Fine-scale genetic structure of a long-lived reptile reflects recent habitat modification

Anthropogenic habitat fragmentation — ubiquitous in modern ecosystems — has strong impacts on gene flow and genetic population structure. Reptiles may be particularly susceptible to the effects of fragmentation because of their extreme sensitivity to environmental conditions and limited dispersal. We investigate fine-scale spatial genetic structure, individual relatedness, and sex-biased dispersal in a large population of a long-lived reptile (tuatara, Sphenodon punctatus) on a recently fragmented island. We genotyped individuals from remnant forest, regenerating forest, and grassland pasture sites at seven microsatellite loci and found significant genetic structuring (R_ST = 0.012) across small distances (< 500 m). Isolation by distance was not evident, but rather, genetic distance was weakly correlated with habitat similarity. Only individuals in forest fragments were correctly assignable to their site of origin, and individual pairwise relatedness in one fragment was significantly higher than expected. We did not detect sex-biased dispersal, but natural dispersal patterns may be confounded by fragmentation. Assignment tests showed that reforestation appears to have provided refuges for tuatara from disturbed areas. Our results suggest that fine-scale genetic structuring is driven by recent habitat modification and compounded by the sedentary lifestyle of these long-lived reptiles. Extreme longevity, large population size, simple social structure and random dispersal are not strong enough to counteract the genetic structure caused by a sedentary lifestyle. We suspect that fine-scale spatial genetic structuring could occur in any sedentary species with limited dispersal, making them more susceptible to the effects of fragmentation.     

The effect of habitat fragmentation on dispersal patterns, mating behavior, and genetic variation in a pika (Ochotona princeps) metapopulation

 Habitat fragmentation is becoming increasingly common, yet, the effect of habitat spatial structure on population dynamics remains undetermined for most species. Populations of a single species found in fragmented and nonfragmented habitat present a rare opportunity to examine the effect of habitat spatial structure on population dynamics. This study investigates the impact of highly fragmented habitat on dispersal patterns, mating behavior, and genetic variation in a pika (Ochotona princeps) population with a mainland-island spatial structure. Juvenile dispersal patterns in fragmented habitat revealed that individuals tended to disperse to neighboring habitat patches. However, within-patch band-sharing scores from multilocus DNA fingerprints did not differ from what would be expected if individuals were assorting randomly among habitat patches each year. Multiple, short-distance dispersal targets for juveniles and occasional long-distance dispersal events suggest that habitat fragmentation on this scale has not resulted in restricted dispersal and a genetically subdivided population. Although pikas tended to mate with the closest available partner, DNA fingerprinting band-sharing scores between mated pairs were consistent with a random mating hypothesis. Random mating in this population appears to be an incidental effect of dispersal in a fragmented habitat. This pattern is distinct from that found in nonfragmented habitat (large talus patches) where mating was non-random and consistent with mating between individuals of intermediate relatedness. DNA fingerprinting data revealed within-species variation in the mating habits of the pika directly attributable to habitat spatial structure. Received: 4 November 1996 / Accepted: 30 June 1997     

Social structure and landscape genetics of the endemic New Caledonian ant <Emphasis Type="Italic">Leptomyrmex pallens</Emphasis> Emery, 1883 (Hymenoptera: Formicidae: Dolichoderinae), in the context of fire-induced rainforest fragmentation

Habitat fragmentation is a major threat to biodiversity, as it can alter ecological processes at various spatial and trophic scales. At the species level, fragmentation leading to the isolation of populations can trigger reductions in genetic diversity, potentially having detrimental effects on population fitness, adaptability and ultimately population persistence. Leptomyrmex pallens is a widespread rainforest ant endemic to New Caledonia but now confined to habitat patches that have been fragmented by anthropogenic fire regimes over the last 200 years. We investigated the social structure of L. pallens in the Aoupinié region (c.a. 4900 ha), and assessed the impacts of habitat fragmentation on its population genetic structure. Allele frequencies at 13 polymorphic microsatellite loci were compared among 411 worker ants from 21 nests distributed across the region. High within-nest relatedness (r = 0.70 ± 0.02), and a single queen found in 38 % of the nests by pedigree analysis indicate that the species is monogynous to weakly polygynous. Estimates of gene flow and genetic structure across the region were subsequently determined using a combined dataset of single workers per nest and of unrelated foraging workers. These estimates coupled with a comprehensive landscape genetic analysis revealed no evidence of significant population structure or habitat effects, suggesting that the Aoupinié region harbours a single panmictic population. In contrast, analyses of mitochondrial DNA sequence data revealed a high degree of genetic structuring, indicating limited maternal gene flow and suggesting that gene flow among nests is driven primarily by winged males. Overall these findings suggest that fire-induced habitat fragmentation has had little impact on the population dynamics of L. pallens. Additional studies of less mobile species should therefore be conducted to gain further insights into fire related disturbances on the unique biodiversity and function of New Caledonian ecosystems.     

Decreased relatedness between male prickly forest skinks (<Emphasis Type="BoldItalic">Gnypetoscincus queenslandiae</Emphasis>) in habitat fragments

In species with low levels of dispersal the chance of closely related individuals breeding may be a potential problem; sex-biased dispersal is a mechanism that may decrease the possibility of cosanguineous mating. Fragmentation of the habitat in which a species lives may affect mechanisms such as sex-biased dispersal, which may in turn exacerbate more direct effects of fragmentation such as decreasing population size that may lead to inbreeding depression. Relatedness statistics calculated using microsatellite DNA data showed that rainforest fragmentation has had an effect on the patterns of dispersal in the prickly forest skink (Gnypetoscincus queenslandiae), a rainforest endemic of the Wet Tropics of north eastern Australia. A lower level of relatedness was found in fragments compared to continuous forest sites due to a significantly lower level of pairwise relatedness between males in rainforest fragments. The pattern of genetic relatedness between sexes indicates the presence of male-biased dispersal in this species, with a stronger pattern detected in populations in rainforest fragments. Male prickly forest skinks may have to move further in fragmented habitat in order to find mates or suitable habitat logs.     

The impact of habitat fragmentation on dispersal of Cunningham's skink (Egernia cunninghami): evidence from allelic and genotypic analyses of microsatellites

The effects of habitat fragmentation on processes within and among populations are important for conservation management. Despite a broad spectrum of lifestyles and the conservation significance of many reptiles, very little work on fine-scale population genetics has been carried out on this group. This study examines the dispersal patterns of a rock crevice-dwelling lizard, Cunningham's skink (Egernia cunninghami), in a naturally vegetated reserve and an adjacent deforested site. Both genotypic and genic approaches were employed, using microsatellite loci. The spatial organization of individuals with respect to pairwise relatedness coefficients and allele frequencies, along with assignment tests, were used to infer dispersal characteristics for both sexes in a natural and a cleared area. The distribution of relatedness in both habitats was spatially structured, with E. cunninghami showing high pairwise relatedness within their rocky retreat sites. Analysis of relatedness over different spatial scales, spatial autocorrelation of alleles and assignment tests, all indicated that both sexes in the cleared area show less dispersal than their counterparts in the reserve. Furthermore, deforestation may inhibit female dispersal to a greater extent than that of males. The geographical structuring of allele frequencies for adults in the cleared area, but not the reserve, indicates that habitat fragmentation has the potential to alter at least the microevolution of E. cunninghami populations.     

Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.     

Population genetic patterns in an irruptive species,the long-nosed bandicoot (<Emphasis Type="Italic">Perameles nasuta</Emphasis>)

Understanding the genetic diversity of a population is important for understanding population persistence and extinction risk. The long-nosed bandicoot (Perameles nasuta) was once regarded as common throughout its range, but it is unknown whether it is at risk of decline and the genetic diversity in this species has not been assessed. We evaluated the genetic structure and diversity of a P. nasuta population from samples collected during a 6 year demographic study that encompassed a cyclical fluctuation in abundance. Genetic diversity was higher compared to other studies on bandicoot species suggesting the population is not genetically impoverished. We detected significant temporal genetic differentiation suggesting turnover of genotypes. There was no strong evidence for population structuring, indicating a panmictic population. Individual-based spatial autocorrelation analysis generated a similar pattern of relatedness across geographical distances for both sexes suggesting no or limited sex-biased dispersal. This study provides useful baseline genetic data for a large P. nasuta population that is not significantly impacted by introduced predators or habitat destruction.     

Gene flow simulations demonstrate resistance of long-lived species to genetic erosion from habitat fragmentation

Habitat fragmentation restricts the movement of individuals across a landscape. In terrestrial and aquatic systems, barriers to movement can modify population and community dynamics at local or regional scales. This study contrasted life history traits related to lifespan with habitat fragmentation to determine impacts on species population genetic structure in the Neuse River Basin, USA. For this, we simulated gene flow among evenly-spaced populations in a river network and tracked individual and population genetics for 200 years. The modeled scenarios represent a full cross between five life history strategies and four riverscapes representing varying degrees of fragmentation. The five life history strategies include species (based on freshwater mussels) with average lifespans ranging from 10 to 50 years and age at maturity from 2 to 6 years. The movement landscapes included a (1) panmictic, (2) stepping-stone landscape allowing movement to only neighboring populations during each dispersal event, (3) partially-fragmented landscape divided by dams currently in the network, and (4) fully-fragmented landscape. Results suggest species with shorter lifespans have higher population genetic structure in fragmented landscapes than species with longer lifespans. Furthermore, species with shorter lifespans in highly fragmented landscapes may be harboring genetic degradation or decline as allele fixation and loss. Although anthropogenic fragmentation of many river systems is only 100–200 years old, the simulation indicates that species can respond genetically in that period of time. Additionally, the time frame of the simulation suggests that genetic impacts of habitat fragmentation in some species present in the Neuse River Basin may not yet be manifesting and restoration activities could be successful.     

Habitat fragmentation and genetic diversity of an endangered, migratory songbird, the golden-cheeked warbler (Dendroica chrysoparia)

Landscape genetic approaches offer the promise of increasing our understanding of the influence of habitat features on genetic structure. We assessed the genetic diversity of the endangered golden-cheeked warbler (Dendroica chrysoparia) across their breeding range in central Texas and evaluated the role of habitat loss and fragmentation in shaping the population structure of the species. We determined genotypes across nine microsatellite loci of 109 individuals from seven sites representing the major breeding concentrations of the species. No evidence of a recent population bottleneck was found. Differences in allele frequencies were highly significant among sites. The sampled sites do not appear to represent isolated lineages requiring protection as separate management units, although the amount of current gene flow is insufficient to prevent genetic differentiation. Measures of genetic differentiation were negatively associated with habitat connectivity and the percentage of forest cover between sites, and positively associated with geographic distance and the percentage of agricultural land between sites. The northernmost site was the most genetically differentiated and was isolated from other sites by agricultural lands. Fragmentation of breeding habitat may represent barriers to dispersal of birds which would pose no barrier to movement during other activities such as migration.     

Intact landscape promotes gene flow and low genetic structuring in the threatened Eastern Massasauga Rattlesnake

Genetic structuring of wild populations is dependent on environmental, ecological, and life‐history factors. The specific role environmental context plays in genetic structuring is important to conservation practitioners working with rare species across areas with varying degrees of fragmentation. We investigated fine‐scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance‐limited dispersal. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity. The low level of genetic structuring contrasts with previous studies in the southern part of the species’ range at comparable fine scales (~7 km), in which much higher levels of structuring were documented. The island population''s genetic structuring more closely resembles that of populations from Ontario, Canada, that occupy similarly intact habitats. Intrapopulation variation in effective migration and genetic diversity likely corresponds to the presence of large inland lakes acting as barriers and more human activity in the southern portion of the island. The observed genetic structuring in this intact landscape suggests that the Eastern Massasauga is capable of sufficient interpatch movements to reduce overall genetic structuring and colonize new habitats. Landscape mosaics with multiple habitat patches and localized barriers (e.g., large water bodies or roads) will promote gene flow and natural colonization for this declining species.     

Keeping it in the family: strong fine-scale genetic structure and inbreeding in <Emphasis Type="Italic">Lodoicea maldivica</Emphasis>, the largest-seeded plant in the world

The fine-scale spatial genetic structure (FSGS) of plant populations is strongly influenced by patterns of seed dispersal. An extreme case of limited dispersal is found in the charismatic yet endangered palm Lodoicea maldivica, which produces large fruits (up to 20 kg) dispersed only by gravity. To investigate patterns of seed dispersal and FSGS in natural populations we sampled 1252 individual adults and regenerating offspring across the species’ natural range in the Seychelles archipelago, and characterised their genotypes at 12 microsatellite loci. The average dispersal distance was 8.7?±?0.7 m. Topography had a significant effect on seed dispersal, with plants on steep slopes exhibiting the longest distances. FSGS was intense, especially in younger cohorts. Contrary to what might be expected in a dioecious species, we found high levels of inbreeding, with most neighbouring pairs of male and female trees (≤10 m) being closely related. Nonetheless, levels of genetic diversity were relatively high and similar in the various sampling areas, although these differed in disturbance and habitat fragmentation. We discuss potential trade-offs associated with maternal resource provisioning of progeny, seed dispersal and inbreeding, and consider the implications of our findings for managing this globally significant flagship species.     

Species-specific traits predict genetic structure but not genetic diversity of three fragmented Afrotropical forest butterfly species

The Upper Guinean forests of Ghana, West Africa, are considered among the most threatened and fragmented in the world. Little is known about the genetic consequences of fragmentation on Ghana’s forest-associated species, but this genetic signature is generally expected to differ across species. We compared patterns of mtDNA cytochrome oxidase I (COI) variation of three Nymphalid forest butterfly species that differ with respect to their relative dispersibilities (Aterica galene: high habitat fidelity, low dispersal ability; Euphaedra medon: high habitat fidelity, strong dispersal ability; Gnophodes betsimena: relaxed habitat fidelity, low dispersal ability). Individuals were collected from two large forest reserves and five small sacred forest groves. Patterns of differentiation across species were broadly coincident with our predicted hierarchy of relative species dispersibility and suggested that genetic connectivity is most compromised by strict fidelity to forest habitat rather than by raw capacity for sustained flight. Connectivity was uncorrelated with geographic distance, but instead seemed best explained by urbanization and the sequential pattern of forest loss. Genetic diversity was dramatically different among species and not easily explained by either species-specific traits or effects of fragmentation. Aterica galene, the species most impacted by fragmentation, exhibited very high diversity, whereas G. betsimena, a broadly distributed, very common species, with relaxed habitat fidelity, was genetically depauperate. There was limited evidence of genetic erosion from the sacred groves despite these small forest patches accounting for less than 1–10 % of the total area of the forest reserves, which indicates these forest relics have high conservation value.     

Cryptic differences in dispersal lead to differential sensitivity to habitat fragmentation in two bumblebee species

Habitat loss has led to fragmentation of populations of many invertebrates, but social hymenopterans may be particularly sensitive to habitat fragmentation due to their low effective population sizes. The impacts of fragmentation depend strongly on dispersal abilities, but these are difficult to quantify. Here, we quantify and compare dispersal abilities of two bumblebee species, Bombus muscorum and Bombus jonellus , in a model island system. We use microsatellites to investigate population genetic structuring, dispersal and spatial patterns in genetic diversity. Populations of both species showed significant structuring, and isolation by distance, but this was markedly greater in B. muscorum (θ = 0.13) than in B. jonellus (θ = 0.034). This difference could reflect a higher effective population size in B. jonellus compared to B. muscorum , but this is not consistent with the observed abundance of the two species. We argue that it is more likely that B. jonellus has a higher propensity to disperse than B. muscorum . This will influence their relative susceptibility to habitat fragmentation and may in part explain differential declines of mainland populations of these and other bumblebee species.     

Fine-scale genetic population structure of an understory rainforest bird in Costa Rica

We studied five populations of a rainforest understory insectivorous bird (Myrmeciza exsul, chestnut-backed antbird) in a fragmented landscape in northeastern Costa Rica in order to test hypotheses about the influence of forest fragmentation on population genetic structure using 16 microsatellite loci. Bayesian assignment approaches—perhaps the most conservative analyses we performed—consistently grouped the sites into two distinct groups, with all individuals from the smallest and most isolated population clustering separately from the other four sites. Additional analyses revealed (1) overall significant genetic structure; (2) a pattern of population differentiation consistent with a hypothesis of isolation by resistance (landscape connectivity), but not distance; and (3) relatively short dispersal distances indicated by elevated mean pairwise relatedness in several of the sites. Our results are somewhat surprising given the small geographic distances between sites (11–34?km) and the short time (~60?years) since wide-spread deforestation in this landscape. We suspect fine-scale genetic structure may occur in many resident tropical bird species, and in the case of the chestnut-backed antbird it appears that anthropogenic habitat fragmentation has important population genetic implications. It appears that chestnut-backed antbirds may persist in fragmented landscapes in the absence of significant migration among patches, but mechanisms that allow this species to persist when many other similar species do not are not well understood.     

Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographical breaks in a Mediterranean endemic marine cave mysid

The marine cave‐dwelling mysid Hemimysis margalefi is distributed over the whole Mediterranean Sea, which contrasts with the poor dispersal capabilities of this brooding species. In addition, underwater marine caves are a highly fragmented habitat which further promotes strong genetic structuring, therefore providing highly informative data on the levels of marine population connectivity across biogeographical regions. This study investigates how habitat and geography have shaped the connectivity network of this poor disperser over the entire Mediterranean Sea through the use of several mitochondrial and nuclear markers. Five deeply divergent lineages were observed among H. margalefi populations resulting from deep phylogeographical breaks, some dating back to the Oligo‐Miocene. Whether looking at the intralineage or interlineage levels, H. margalefi populations present a high genetic diversity and population structuring. This study suggests that the five distinct lineages observed in H. margalefi actually correspond to as many separate cryptic taxa. The nominal species, H. margalefi sensu stricto, corresponds to the westernmost lineage here surveyed from the Alboran Sea to southeastern Italy. Typical genetic breaks such as the Almeria‐Oran Front or the Siculo‐Tunisian Strait do not appear to be influential on the studied loci in H. margalefi sensu stricto. Instead, population structuring appears more complex and subtle than usually found for model species with a pelagic dispersal phase. The remaining four cryptic taxa are all found in the eastern basin, but incomplete lineage sorting is suspected and speciation might still be in process. Present‐day population structure of the different H. margalefi cryptic species appears to result from past vicariance events started in the Oligo‐Miocene and maintained by present‐day coastal topography, water circulation and habitat fragmentation.     

Genetic structure and genetic diversity of the endangered grassland plant <Emphasis Type="Italic">Crepis mollis</Emphasis> (Jacq.) Asch. as a basis for conservation management in Germany

Plant diversity is decreasing mainly through anthropogenic factors like habitat fragmentation, which lead to spatial separation of remaining populations and thereby affect genetic diversity and structure within species. Twenty populations of the threatened grassland species Crepis mollis were studied across Germany (578 individual plants) based on microsatellite genotyping. Genetic diversity was significantly higher in populations from the Alpine region than from the Central Uplands. Furthermore, genetic diversity was significantly positively correlated with population size. Despite smaller populations in the Uplands there were no signs of inbreeding. Genetic differentiation between populations was moderate (F _ST?=?0.09) and no isolation by distance was found. In contrast, large-scale spatial genetic structure showed a significant decrease of individual pairwise relatedness, which was higher than in random pairs up to 50 km. Bayesian analyses detected three genetic clusters consistent with two regions in the Uplands and an admixture group in the Alpine region. Despite the obvious spatial isolation of the currently known populations, the absence of significant isolation by distance combined together with moderate population differentiation indicates that drift rather than inter-population gene flow drives differentiation. The absence of inbreeding suggests that pollination is still effective, while seed dispersal by wind is likely to be impaired by discontinuous habitats. Our results underline the need for maintaining or improving habitat quality as the most important short term measure for C. mollis. For maintaining long-term viability, establishing stepping stone habitats or, where this is not possible, assisted gene flow needs to be considered.     

Population genetics and relatedness in a critically endangered island raptor, Ridgway’s Hawk Buteo ridgwayi

Many island avian populations are of conservation interest because they have a higher risk of extinction than mainland populations. Susceptibility of island birds to extinction is primarily related to human induced change through habitat loss, persecution, and introduction of exotic species, in combination with genetic factors. We used microsatellite profiles from 11 loci to assess genetic diversity and relatedness in the critically endangered hawk Buteo ridgwayi endemic to the island of Hispaniola in the Caribbean. Using samples collected between 2005 and 2009, our results revealed a relatively high level of heterozygosity, evidence of a recent genetic bottleneck, and the occurrence of inbreeding within the population. Pair relatedness analysis found 4 of 7 sampled breeding pairs to be related similar to that of first cousin or greater. Pedigree estimates indicated that up to 18 % of potential pairings would be between individuals with relatedness values similar to that of half-sibling. We discuss our findings in the context of conservation genetic management suggesting both carefully managed translocations and the initiation of a captive population as a safeguard of the remaining genetic diversity.     

Water availability strongly impacts population genetic patterns of an imperiled Great Plains endemic fish

Genetic, demographic, and environmental processes affect natural populations synergistically, and understanding their interplay is crucial for the conservation of biodiversity. Stream fishes in metapopulations are particularly sensitive to habitat fragmentation because persistence depends on dispersal and colonization of new habitat but dispersal is constrained to stream networks. Great Plains streams are increasingly fragmented by water diversion and climate change, threatening connectivity of fish populations in this ecosystem. We used seven microsatellite loci to describe population and landscape genetic patterns across 614 individuals from 12 remaining populations of Arkansas darter (Etheostoma cragini) in Colorado, a candidate species for listing under the U.S. Endangered Species Act. We found small effective population sizes, low levels of genetic diversity within populations, and high levels of genetic structure, especially among basins. Both at- and between-site landscape features were associated with genetic diversity and connectivity, respectively. Available stream habitat and amount of continuous wetted area were positively associated with genetic diversity within a site, while stream distance and intermittency were the best predictors of genetic divergence among sites. We found little genetic contribution from historic supplementation efforts, and we provide a set of management recommendations for this species that incorporate a conservation genetics perspective.     

Spatial genetic structuring in a vagile species, the European wood mouse

We examined the genetic structure of natural populations of the European wood mouse Apodemus sylvaticus at the microgeographic (<3 km) and macrogeographic (>30 km) scales. Ecological and behavioural studies indicate that this species exhibits considerable dispersal relative to its home-range size. Thus, there is potential for high gene flow over larger geographic areas. As levels of population genetic structure are related to gene flow, we hypothesized that population genetic structuring at the microgeographic level should be negligible, increasing only with geographic distance. To test this, four sites were sampled within a microgeographic scale with two additional samples at the macrogeographic level. Individuals ( n =415) were screened and analysed for seven polymorphic microsatellite loci. Contrary to our hypothesis, significant levels of population structuring were detected at both scales. Comparing genetic differentiation with geographic distance suggests increasing genetic isolation with distance. However, this distance effect was non-significant being confounded by surprisingly high levels of differentiation among microgeographic samples. We attribute this pattern of genetic differentiation to the effect of habitat fragmentation, splitting large populations into components with small effective population sizes resulting in enhanced genetic drift. Our results indicate that it is incorrect to assume genetic homogeneity among populations even where there is no evidence of physical barriers and dispersal can occur freely. In the case of A. sylvaticus , it is not clear whether dispersal does not occur across habitat barriers or behavioural dispersal occurs without consequent gene flow.     

Contrasting demographic and genetic estimates of dispersal in the endangered Coahuilan box turtle: a contemporary approach to conservation

The evolutionary viability of an endangered species depends upon gene flow among subpopulations and the degree of habitat patch connectivity. Contrasting population connectivity over ecological and evolutionary timescales may provide novel insight into what maintains genetic diversity within threatened species. We employed this integrative approach to evaluating dispersal in the critically endangered Coahuilan box turtle (Terrapene coahuila) that inhabits isolated wetlands in the desert‐spring ecosystem of Cuatro Ciénegas, Mexico. Recent wetland habitat loss has altered the spatial distribution and connectivity of habitat patches; and we therefore predicted that T. coahuila would exhibit limited movement relative to estimates of historic gene flow. To evaluate contemporary dispersal patterns, we employed mark–recapture techniques at both local (wetland complex) and regional (intercomplex) spatial scales. Gene flow estimates were obtained by surveying genetic variation at nine microsatellite loci in seven subpopulations located across the species’ geographical range. The mark–recapture results at the local spatial scale reveal frequent movement among wetlands that was unaffected by interwetland distance. At the regional spatial scale, dispersal events were relatively less frequent between wetland complexes. The complementary analysis of population genetic substructure indicates strong historic gene flow (global F_ST = 0.01). However, a relationship of genetic isolation by distance across the geographical range suggests that dispersal limitation exists at the regional scale. Our approach of contrasting direct and indirect estimates of dispersal at multiple spatial scales in T. coahuila conveys a sustainable evolutionary trajectory of the species pending preservation of threatened wetland habitats and a range‐wide network of corridors.