain coniferous forests, refugia and butterﬂies. Mol. Ecol. 17, 2101–2106. Vaughan, S.P., Cottrell, J.E., Moodley, D.J., Connolly, T., Russell, K., 2007. Clonal structure and recruitment in British wild cherry (Prunus avium L.). For. Ecol. Manage. 242, 419–430. Vaxevanidou, Z., González-Martı́nez, S.C., Climent, J., Gil, L., 2006. Tree populations bordering on extinction: a case study in the endemic Canary Island pine. Biol. Conserv. 129, 451–460. Vellend, M., 2005. Species diversity and genetic diversity: parallel processes and correlated patterns. Am. Nat. 166, 199–215. Vellend, M., Geber, M.A., 2005. Connections between species diversity and genetic diversity. Ecol. Lett. 8, 767–781. Vendramin, G.G., Anzidei, M., Madaghiele, A., Sperisen, C., Bucci, G., 2000. Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abies K.). Genome 43, 68–78. Vendramin, G.G., Fady, B., González-Martinez, S.C., Hu, F.S., Scotti, I., Sebastiani, F., Soto, A., Petit, R.J., 2008. Genetically depauperate but widespread: the case of an emblematic Mediterranean pine. Evolution 62, 680–688. Victory, E.R., Glaubitz, J.C., Rhodes Jr, O.E., Woeste, K.E., 2006. Genetic homogeneity in Juglans nigra (Juglandaceae) at nuclear microsatellites. Am. J. Bot. 93, 118–126. Vieira, F.D., de Carvalho, D., 2008. Genetic structure of an insect-pollinated and bird-dispersed tropical tree in vegetation fragments and corridors: implications for conservation. Biodiv. Conserv. 17, 2305–2321. Voigt, F.A., Arafeh, R., Farwig, N., Griebeler, E.M., Boehning-Gaese, K., 2009. Linking seed dispersal and genetic structure of trees: a biogeographical approach. J. Biogeogr. 36, 242–254. Wachowiak, W., Celinski, K., Prus-Glowacki, W., 2005. Evidence of natural reciprocal hybridisation between Pinus uliginosa and P. sylvestris in the sympatric population of the species. Flora 200, 563–568. Wachowiak, W., Odrzykoski, I., Myczko, L., Prus-Glowacki, W., 2006. Lack of evidence on hybrid swarm in the sympatric population of Pinus mugo and P. sylvestris. Flora 201, 307–316. Wachowiak, W., Prus-Glowacki, W., 2008. Hybridisation processes in sympatric populations of pines Pinus sylvestris L., P. mugo Turra and P. uliginosa Neumann. Plant Syst. Evol. 271, 29–40. Wang, H.-W., Ge, S., 2006. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA. Mol. Ecol. 15, 4109–4122. Wang, X.-R., Szmidt, A.E., 2001. Molecular markers in population genetics of forest trees. Scand. J. For. Res. 16, 199–220. Wang, X.-R., Chhatre, V.E., Nilsson, M.-C., Song, W., Zackrisson, O., Szmidt, A.E., 2003. Island population structure of Norway spruce (Picea abies) in Northern Sweden. Int. J. Plant Sci. 164, 711–717. Wang, Y., Luo, J., Xue, X., Korpelainen, H., Li, C., 2005. Diversity of microsatellite markers in the populations of Picea asperata originating from the mountains of China. Plant Sci. 168, 707–714. ARTICLE IN PRESS M. Pautasso / Perspectives in Plant Ecology, Evolution and Systematics 11 (2009) 157–189 Wehenkel, C., Bergmann, F., Gregorius, H.-R., 2006. Is there a trade-off between species diversity and genetic diversity in forest tree communities? Plant Ecol. 185, 151–161. Wehenkel, C., Bergmann, F., Gregorius, H.R., 2007. Genotype-species interactions in neighbourhoods of forest tree communities. Silvae Genet. 56, 101–110. White, G.M., Boshier, D.H., Powell, W., 1999. Genetic variation within a fragmented population of Swietenia humilis Zucc. Mol. Ecol. 8, 1899–1909. Whitham, T.G., DiFazio, S.P., Schweitzer, J.A., Shuster, S.P., Allan, G.J., Bailey, J.K., Woolbright, S.A., 2008. Extending genomics to natural communities and ecosystems. Science 320, 492–495. Williams, D.A., Wang, Y., Borchetta, M., Gaines, M.S., 2007. Genetic diversity and spatial structure of a keystone species in fragmented pine rockland habitat. Biol. Conserv. 138, 256–268. Williams, J.H., Boecklen, W.J., Howard, D.J., 2001. Reproductive processes in two oak (Quercus) contact zones with different levels of hybridization. Heredity 87, 680–690. Wisdom, M.J., Bate, L.J., 2008. Snag density varies with intensity of timber harvest and human access. For. Ecol. Manage. 255, 2085–2093. Woo, L.S., Hoon, Y.B., Don, H.S., Ho, S.H., Joo, L.J., 2008. Genetic variation in natural populations of Abies nephrolepis Max. in South Korea. Ann. For. Sci. 65, 302. Wright, J.P., Jones, C.G., 2006. The concept of organisms as ecosystem engineers ten years on: progress, limitations, and challenges. BioScience 56, 203–209. Xia, T., Meng, L., Mao, K., Tian, B., Miehe, G., Liu, J., 2008. Genetic variation in the Qinghai–Tibetan Plateau endemic and endangered conifer Cupressus gigantea, detected using RAPD and ISSR markers. Silvae Genet. 57, 85–92. Xu, S.Q., Tauer, C.G., Nelson, C.D., 2008. Genetic diversity within and among populations of shortleaf pine (Pinus echinata Mill.) and loblolly pine (Pinus taeda L.). Tree Genet. Genomes 4, 859–868. Yaacobi, G., Ziv, Y., Rosenzweig, M.L., 2007. Habitat fragmentation may not matter to species diversity. Proc. R. Soc. London B 274, 2409–2412. Yamada, H., Ubukata, M., Hashimoto, R., 2006. Microsatellite variation and differentiation among local popula- 189 tions of Castanopsis species in Japan. J. Plant Res. 119, 69–78. Yang, R.C., Yeh, F.C., 1992. Genetic consequences of in-situ and ex-situ conservation of forest trees. For. Chron. 68, 720–729. Yao, X., Ye, Q., Kang, M., Huang, H., 2007. Microsatellite analysis reveals interpopulation differentiation and gene ﬂow in the endangered tree Changiostyrax dolichocarpa (Styracaceae) with fragmented distribution in central China. New Phytol. 176, 472–480. Ying, W., Ming, K., Hongwen, H., 2007. Subpopulation genetic structure of a plant panmictic population of Castanea sequinii as revealed by microsatellite markers. Front. Biol. China 2, 187–195. Zanetto, A., Kremer, A., 1995. Geographical structure of gene diversity in Quercus petraea (Matt) Liebl. 1. Monolocus patterns of variation. Heredity 75, 506–517. Zelener, N., Poltri, S.N.M., Bartoloni, N., Lopez, C.R., Hopp, H.E., 2005. Selection strategy for a seedling seed orchard design based on trait selection index and genomic analysis by molecular markers: a case study for Eucalyptus dunnii. Tree Physiol. 25, 1457–1467. Zeng, J., Zou, Y., Bai, J., Zheng, H., 2003. RAPD analysis of genetic variation in natural populations of Betula alnoides from Guangxi, China. Euphytica 134, 33–41. Zhang, X., Korpelainen, H., Li, C., 2006. Microsatellite variation of Quercus aquifolioides populations at varying altitudes in the Wolong Natural Reserve of China. Silva Fenn. 40, 407–415. Zhang, Z.-Y., Chen, Y.-Y., Li, D.-Z., 2005. Detection of low genetic variation in a critically endangered Chinese pine, Pinus squamata, using RAPD and ISSR markers. Biochem. Genet. 43, 239–249. Zheng, J.-W., An, S.-Q., Chen, L., Leng, X., Wang, Z.-S., Ziang, H.-J., 2005. Effects of logging on the genetic diversity of Quercus tialoshanica Chun et Ko in a tropical montane forest of Hainan Island, Southern China. J. Integr. Plant Biol. 47, 1184–1192. Zhou, J.Z., Kang, S., Schadt, C.W., Garten, C.T., 2008. Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. USA 105, 7768–7773. Ziegenhagen, B., Gneuss, S., Rathmacher, G., Leyer, I., Bialozyt, R., Heinze, B., Liepelt, S., 2008. A fast and simple genetic survey reveals the spread of poplar hybrids at a natural Elbe river site. Conserv. Genet. 9, 373–379.

RELATED PAPERS

RELATED TOPICS

Log In

Geographical genetics and the conservation of forest trees

Geographical genetics and the conservation of forest trees

Related Papers

RELATED PAPERS

RELATED TOPICS