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Map of Mexico and Guatemala showing the location of the Pinus chiapensis populations investigated in this study. Population numbers as in Table 1.
Source publication
Pioneer species are essential for forest regeneration and ecosystem resilience. Pinus chiapensis is an endangered pioneer key species for tropical montane cloud forest regeneration in Mesoamerica. Human activities have severely reduced some P. chiapensis populations, which exhibited a small or null colonization potential suggesting the involvement...
Context in source publication
Context 1
... sampled 15 populations of contrasting size through- out the range of P. chiapensis (Fig. 1, Table 1). A popula- tion was defined as a group of individuals of P. chiapensis occupying a uniform piece of land, clearly separated from other populations by distances not shorter than 10 km, and habitats distinct from those occupied by the popula- tion. Extensive walks, vehicle ridings, and the inspection of 1:70000 aerial ...
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Eastern white pine (Pinus strobus L.) is a widespread conifer in eastern North America. A novel dieback phenomenon, as well as increasing global temperatures contributing to the contraction of suitable habitat, is threatening this species’ long-term persistence in the Southern Appalachian Mountains. This southern extent of its current range is wher...
Citations
... Here, we quantify these interactions to understand how to maintain genetic variation in recovering populations when repairing corridors or otherwise encouraging movement of genetic variants is desirable. When genetic diversity is diminished and inbreeding increases, populations often face increased inbreeding depression through the expression of recessive traits and accumulation of maladapted alleles [2,3]. Small populations, in particular, are often at high extinction risk due to these effects because they are typically isolated and lose genetic variants quickly through drift [4]. ...
As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression. However, the rescued populations were more similar to the migrant source population (average FST range 0.05–0.10) compared to the historical recipient population (average FST range 0.23–0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.
... Such high intraspecific sequence divergence has also been reported previously in haiwels (Pangasius macronema) and striped catfish (Pangasianodon hypophthalmus), resulting from geographical isolation and substantial habitat reorganization [50]. Intraspecific sequence divergence between these two species was likely overlapped with the interspecific sequence divergence, and significantly different genetic or population structures cannot be ruled out, particularly in small-sized samples [65]. Our results showed that mismatches between nomenclature and barcode by sequence errors of clariid catfish in repositories is most probable cause of the existence of cryptic species complexes due to misidentification of species. ...
DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylo-genetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest in-traspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcod-ing. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intra-specific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.
... For example, Pinus chiapensis of Holarctic origin and endemic to southern Mexico and Guatemala (Farjon, 2018), shows an unusually low population genetic diversity compared with other pine species, including its nearest closest extant relatives: the North American white pines, P. monticola and P. strobus (Syring et al., 2007). Genetic bottlenecks derived from glacial fluctuations and anthropogenic habitat losses may explain this result (del Castillo et al., 2011). ...
... Nevertheless, climate change and habitat destruction may increase their extinction risks. Colonization potential was associated with heterozygosity, genetic diversity, and population size in the pioneer pine Pinus chiapensis, Pinaceae (del Castillo et al., 2011), some of whose small populations are at high extinction risk (e.g., Martínez-Carrasco, 1998). Lack of ectomycorrhizal fungi (EMF) in soil deter the establishment of pine species in open areas, requiring EMF inoculation from forest soils (e.g., Sánchez-Montalvo et al., 2005). ...
Three upheavals shaped southern Mexico to Panama (SMP) biodiversity:
1. The Great American Interchange that allowed migrations between the Neotropical and the Nearctic biogeographic realms;
2. human colonization with the generation of Mesoamerican cultures; and
3. the Spaniards’ arrival and globalization.
Tectonic events generated a narrow piece of land with steep topography and high environmental heterogeneity, demanding high levels of local adaptation. Habitat size is usually restricted and reduced by frequent disturbances. Topography imposes few options for individuals forced to displace. Thus, extinction risks should be unusually high. Humans initiated an ongoing defaunation process and introduced the maize and the milpa, an itinerant maize-based slash-and-burn polyculture, which depends on revegetation to re-establish soil fertility. Also, the milpa is a most important pre-Hispanic legacy, a biocultural and landrace reservoir actively affecting landscape configuration, succession, soil development, and the genetic architecture of the species. Unprecedented human epidemics and soil, biodiversity, and culture erosion followed behind the Spanish aftermath and the subsequent globalization. > 63 million people and ≈100 ethnic groups inhabit SMP in 2020, which, with the biota, share the same problems of climate change, disturbance, and acculturation. SMP has been the scenario of severe climate change, fastest and deadliest extinction events (amphibians), a most spectacular exotic-species invasion (Africanized honeybees), and accelerated deforestation, defaunation, and acculturation. Biocultural conflicts between native and non-native people are globalization byproducts and sources of habitat destruction and species decline. Bottom-up initiatives are likely the best option for conservation in indigenous areas, whereas honest (i.e., with truly conservation intentions) top-down initiatives are helpful if the affected people are considered subjects (no objects) of conservation plans. We suggest some unique areas requiring conservation attention and analyzed current conservation initiatives. Not a single initiative is best suited for all conservation needs in SMP. Protection of all successional stages is critical for resilience and revegetation. Conservation of the milpa system (crop fields and subsequent fallows) is an optimal option for minimizing tradeoffs between conservation and people needs and safeguarding traditional culture and local landraces but is limited to areas with indigenous people and may not work for species with large home ranges.
... This is also a plausible explanation for the lower germination, as fitness and variability are associated with genetic diversity in forest trees [46]. Such correlation between poorer seed performance and restricted population size was previously detected in other conifers [47,48]. For example, increased formation of empty seeds and lowered germination rate dependent on population size had been found in artificial Douglas-fir (Pseudotsuga menziesii [Mirbel] Franco) stands of different size [47], and decreased germination and seedling performance dependent on population size were observed in the tropical pine Pinus chiapensis [MartÍnez] Andresen [48]. ...
... Such correlation between poorer seed performance and restricted population size was previously detected in other conifers [47,48]. For example, increased formation of empty seeds and lowered germination rate dependent on population size had been found in artificial Douglas-fir (Pseudotsuga menziesii [Mirbel] Franco) stands of different size [47], and decreased germination and seedling performance dependent on population size were observed in the tropical pine Pinus chiapensis [MartÍnez] Andresen [48]. In both cited studies the population size was calculated from census data of the parental population, whereas here it was estimated from genetic data of the pollen haploid contributions to the embryos. ...
Norway spruce differs little in neutral genetic markers among populations and provenances often reported, but in terms of putative adaptive traits and their candidate genes, some clear differences have been observed. This has previously been shown for crown morphotypes. Stands with mostly narrow crown shapes are adapted to high elevation conditions, but these stands are scattered, and the forest area is often occupied by planted stands with predominantly broad crowned morphotypes. This raises questions on whether this differentiation can remain despite gene flow, and on the level of gene flow between natural and planted stands growing in close neighbourhood. The locally adapted stands are a valuable seed source, the progeny of which is expected to have high genetic quality and germination ability. The presented case study is useful for spruce plantation by demonstrating evaluation of these expectations. Immigrant pollen and seeds from planted trees could be maladaptive and may alter the genetic composition of the progeny. This motivated us to study single tree progenies in a locally adapted stand with narrow crowned trees in a partial mast year at nuclear genomic simple sequence repeat (SSR) markers. Spruce is a typical open-pollinated conifer tree species with very low selfing rates, which were also observed in our study (s = 0.3-2.1%) and could be explained by efficient cross-pollination and postzygotic early embryo abortion, common in conifers. The estimated high amount of immigrant pollen found in the pooled seed lot (70.2-91.5%) is likely to influence the genetic composition of the seedlings. Notably, for individual mother trees located in the centre of the stand, up to 50% of the pollen was characterised as local. Seeds from these trees are therefore considered to retain most of the adaptive variance of the stand. Germination percentage varied greatly between half-sib families (3.6-61.9%) and was negatively correlated with relatedness and positively with effective pollen population size of the respective families. As pollen mostly originated from outside the stand and no family structures in the stand itself were found, germination differences can likely be explained by diversity differences in the individual pollen cloud.
... Nevertheless, we have to be careful with generalising our results. First, we chose small populations sizes as they are more biologically relevant, but this may limit adaptation and establishment (Del Castillo et al., 2011;Yates & Fraser, 2014). We also used populations that have been maintained in the lab for many generations, probably leading to a decrease in genetic variation compared to wild populations. ...
... Second, it is impossible to add a competitor without changing total population sizes, population densities, or island sizes; all of these affect genetic variation and drift (Del Castillo et al., 2011;Alzate, Etienne & Bonte, 2019). As it is known that larger populations usually contain more genetic variation, we chose to standardise this by means of isofemale lines, knowing that this might create differences in drift among treatments. ...
Background
A central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary dynamics within the community.
Methods
Here we report the long-term influence of a ghost competitor on the performance of a more successful species using experimental evolution. We transferred the spider mite Tetranychus urticae onto a novel host plant under initial presence or absence of a competing species, the congeneric mite T. ludeni .
Results
The competitor species, T. ludeni , unintentionally went extinct soon after the start of the experiment, but we nevertheless completed the experiment and found that the early competitive pressure of this ghost competitor positively affected the performance (i.e., fecundity) of the surviving species, T. urticae . This effect on T. urticae lasted for at least 25 generations.
Discussion
Our study suggests that early experienced selection pressures can exert a persistent evolutionary signal on species’ performance in novel environments.
... Thus, broadening of the study to include a wide variety of species makes it possible to clarify the relationships among them from the perspective of species characteristics. However, previous studies on plants have mainly focused on short-lived and insect-pollinated species (Leimu et al. 2006;Ilves et al. 2013;Busch and Reisch 2016), and studies on long-lived tree species and wind-pollinated species are relatively limited (Billington 1991;del Castillo et al. 2011;Chybicki et al. 2012). Previous studies have tested the above hypothesis mostly in artificially fragmented areas, with the aim to detect deleterious effects of human-caused fragmentation on the genetic diversity of local populations. ...
... The lack of significant associations of census population size with expected heterozygosity and allelic richness in this study is not in accordance with previous reports showing significant positive relationships between these features (del Castillo et al. 2011;Ilves et al. 2013;Busch and Reisch 2016). This inconsistency might be clarified by a focus on the range of population sizes included in this study. ...
Rare species consisting of small populations are subject to random genetic drift, which reduces genetic diversity. Thus, determining the relationship between population size and genetic diversity would provide key information for planning a conservation strategy for rare species. We used six microsatellite markers to investigate seven extant populations of the rare conifer Pseudotsuga japonica, which is endemic to the Kii Peninsula and Shikoku Island regions that are geographically separated by the Kii Channel in southwest Japan. The population differentiation of P. japonica was relatively high (FST = 0.101) for a coniferous species, suggesting limited gene flow among populations. As expected, significant regional differentiation (AMOVA; p < 0.05) indicated genetic divergence across the Kii Channel. A strong positive correlation between census population size and the number of rare alleles (r = 0.862, p < 0.05) was found, but correlations with major indices of genetic diversity were not significant (allelic richness: r = 0.649, p = 0.104, expected heterozygosity: r = 0.361, p = 0.426). The observed order of magnitude of correlation with three genetic diversity indices corresponded with the theoretically expected order of each index’ sensitivity (i.e., the rate of decline per generation) to the bottleneck event. Thus, features that exhibit a faster response, i.e., the number of rare alleles, would have been subject to deleterious effects of the recent decline in population size, which is presumably caused by the development of extensive artificial plantations of other tree species over the last several decades. Finally, we propose a conservation plan for P. japonica based on our findings.
... Populations that have been reduced in size by anthropogenic forces typically display low genetic diversity and high levels of inbreeding (Bouzat 2010;Campanella et al. 2010;Del Castillo et al. 2011;Faulks et al. 2012;Reed & Frankham 2003;Tucker et al. 2012). For example, small populations of Florida manatees had positive inbreeding coefficients (up to 0.052) and less genetic diversity than expected for a placental mammal (Tucker et al. 2012). ...
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulfide rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of P. sulphuraria and one population of P. thermalis. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. The genetic data was also used to infer the demographic history of these populations to obtain estimates for effective population sizes and migration rates. Effective population sizes were large given the small habitats of these populations. Our results imply that these three endemic extremophile populations should each be considered separately for conservation purposes. Additionally, this study suggests that populations in naturally small habitats may generally have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated. We caution, however, that the inferred lack of inbreeding and the large effective population sizes could potentially be a result of colonization by genetically diverse ancestors.
... In dipterocarps, fruits of Neobalanocarpus heimii (King) P. Ashton and Shorea acuminata Dyer produced through outcrossing are heavier than selfed fruits, and therefore are more likely to germinate and survive to emergence of first leaves (Naito et al. 2005(Naito et al. , 2008. Recent studies have also reported declines in fitness associated with reduced heterozygosity in the tropical trees Swietenia macrophylla King (Breed et al. 2012), Pinus chiapensis (Martínez) Andresen (Del Castillo et al. 2011), and Dysoxylum malabaricum Bedd. ex C.DC. (Ismail et al. 2014b). ...
... Our results are consistent with studies that have observed a relationship between heterozygosity or outcrossing and plant growth or survival (e.g. Del Castillo et al. 2011), including the dipterocarps S. acuminata (Naito et al. 2008) and Vateria indica L. (Ismail et al. 2014a). In addition, reduced heterozygosity in nursery-raised compared to wild seedlings has been reported in other tropical trees, which suggests that the forest floor environment provides an important selective force against survival of inbred progeny (Kettle et al. 2008). ...
Background: Logging and habitat fragmentation of tropical rain forests may disrupt patterns of gene flow and genetic diversity. Consequently, inbreeding in tree populations may reduce fitness and increase extinction risks, especially among species that are predominantly outcrossing, dependent on biotic pollination and/or display limited seed dispersal such as species of the Dipterocarpaceae.
Aims: To test the hypothesis that heterozygosity of individual progeny affects their likelihood of germination and the growth and survival of seedlings.
Methods: Standardised measure of multilocus heterozygosity (sMLH) was estimated from seven microsatellite loci for individual progeny collected from 18 mother trees of the large dipterocarp Parashorea tomentella. The relationships among sMLH, germination and seedling growth and survival were determined for the progeny.
Results: Seedling survival over 18 months increased with greater sMLH and fresh fruit weight. This result was expressed under all experimentally controlled combinations of light and nutrient availability in the nursery and in the shaded understorey of primary forest where survival overall was much lower than in the nursery. sMLH did not affect the probability of germination or seedling growth rate in any experimental treatment.
Conclusions: These results provide evidence that reduced heterozygosity is associated with reduced seedling survival in a tropical forest tree species.
... Liverworts, mostly Jungermanniales, are the fastest colonizers, followed by mosses, while ferns and flowering plants are the latest colonizers (Cordova and del Castillo 2001). Because of its relationship with population size, fragment age can be indirectly associated with fitness and genetic diversity on a species-specific basis, affecting colonization and the persistence of the species (e.g., Pinus chiapenesis; del Castillo et al. 2011). ...
The study of the ecology of fragmented landscapes has been dominated by two assumptions: the unique unidirectional path from larger to smaller fragments and the negligible role of fragment species on fragment properties. An accurate conceptualization of fragmented landscapes requires consideration of the age and origin of the fragments, i.e., direct fragmentation or reverse fragmentation (generation or increase of vegetated fragments by colonization), and the habitat modifications of fragment species (autogenic processes). Colonization and autogenic processes alter the fragments' composition and function. Fragment metrics affect colonization. Autogenic processes are antagonized by disturbances and modulated by abiotic inputs. Fragment alterations by autogenic processes may explain the continuous species substitution detected in some fragments or the species persistence in others. Reverse fragmentation, a natural process in commonly disturbed landscapes, challenges the avoidance-of-habitat disturbance as the ultimate strategy for biodiversity conservation and stresses the importance of pioneer species that promote succession as resilience elements in fragmented landscapes. Among-fragment diversity, generated by local disturbances, can be essential for the resilience of fragmented landscapes, suggesting that conservation and habitat utilization can be complementary processes. Traditional agroforestry systems that depend on disturbance, fragmentation, colonization, and autogenic processes may provide important insights into fragmentation ecology.
... Theory predicts that the capability of populations to respond to environmental changes depends on their genetic diversity. This appears to be the case for climate change in aquatic plant species (Ehlers and Reusch 2008), and for fragmentation in tropical tree species (del Castillo et al. 2011). Human activities have yielded conflicting results in epiphyte genetic diversity. ...
Climate change, habitat loss, and harvesting are potential drivers of species extinction. These factors are unlikely to act on isolation, but their combined effects are poorly understood. We explored these effects in Catopsis compacta, an epiphytic bromeliad commercially harvested in Oaxaca, Mexico. We analyzed local climate change projections, the dynamics of the vegetation patches, the distribution of Catopsis in the patches, together with population genetics and demographic information. A drying and warming climate trend projected by most climate change models may contribute to explain the poor forest regeneration. Catopsis shows a positive mean stochastic population growth. A PVA reveals that quasi-extinction probabilities are not significantly affected by the current levels of harvesting or by a high drop in the frequency of wet years (2%) but increase sharply when harvesting intensity duplicates. Genetic analyses show a high population genetic diversity, and no evidences of population subdivision or a past bottleneck. Colonization mostly takes place on hosts at the edges of the fragments. Over the last 27 years, the vegetation cover has being lost at a 0.028 years(-1) rate, but fragment perimeter has increased 0.076 years(-1). The increases in fragment perimeter and vegetation openness, likely caused by climate change and logging, appear to increase the habitat of Catopsis, enhance gene flow, and maintain a growing and highly genetically diverse population, in spite of harvesting. Our study evidences conflicting requirements between the epiphytes and their hosts and antagonistic effects of climate change and fragmentation with harvesting on a species that can exploit open spaces in the forest. A full understanding of the consequences of potential threatening factors on species persistence or extinction requires the inspection of the interactions of these factors among each other and their effects on both the focus species and the species on which this species depends.
