A genetic survey of heavily exploited, endangered turtles: caveats on the conservation value of trade animals

Asian turtles face an extinction crisis, and so it is imperative that systematists accurately determine species diversity in order to guide conservation strategies effectively. We surveyed mitochondrial and nuclear DNA (mtDNA and nuDNA) variation of the heavily exploited Mauremys mutica complex, a clade of Asian turtles that contains the endangered M. mutica from Japan, Taiwan, China and Vietnam, and the critically endangered Mauremys annamensis from central Vietnam. We discovered extensive mtDNA and nuDNA variation among samples that did not correspond to the currently recognized taxonomy. Both nuDNA and mtDNA data suggest that M. mutica is paraphyletic with respect to M. annamensis . Surprisingly, M. annamensis exhibits a previously unknown mtDNA structure in the form of two clades that are paraphyletic to M. mutica . These data reveal that the currently recognized taxonomy of the mutica complex does not reflect the genetic diversity of our samples. Unfortunately, many conservation-oriented captive-breeding efforts for turtles are also based on trade samples such as the ones studied here. These efforts include plans to breed trade-rescued individuals and release their progeny into the wild. Because our genetic survey reveals that the taxonomic identity of these samples does not reflect genetic diversity, we raise serious questions about the efficacy of these programs. In order to address conservation issues and provide more accurate estimates of evolutionary lineages within Mauremys , we recommend continued surveys for wild populations of the mutica complex to provide new genetic material and additional distributional data, attempts to extract DNA from historic museum specimens and a shift in conservation focus to in situ preservation of wild populations and associated habitat.     

Comparative phylogeography and demographic history of the wood lemming (Myopus schisticolor): implications for late Quaternary history of the taiga species in Eurasia

The association between demographic history, genealogy and geographical distribution of mitochondrial DNA cytochrome b haplotypes was studied in the wood lemming (Myopus schisticolor), a species that is closely associated with the boreal forest of the Eurasian taiga zone from Scandinavia to the Pacific coast. Except for a major phylogeographic discontinuity (0.9% nucleotide divergence) in southeastern Siberia, only shallow regional genetic structure was detected across northern Eurasia. Genetic signs of demographic expansions imply that successive range contractions and expansions on different spatial scales represented the primary historical events that shaped geographical patterns of genetic variation. Comparison of phylogeographic structure across a taxonomically diverse array of other species that are ecologically associated with the taiga forest revealed similar patterns and identified two general aspects. First, the major south-north phylogeographic discontinuity observed in five out of six species studied in southeastern Siberia and the Far East implies vicariant separation in two different refugial areas. The limited distribution range of the southeastern lineages provides no evidence of the importance of the putative southeastern refugial area for postglacial colonization of northern Eurasia by boreal forest species. Second, the lack of phylogeographic structure associated with significant reciprocal monophyly and genetic signatures of demographic expansion in all nine boreal forest animal species studied to date across most of northern Eurasia imply contraction of each species to a single refugial area during the late Pleistocene followed by range expansion on a continental scale. Similar phylogeographic patterns observed in this taxonomically diverse set of organisms with different life histories and dispersal potentials reflect the historical dynamics of their shared environment, the taiga forest in northern Eurasia.     

Marine turtle mitogenome phylogenetics and evolution

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.     

Comparative phylogeography of Nearctic and Palearctic fishes

Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.     

Intraspecific phylogeography of the gopher tortoise, Gopherus polyphemus: RFLP analysis of amplified mtDNA segments

The slow rate of mtDNA evolution in turtles poses a limitation on the levels of intraspecific variation detectable by conventional restriction fragment surveys. We examined mtDNA variation in the gopher tortoise (Gopherus polyphemus) using an alternative restriction assay, one in which PCR-amplified segments of the mitochondrial genome were digested with tetranucleotide-site endonucleases. Restriction fragment polymorphisms representing four amplified regions were analysed to evaluate population genetic structure among 112 tortoises throughout the species' range. Thirty-six haplotypes were identified, and three major geographical assemblages (Eastern, Western, and Mid-Florida) were resolved by UPGMA and parsimony analyses. Eastern and Western assemblages abut near the Apalachicola drainage, whereas the Mid-Florida assemblage appears restricted to the Brooksville Ridge. The Eastern/Western assemblage boundary is remarkably congruent with phylogeographic profiles for eight additional species from the southeastern U.S., representing both freshwater and terrestrial realms.     

Phylogeography of the salamander genus Pseudobranchus in the southeastern United States

This study provides an extensive set of mitochondrial cytochrome b sequences for the salamander genus Pseudobranchus of the southeastern United States. These sequences were analysed by multiple phylogenetic methods that support a single set of major phylogeographic divisions for its two corroborated species (P. axanthus and P. striatus). These phylogeographic divisions overlap with the geographic breakpoints of other freshwater and terrestrial taxa in this region. Collectively, these overlapping patterns highlight the Central Highland and Tifton/Vidalia uplands as a significant barrier to Atlantic vs. Gulf coast groups, while reconfirming the phylogeographic significance of the Altamaha and Apalachicola river drainages. Despite their distinct phylogeographic split, P. striatus from west and east of these uplands are not currently recognizable as separate species according to the concordance principles for species definition.     

Evolution of the gene network underlying gonadogenesis in turtles with temperature-dependent and genotypic sex determination

The evolution of sex determination has long fascinated biologists, as it has paramount consequences for the evolution of a multitude of traits, from sex allocation to speciation and extinction. Explaining the diversity of sex-determining systems found in vertebrates (genotypic or GSD and temperature-dependent or TSD) requires a comprehensive and integrative examination from both a functional and an evolutionary perspective. Particularly revealing is the examination of the gene network that regulates gonadogenesis. Here, I review some advances in this field and propose some additional hypotheses about the composition of the gene network underlying sexual development, the functional links among some of its elements and their evolution in turtles. I focus on several pending questions about: (1) What renders TSD systems thermo-sensitive? (2) Is there one developmentally conserved or multiple TSD mechanisms? (3) Have evolutionarily derived GSD species lost all ancestral thermal-sensitivity? New data are presented on embryonic expression of Dax1 (the dosage-sensitive sex-reversal adrenal hypoplasia congenital on the X chromosome gene in the turtles Chrysemys picta (TSD) and Apalone mutica (GSD). No differential Dax1 expression was detected in C. picta at any of the stages examined, consistent with reports on two other TSD turtles and alligators. Notably, significantly higher Dax1 expression was found at 30°C than at 25°C at stage 15 in A. mutica (GSD), likely caused by Wt1's identical expression pattern previously reported. Because Sf1 is an immediate downstream target of Dax1 and its expression is not affected by temperature, it is proposed that Sf1 renders Dax1's differential signal ineffective to induce biased sex ratios in A. mutica, as previously proposed for Wt1's thermosensitive expression. Thus, it is hypothesized that Sf1 plays a major role in the lack of response of sex ratio to temperature of A. mutica, and may function as a sex-determining gene in this GSD species. These and previous data permit formulating several mechanistic hypotheses: (1) the postulation of Wt1 as a candidate thermal master switch alone, or in combination with Sf1, in the TSD turtle C. picta; (2) the proposition of Sf1 as a sex-determining gene in the GSD turtle A. mutica; and (3) the hypothesis that differing patterns of gene expression among TSD taxa reflect multiple traits from a developmental perspective. Moreover, the recent finding of relic differential Wt1 expression in A. mutica and the results for Dax1 in this species provide empirical evidence that GSD taxa can harbor thermal sensitivity at the level of gene expression, potentially co-optable during TSD evolution.     

Fat frogs,mobile genes: unexpected phylogeographic patterns for the ornate chorus frog (Pseudacris ornata)

The southeastern coastal plain of the United States is a region marked by extraordinary phylogeographic congruence that is frequently attributed to the changing sea levels that occurred during the glacial‐interglacial cycles of the Pleistocene epoch. A phylogeographic break corresponding to the Apalachicola River has been suggested for many species studied to date that are endemic to this region. Here, we used this pattern of phylogeographic congruence to develop and test explicit hypotheses about the genetic structure in the ornate chorus frog (Pseudacris ornata). Using 1299 bp of mtDNA sequence and seven nuclear microsatellite markers in 13 natural populations of P. ornata, we found three clades corresponding to geographically distinct regions; one spans the Apalachicola River (Southern Clade), one encompasses Georgia and South Carolina (Central Clade) and a third comprises more northerly individuals (Northern Clade). However, it does not appear that typical phylogeographic barriers demarcate these clades. Instead, isolation by distance across the range of the entire species explained the pattern of genetic variation that we observed. We propose that P. ornata was historically widespread in the southeastern United States, and that a balance between genetic drift and migration was the root of the genetic divergence among populations. Additionally, we investigated fine‐scale patterns of genetic structure and found the spatial scale at which there was significant genetic structure varied among the regions studied. Furthermore, we discuss our results in light of other phylogeographic studies of southeastern coastal plain organisms and in relation to amphibian conservation and management.     

Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution

Codistributed species may display either congruent phylogeographic patterns, indicating similar responses to a series of shared climatic and geologic events, or discordant patterns, indicating independent responses. This study compares the phylogeographic patterns of two similarly distributed salamander species within the Pacific Northwest of the United States: Cope's giant salamander (Dicamptodon copei) and Van Dyke's salamander (Plethodon vandykei). Previous studies of P. vandykei support two reciprocally monophyletic lineages corresponding to coastal populations, located from the Olympic Mountains to the mouth of the Columbia River, and inland populations within the Cascade Mountains. We hypothesized that D. copei would have a congruent phylogeographic pattern to P. vandykei due to similarity in distribution and dependence upon similar stream and stream-side habitats. We test this hypothesis by estimating the phylogeny of D. copei using approximately 1800bp of mitochondrial DNA and comparing it to that of P. vandykei. Sympatric populations of D. copei and of P. vandykei display an identical phylogeographic pattern, suggesting similar responses within their shared distribution. Populations of D. copei occurring outside the range of P. vandykei displayed high levels of genetic divergence from those sympatric to P. vandykei. Overall, phylogeographic patterns between the two species were ultimately incongruent due to the high divergence of these allopatric populations. These results provide an example of codistributed species displaying overall incongruent phylogeographic patterns while simultaneously displaying congruent patterns within portions of their shared geographic distribution. This pattern demonstrates that a simple dichotomy of congruent and incongruent phylogeographic patterns of codistributed species may be too simplistic and that more complex intermediate patterns can result even from minor differences in species' ranges.     

Isolation and characterization of 15 microsatellite loci in four endangered Amentotaxus species (Taxaceae)

? Premise of the study: Fifteen microsatellite loci were developed in an endangered species, Amentotaxus formosana, and were tested in an additional three species, A. argotaenia, A. yunnanensis, and A. poilanei, to evaluate the population structure for conservation efforts and reconstruct the phylogeographic patterns of this ancient lineage. ? Methods and Results: Polymorphic primer sets were developed from A. formosana; the number of alleles ranged from two to 10, with an observed heterozygosity ranging from 0 to 0.60. All of the loci were found to be interspecifically amplifiable. ? Conclusions: These polymorphic and transferable loci will be potentially useful for future studies that will focus on identifying distinct genetic units within species and establishing the phylogeographic patterns and the process of speciation among closely related species.     

Phylogeographic patterns of decapod crustaceans at the Atlantic-Mediterranean transition

Comparative multispecies studies allow contrasting the effect of past and present oceanographic processes on phylogeographic patterns. In the present study, a fragment of the COI gene was analyzed in seven decapod crustacean species from five families and with different bathymetric distributions. A total of 769 individuals were sampled along the Atlantic-Mediterranean transition area in order to test the effect of three putative barriers to gene flow: Strait of Gibraltar, Almeria-Oran Front and Ibiza Channel. A significant effect of the Strait of Gibraltar was found in the crabs Liocarcinus depurator and Macropipus tuberculatus. The Ibiza Channel had a significant effect for L. depurator. However, the Almeria-Oran front was not found to have a significant effect on any of the studied species. Higher levels of population structure were found in shallow-water species, although the number of species sampled should be increased to obtain a conclusive pattern. The haplotypes within the different species coalesced at times that could be related with past climatic events occurring before, during and after the last glacial maximum. Given the large diversity of phylogeographic patterns obtained within decapods, it is concluded that both historical and contemporary processes (marine current patterns, bathymetry and life-history traits) shape the phylogeographic patterns of these crustaceans.     

Survival and physiological responses of hatchling blanding's turtles (Emydoidea blandingii) to submergence in normoxic and hypoxic water under simulated winter conditions

Overwintering habits of hatchling Blanding's turtles (Emydoidea blandingii) are unknown. To determine whether these turtles are able to survive winter in aquatic habitats, we submerged hatchlings in normoxic (155 mmHg Po2) and hypoxic (6 mmHg Po2) water at 4 degrees C, recording survival times and measuring changes in key physiological variables. For comparison, we simultaneously studied hatchling softshell (Apalone spinifera) and snapping (Chelydra serpentina) turtles, which are known to overwinter in aquatic habitats. In normoxic water, C. serpentina and A. spinifera survived to the termination of the experiment (76 and 77 d, respectively). Approximately one-third of the E. blandingii died during 75 d of normoxic submergence, but the cause of mortality was unclear. In hypoxic water, average survival times were 6 d for A. spinifera, 13 d for E. blandingii, and 19 d for C. serpentina. Mortality during hypoxic submergence was probably caused by metabolic acidosis, which resulted from accumulated lactate. Unlike the case with adult turtles, our hatchlings did not increase plasma calcium and magnesium, nor did they sequester lactate within the shell. Our results suggest that hatchling E. blandingii are not particularly well suited to hibernation in hypoxic aquatic habitats.     

Evolutionary origins and diversification of dragon lizards in Australia's tropical savannas

Australia's monsoonal tropics are dominated by the largest and least modified savanna woodlands in the world, and they are globally significant for their high biodiversity and regional endemism. Despite this, there have been very few molecular studies of the evolutionary origins and diversification of vertebrates in this region. The semi-arboreal dragon lizards of Lophognathus and Amphibolurus are widely distributed in the savanna and dry sclerophyll woodlands of Australasia, including the monsoon tropics. We sequenced a ~1400 bp region of mitochondrial DNA and a ~1400 bp nuclear gene (RAG1) to investigate the phylogenetic relationships and phylogeographic structuring of all seven species of Lophognathus and Amphibolurus. Our analyses show that there is a higher level of species and generic diversity in the monsoon tropics than previously thought, and a full morphological review and taxonomic revision of these genera is required. Relaxed molecular clock analyses indicate that species across both genera originated in the late Miocene and early Pliocene, with significant phylogeographic structure within species. We did not find any evidence that the monsoon tropics species were a monophyletic group that had diversified within the region; instead Amphibolurus and Lophognathus represent at least three independent evolutionary colonizations of the monsoon tropics. It is probable that the origins and phylogeographic patterns of the northern Lophognathus species have evolved under the climatic influence of the Australian monsoon, rather than being either an ancient Gondwanan lineage that pre-dates the monsoon or the result of a more recent dispersal event across Wallace's Line.     

Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces

Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.     

黄喉拟水龟（♀）与三线闭壳龟（♂）杂交后代的形态特征及其与父母本的比较研究

本研究通过黄喉拟水龟Mauremys mutica（♀）与三线闭壳龟Cuora trifasciata（♂）进行杂交,成功获得了杂种龟。这说明黄喉拟水龟和三线闭壳龟是可以进行属间远缘杂交的,但杂交组合的受精率及孵化成功率均低于黄喉拟水龟的同种组合。杂种稚龟与黄喉拟水龟稚龟在背甲纹路、腹甲黑斑、四肢和尾腹面的皮肤颜色、喉盾前端形状及起点位置、喉盾宽/喉盾缝长、喉盾缝长/肱盾缝长、股盾缝长/肛盾缝长存在差异。1龄前,杂种龟生长快于黄喉拟水龟。形态特征上,杂种龟头顶部淡棕黄色,头侧眼后有两条黑色纵纹,颈腹部淡黄色;背甲棕色,腹甲浅黄色,每一盾片中间都有边缘呈放射状的黑斑;四肢、尾腹面及裸露皮肤部分为黄褐色。形态可量数据分析显示杂种龟在形态上接近黄喉拟水龟。建立了三种龟的形态判别公式,判别的准确率为100%（p<0.01）,判别分析中贡献最大的4个变量分别是腹甲后半部长/背甲长、喉盾宽/背甲长、肱盾缝长/背甲长、股盾缝长/背甲长,可见三线闭壳龟、黄喉拟水龟与杂交种腹部的腹甲后半部长、喉盾宽、肱盾缝长、股盾缝长等参数可作为鉴别三者的直接依据。本实验的结果对杂种龟的鉴定、龟类的杂交育种及养殖生产实践都有一定的借鉴作用。     

Range-wide phylogeography of a temperate lizard, the five-lined skink (Eumeces fasciatus)

We used mitochondrial DNA and microsatellite loci to examine the phylogeographic patterns of the most broadly distributed lizard in eastern North America, the five-lined skink (Eumeces fasciatus). We infer that longitudinal phylogeographic patterns in E. fasciatus are consistent with fragmentation due to refugial and post-glacial dynamics, but that deep divergences within the species imply historical fragmentation that predates the Pleistocene. The effect of multiple refugia is implied from our nested clade analyses, including a northern refugium in Wisconsin. Analysis of population structure using nuclear microsatellite data within the species suggests the importance of glacial dynamics in shaping more recent genetic structuring within one widely distributed lineage that ranges from the Mississippi River to the Atlantic Ocean in longitude and from southern Ontario to the Gulf of Mexico in latitude. Results shed light on the historical processes that have influenced current population structure of a temperate lizard, support the striking similarity of longitudinal phylogeographic structure across many herpetofaunal species in eastern North America, and illustrate the utility of employing multiple markers in phylogeographic studies.     

Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia

We examine the effects of historical climate change on vertebrate differentiation in tropical rainforest by comparing phylogeographic patterns in six species of widespread rainforest-restricted herpetofauna from throughout the Wet Tropics of Australia. Qualitative and quantitative comparisons of phylogeographic structure reveal strikingly similar patterns of pre-Pleistocene vicariant population differentiation on either side of a previously identified biogeographic break (variously referred to as the Black Mountain Barrier or Corridor; BMC). While divergence across the BMC antedates the Pleistocene, the impact of Quaternary climate change is apparent in populations on either side of the BMC. Consistent with palaeoclimatological reconstructions for the region, the distribution and degree of mtDNA diversity suggests that populations were fragmented and reduced to multiple refugia during Pleistocene glacial periods, with expansion following Holocene rainforest recovery. This pattern is repeated on both sides of the BMC, but substantial differences in the amount and distribution of mtDNA diversity within species indicate the importance of species-specific ecological characteristics. The historical processes of extinction and (re)colonization revealed by the comparative phylogeographic analysis of mtDNA sequences substantiate earlier suggestions that current regional patterns of species distribution and diversity in the Wet Tropics are largely determined by local extinctions and subsequent recolonization driven by Quaternary climate changes.     

Testing phylogeographic predictions on an active volcanic island: Brachyderes rugatus (Coleoptera: Curculionidae) on La Palma (Canary Islands)

Volcanic islands with well-characterized geological histories can provide ideal templates for generating and testing phylogeographic predictions. Many studies have sought to utilize these to investigate patterns of colonization and speciation within groups of closely related species across a number of islands. Here we focus attention within a single volcanic island with a well-characterized geological history to develop and test phylogeographic predictions. We develop phylogeographic predictions within the island of La Palma of the Canary Islands and test these using 69 haplotypes from 570 base pairs of mitochondrial DNA cytochrome oxidase II sequence data for 138 individuals of Brachyderes rugatus rugatus, a local endemic subspecies of curculionid beetle occurring throughout the island in the forests of Pinus canariensis. Although geological data do provide some explanatory power for the phylogeographic patterns found, our network-based analyses reveal a more complicated phylogeographic history than initial predictions generated from data on the geological history of the island. Reciprocal illumination of geological and phylogeographic history is also demonstrated with previous geological speculation gaining phylogeographic corroboration from our analyses.     

Out of Florida: mtDNA reveals patterns of migration and Pleistocene range expansion of the Green Anole lizard (Anolis carolinensis)

Anolis carolinensis is an emerging model species and the sole member of its genus native to the United States. Considerable morphological and physiological variation has been described in the species, and the recent sequencing of its genome makes it an attractive system for studies of genome variation. To inform future studies of molecular and phenotypic variation within A. carolinensis, a rigorous account of intraspecific population structure and relatedness is needed. Here, we present the most extensive phylogeographic study of this species to date. Phylogenetic analyses of mitochondrial DNA sequence data support the previous hypothesis of a western Cuban origin of the species. We found five well‐supported, geographically distinct mitochondrial haplotype clades throughout the southeastern United States. Most Florida populations fall into one of three divergent clades, whereas the vast majority of populations outside Florida belong to a single, shallowly diverged clade. Genetic boundaries do not correspond to major rivers, but may reflect effects of Pleistocene glaciation events and the Appalachian Mountains on migration and expansion of the species. Phylogeographic signal should be examined using nuclear loci to complement these findings.