Genetic variability,management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis

Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as Bothrops insularis, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (a) characterize the genetic diversity of ex situ and in situ populations of B. insularis using heterologous microsatellites; (b) investigate genetic structure among and within these populations; and (c) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the B. neuwiedi group were used to access genetic diversity indexes of ex situ and in situ populations. Low‐to‐medium genetic diversity parameters were found. Both populations showed low—albeit significant—values of system of mating inbreeding coefficient, whereas only the in situ population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the in situ one, which is crucial for considering a reintroduction process into the island.     

Genetic diversity is retained in a bottlenecked Cinereous Vulture population in Turkey

Vulture populations worldwide have suffered precipitous declines in recent decades. The Cinereous Vulture Aegypius monachus, a highly philopatric scavenger distributed across southern Europe and the central Asian plateau, is threatened in many parts of its range. Turkey holds the second largest population of this species in the Western Palaearctic, but there has been no research on its genetic structure and the possible implications of this structure for the future of the species. Here we report nuclear diversity and relatedness determined by short tandem repeat genotyping of 81 individuals from the four largest colonies. Our results demonstrated no significant genetic structuring, suggesting a single panmictic metapopulation connected by frequent dispersal. Furthermore, we show that the study population has retained moderate levels of genetic diversity, despite passing through a recent demographic bottleneck. We estimated the effective population size to be 112 individuals (95% confidence interval 74–201). Our results imply that the observed lack of increase in population size since the 1990s has not been caused by lowered fitness due to genetic inbreeding but rather by increased mortality via demographic processes. In the short term, we suggest that conservation efforts should treat the Turkish subpopulations as a single management unit and aim to increase population size through effective protection, especially during the breeding season.     

Role of evolutionary and ecological factors in the reproductive success and the spatial genetic structure of the temperate gorgonian Paramuricea clavata

Dispersal and mating features strongly influence the evolutionary dynamics and the spatial genetic structure (SGS) of marine populations. For the first time in a marine invertebrate, we examined individual reproductive success, by conducting larval paternity assignments after a natural spawning event, combined with a small‐scale SGS analysis within a population of the gorgonian Paramuricea clavata. Thirty four percent of the larvae were sired by male colonies surrounding the brooding female colonies, revealing that the bulk of the mating was accomplished by males from outside the studied area. Male success increased with male height and decreased with increasing male to female distance. The parentage analyses, with a strong level of self‐recruitment (25%), unveiled the occurrence of a complex family structure at a small spatial scale, consistent with the limited larval dispersal of this species. However, no evidence of small scale SGS was revealed despite this family structure. Furthermore, temporal genetic structure was not observed, which appears to be related to the rather large effective population size. The low level of inbreeding found suggests a pattern of random mating in this species, which disagrees with expectations that limited larval dispersal should lead to biparental inbreeding. Surface brooding and investment in sexual reproduction in P. clavata contribute to multiple paternity (on average 6.4 fathers were assigned per brood), which enhance genetic diversity of the brood. Several factors may have contributed to the lack of biparental inbreeding in our study such as (i) the lack of sperm limitation at a small scale, (ii) multiple paternity, and (iii) the large effective population size. Thus, our results indicate that limited larval dispersal and complex family structure do not necessarily lead to biparental inbreeding and SGS. In the framework of conservation purposes, our results suggested that colony size, proximity among colonies and the population size should be taken into consideration for restoration projects.     

Genetic structure and mating system of Manilkara huberi (Ducke) A. Chev., a heavily logged Amazonian timber species

In this work, we report on the population genetic structure of the endangered tree species Manilkara huberi, an Amazonian tree species intensely exploited due to the high density and resistance of its wood. We investigated the patterns of spatial distribution, genetic structure, and mating system using 7 microsatellite loci and here discuss the consequences for conservation and management of the species. To examine the population genetic structure, 481 adult trees and 810 seedlings were sampled from an area of 200 ha from a natural population in FLONA Tapajós, PA, Brazil. We found relatively high and consistent inbreeding levels (intrapopulation fixation index [f] 0.175 and 0.240) and a significant spatial genetic structure up to a radius of approximately 300 m, most likely due to a limited seed and pollen flow. The multilocus (tm) population outcrossing rate was high (0.995), suggesting that the species is predominantly allogamous with a pollen flow restricted to 47 m. These results suggest that M. huberi is spatially structured, consistent with a model of isolation by distance. Fragmentation may therefore cause the loss of subpopulations, suggesting that management programs for production and conservation should include large areas. The genetic data also revealed that for ex situ conservation, seeds should be collected from more than 175 maternal trees, in order to keep an effective population size of 500. Furthermore, as the species is widely distributed across the Amazon Forest, samples should include several populations in order to represent the highest genetic diversity possible. These results provide a blueprint to guide the production and conservation management policies of this valuable timber species.     

Habitat fragmentation in forests affects relatedness and spatial genetic structure of a native rodent,Rattus lutreolus

Habitat fragmentation can have a range of negative demographic and genetic impacts on disturbed populations. Dispersal barriers can be created, reducing gene flow and increasing population differentiation and inbreeding in isolated habitat remnants. Aggregated retention is a form of forestry that retains patches of forests as isolated island or connected edge patches, with the aim of ‘lifeboating’ species and processes, retaining structural features and improving connectivity. Swamp rats (Rattus lutreolus) are a cover‐dependent species that are sensitive to habitat removal. We examined the effects of aggregated retention forestry and forestry roads in native wet Eucalyptus forests on swamp rat gene flow and population genetic structure. We characterized neighbourhood size in unlogged forest to provide a natural state for comparison, and examined population structure at a range of spatial scales, which provided context for our findings. Tests of pairwise relatedness indicated significant differentiation between island and edge populations in aggregated retention sites, and across roads in unlogged sites. Spatial autocorrelation suggested a neighbourhood size of 42–55 m and revealed male‐biased dispersal. We found no genetic isolation by geographical distance at larger (>2.3 km) scales and populations were all significantly differentiated. Our results suggest that removal of mature forest creates barriers for swamp rat dispersal. In particular, roads may have long‐term impacts, while harvesting of native forests is likely to create only short‐term dispersal barriers at the local scale, depending on the rate of regeneration.     

Extreme population differentiation in a vulnerable slavemaking ant with a fragmented distribution

Understanding levels of population differentiation and inbreeding are important issues in conservation biology, especially for social Hymenoptera with fragmented and small population sizes. Isolated populations are more vulnerable to genetic loss and extinction than those with extended continuous distributions. However, small populations are not always a consequence of a recent reduction of their habitat. Thus, determining the history of population isolation and current patterns of genetic variation of a species is crucial for its conservation. Rossomyrmex minuchae is a slave-making ant with patchy distribution in South Eastern Spain and is classified as vulnerable by the IUCN. In contrast, the other three known species of the genus are presumed to show more uniform distributions. Here we investigate the genetic diversity and population structure of R. minuchae and compare it with that found in two other species of the genus: R. anatolicus and R. quandratinodum. We conclude that although genetic diversity of R. minuchae is low, there is no evidence of a recent bottleneck, suggesting a gradual and natural fragmentation process. We also show extreme population differentiation at nuclear and mitochondrial markers, and isolation by distance at a local scale. Despite some evidence for inbreeding and low genetic variation within populations, we found almost no diploid males, a finding which contrasts with that expected in inbred Hymenoptera with single locus complementary sex determination. This could mean that sex is determined by another mechanism. We argue that continued low population size means that detrimental effects of inbreeding and low genetic variation are likely in the future. We suggest that a policy of artificial gene flow aimed at increasing within population variation is considered as a management option.     

The influence of landscape,climate and history on spatial genetic patterns in keystone plants (Azorella) on sub‐Antarctic islands

The distribution of genetic variation in species is governed by factors that act differently across spatial scales. To tease apart the contribution of different processes, especially at intermediate spatial scales, it is useful to study simple ecosystems such as those on sub‐Antarctic oceanic islands. In this study, we characterize spatial genetic patterns of two keystone plant species, Azorella selago on sub‐Antarctic Marion Island and Azorella macquariensis on sub‐Antarctic Macquarie Island. Although both islands experience a similar climate and have a similar vegetation structure, they differ significantly in topography and geological history. We genotyped six microsatellites for 1,149 individuals from 123 sites across Marion Island and 372 individuals from 42 sites across Macquarie Island. We tested for spatial patterns in genetic diversity, including correlation with elevation and vegetation type, and clines in different directional bearings. We also examined genetic differentiation within islands, isolation‐by‐distance with and without accounting for direction, and signals of demographic change. Marion Island was found to have a distinct northwest–southeast divide, with lower genetic diversity and more sites with a signal of population expansion in the northwest. We attribute this to asymmetric seed dispersal by the dominant northwesterly winds, and to population persistence in a southwestern refugium during the Last Glacial Maximum. No apparent spatial pattern, but greater genetic diversity and differentiation between sites, was found on Macquarie Island, which may be due to the narrow length of the island in the direction of the dominant winds and longer population persistence permitted by the lack of extensive glaciation on the island. Together, our results clearly illustrate the implications of island shape and geography, and the importance of direction‐dependent drivers, in shaping spatial genetic structure.     

Demographic and genetic collapses in spatially structured populations: insights from a long‐term survey in wild fish metapopulations

Unraveling the relationship between demographic declines and genetic changes over time is of critical importance to predict the persistence of at‐risk populations and to propose efficient conservation plans. This is particularly relevant in spatially structured populations (i.e. metapopulations) in which the spatial arrangement of local populations can modulate both demographic and genetic changes. We used ten‐year demo‐genetic monitoring to test 1) whether demographic declines were associated with genetic diversity declines and 2) whether the spatial structure of a metapopulation can weaken or reinforce these demographic and genetic temporal trends. We continuously surveyed, over time and across their entire range, two metapopulations of an endemic freshwater fish species Leuciscus burdigalensis: one metapopulation that had experienced a recent demographic decline and a second metapopulation that was stable over time. In the declining metapopulation, the number of alleles rapidly decreased, the inbreeding coefficient increased, and a genetic bottleneck emerged over time. In contrast, genetic indices were constant over time in the stable metapopulation. We further show that, in the declining metapopulation, demographic and genetic declines were not homogeneously distributed across the metapopulation. We notably identify one local population situated downstream as a ‘reservoir’ of individuals and genetic variability that dampens both the demographic and genetic declines measured at the metapopulation level. We demonstrate the usefulness of long‐term monitoring that combines both genetic and demographic parameters to understand and predict temporal population fluctuations of at‐risk species living in a metapopulation context.     

Consistent loss of genetic diversity in isolated cutthroat trout populations independent of habitat size and quality

Fragmentation and isolation of wildlife populations has reduced genetic diversity worldwide, leaving many populations vulnerable to inbreeding depression and local extinction. Nonetheless, isolation is protecting many native aquatic species from interactions with invasive species, often making reconnection an unrealistic conservation strategy. Isolation management is widely used to protect extant cutthroat trout (Oncorhynchus clarkii) populations from invasive species. Despite this, few studies have empirically examined how predictor variables including habitat length, population size, time since isolation and habitat quality, relate to levels of genetic diversity in isolated trout populations. We compared allelic richness of cutthroat trout across 14 microsatellite loci in two connected and 12 anthropogenically isolated populations of the Flathead River basin, Montana. Isolated populations in habitat fragments <8 km stream length had reduced genetic diversity, but diversity was not significantly related to any of our predictor variables. To broaden our scope, we analyzed seven geologically isolated populations from the same river basin occupying habitat fragments up to 18 km in length. These populations showed reduced diversity, regardless of fragment size. Furthermore, geologically isolated populations had significantly lower average allelic richness compared to streams recently isolated by anthropogenic activities. These results demonstrate a consistent loss of genetic diversity through time in isolated populations, emphasizing the need to explore strategies to minimize risks of inbreeding depression. Testing conservation theory and subsequent assumptions broadly across taxa is necessary to ensure efficacy of conservation efforts.     

Using phylogenetic, genetic and demographic evidence for setting conservation priorities for Mexican rare pines

Phylogenetic, genetic and demographic information are key issues for establishing priorities for conservation. In this study we explored the Vane-Wrigth measure of phylogenetic diversity for establishing criteria for conservation, when intra as well as interpopulation level demographic (population size) and genetic (heterozygosity, inbreeding and genetic distances among populations) parameters are taken into consideration. The data were standardized and analyzed independently and integratively enabling the calculation of indices or criteria for conservation priorities. We illustrate the application of this approach in populations of four Mexican pine species that have been considered rare and endangered, Pinus rzedowzkii, P. pinceana, P. lagunae and P. muricata. The application of several independent diversity indices did not allow us to resolve prioritization. However, the integration of all indices generated different values of importance to conservation, and suggested that the populations with the highest priorities for conservation are: two for Pinus rzedowskii, P. pinceana, and P. lagunae, and one for P. muricata. These populations have intermediate sizes, are the most divergent in the phylogeny and contain genetic variation that is representative of the gene pool of each species. Finally, we demonstrated the functionality of some genetic and demographic parameters; the genetic structure, recruitment rate, geographic distribution and demographic stochasticity, as complementary indicators for evaluating the conservation priority among populations and species.     

Effects of population size and forest management on genetic diversity and structure of the tuberous orchid Orchis mascula

Due to societal changes and altered demands for firewood, the traditional forest management of coppicing has been largely abandoned. As a result, many forest herbs that are specifically adapted to regular opening of the canopy, have suffered significant declines in abundance, and the remaining populations of these species often tend to be small and isolated. Reduced population sizes and pronounced spatial isolation may cause loss of within-population genetic diversity and increased between-population differentiation through random genetic drift and inbreeding. In this study, we investigated genetic diversity and genetic structure of 15 populations of the food-deceptive orchid Orchis mascula using AFLP markers. Within-population genetic diversity significantly increased with increasing population size, indicating genetic impoverishment in small populations. Genetic differentiation, on the other hand, was rather low (Φ_ST = 0.083) and there was no significant relationship between genetic and geographic distances, suggesting substantial gene flow within the study area. However, strong differences in levels of within-population diversity and among-population differentiation were found for populations located in forests that have been regularly coppiced and populations found in forests that were neglected for more than 50 years and that were totally overgrown by shrubs. Our data thus indicate that a lack of coppicing leads to decreased genetic diversity and increased differentiation in this orchid species, most likely as a result of genetic drift following demographic bottlenecks. From a conservation point of view, this study combined with previous results on the demography of O. mascula in relation to forest management illustrates the importance of coppicing in maintaining viable populations of forest herbs in the long-term.     

Population structure and inbreeding in a rare and declining bumblebee, Bombus muscorum (Hymenoptera: Apidae)

Owing to habitat loss populations of many organisms have declined and become fragmented. Vertebrate conservation strategies routinely consider genetic factors, but their importance in invertebrate populations is poorly understood. Bumblebees are important pollinators, and many species have undergone dramatic declines. As monoandrous social hymenopterans they may be particularly susceptible to inbreeding due to low effective population sizes. We study fragmented populations of a bumblebee species, on a model island system, and on mainland Great Britain where it is rare and declining. We use microsatellites to study: population genetic structuring and gene flow; the relationships between genetic diversity, population size and isolation; and frequencies of (sterile) diploid males - an indicator of inbreeding. We find significant genetic structuring (theta = 0.12) and isolation by distance. Populations > 10 km apart are all significantly differentiated, both on oceanic islands and on the mainland. Genetic diversity is reduced relative to closely related common species, and isolated populations exhibit further reductions. Of 16 populations, 10 show recent bottlenecking, and 3 show diploid male production. These results suggest that surviving populations of this rare insect suffer from inbreeding as a result of geographical isolation. Implications for the conservation of social hymenopterans are discussed.     

sGD: software for estimating spatially explicit indices of genetic diversity

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans.     

Significant demographic and fine-scale genetic structure in expanding and senescing populations of the terrestrial orchid Cymbidium goeringii (Orchidaceae)

? Premise of the study: Fine-scale genetic structure (FSGS) in plants is influenced by variation in spatial and temporal demographic processes. To determine how demographic structure and FSGS change with stages of population succession, we studied replicate expanding and senescing populations of the Asian terrestrial orchid Cymbidium goeringii. ? Methods: We used spatial autocorrelation methods (O-ring and kinship statistics) to quantify spatial demographic structure and FSGS in two expanding and two senescing populations, also measuring genetic diversity and inbreeding in each. ? Key results: All populations exhibited significant aggregation of individuals and FSGS at short spatial scales. In expanding populations, this finding was associated with high recruitment rates, suggesting restricted seed dispersal. In senescing populations, recruitment was minimal, suggesting alternative mechanisms of aggregation, perhaps including spatial associations with mycorrhizal fungi. All populations had significant evidence of genetic bottlenecks, and inbreeding levels were consistently high. ? Conclusions: Our results indicate that different successional stages can generate similar patterns of spatial demographic and genetic structure, but as a consequence of different processes. These results contrast with the only other study of senescence effects on population genetic structure in an herbaceous perennial, which found little to no FSGS in senescing populations. With the exception of populations subject to mass collection by orchid sellers, significant FSGS is characteristic of the 16 terrestrial orchid species examined to date. From a conservation perspective, this result suggests that inference of orchid population history will benefit from analyses of both FSGS and demographic structure in combination with other ecological field data.     

Increased inbreeding but not homozygosity in small populations of Sabatia angularis (Gentianaceae)

Understanding how the mating system varies with population size in plant populations is critical for understanding their genetic and demographic fates. We examined how the mating system, characterized by outcrossing rate, biparental inbreeding rate, and inbreeding coefficient, and genetic diversity varied with population size in natural populations of the biennial Sabatia angularis. We found a significant, positive relationship between outcrossing and population size. Selfing was as high as 40% in one small population but was only 7% in the largest population. Despite this pattern, observed heterozygosity did not vary with population size, and we suggest that selection against inbred individuals maintains observed heterozygosity in small populations. Consistent with this hypothesis, we found a trend of lower inbreeding coefficients in the maternal than progeny generation in all of the populations, and half of the populations exhibited significant excesses of adult heterozygosity. Moreover, genetic diversity was not related to population size and was similar across all populations examined. Our results suggest that the consequences of increased selfing for population fitness in S. angularis, a species that experiences significant inbreeding depression, will depend on the relative magnitude and consistency of inbreeding depression and the demographic cost of selection for outcrossed progeny in small populations.     

A complex history of introgression and vicariance in a threatened montane skink (<Emphasis Type="Italic">Pseudemoia cryodroma</Emphasis>) across an Australian sky island system

Species endemic to sky island systems are isolated to mountain peaks and high elevation plateaux both geographically and ecologically, making them particularly vulnerable to the effects of climate change. Pressures associated with climate change have already been linked to local extinctions of montane species, emphasizing the importance of understanding the genetic diversity and population connectivity within sky islands systems for the conservation management of remaining populations. Our study focuses on the endangered alpine skink Pseudemoia cryodroma, which is endemic to the Victorian Alps in south-eastern Australia, and has a disjunct distribution in montane habitats above 1100 m a.s.l. Using mitochondrial DNA (mtDNA) and microsatellite loci, we investigated species delimitation, genetic connectivity and population genetic structure across the geographic range of this species. We found discordance between genetic markers, indicating historical mtDNA introgression at one of the study sites between P. cryodroma and the closely related, syntopic P. entrecasteauxii. Molecular diversity was positively associated with site elevation and extent of suitable habitat, with inbreeding detected in three of the five populations. These results demonstrate the complex interaction between geography and habitat in shaping the population structure and genetic diversity of P. cryodroma, and highlight the importance of minimising future habitat loss and fragmentation for the long-term persistence of this species.     

Population genetics of the endangered Crowned Solitary Eagle (<Emphasis Type="Italic">Buteogallus coronatus</Emphasis>) in South America

The Crowned Solitary Eagle (Buteogallus coronatus) is one of the rarest and most severely threatened birds of prey in the Neotropical region. We studied levels of neutral genetic diversity, population structure, and the demographic history of the species using 55 contemporary samples covering a large fraction of the species range, which were genotyped at 17 microsatellite loci. Our results indicated genetic homogeneity across the sampled regions, which may be explained by a high dispersal capability of Crowned Solitary Eagles resulting in high gene flow or relatively recent population expansion. Further demographic tests revealed that the species has experienced a recent demographic reduction, but inbreeding was not detected. The existing connectivity between geographically separated populations may have buffered the negative effects of the demographic bottleneck. Alternatively, the demographic reduction may be too recent to detect a genetic signature due to the long generation time of the species. Potential conservation strategies, including the possibility of translocations of individuals, are discussed.     

Automated DNA mutation detection using universal conditions direct sequencing: application to ten muscular dystrophy genes

Background

Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti) of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size.

Results

We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation.

Conclusion

Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity are likely the result of animal-mediated long-distance seed dispersal. The greatest present threat to the species is the potential onset of inbreeding depression as the result of increased human harvesting activities. Future genetic studies in understory palms should focus on both fine-scale and landscape-level genetic structure.     

When landscape modification is advantageous for protected species. The case of a synanthropic tarantula, Brachypelma vagans

Landscape fragmentation usually has a considerable effect on the genetic and demographic viability of most species because it reduces population size and increases isolation among populations. This situation provokes loss of genetic diversity and increased inbreeding that can lead to population or species extinctions. Some studies also show that landscape fragmentation may have no effect on or even positive consequences for species genetic diversity. The protected tarantula, Brachypelma vagans, exhibits a particular situation in the Mexican Caribbean, which has experienced high lowland and coastal fragmentation because of recent increases in agricultural, urban and touristic development. This modified landscape structure creates favorable conditions for establishment of B. vagans populations in rural settlements. Populations of this tarantula have high densities of individuals, principally females and juveniles, and gene dispersion is assumed by the rare males. Within this context, we studied the influence of natural and anthropogenic fragmentation on the genetic diversity of six B. vagans populations (five continental, one insular), together with their spatial organization. Our approach used seven inter simple sequence repeat markers, which are highly polymorphic markers. The 76 loci selected revealed high genetic variability for continental populations and a low, but not critical situation, for the insular population. We detected a good level of gene exchange among continental populations, and an evident and recent isolation of the island population. This species exhibits a metapopulation structure in the lowlands with numerous local populations where mature females exhibit high birth site fidelity. We conclude that this protected species does not exhibit characteristics to warrant its current conservation status, and we propose complete revision of the ecological and genetic situation for B. vagans in particular, and for all species within the genus Brachypelma in general.