Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus

Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally‐dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.     

Diversity and structure of fragmented populations of a threatened endemic cyprinodontid (Aphanius sophiae) inferred from genetics and otolith morphology: Implications for conservation and management

The assessment of population structure and genetic diversity is crucial for the management and conservation of threatened species. Natural and artificial barriers to dispersal (i.e., gene flow) increase populations’ differentiation and isolation by reducing genetic exchange and diversity. Freshwater ecosystems are highly fragmented because of human activities. Threatened species with small population sizes are more sensitive to habitat fragmentation effects. Here, we investigate the genetic population structure and gene flow among seven populations of Aphanius sophiae in the Kor Basin by using sequences of the complete Cyt b gene and otolith morphometry. The Cyt b gene showed low level of genetic variation, only 4.12% of the identified sites were variable, and 2.42% were parsimony informative. Overall, haplotype diversity was low to moderate and nucleotide diversity was low to extremely low. Fish populations exhibited high levels of genetic differentiation, suggesting limited gene flow among them. These differences were obtained not only among geographically distant populations, but also among neighboring localities. Genetic population structure was supported by the AMOVA analysis and by the haplotype network (only one of 21 haplotypes were shared by two localities). Otolith morphometric analysis was in agreement with genetic results, the two most distant and isolated populations were clearly separated, and genetically close populations showed less differences in morphometry. A significant pattern of isolation by distance was also detected among A. sophiae populations, with genetic distance more correlated with hydrological distance than with geographic distance. Results suggested that limited gene flow due to habitat fragmentation is an important factor contributing to genetic structuring and to the loss of genetic variation of A. sophiae populations. Aphanius sophiae population structure seems to be the result of habitat fragmentation and water pollution, but other factors such as introduced species should be considered. Given the high degree of genetic structuring, the definition of conservation groups is of particular importance for A. sophiae, which should be considered endangered according to the IUCN criteria. Conservation plans must recognize the genetic independence of populations and manage separately preventing the loss of locally adapted genotypes.     

Habitat fragmentation influences genetic diversity and differentiation: Fine‐scale population structure of Cercis canadensis (eastern redbud)

Forest fragmentation may negatively affect plants through reduced genetic diversity and increased population structure due to habitat isolation, decreased population size, and disturbance of pollen‐seed dispersal mechanisms. However, in the case of tree species, effective pollen‐seed dispersal, mating system, and ecological dynamics may help the species overcome the negative effect of forest fragmentation. A fine‐scale population genetics study can shed light on the postfragmentation genetic diversity and structure of a species. Here, we present the genetic diversity and population structure of Cercis canadensis L. (eastern redbud) wild populations on a fine scale within fragmented areas centered around the borders of Georgia–Tennessee, USA. We hypothesized high genetic diversity among the collections of C. canadensis distributed across smaller geographical ranges. Fifteen microsatellite loci were used to genotype 172 individuals from 18 unmanaged and naturally occurring collection sites. Our results indicated presence of population structure, overall high genetic diversity (H_E = 0.63, H_O = 0.34), and moderate genetic differentiation (F_ST = 0.14) among the collection sites. Two major genetic clusters within the smaller geographical distribution were revealed by STRUCTURE. Our data suggest that native C. canadensis populations in the fragmented area around the Georgia–Tennessee border were able to maintain high levels of genetic diversity, despite the presence of considerable spatial genetic structure. As habitat isolation may negatively affect gene flow of outcrossing species across time, consequences of habitat fragmentation should be regularly monitored for this and other forest species. This study also has important implications for habitat management efforts and future breeding programs.     

Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna

Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present‐day tropical biota. Using genome‐wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post‐Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as “isolation by instability,” highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.     

Genetic footprints of habitat fragmentation in the extant populations of Sinojackia (Styracaceae): implications for conservation

Sinojackia, a member of the family Styracaceae, is an endangered genus endemic to China. The number of populations and population size of Sinojackia have decreased sharply because of habitat fragmentation and destruction. We studied the genetic diversity of extant populations in two different cohorts (adult and seedling) using eight microsatellite markers to investigate the genetic footprints of habitat fragmentation in four recognized Sinojackia spp. and to develop appropriate conservation measures. Data on intrapopulational genetic diversity suggest that Sinojackia populations have maintained relatively high levels of genetic diversity and low levels of genetic differentiation despite severe fragmentation. The high genetic diversity may be explained by the outcrossing mating system and high longevity of Sinojackia spp. The amount of genetic variation is not associated with population size, which was also supported by bottleneck analysis. In the species studied, there was no significant difference in the genetic diversity between the two cohorts analysed. However, inbreeding increased from adult trees to seedling populations, suggesting that the higher proportion of biparental inbreeding in the recent generations of seedlings is the result of restricted current genetic flow caused by habitat fragmentation. Average seed set per population was not significantly correlated with either population size or genetic diversity. Conservation management should aim to monitor inbreeding and outbreeding depression carefully to ensure the in situ and ex situ conservation of Sinojackia spp. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.     

Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog

The Eastern Afromontane Biodiversity Hotspot is known for microendemism and exceptional population genetic structure. The region's landscape heterogeneity is thought to limit gene flow between fragmented populations and create opportunities for regional adaptation, but the processes involved are poorly understood. Using a combination of phylogeographic analyses and circuit theory, I investigate how characteristics of landscape heterogeneity including regional distributions of slope, rivers and streams, habitat and hydrological basins (drainages) impact genetic distance among populations of the endemic spotted reed frog (Hyperolius substriatus), identifying corridors of connectivity as well as barriers to dispersal. Results show that genetic distance among populations is most strongly correlated to regional and local hydrologic structure and the distribution of suitable habitat corridors, not isolation by distance. Contrary to expectations, phylogeographic structure is not coincident with the two montane systems, but instead corresponds to the split between the region's two major hydrological basins (Zambezi and East Central Coastal). This results in a paraphyletic relationship for the Malawian Highlands populations with respect to the Eastern Arc Mountains and implies that the northern Malawian Highlands are the diversity centre for H. substriatus. Although the Malawian Highlands collectively hold the greatest genetic diversity, individual populations have lower diversity than their Eastern Arc counterparts, with an overall pattern of decreasing population diversity from north to south. Through the study of intraspecific differentiation across a mosaic of ecosystem and geographic heterogeneity, we gain insight into the processes of diversification and a broader understanding of the role of landscape in evolution.     

Comprehensive analysis of population genetics of Phoxinus phoxinus ujmonensis in the Irtysh River: Abiotic and biotic factors

As a widely distributed species along the Irtysh River, Phoxinus phoxinus ujmonensis (Kaschtschenko, 1899) was used as a model to investigate genetic diversity and population structure as well as the influence of environmental factors on population genetics. In this study, we specifically developed 12 polymorphic microsatellite loci. The analysis of microsatellite and mtDNA markers revealed a high and a moderate genetic diversity across seven populations, respectively. Moderate differentiation was also detected among several populations, indicating the impact of habitat fragmentation and divergence. The absence of isolation by distance implied an extensive gene flow, while the presence of isolation by adaptation implied that these populations might be in the process of adapting to divergent habitats. Correlation analysis showed that abiotic factors like dissolved oxygen, pH, total dissolved solids, and conductivity in water as well as biotic factors like plankton diversity and fish species diversity had impact on genetic diversity and divergence in P. phoxinus ujmonensis populations. The results of this study will provide an insight into the effect of environmental factors on genetic diversity and contribute to the study of population genetics of sympatric species.     

Conservation genetics of Amorpha georgiana (Fabaceae), an endangered legume of the Southeastern United States

Amorpha georgiana (Fabaceae) is an endangered legume species found in longleaf pine savannas in the Southeastern United States. Approximately 900 individuals and 14 populations remain, most of which are concentrated in North Carolina. Eleven microsatellite loci were used to explore genetic diversity, population structure and recent population bottlenecks using genotypic data from 132 individuals collected at ten different localities. Although A. georgiana is quite rare, it exhibited high levels of genetic diversity (17.7 alleles/locus; H _o = 0.65, H _E = 0.75). Most of the genetic variation was found within rather than between populations of this species. The single remaining Georgia population was well differentiated from populations of the Carolinas ( F _ST > 0.1), which had weaker structure among them ( F _ST < 0.1). Only a geographically disjunct population showed strong evidence of a recent population bottleneck, perhaps due to a recent founder event. Hybridization with A. herbacea was also detected. For conservation management plans, A. georgiana populations in each geographic region (North Carolina, South Carolina and Georgia) plus a disjunct population in North Carolina (Holly Shelter) should be treated as separate management units for which in situ conservation, including habitat restoration and use of prescribed burns, should ensure persistence of this species and preservation of its evolutionary potential.     

Small-Scale Fragmentation Effects on Local Genetic Diversity in Two Phyllostomid Bats with Different Dispersal Abilities in Panama

Habitat fragmentation is one of the greatest threats to biodiversity. Despite their importance for conservation, the genetic consequences of small-scale habitat fragmentation for bat populations are largely unknown. In this study, we linked genetic with ecological and demographic data to assess the effects of habitat fragmentation on two species of phyllostomid bats ( Uroderma bilobatum and Carollia perspicillata ) that differ in their dispersal abilities and demographic response to fragmentation. We hypothesized that population differentiation and the effect of habitat fragmentation on levels of genetic diversity will be a function of the species' mobility. We sequenced mtDNA from 232 bats caught on 11 islands in Gatún Lake, Panamá, isolated from the mainland for ca 90 yr, and in adjacent, continuous forest on the mainland. Populations of both species showed significant genetic differentiation ( F _ST). Consistent with our prediction, population subdivision was lower in the highly mobile U. bilobatum ( F _ST= 0.01) compared to the less vagile C. perspicillata ( F _ST= 0.06), and only the latter species showed a pattern indicative of isolation by distance and, in addition, an effect of fragmentation. Genetic erosion as a result of fragmentation was also only detectable in the less mobile species, C. perspicillata , where haplotype diversity was lower in island compared to mainland populations. Our results suggest that some Neotropical bat species are prone to loss of genetic variation in response to anthropogenic small-scale habitat fragmentation. In this context, our findings point toward mobility as a good predictor of a species' vulnerability to fragmentation and altered population genetic structure.     

Population structure and landscape genetics in the endangered subterranean rodent Ctenomys porteousi

In order to devise adequate conservation and management strategies for endangered species, it is important to incorporate a reliable understanding of its spatial population structure, detecting the existence of demographic partitions throughout its geographical range and characterizing the distribution of its genetic diversity. Moreover, in species that occupy fragmented habitats it is essential to know how landscape characteristics may affect the genetic connectivity among populations. In this study we use eight microsatellite markers to analyze population structure and gene flow patterns in the complete geographic range of the endangered rodent Ctenomys porteousi. Also, we use landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. In spite of geographical proximity of the sampling sites (8–27 km between the nearest sites) and the absence of marked barriers to individual movement, strong population structure and low values of gene flow were observed. Genetic differentiation among sampling sites was consistent with a simple model of isolation by distance, where peripheral areas showed higher population differentiation than those sites located in the central area of the species’ distribution. Landscape genetics analysis suggested that habitat fragmentation at regional level has affected the distribution of genetic variation among populations. The distance of sampling sites to areas of the landscape having higher habitat connectivity was the environmental factor most strongly related to population genetic structure. In general, our results indicate strong genetic structure in C. porteousi, even at a small spatial scale, and suggest that habitat fragmentation could increase the population differentiation.     

Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas

Genetic effects of habitat fragmentation may be undetectable because they are generally a recent event in evolutionary time or because of confounding effects such as historical bottlenecks and historical changes in species'' distribution. To assess the effects of demographic history on the genetic diversity and population structure in the Neotropical tree Dipteryx alata (Fabaceae), we used coalescence analyses coupled with ecological niche modeling to hindcast its distribution over the last 21 000 years. Twenty-five populations (644 individuals) were sampled and all individuals were genotyped using eight microsatellite loci. All populations presented low allelic richness and genetic diversity. The estimated effective population size was small in all populations and gene flow was negligible among most. We also found a significant signal of demographic reduction in most cases. Genetic differentiation among populations was significantly correlated with geographical distance. Allelic richness showed a spatial cline pattern in relation to the species'' paleodistribution 21 kyr BP (thousand years before present), as expected under a range expansion model. Our results show strong evidences that genetic diversity in D. alata is the outcome of the historical changes in species distribution during the late Pleistocene. Because of this historically low effective population size and the low genetic diversity, recent fragmentation of the Cerrado biome may increase population differentiation, causing population decline and compromising long-term persistence.     

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

ABSTRACT: BACKGROUND: As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. RESULTS: Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; pi = 0.00314) were almost as high as at PAL (h = 0.836; pi = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel's test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species. CONCLUSIONS: We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.     

Gene flow and population structure of a solitary top carnivore in a human‐dominated landscape

While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free‐roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human–carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human‐caused extinctions.     

Exploring the legacy of goat grazing: signatures of habitat fragmentation on genetic patterns of endemic weevil populations in Northern Isabela Island,Galápagos (Ecuador)

Together with reduction in habitat area and quality, reduction in habitat connectivity is one of the major factors influencing species’ persistence in fragmented landscapes. We explore the consequences of recent habitat fragmentation on volcanoes across Isabela Island, Galápagos by analyzing genetic patterns of populations of endemic weevils whose host plants have been depleted by indiscriminate goat grazing. We predicted that if grazing on the weevils’ host plants has caused habitat fragmentation on the weevils populations themselves, then the effects on the genetic architecture of populations should be more severe on Galapaganus conwayensis populations from volcanoes on Northern Isabela than on those from Santa Cruz or Pinta islands where vegetation destruction was not as extensive. We used mitochondrial sequences to reveal historical colonization patterns and microsatellite variation to understand more contemporary genetic changes. We found significantly lower microsatellite genetic diversity and population size within localities and increased genetic differentiation at a small geographic scale with a stronger isolation by distance pattern and larger numbers of genetic clusters on Isabela. In the absence of long-standing mitochondrial structure within each volcano, we interpret the microsatellite results as suggesting that recent host plant habitat fragmentation may indeed influence the genetic patterns of plant feeding insects and highlight the importance of controlling the spread of introduced herbivores in the Galápagos Islands.     

Montane refugia predict population genetic structure in the Large‐blotched Ensatina salamander

Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate‐induced habitat shifts on population genetic structure in the Large‐blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high‐elevation conifer forest in the Transverse and Peninsular Ranges of southern California and northern Baja California. A composite SDM representing the range through time predicts two disjunct refugia, one in southern California encompassing the core of the species range and the other in the Sierra San Pedro Mártir of northern Baja California at the southern limit of the species range. Based on our spatial model, we would expect a pattern of high connectivity among populations within the northern refugium and, conversely, a pattern of isolation due to long‐term persistence of the Sierra San Pedro Mártir population. Our genetic results are consistent with these predictions based on the hypothetical refugia in that (i) historical measures of population connectivity among stable areas are correlated with gene flow estimates; and (ii) there is strong geographical structure between separate refugia. These results provide evidence for the role of recent climatic change in shaping patterns of population persistence and connectivity within the Transverse and Peninsular Ranges, an evolutionary hotspot.     

Genetic costructure in a meta‐community under threat of habitat fragmentation

Habitat fragmentation increasingly threatens the services provided by natural communities and ecosystem worldwide. An understanding of the eco‐evolutionary processes underlying fragmentation‐compromised communities in natural settings is lacking, yet critical to realistic and sustainable conservation. Through integrating the multivariate genetic, biotic and abiotic facets of a natural community module experiencing various degrees of habitat fragmentation, we provide unique insights into the processes underlying community functioning in real, natural conditions. The focal community module comprises a parasitic butterfly of conservation concern and its two obligatory host species, a plant and an ant. We show that both historical dispersal and ongoing habitat fragmentation shape population genetic diversity of the butterfly Phengaris alcon and its most limited host species (the plant Gentiana pneumonanthe). Genetic structure of each species was strongly driven by geographical structure, altitude and landscape connectivity. Strikingly, however, was the strong degree of genetic costructure among the three species that could not be explained by the spatial variables under study. This finding suggests that factors other than spatial configuration, including co‐evolutionary dynamics and shared dispersal pathways, cause parallel genetic structure among interacting species. While the exact contribution of co‐evolution and shared dispersal routes on the genetic variation within and among communities deserves further attention, our findings demonstrate a considerable degree of genetic parallelism in natural meta‐communities. The significant effect of landscape connectivity on the genetic diversity and structure of the butterfly also suggests that habitat fragmentation may threaten the functioning of the community module on the long run.     

Development of genetic diversity,differentiation and structure over 500 years in four ponderosa pine populations

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range‐margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range‐margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500‐year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within‐population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F_ST and Jost's D_est) and diversity within populations (F_IS) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.     

Genetic connectivity and diversity in inselberg populations of Acacia woodmaniorum,a rare endemic of the Yilgarn Craton banded iron formations

Historically rare plant species with disjunct population distributions and small population sizes might be expected to show significant genetic structure and low levels of genetic diversity because of the effects of inbreeding and genetic drift. Across the globe, terrestrial inselbergs are habitat for rich, often rare and endemic flora and are valuable systems for investigating evolutionary processes that shape patterns of genetic structure and levels of genetic diversity at the landscape scale. We assessed genetic structure and levels of genetic diversity across the range of the historically rare inselberg endemic Acacia woodmaniorum. Phylogeographic and genetic structure indicates that connectivity is not sufficient to produce a panmictic population across the limited geographic range of the species. However, historical levels of gene flow are sufficient to maintain a high degree of adaptive connectivity across the landscape. Genetic diversity indicates gene flow is sufficient to largely counteract any negative genetic effects of inbreeding and random genetic drift in even the most disjunct or smallest populations. Phylogeographic and genetic structure, a signal of isolation by distance and a lack of evidence of recent genetic bottlenecks suggest long-term stability of contemporary population distributions and population sizes. There is some evidence that genetic connectivity among disjunct outcrops may be facilitated by the occasional long distance dispersal of Acacia polyads carried by insect pollinators moved by prevailing winds.     

Population genetic consequences of geographic disjunction: a prairie plant isolated on Great Lakes alvars

Species may often exhibit geographic variation in population genetic structure due to contemporary and historical variation in population size and gene flow. Here, we test the predictions that populations on the margins of a species' distribution contain less genetic variation and are more differentiated than populations towards the core of the range by comparing patterns of genetic variation at five microsatellite loci between disjunct and core populations of the perennial, allohexaploid herb Geum triflorum. We sampled nine populations isolated on alvar habitat within the eastern Great Lakes region in North America, habitats that include disjunct populations of several plant species, and compared these to 16 populations sampled from prairie habitat throughout the core of the species' distribution in midwestern Canada and the USA. Alvar populations exhibited much lower within-population diversity and contained only a subset of alleles found in prairie populations. We detected isolation by distance across the species' range and within alvar and prairie regions separately. As predicted, genetic differentiation was higher among alvar populations than among prairie populations, even after controlling for the geographic distance between sampled populations. Low diversity and high differentiation can be accounted for by the greater contemporary spatial isolation of alvar populations. However, the genetic structure of alvar populations may also have been influenced by postglacial range expansion and contraction. Our results are consistent with alvar populations being founded during an expansion of prairie habitat during the warmer, hypsithermal period approximately 5000 bp and subsequently becoming stranded on isolated alvar habitat as the climate grew cooler and wetter.     

Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction

Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farmland, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation-by-distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess differences in effective population density and dispersal between the contrasted landscapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.