Evolutionary distinctiveness and historical decline in genetic diversity in the Seychelles Black Parrot Coracopsis nigra barklyi

Island endemic species are acutely vulnerable to extinction as a result of stochastic and human impacts. Conservation of unique island biodiversity is high priority, and an understanding of the evolutionary history of vulnerable island species is important to inform conservation management. The Seychelles Black Parrot Coracopsis nigra barklyi is an island endemic threatened with extinction. The total population of 520–900 individuals is restricted to the 38‐km² island of Praslin, and it is one of the last few remaining endemic island parrots that survive in the Indian Ocean. We combined mitochondrial and microsatellite DNA markers with morphological data to examine the evolutionary distinctiveness of C. n. barklyi within Coracopsis, and to compare levels of genetic diversity between historical and contemporary specimens. Phylogenetic analyses revealed C. n. barklyi as sister to the remaining three C. nigra subspecies, and discriminant function analysis suggested the Seychelles Black Parrot is the smallest of the four subspecies. Higher levels of genetic diversity were observed in historical specimens, whereas only one mtDNA haplotype was observed in the contemporary specimens, suggesting that C. n. barklyi has lost genetic diversity as a consequence of substantial recent population decline. This study provides a first insight into the evolutionary, genetic and morphological processes that have shaped C. n. barklyi and provides an important perspective on this parrot's current genetic status to guide its future conservation management. Further ecological studies are essential but we suggest that C. n. barklyi should be managed as an evolutionary significant unit to conserve its unique evolutionary pathway.     

Population structure and genetic diversity distribution in wild and cultivated populations of the traditional Chinese medicinal plant Magnolia officinalis subsp. biloba (Magnoliaceae)

Magnolia officinalis subsp. biloba, a traditional Chinese medicinal plant, experienced severe declines in the number of populations and the number of individuals in the late 20th century due to the widespread harvest of the subspecies. A large-scale cultivation program was initiated and cultivated populations rapidly recovered the loss in individual plant numbers, but wild populations remained small as a consequence of cutting. In this study, the levels of genetic variation and genetic structure of seven wild populations and five domestic populations of M. officinalis subsp. biloba were estimated employing an AFLP methodology. The plant exhibited a relatively high level of intra-population genetic diversity (h = 0.208 and H _j = 0.268). The cultivated populations maintained approximately 95% of the variation exhibited in wild populations, indicating a slight genetic bottleneck in the cultivated populations. The analysis of genetic differentiation revealed that most of the AFLP diversity resided within populations both for the wild group (78.22%) and the cultivated group (85.92%). Genetic differentiation among populations in the wild group was significant (F _ST = 0.1092, P < 0.005), suggesting wild population level genetic structure. Principal coordinates analysis (PCO) did not discern among wild and cultivated populations, indicating that alleles from the wild population were maintained in the cultivated gene pool. Results from the present study provide important baseline data for effectively conserving the genetic resources of this medicinal subspecies.     

Genetic structure of the critically endangered Red‐headed Wood Pigeon Columba janthina nitens and its implications for the management of threatened island populations

The Red‐headed Wood Pigeon Columba janthina nitens is endemic to the Ogasawara Islands, an oceanic island chain located 1000 km south of the main islands of Japan. The subspecies is at high risk of extinction because of its small population size and restricted habitat range. We undertook genetic analyses of this pigeon using sequences of a portion of the mitochondrial control region and five microsatellite markers to estimate the genetic characteristics of two wild populations from the Bonin and Volcano Islands, as well as one captive breeding population. The genetic diversity of the wild individuals was exceptionally low in both the mitochondria (nucleotide diversity = 0.00105) and at the microsatellite (3.2 alleles per locus and H_E = 0.12) loci. Higher numbers of microsatellite genotypes were observed in the Volcano Islands population than in the Bonin Islands population, which may be because of the relatively low impact of human disturbance. The most common mitochondrial haplotypes and microsatellite alleles observed in the two wild populations were completely fixed in the captive population. Our results suggest that the genetic diversity of the captive population needs to be increased. However, introduction of a wild individual into a captive population can lead to a decreased genetic diversity in the wild population and therefore should be done with caution. The genetic differentiation between the Bonin and the Volcano island groups was low, and the populations of the two island groups should be regarded as a single evolutionarily significant unit. However, special consideration is required for habitat conservation in the Volcano Islands, which may be functioning as a sanctuary for the Red‐headed Wood Pigeon. For the long‐term conservation of threatened bird species that live on remote oceanic islands, determination of management units considering gene flow caused by their flying capacity and maintenance of genetically suitable wild and captive populations are essential.     

Conservation genetics of the black rhinoceros, <Emphasis Type="Italic">Diceros bicornis bicornis</Emphasis>, in Namibia

Poaching and habitat destruction across sub-Saharan Africa brought the black rhinoceros (Diceros bicornis) close to extinction. Over the past few decades, however, one of four subspecies, D. b. bicornis, has experienced a significant population increase as a consequence of its protection within Etosha National Park (ENP), Namibia. We report here on the level and spatial distribution of black rhinoceros genetic diversity within ENP. Using nine microsatellite loci, genetic variation was assessed from 144 individuals. Our results are consistent with the observation of lower levels of genetic diversity in D. b. bicornis, when compared to D. b. michaeli, but greater diversity when compared to D. b. minor. We also showed that ENP’s black rhino genetic diversity is well represented in Waterberg National Park, originally founded with ENP individuals. We found no genetic signature of a recent bottleneck in ENP, however, suggesting that the genetic diversity within ENP has not been adversely affected by the recent severe population decline. Using Bayesian clustering methods, we observed no significant population structure within ENP, but positive spatial genetic correlation is observed at distances up to 25 km. This relationship exists in females but not males, suggesting reduced dispersal among females, the first evidence of limited female dispersal or philopatry in any species of rhinoceros.     

Development and characterization of polymorphic microsatellite loci in the endangered Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis)

The finless porpoise (Neophocaena phocaenoides) is one of the smallest cetacean species widely distributed in the shallow coastal waters of the Indo-Pacific Oceans. The population size of the Yangtze subspecies (N. p. asiaeorientalis) has sharply decreased in the last two decades and access to objective data on its population structure and genetic diversity would be of great assistance for their proper management. Here we report on the isolation of nine polymorphic microsatellite using the “Fast Isolation by AFLP of Sequences Containing repeats” (FIASCO) protocol. Polymorphism was assessed using 30 porpoise individuals randomly sampled in the Yangtze River. The number of alleles per locus varies from 2 to 9, with an average value of 5.56, whereas the ranges of observed and expected heterozygosities were 0.300–0.633 (mean 0.496) and 0.473–0.804 (mean 0.659), respectively.     

Genetic divergence between the South Korean and Mongolian populations of the dung beetle,Gymnopleurus mopsus (Coleoptera: Scarabaeidae) based on mitochondrial cytochrome c oxidase subunit I (COI) gene sequences

The locally extinct dung beetle, Gymnopleurus mopsus Pallas, 1781 (Coleoptera: Scarabaeidae), has not been found in South Korea since the 1970s. This research was conducted to understand the genetic divergence between the South Korean and Mongolian populations of G. mopsus as a part of its reintroduction program in South Korea. The genetic distance and diversity were determined using the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence (658 bp ) corresponding to the DNA barcode region. The mitochondrial COI gene sequences of 64 individuals of G. mopsus collected in South Korea (7 individuals) and Mongolia (57 individuals) showed a relatively high level of genetic diversity (nucleotide diversity, 0.0078 ± 0.0007; Haplotype diversity, 0.965 ± 0.017). The genetic distances between the South Korean and Mongolian populations lay within the intraspecific level and the phylogenetic reconstruction using the neighbor‐joining (NJ) method showed that all individuals belonged to a single clade. This result indicates that the current Mongolian population of G. mopsus is a good candidate source population to restore the locally extinct population of the species in South Korea.     

The genetic consequence of differing ecological demands of a generalist and a specialist butterfly species

Many studies aim at testing the impact of recent fragmentation on the genetic diversity and connectivity of populations, while some species do exist naturally in fragmented landscapes because of their habitat requirements. Therefore, it is important to look at the genetic signatures of species occurring in naturally fragmented landscapes in order to disentangle the effect of fragmentation from the effect of habitat requirements. We selected two Nymphalid butterflies for this purpose. While Melanargia galathea is a common butterfly in flower-rich meadows, Melitaea aurelia is closely connected to calcareous grasslands, thus being historically fragmented due to its ecological demands. For the analysis of the genetic response on these opposed patterns, we analysed 18 allozyme loci for 789 individuals (399 individuals of M. galathea and 390 individuals of M. aurelia) in a western German study region with adjacent areas in Luxemburg and northeastern France. Both species showed similarly low genetic differentiations among local populations (M. galathea: F _ST 3.3%; M. aurelia: F _ST 3.6%), both combined with a moderate level of inbreeding. Isolation-by-distance analysis revealed a significant correlation for both species with similar amounts of explained variances (M. galathea: r ² = 27.8%; M. aurelia: r ² = 28.5%). Most parameters of genetic diversity were higher in M. galathea than in M. aurelia, but the latter species had a considerably higher amount of rare or locally restricted genes; the differing ecological demands are thus reflected in these differences. Both species thus seem to be genetically well suited to their respective ecological requirements. In the light of conservation genetics, we deduce that highly fragmented populations are not necessarily prone to extinction. The extinction risk might be linked to the life history of an organism and its population genetic structure.     

Microsatellites from the vairone Leuciscus souffia (Pisces: Cyprinidae) and their application to closely related species

Eleven microsatellites were isolated from the vairone Leuciscus souffia (Risso 1826), an endangered fish that inhabits river systems in and around the Alps in Europe. The level of genetic diversity was assessed in 29 individuals of the subspecies L. s. souffia, and their variability was further estimated in seven individuals of a different subspecies, L. s. muticellus. Eight of these microsatellite loci were also applied to seven closely related cyprinid species. Availability of the reported microsatellite loci will facilitate the investigation of population genetic structure of these species with applications for the development of conservation strategies and phylogeographical approaches.     

A rapid PCR-based diagnostic test for the identification of subspecies of <Emphasis Type="Italic">Acacia saligna</Emphasis>

Subspecific taxa of species complexes can display cryptic morphological variation, and individuals and populations can often be difficult to identify with certainty. However, accurate population identification is required for comprehensive conservation and breeding strategies and for studies of invasiveness and gene flow. Using five informative microsatellite markers and a Bayesian statistical approach, we developed an efficient polymerase chain reaction-based diagnostic tool for the rapid identification of individuals and populations of the Acacia saligna species complex of Western Australia. We genotyped 189 individuals from 14 reference populations previously characterised based on morphology and used these data to investigate population structure in the species complex. High total genetic diversity (H _T = 0.729) and high population differentiation (θ = 0.355) indicated strong intraspecific structuring. With the provision of prior population information, the reference data set was optimally resolved into four clusters, each corresponding to one of the four main proposed subspecies, with very high membership values (Q > 97%). The reference data set was then used to assign individuals and test populations to one of the four subspecies. Assignment was unequivocal for all test individuals from two populations of subsp. lindleyi and for all but one individual of subsp. stolonifera. Individuals from populations of subsp. saligna and subsp. pruinescens showed a degree of genetic affinity for the two subspecies in their assignments, although the majority of individuals were correctly assigned to subspecies. The diagnostic tool will assist in characterising populations of A. saligna, especially naturalised and invasive populations of unknown origin.     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

Analysis of genetic structure of the red shrimp <Emphasis Type="Italic">Aristeus antennatus</Emphasis> from the Western Mediterranean employing two mitochondrial regions

In this paper we addressed the phylogeographical genetic structure of the economically important red shrimp, Aristeus antennatus (Crustacea, Aristeidae) in the Western Mediterranean. Partial mitochondrial regions of the cytochrome c oxidase subunit I (514 bp) and ribosomal 16S subunit (547 bp) were sequenced in 137 individuals collected at three localities: Catalan Sea, Ligurian Sea and the southern Tyrrhenian Sea. Values of haplotypic diversity were h = 0.552–0.724, whereas those for nucleotide diversity were π = 0.0012–0.0026. Among-sample genetic diversity was not significant and no geographical patterns in the distribution of haplotypes were apparent. Results of the present study are consistent with a past population expansion that occurred <2,000 years ago. Despite the current fishing pressure, genetic variability appears to be sufficiently high to keep A. antennatus populations stable over time. Dispersal-related life history traits may account for the shallow genetic structure. Our results are not in contrast with the hypothesis of sustainability of Western Mediterranean red shrimp fisheries predicted on the basis of previously obtained biological results.     

Phylogeography and population structure of the endangered Tehuantepec jackrabbit <Emphasis Type="Italic">Lepus flavigularis</Emphasis>: implications for conservation

The Tehuantepec jackrabbit (Lepus flavigularis) is an endangered species restricted to a small area in the Isthmus of Tehuantepec, Oaxaca, Mexico. To evaluate its phylogeographic structure, population genetics, and demographic history we sequenced the mitochondrial Control Region hypervariable domain (CR-1) for 42 individuals representing the entire species range. Phylogenetic patterns indicated that this species is subdivided into two highly divergent clades, with an average nucleotide genetic distance of 3.7% (TrN) between them. Clades A and B are geographically distributed in non-overlapping areas to the west and to the east of the Isthmus of Tehuantepec, respectively. Genetic diversity indices showed reduced genetic variability in L. flavigularis when compared to other species of Lepus within main clades and within populations. This low genetic diversity coupled with the restricted distribution to very small areas of occurrence and limited gene flow suggest that genetic drift has played an important role in the evolution of this species. Historical demographic analysis also pointed out that these two clades underwent a recent population expansion that started about 9,000 years ago for clade A and 3,200 years ago for clade B during the Holocene. Consequently, from the conservation perspective our results suggest that populations included in clades A and B should be regarded as distinct evolutionary lineages.     

Species‐level view of population structure and gene flow for a critically endangered primate (Varecia variegata)

Lemurs are among the world's most threatened mammals. The critically endangered black‐and‐white ruffed lemur (Varecia variegata), in particular, has recently experienced rapid population declines due to habitat loss, ecological sensitivities to habitat degradation, and extensive human hunting pressure. Despite this, a recent study indicates that ruffed lemurs retain among the highest levels of genetic diversity for primates. Identifying how this diversity is apportioned and whether gene flow is maintained among remnant populations will help to diagnose and target conservation priorities. We sampled 209 individuals from 19 sites throughout the remaining V. variegata range. We used 10 polymorphic microsatellite loci and ~550 bp of mtDNA sequence data to evaluate genetic structure and population dynamics, including dispersal patterns and recent population declines. Bayesian cluster analyses identified two distinct genetic clusters, which optimally partitioned data into populations occurring on either side of the Mangoro River. Localities north of the Mangoro were characterized by greater genetic diversity, greater gene flow (lower genetic differentiation) and higher mtDNA haplotype and nucleotide diversity than those in the south. Despite this, genetic differentiation across all sites was high, as indicated by high average F_ST (0.247) and Φ_ST (0.544), and followed a pattern of isolation‐by‐distance. We use these results to suggest future conservation strategies that include an effort to maintain genetic diversity in the north and restore connectivity in the south. We also note the discordance between patterns of genetic differentiation and current subspecies taxonomy, and encourage a re‐evaluation of conservation management units moving forward.     

Genetic diversity in the mtDNA control region and population structure in the small yellow croaker <Emphasis Type="Italic">Larimichthys polyactis</Emphasis>

The genetic diversity and population genetic structure of the small yellow croaker (Larimichthys polyactis) were investigated. One hundred and fourteen individuals were sampled from 8 localities of the Yellow Sea and the northern East China Sea. Genetic variation in DNA sequences were examined from the first hypervariable region (HVR-1) of the mitochondrial DNA control region. High levels of haplotype diversity (h = 0.98 ± 0.87%) in the HVR-1 region were detected, indicating a high level of genetic diverstiy. A total of 84 polymorphic sites were found, and 87 haplotypes were defined. The pairwise nucleotide differences between samples ranged from 3.83 ± 2.19 to 6.56 ± 3.25. The demographic history of L. polyactis was examined by using neutrality tests and mismatch distribution analysis, which indicated a Pleistocene population expansion at about 49,300–197,000 years. The star burst structure of the minimum spanning tree also suggestted a very recent origin for most haplotypes. Hierarchical molecular variance analysis (AMOVA) and conventional population Fst comparisons revealed no significant genetic structure throughout the examined range, which is inconsistent with previous findings based on the morphological and ecological studies. Long-term dispersal and high gene flow likely have contributed to the genetically homogeneous population structure of the species. The knowledge on genetic diversity and genetic structure will be crucial to establish appropriate fishery management stocks for the species.     

Mitochondrial DNA sequence variability in red-legged partridge, <Emphasis Type="Italic">Alectoris rufa</Emphasis>, Spanish populations and the origins of genetic contamination from <Emphasis Type="Italic">A. chukar</Emphasis>

The analysis of 135 mitochondrial D-loop sequences of the Iberian autochthonous red-legged partridge (Alectoris rufa) from wild population hunting bags from various locations and fowl runs in Spain yielded 37 different haplotypes. Among these, three haplotypes correspond to chukar partridges (Alectoris chukar), indicating genetic introgression from birds illegally introduced for restocking: three individuals carrying such haplotypes where found in natural populations, one appeared among those sampled on a mass reproduction farm and the remaining 10 in another fowl-run. The geographical origin of the contaminating chukar haplotypes could be assigned to the most easterly area of the chukar partridge geographical distribution in China. Molecular diversity parameters in the A. rufa samples indicate a considerable amount of genetic variation. Φ_ST showed significant differences among populations that are not explained by geographical distance alone. Particularly, one northern population (Palencia) shows a certain degree of genetic differentiation that could reflect a previously suggested subspecies division. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Patterns of nuclear and mitochondrial DNA variation in Iberian populations of <Emphasis Type="Italic">Emys orbicularis</Emphasis> (Emydidae): conservation implications

The European pond turtle (Emys orbicularis) is threatened and in decline in several regions of its natural range, due to habitat loss combined with population fragmentation. In this work, we have focused our efforts on studying the genetic diversity and structure of Iberian populations with a fine-scale sampling (254 turtles in 10 populations) and a representation from North Africa and Balearic island populations. Using both nuclear and mitochondrial markers (seven microsatellites, ∼1048 bp nDNA and ∼1500 bp mtDNA) we have carried out phylogenetic and demographic analyses. Our results show low values of genetic diversity at the mitochondrial level although our microsatellite dataset revealed relatively high levels of genetic variability with a latitudinal genetic trend decreasing from southern to northern populations. A moderate degree of genetic differentiation was estimated for Iberian populations (genetic distances, F _ST values and clusters in the Bayesian analysis). The results in this study combining mtDNA and nDNA, provide the most comprehensive population genetic data for E. orbicularis in the Iberian Peninsula. Our results suggest that Iberian populations within the Iberian–Moroccan lineage should be considered as a single subspecies with five management units, and emphasize the importance of habitat management rather than population reinforcement (i.e. captive breeding and reintroduction) in this long-lived species.     

Genetic structure of an isolated population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island, Panama

Habitat fragmentation may influence genetic variability through reductions in population size and the physical isolation of conspecifics. We explored the effects of these factors on genetic diversity in a population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island (BCI), Panama. The study population was established in 1914 when an unknown number of resident individuals were isolated from the surrounding mainland by damming of the Río Chagres to create the Panama Canal. Analyses of 10 microsatellite loci indicated that, despite this isolation, the howler monkeys on BCI exhibit levels of genetic diversity (H _S = 0.584 ± 0.063) among the highest reported for any species of Alouatta. These data also revealed that although relatedness among adults in a social group was significantly greater than zero, the BCI population is not highly genetically structured. Tests for genetic bottlenecks based on departures from equilibrium expectations failed to reveal evidence of a recent reduction in population size. In contrast, coalescent modeling indicated that this population has likely experienced a marked decline within the last few 100 years. These findings generate new insights into the genetic structure of A. palliata and suggest that while the formation of BCI may not have substantially reduced genetic variation in these animals, genetic diversity has been influenced by historical changes in population size.     

Genetic diversity and population structure of Schizopygopsis younghusbandi Regan in the Yarlung Tsangpo River inferred from mitochondrial DNA sequence analysis

The genetic diversity and population structure of Schizopygopsis younghusbandi from six sites in the middle reach of the Yarlung Tsangpo River were examined based on mitochondrial DNA cytochrome b (Cyt b) gene and control region (D-loop) sequences. 1141 bp of complete Cyt b sequences and 737 bp of partial D-loop sequences for 153 individuals of S. younghusbandi were obtained by using PCR amplification and sequencing. The results showed that S. younghusbandi populations had high haplotype diversity and low nucleotide diversity, and the population genetic diversity of this species was at a low level. Analysis of molecular variance revealed that most genetic variation occurred within populations, and that genetic differentiation was at low or moderate levels. The network of haplotypes based on Cyt b gene showed that there were two groups within the examined populations. Neutrality tests and mismatch distribution analysis suggested that this species might have undergone a population expansion and the expansion time was estimated to be 0.25–0.46 Ma BP. All these results would be crucial to establish scientific strategies for effective conservation and sustainable exploitation of wild resources of S. younghusbandi.     

Subspecific identity and a comparison of genetic diversity between wild and ex situ wildebeest

The original North American ex situ wildebeest population was believed to originate from the white-bearded wildebeest (Connochaetes taurinus albojubatus), which is both morphologically distinct and geographically separated from the brindled wildebeest (C. t. taurinus). However, after an import of wildebeest into North America in 2001, managers have suspected that white-bearded and brindled wildebeest were mixed in herds at multiple institutions. We sequenced the mitochondrial control region (d-loop) from a portion of the managed North American population and compared our sequences with previously published sequences from wild individuals to determine the subspecific identity and genetic diversity of our ex situ population. We were able to confidently identify C. t. albojubatus as the subspecies identity of the sampled portion of our population. Within our population, haplotype and nucleotide diversity were low (0.169 and 0.001, respectively) with a single common haplotype (H1) containing 41 of the 45 individuals sequenced, while two rare haplotypes (H2 and H3) were derived from three individuals and a single individual, respectively. Nucleotide and haplotype diversity were greater overall in the wild populations compared with our managed population. However, C. t. albojubatus was found to exhibit lower nucleotide diversity in both wild and ex situ populations when compared to other wild subspecies. Though the overall goal of the North American wildebeest population is for public education and not reintroduction, maintaining genetic diversity is vital for the long-term viability of this managed population, which may benefit from periodic supplementation of wild animals.     

Low genetic diversity and strong but shallow population differentiation suggests genetic homogenization by metapopulation dynamics in a social spider

Mating systems and population dynamics influence genetic diversity and structure. Species that experience inbreeding and limited gene flow are expected to evolve isolated, divergent genetic lineages. Metapopulation dynamics with frequent extinctions and colonizations may, on the other hand, deplete and homogenize genetic variation, if extinction rate is sufficiently high compared to the effect of drift in local demes. We investigated these theoretical predictions empirically in social spiders that are highly inbred. Social spiders show intranest mating, female‐biased sex ratio, and frequent extinction and colonization events, factors that deplete genetic diversity within nests and populations and limit gene flow. We characterized population genetic structure in Stegodyphus sarasinorum, a social spider distributed across the Indian subcontinent. Species‐wide genetic diversity was estimated over approximately 2800 km from Sri Lanka to Himalayas, by sequencing 16 protein‐coding nuclear loci. We found 13 SNPs in 6592 bp (π = 0.00045) indicating low species‐wide nucleotide diversity. Three genetic lineages were strongly differentiated; however, only one fixed difference among them suggests recent divergence. This is consistent with a scenario of metapopulation dynamics that homogenizes genetic diversity across the species' range. Ultimately, low standing genetic variation may hamper a species' ability to track environmental change and render social inbreeding spiders ‘evolutionary dead‐ends’.