Population structure and genetic variation in the endangered Giant Kangaroo Rat (<Emphasis Type="Italic">Dipodomys ingens</Emphasis>)

Populations of the endangered giant kangaroo rat, Dipodomys ingens (Heteromyidae), have suffered increasing fragmentation and isolation over the recent past, and the distribution of this unique rodent has become restricted to 3% of its historical range. Such changes in population structure can significantly affect effective population size and dispersal, and ultimately increase the risk of extinction for endangered species. To assess the fine-scale population structure, gene flow, and genetic diversity of remnant populations of Dipodomys ingens, we examined variation at six microsatellite DNA loci in 95 animals from six populations. Genetic subdivision was significant for both the northern and southern part of the kangaroo rat’s range although there was considerable gene flow among southern populations. While regional gene diversity was relatively high for this endangered species, hierarchical F-statistics of northern populations in Fresno and San Benito counties suggested non-random mating and genetic drift within subpopulations. We conclude that effective dispersal, and therefore genetic distances between populations, is better predicted by ecological conditions and topography of the environment than linear geographic distance between populations. Our results are consistent with and complimentary to previous findings based on mtDNA variation of giant kangaroo rats. We suggest that management plans for this endangered rodent focus on protection of suitable habitat, maintenance of connectivity, and enhancement of effective dispersal between populations either through suitable dispersal corridors or translocations.     

Conservation genetics of Blanding’s turtle and its application in the identification of evolutionarily significant units

Blanding’s turtle is a North American freshwater turtle whose main range occurs south of the Great Lakes; disjunct populations occur east of the Appalachian Mountains from New York to Nova Scotia. The species is listed as threatened or endangered in most of its range. We employed five variable microsatellites to examine samples of 300 individuals in 12 populations. Estimates of F _ST based on pairwise comparisons of populations ranged from 0.000 to 0.465. Phylogenetic analysis of these F _ST values reveals that the Appalachian Mountains and the Hudson River appear to present major barriers to gene flow in Blanding’s turtle. The extent of fine-scale genetic structure previously reported in the Nova Scotian populations was not found in other parts of the species’ range. We recommend that populations separated by the Appalachian Mountains as well as the highly disjunct Nova Scotian populations of Blanding’s turtle be recognized as evolutionarily significant units.     

Potential loss of genetic variability despite well established network of reserves: the case of the Iberian endemic lizard <Emphasis Type="Italic">Lacerta schreiberi</Emphasis>

Although future anthropogenic climate change is recognized as one of the major threats to European species, its implementation during reserve planning has only been started recently. We here describe climate change impacts on the Iberian endemic lizard Lacerta schreiberi expecting serious declines and range reductions due to a loss of suitable climate space in the next future. We apply species distribution models to assess possible future changes in the lizard’s range, identify areas with high extinction risk meriting conservation efforts and analyze whether the Natura 2000 network in its current stage will offer a sufficient protection for the genetically most valuable lineages. Despite a very good coverage and connectivity of the most valuable populations of L. schreiberi with the existing protected sites network, our results predict a strong loss of genetic variability by 2080. Also, two main patterns become evident: While the genetically less diverse north-western populations may be less affected by climate change, the climate change effects on the southern isolates and the genetically most diverse populations within the Central System may be devastating. To improve a successful prospective conservation of L. schreiberi the management of protected sites needs to consider the processes that threaten this species. Furthermore, our study highlights the urgent need to consider climate change effects on evolutionary significant units within the Natura 2000 framework.     

DECOUPLING OF SHORT‐ AND LONG‐DISTANCE DISPERSAL PATHWAYS IN THE ENDEMIC NEW ZEALAND SEAWEED CARPOPHYLLUM MASCHALOCARPUM (PHAEOPHYCEAE,FUCALES)1

The processes that produce and maintain genetic structure in organisms operate at different timescales and on different life‐history stages. In marine macroalgae, gene flow occurs through gamete/zygote dispersal and rafting by adult thalli. Population genetic patterns arise from this contemporary gene flow interacting with historical processes. We analyzed spatial patterns of mitochondrial DNA variation to investigate contemporary and historical dispersal patterns in the New Zealand endemic fucalean brown alga Carpophyllum maschalocarpum (Turner) Grev. Populations bounded by habitat discontinuities were often strongly differentiated from adjoining populations over scales of tens of kilometers and intrapopulation diversity was generally low, except for one region of northeast New Zealand (the Bay of Plenty). There was evidence of strong connectivity between the northern and eastern regions of New Zealand’s North Island and between the North and South Islands of New Zealand and the Chatham Islands (separated by 650 km of open ocean). Moderate haplotypic diversity was found in Chatham Islands populations, while other southern populations showed low diversity consistent with Last Glacial Maximum (LGM) retreat and subsequent recolonization. We suggest that ocean current patterns and prevailing westerly winds facilitate long‐distance dispersal by floating adult thalli, decoupling genetic differentiation of Chatham Island populations from dispersal potential at the gamete/zygote stage. This study highlights the importance of encompassing the entire range of a species when inferring dispersal patterns from genetic differentiation, as realized dispersal distances can be contingent on local or regional oceanographic and historical processes.     

What parts of the US mainland are climatically suitable for invasive alien pythons spreading from Everglades National Park?

The Burmese Python (Python molurus bivittatus) is now well established in southern Florida and spreading northward. The factors likely to limit this spread are unknown, but presumably include climate or are correlated with climate. We compiled monthly rainfall and temperature statistics from 149 stations located near the edge of the python’s native range in Asia (Pakistan east to China and south to Indonesia). The southern and eastern native range limits extend to saltwater, leaving unresolved the species’ climatic tolerances in those areas. The northern and western limits are associated with cold and aridity respectively. We plotted mean monthly rainfall against mean monthly temperature for the 149 native range weather stations to identify the climate conditions inhabited by pythons in their native range, and mapped areas of the coterminous United States with the same climate today and projected for the year 2100. We accounted for both dry-season aestivation and winter hibernation (under two scenarios of hibernation duration). The potential distribution was relatively insensitive to choice of scenario for hibernation duration. US areas climatically matched at present ranged up the coasts and across the south from Delaware to Oregon, and included most of California, Texas, Oklahoma, Arkansas, Louisiana, Mississippi, Alabama, Florida, Georgia, and South and North Carolina. By the year 2100, projected areas of potential suitable climate extend northward beyond the current limit to include parts of the states of Washington, Colorado, Illinois, Indiana, Ohio, West Virginia, Pennsylvania, New Jersey, and New York. Thus a substantial portion of the mainland US is potentially vulnerable to this ostensibly tropical invader.     

Phylogeography and Pleistocene demographic history of the endangered marsh deer (Blastocerus dichotomus) from the Río de la Plata Basin

The marsh deer is the largest neotropical cervid with morphological and ecological adaptations to wetlands and riparian habitats. Historically, this now endangered species occupied habitats along the major river basins in South America, ranging from southern Amazonia into northern Argentina to the Paraná river delta. This particularly close association with wetlands makes marsh deer an excellent species for studying the effects of Pleistocene climatic changes on their demographic and phylogeographic patterns. We examined mitochondrial DNA variation in 127 marsh deer from 4 areas distributed throughout the Río de la Plata basin. We found 17 haplotypes in marsh deer from Brazil, Bolivia and Argentina that differed by 1–8 substitutions in a 601 bp fragment of mitochondrial control region sequence, and 486 bp of cytochrome b revealed only 3 variable sites that defined 4 haplotypes. Phylogeny and distribution of control region haplotypes suggest that populations close to the Pantanal area in central Brazil underwent a rapid population expansion and that this occurred approximately 28,000–25,000 years BP. Paleoclimatic data from this period suggests that there was a dramatic increase for precipitation in the medium latitudes in South America and these conditions may have fostered marsh deer’s population growth.     

Genetic analyses of the Asian longhorned beetle (Coleoptera,Cerambycidae, <Emphasis Type="Italic">Anoplophora glabripennis</Emphasis>), in North America,Europe and Asia

The Asian longhorned beetle, (Coleoptera, Cerambycidae, Anoplophora glabripennis (Motschulsky)), is endemic to China and Korea and an important invasive insect in North America and Europe. We analyzed mitochondrial DNA sequence data of invasive populations of A. glabripennis in North America and Europe, and microsatellite allele frequency data of beetles from North America. We show that populations in New York City and Long Island NY; New Jersey, Chicago, IL, and Toronto, Canada have limited genetic diversity compared to populations in China. In addition, the data suggest that separate introduction events were responsible for many of the populations in North America and for European populations in Austria, France, Germany and Italy. Populations on Long Island, NY are suspected to have been initiated by the transport of cut wood from New York City. A. glabripennis beetles found in Jersey City, NJ appear to be derived from an expansion of the New York City, NY population, whereas beetles found in Linden, NJ are an expansion from the Carteret, NJ population. Limited genetic diversity did not stop this invasive insect from establishing damaging populations in North America. Founders of introduced A. glabripennis populations in North America and Europe are likely derived from populations in China that are themselves invasive, rendering difficult the identification of source populations. Invasiveness in an insect’s natural range could be an important predictor of potential pest status of introduced populations.     

Microclimatic buffering and resource‐based habitat in a glacial relict butterfly: significance for conservation under climate change

In contrast to several organisms that have already shown range shifts to the north as a response to climate change, southern populations of relict species are trapped in isolated altitudinal habitats. Therefore, there is a growing interest to better understand their habitat use, with particular attention to the thermal aspects and associated significance for their habitat management. We address this issue by a study of larval habitat use relative to vegetation structure and microclimate in a glacial relict butterfly of peat bog ecosystems, using a functional, resource‐based habitat approach. We analysed caterpillar presence and density relative to vegetation composition (reflecting gradients of humidity, temperature, and natural succession of the peat bog) and to the availability and quality of thermal refuges for caterpillars (i.e., structures provided by Sphagnum hummocks). We also tested caterpillar survival rates under different temperature and humidity treatments. We found that (1) Boloria aquilonaris was a specialist butterfly of early successional stages with very humid zones of peat bog, (2) the lack of Sphagnum hummocks reduced larval habitat suitability, and hence the population density, and (3) a reduction of the thermal buffering ability of Sphagnum hummocks was observed in less humid, degraded parts, or late‐successional stages of peat bog. A larval rearing experiment showed a significant impact of temperature on caterpillar survival; survival being higher at lower temperature. Our field and laboratory results support the idea that the thermal environment exploited by caterpillars should be considered as a functional resource and included in a population‐specific habitat definition. Appropriate management of the peat bog habitat of this glacial relict species should not exclusively focus on the larval and adult feeding resources, but also on the quality of thermal refuges provided by Sphagnum hummocks in humid zones of the peat bog, especially in the current critical context of climate warming.     

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.     

Postglacial northward expansion and genetic differentiation between migratory and sedentary populations of the broad‐tailed hummingbird (Selasphorus platycercus)

Unlike other migratory hummingbirds in North America, the broad‐tailed hummingbird (Selasphorus platycercus) exhibits both long‐distance migratory behaviour in the USA and sedentary behaviour in Mexico and Guatemala. We examined the evolution of migration linked to its northward expansion using a multiperspective approach. We analysed variation in morphology, mitochondrial and nuclear DNA, estimated migration rates between migratory and sedentary populations, compared divergence times with the occurrence of Quaternary climate events and constructed species distribution models to predict where migratory and sedentary populations resided during the Last Glacial Maximum (LGM) and Last Interglacial (LIG) events. Our results are consistent with a recent northward population expansion driven by migration from southern sedentary populations. Phylogeographical analyses and population genetics methods revealed that migratory populations in the USA and sedentary populations in Mexico of the platycercus subspecies form one admixed population, and that sedentary populations from southern Mexico and Guatemala (guatemalae) undertook independent evolutionary trajectories. Species distribution modelling revealed that the species is a niche tracker and that the climate conditions associated with modern obligate migrants in the USA were not present during the LIG, which provides indirect evidence for recent migratory behaviour in broad‐tailed hummingbirds on the temporal scale of glacial cycles. The finding that platycercus hummingbirds form one genetic population and that suitable habitat for migratory populations was observed in eastern Mexico during the LIG also suggests that the conservation of overwintering sites is crucial for obligate migratory populations currently facing climate change effects.     

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.     

Predicted range shifts in North American boreal forest birds and the effect of climate change on genetic diversity in blackpoll warblers (Setophaga striata)

As North American species’ ranges shift northward in response to climate change, populations isolated in high-elevation habitat “islands” at the southern edge of distributions are predicted to decrease in size or be extirpated. Levels of genetic structure and gene flow and the number of private alleles held within these peripheral populations can be used as a measure of the potential loss of genetic diversity due to climate change. We use GIS-based climate niche models to project geographic distributions of 15 boreal forest bird species for the year 2080 under two carbon emissions scenarios to predict the extent to which ranges will shift, leading to the extirpation of isolated populations at the southern periphery of the boreal forest. Breeding distributions of nearly all boreal bird species are predicted to expand as they shift northward, but will dramatically decrease or be completely lost from mountain populations in New York, Vermont, and New Hampshire by 2080. To examine the effect of these shifts on gene pools of migratory bird species we genotyped 178 blackpoll warblers (Setophaga striata) at nine microsatellite loci, sampling four imperiled high-elevation populations and four northern populations. In S. striata 10.4 % of microsatellite alleles were confined to populations expected to be lost due to climate change. However, these accounted for a nonsignificant percent of the genetic structure, and loss of these alleles would not significantly erode species heterozygosity or allelic richness. Our results indicate that isolated southern populations of S. striata, and possibly other migratory species with high gene flow, do not represent genetically isolated, independently evolving units. Efforts to mitigate the effect of climate change on boreal forest birds should focus on species in which peripheral populations harbor significant genetic diversity.     

Population structure and loss of genetic diversity in the endangered white-headed duck, <Emphasis Type="Italic">Oxyura leucocephala</Emphasis>

The white-headed duck is a globally threatened species native to the Palaearctic with a range extending from Spain in the west to the western edge of China in the east. Its populations have become fragmented and undergone major declines in recent decades. To study genetic differences between populations across the range and change in genetic diversity over time, we sequenced a portion of the mitochondrial DNA control region from 67 museum specimens (years 1861–1976) as well as 39 contemporary samples from Spain and seven from Greece (years 1992–2003). In the historical sample, we found a lack of significant genetic structure between populations in different areas. We found evidence that the species experienced a rapid expansion in the past, perhaps from glacial refugia centred around the Mediterranean following the last ice age. In Spain, the population went through a dramatic bottleneck in the 1970s and early 1980s, when only a few dozens individuals remained in the wild. Although population size has since recovered to a few thousand individuals, we found a highly significant loss of mitochondrial haplotype diversity between the historical and contemporary samples. Given ongoing declines in other areas, losses in genetic diversity that may reduce the adaptive potential of white-headed ducks in the future are a continuing concern throughout the geographic range of this species.     

Molecular biodiversity in the moss <Emphasis Type="Italic">Leptodon smithii</Emphasis> (Neckeraceae) in relation to habitat disturbance and fragmentation

Bryophytes seem particularly suitable to investigate genetic diversity in relation to habitat disturbance due to their large employment as bioindicators and to the recent application of molecular markers to moss population studies. Genetic variation and structure were analysed in seven urban, extraurban and remote populations of Leptodon smithii, an epiphytic moss of Quercus ilex, a phanerogamic species of Mediterranean climax vegetation. A total of 210 individual shoots were DNA extracted and amplified with internal simple sequence repeat (ISSR) primers, and 54 haplotypes were identified. An uneven distribution of haplotype number and frequencies was observed among sites, with a higher number of haplotypes and more homogeneous haplotype frequencies in the extraurban/remote populations. Molecular diversity indices were overall higher in the extraurban sites than in the urban ones. Multilocus linkage disequilibrium values were in line with the occurrence of sexual/asexual reproduction in the seven populations. The isolation-by-distance model was not supported by Mantel test among sites; however, within-population fixation index (F_ST) highlighted a clear relation between genetic and physic distances among trees, suggesting a limited dispersal range for L. smithii’s spores. The genetic structure was mainly affected by population size, wood structure and extent, and genetic drift consequent to habitat fragmentation and human-induced disturbance.     

Population genetic structure and history of fragmented remnant populations of the New England cottontail (<Emphasis Type="Italic">Sylvilagus transitionalis</Emphasis>)

The New England cottontail (Sylvilagus transitionalis) has suffered from extensive loss and fragmentation of its habitat and is now a species of conservation priority in the northeastern United States. Remnant New England cottontail populations currently occur in five geographically disjunct locations: southern Maine and southeastern New Hampshire (MENH); the Merrimack Valley in central New Hampshire (NH-MV); Cape Cod, Massachusetts (CC); parts of eastern Connecticut and Rhode Island (CTRI); and western Connecticut, southeastern New York and southwestern Massachusetts (CTNY). We used microsatellite genotyping to discern patterns of population structure, genetic variability, and demographic history across the species’ range and to assess whether the observed patterns are a consequence of recent habitat loss and fragmentation. Our findings show that the geographic populations are highly differentiated (overall F _ST = 0.145; P < 0.001). Using Bayesian clustering analyses, we identified five genetic clusters, which corresponded closely to the geographic populations, but grouped MENH & NH-MV together (ME/NH) and identified an isolated population in eastern Connecticut (Bluff Point). The genetic clusters showed little evidence of recent gene flow and are highly influenced by genetic drift. The CC and Bluff Point populations show signs they experienced a genetic bottleneck, whereas the ME/NH population shows evidence of ongoing decline. Populations in Bluff Point, CC, and ME/NH also show significantly reduced genetic variation relative to the other clusters (CTNY and CTRI without Bluff Point). Without immediate human intervention, the short-term persistence of New England cottontail populations in Maine, New Hampshire and Cape Cod is at great risk. Conservation efforts at this time should focus on within-population sustainability and eventually restoring connectivity among these isolated populations.     

Population structuring in mountain zebras (<Emphasis Type="Italic">Equus zebra</Emphasis>): The molecular consequences of divergent demographic histories

The endangered mountain zebra (Equus zebra) is endemic to the semi-arid inhospitable mountainous escarpments of southern Africa. The species is divided taxonomically into two geographically separated subspecies, each with differing recent population histories. In Namibia, Hartmann’s mountain zebra (E. z. hartmannae) is common and occurs in large free-ranging populations, whereas in South Africa, prolonged hunting and habitat destruction over the last 300 years has decimated populations of the Cape mountain zebra (E. z. zebra). In this study, we investigate the consequences of these divergent demographic histories for population genetic diversity and structure. We also examine the phylogeographic relationship between the two taxonomic groups. Genetic information was obtained at 15 microsatellite loci for 291 individuals from a total of 10 populations as well as 445 bp of the mitochondrial control region sequence data from 77 individuals. Both model-based and standard analytical approaches were used to examine the data. Both types of marker returned levels of diversity and structure that were consistent with population history. Low genetic variation within individual Cape mountain zebra populations, the characteristic indicator of population fragmentation and drift, was offset by moderate variation in the entire E. z. zebra sample. This implies that higher levels of diversity still exist within the Cape mountain zebra gene pool. A management strategy that entailed the mixing of aboriginal populations is therefore advocated in order to halt the further loss of Cape mountain zebra genetic diversity. Allele frequencies in Hartmann’s mountain zebra were relatively resilient to demographic fluctuations. Due to the high incidence of mitochondrial haplotype sharing between populations, the hypothesis that Cape and Hartmann’s mountain zebra mitochondrial lineages were reciprocally monophyletic was not supported. However, the presence of private alleles at nuclear loci rendered the two subspecies genetically distinct evolutionary significant units.     

Investigating the cause of the disjunct distribution of <Emphasis Type="Italic">Amietophrynus pantherinus</Emphasis>, the Endangered South African western leopard toad

More amphibians are threatened through loss of habitat than any other single factor. Conservation measures to restore habitat are dependent on historical data indicating the original extent of a species. When historical data is absent, disjunct distributions create a special problem for conservationists who need to determine whether they have an anthropogenic cause. The Endangered western leopard toad (Amietophrynus pantherinus) has a disjunct distribution in the south-western tip of South Africa. We use mitochondrial sequences from 153 individuals to show that the disjunct distribution is unlikely to have an anthropogenic origin. Two distinct populations are separated by 100 km, with highest probability for the most recent common ancestor arising some 5 Kya. The causes of this disjunct distribution appear to be too recent to be attributable to changes in sea level; instead we suggest that there was a range retraction associated with a distinct drying period in the area during the Holocene, possibly indicating that this species will be susceptible to future climate change. Further, we find that the eastern population is less genetically diverse and appears to be undergoing a serious reduction in range, despite its occurrence in the least urbanized habitat. Conservation measures suggested include surveys for breeding sites in the eastern population, custodian agreements for existing breeding sites and foraging areas and the need for a Biodiversity Management Plan to be drawn up and implemented.     

Ecological Predictors of Extinction Risk in the Flora of Lowland England, UK

We used historical and contemporary records to determine the scale of plant extinction in Bedfordshire and Northamptonshire, and to assess whether extinct species share a range of ecological and phytogeographical traits. Since 1700 both counties have lost 94 species (11% of their native floras) with the rate of extinction increasing from 3.8 to 4.8 species per decade in the 19th century to 6–8 species per decade after 1950. The most important predictors of extinction risk were English range size and traits associated with habitat specialisation and competitive ability: poor competitors (i.e. short stress-tolerators) associated with open habitats with very low or high pH and soil moisture (e.g. lowland bogs, dwarf-shrub heath and acid and calcareous grassland) were much more likely to have become extinct in the study region than would have been expected by chance alone. Many of these species have very localised distributions and/or occur at the northern, southern or eastern edges of their range in southern England (i.e. Northern and Oceanic). In contrast, there was no clear or significant relationship between extinction and dispersal ability or reproductive mode. These findings, which parallel national trends, indicate that habitat loss and eutrophication have been the main causes of population extinction in lowland England over the last 300 years. However, more fine-scaled studies are required to assess whether ‘low-level’ stresses, such as habitat fragmentation, climate change and atmospheric pollution, are having additional impacts on populations already severely depleted by habitat loss, as well as to quantify changes in the abundance of more widespread species which are known to have declined over the same period.     

The origin of Indian Star tortoises (Geochelone elegans) based on nuclear and mitochondrial DNA analysis: A story of rescue and repatriation

The Indian Star tortoise (Geochelone elegans) belongs to the family Testunidae and is distributed in southwest India and Sri Lanka. In addition to facing loss of its natural habitat, the species is also illegally traded as food and as an exotic pet internationally. Here we report DNA-based analyses for identification and repatriation of these tortoises into their natural habitat. We have attempted to establish the geographical origin of these tortoises rescued from smugglers, by comparing the microsatellite and mitochondrial markers of rescued animals with animals of known provenance. Star tortoises exhibited strong genetic structure in India. The populations from western India were genetically distinct at microsatellite and mitochondrial loci from southern populations. The rescued individuals had similar multilocus genotypes and mitochondrial DNA haplotypes as the reference individuals from south India. However, the precise geographic origin of many of the rescued samples remains unresolved, because we could not assign them to southern populations and the Neighbor-Joining cluster analysis indicated that some of rescued tortoises formed distinct clusters. These data strongly suggest that the rescued group of tortoises is composed of a mix of individuals from differentiated source populations that are probably located in southern India and possibly Sri Lanka. Our study provides valuable information based on molecular markers for the assessment of genetic diversity in Indian Star tortoises.