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Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities., Competing Interests: The authors declare no competing interest.

Genomic data are increasingly used for high resolution population genetic studies including those at the forefront of biological conservation. A key methodological challenge is determining sequence similarity clustering thresholds for RADseq data when no reference genome is available. These thresholds define the maximum permitted divergence among allelic variants and the minimum divergence among putative paralogues and are central to downstream population genomic analyses. Here we develop a novel set of metrics to determine sequence similarity thresholds that maximize the correct separation of paralogous regions and minimize oversplitting naturally occurring allelic variation within loci. These metrics empirically identify the threshold value at which true alleles at opposite ends of several major axes of genetic variation begin to incorrectly separate into distinct clusters, allowing researchers to choose thresholds just below this value. We test our approach on a recently published data set for the protected foothill yellow-legged frog (Rana boylii). The metrics recover a consistent pattern of roughly 96% similarity as a threshold above which genetic divergence and data missingness become increasingly correlated. We provide scripts for assessing different clustering thresholds and discuss how this approach can be applied across a wide range of empirical data sets., (© 2019 John Wiley & Sons Ltd.)

Newts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remained unclear. To resolve the phylogeny of Triturus, we generated a c. 6000 transcriptome-derived marker data set using a custom target enrichment probe set, and conducted phylogenetic analyses using: (1) data concatenation with RAxML, (2) gene-tree summary with ASTRAL, and (3) species-tree estimation with SNAPP. All analyses produce the same, highly supported topology, despite cladogenesis having occurred over a short timeframe, resulting in short internal branch lengths. Our new phylogenetic hypothesis is consistent with the minimal number of inferred changes in NTV count necessary to explain the diversity in NTV observed today. Although a causal relationship between NTV, body form, and aquatic ecology has yet to be experimentally established, our phylogeny indicates that these features have evolved together, and suggest that they may underlie the adaptive radiation that characterizes Triturus., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies. We make use of an empirical prior on rates of molecular evolution to estimate divergence times with a molecular clock under a coalescent framework. Together, the phylogeny and divergence time estimates suggest that diversification has been both more recent and more rapid than has so far been suspected. We provide a well-supported evolutionary framework for Graptemys that is necessary for understanding map turtle diversity, biogeography, and for conservation of this threatened clade of turtles., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing., Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented., Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome-wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next-generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander (Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this large data set (344 330 reads), we developed a pipeline that sorts PTS data by barcode and locus, identifies high-quality variable nucleotides and yields phased haplotype sequences for each individual at each locus. Our sequencing and bioinformatic strategy resulted in a genome-wide data set with relatively low levels of missing data and a wide range of nucleotide variation. structure analyses of these data in a genotypic format resulted in strongly supported assignments for the majority of individuals into nine geographically defined genetic clusters. Species tree analyses of the most variable loci using a multi-species coalescent model resulted in strong support for most branches in the species tree; however, analyses including more than 50 loci produced parameter sampling trends that indicated a lack of convergence on the posterior distribution. Overall, these results demonstrate the potential for amplicon-based PTS to rapidly generate large-scale data for population genetic and phylogenetic-based research., (© 2012 Blackwell Publishing Ltd.)

Turtles are currently the most endangered major clade of vertebrates on earth, and Asian box turtles (Cuora) are in catastrophic decline. Effective management of this diverse turtle clade has been hampered by human-mediated, and perhaps natural hybridization, resulting in discordance between mitochondrial and nuclear markers and confusion regarding species boundaries and phylogenetic relationships among hypothesized species of Cuora. Here, we present analyses of mitochondrial and nuclear DNA data for all 12 currently hypothesized species to resolve both species boundaries and phylogenetic relationships. Our 15-gene, 40-individual nuclear data set was frequently in conflict with our mitochondrial data set; based on its general concordance with published morphological analyses and the strength of 15 independent estimates of evolutionary history, we interpret the nuclear data as representing the most reliable estimate of species boundaries and phylogeny of Cuora. Our results strongly reiterate the necessity of using multiple nuclear markers for phylogeny and species delimitation in these animals, including any form of DNA "barcoding", and point to Cuora as an important case study where reliance on mitochondrial DNA can lead to incorrect species identification., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Past confusion about leopard frog (genus Rana) species composition in the Tri-State area of the US that includes New York (NY), New Jersey (NJ), and Connecticut (CT) has hindered conservation and management efforts, especially where populations are declining or imperiled. We use nuclear and mitochondrial genetic data to clarify the identification and distribution of leopard frog species in this region. We focus on four problematic frog populations of uncertain species affiliation in northern NJ, southeastern mainland NY, and Staten Island to test the following hypotheses: (1) they are conspecific with Rana sphenocephala or R. pipiens, (2) they are hybrids between R. sphenocephala and R. pipiens, or (3) they represent one or more previously undescribed cryptic taxa. Bayesian phylogenetic and cluster analyses revealed that the four unknown populations collectively form a novel genetic lineage, which represents a previously undescribed cryptic leopard frog species, Rana sp. nov. Statistical support for R. sp. nov. was strong in both the Bayesian (pp=1.0) and maximum-likelihood (bootstrap=99) phylogenetic analyses as well as the Structure cluster analyses. While our data support recognition of R. sp. nov. as a novel species, we recommend further study including fine-scaled sampling and ecological, behavioral, call, and morphological analyses before it is formally described., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Advances in molecular biology have expanded our understanding of patterns of evolution and our ability to infer phylogenetic relationships. Despite many applications of molecular methods in attempts at resolving the evolutionary relationships among the major clades of turtles, some nodes in the tree have proved to be extremely problematic and have remained unresolved. In this study, we use 14 nuclear loci to provide an in depth look at several of these troublesome nodes and infer the systematic relationships among 11 of the 14 turtle families. We find strong support for two of the most problematic nodes in the deep phylogeny of turtles that have traditionally defied resolution. In particular, we recover strong support for a sister relationship between the Emydidae and the monotypic bigheaded-turtle, Platysternon megacephalum. We also find strong support for a clade consisting of sea turtles, mud and musk turtles, and snapping turtles. Within this clade, snapping turtles (Chelydridae) and mud/musk turtles (Kinosternidae) are sister taxa, again with strong support. Our results emphasize the utility of multi-locus datasets in phylogenetic analyses of difficult problems., (2009 Elsevier Inc. All rights reserved.)

The historical biogeography of California's taxa has been the focus of extensive research effort. The western pond turtle (Emys marmorata) is an example of a wide-ranging taxon that spans several well-known California diversity hotspots. Using a dataset comprised of one mitochondrial and five nuclear loci, we elucidate the major biogeographic patterns of the western pond turtle across the California landscape. By employing a combination of phylogenetic and network-based approaches, we recovered a relatively ancient (c. 2-8 Ma) north/south split among populations of E. marmorata and find an area of intergradation centred in the Central Coast Ranges of California. In addition, discordant mitochondrial/nuclear genetic patterns suggest subsequent gene flow from northern populations and from San Joaquin Valley populations into the Central Coast Ranges after the Pliocene-Pleistocene marine embayment of the Great Central Valley subsided. Our results emphasize the utility of nuclear DNA phylogeography for recovering the impact of relatively ancient biogeographic events, and suggest that the Central Coast Ranges of California have played a major role in the geographic structuring of the western pond turtle, and possibly other co-distributed taxa.

As phylogenetic data sets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two-thirds of all turtle species based on a approximately 50 kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.

Background: Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, and simulations have been used to examine this question. Most simulations have been based on few empirical loci, and suggest that well supported phylogenies can be determined with a very modest amount of data. Here we report the results of an empirical phylogenetic analysis of all 10 genera and 25 of 48 species of the new world pond turtles (family Emydidae) based on one mitochondrial (1070 base pairs) and seven nuclear loci (5961 base pairs), and a more biologically realistic simulation analysis incorporating variation among gene trees, aimed at determining how much more data might be necessary to recover weakly-supported nodes with strong support., Results: Our mitochondrial-based phylogeny was well resolved, and congruent with some previous mitochondrial results. For example, all genera, and all species except Pseudemys concinna, P. peninsularis, and Terrapene carolina were monophyletic with strong support from at least one analytical method. The Emydinae was recovered as monophyletic, but the Deirochelyinae was not. Based on nuclear data, all genera were monophyletic with strong support except Trachemys, and all species except Graptemys pseudogeographica, P. concinna, T. carolina, and T. coahuila were monophyletic, generally with strong support. However, the branches subtending most genera were relatively short, and intergeneric relationships within subfamilies were mostly unsupported. Our simulations showed that relatively high bootstrap support values (i.e. >or= 70) for all nodes were reached in all datasets, but an increase in data did not necessarily equate to an increase in support values. However, simulations based on a single empirical locus reached higher overall levels of support with less data than did the simulations that were based on all seven empirical nuclear loci, and symmetric tree distances were much lower for single versus multiple gene simulation analyses., Conclusion: Our empirical results provide new insights into the phylogenetics of the Emydidae, but the short branches recovered deep in the tree also indicate the need for additional work on this clade to recover all intergeneric relationships with confidence and to delimit species for some problematic groups. Our simulation results suggest that moderate (in the few-to-tens of kb range) amounts of data are necessary to recover most emydid relationships with high support values. They also suggest that previous simulations that do not incorporate among-gene tree topological variance probably underestimate the amount of data needed to recover well supported phylogenies.

We present a strategy for phylogenetic marker development in non-model systems. Rather than using the traditional approach of comparing distantly related taxa to develop conserved primers for unknown species, we explore an alternative strategy that builds primers directly from a single, relatively well characterized species and applies those primers to increasingly distantly related taxa. We develop and test our protocol with turtles. Using a single BAC end-sequence library consisting of 3461 sequences totaling 2.43 million base pairs of data, we outline a procedure to flag repeat elements, followed by a BLAST approach to categorize sequences into high, low, and no similarity compartments compared to GenBank sequences. We developed and tested a panel of 96 primer pairs with a set of turtle tissues that forms a series of increasingly distantly related taxa with respect to the BAC reference species. Finally, we sequenced 11 of these newly discovered markers across a diverse set of 18 turtle species that spans the 210 million years of chelonian crown-group history and that includes representatives of most of the major clades of extant turtles. Our results indicate that large numbers of new, phylogenetically informative markers can be developed quickly and inexpensively from a single BAC, EST, or similar genomic resource, and that those markers provide reliable phylogenetic information across both shallow and deep levels of phylogenetic history. Our results also highlight the importance of screening for and managing repetitive elements found in randomly sequenced DNA fragments. We presume that our strategy should work well across any similarly divergent clade, suggesting that many-marker datasets can be developed quickly and efficiently for phylogenetic analysis.

Well-supported, congruent phylogeographic and biogeographic patterns permit the development of a priori phylogeographic and distributional predictions. In the southeastern Coastal Plain of the United States, the common discovery of east-west disjunctions (phylogeographic breaks and species' distributional boundaries) suggests that similar disjunctions should occur in codistributed taxa. Despite the near ubiquity of these disjunctions, the most recent morphological analyses of the flatwoods salamander, Ambystoma cingulatum, indicate that none occur in this low-vagility, Coastal Plain endemic. We conducted molecular and morphological analyses to test whether the flatwoods salamander is an exception to this common biogeographic pattern. Assessing geographic variation in this species is also an important management tool for this threatened, declining amphibian. We demonstrate that flatwoods salamanders, as predicted by comparisons to codistributed taxa, are polytypic with a major disjunction at the Apalachicola River. This drainage is a common site for east-west phylogeographic breaks, probably because repeated marine embayments during the Pliocene and Pleistocene interglacials generated barriers to gene flow. Based on mitochondrial DNA, morphology, and allozymes, we recognize two species of flatwoods salamanders -- Ambystoma cingulatum to the east of the Apalachicola drainage and Ambystoma bishopi to the west. Given this increased diversity, the conservation status of these two taxa may warrant re-evaluation. More generally, these results emphasize that in the absence of taxon-specific data, established comparative patterns can provide strong expectations for designing management units for unstudied species of conservation concern.

Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinarium, a member of an adaptive radiation of metamorphic and paedomorphic salamanders (the Ambystoma tigrinum complex) that have diversified across terrestrial and aquatic environments. Gene tree comparisons demonstrate extensive nonmonophyly in the mtDNA genealogy of A. ordinarium, while seven of eight independent nuclear loci resolve the species as monophyletic or nearly so, and diagnose it as a well-resolved genealogical species. A differential introgression hypothesis is supported by the observation that western A. ordinarium localities contain mtDNA haplotypes that are identical or minimally diverged from haplotypes sampled from a nearby paedomorphic species, Ambystoma dumerilii, while most nDNA trees place these species in distant phylogenetic positions. These results provide a strong example of how historical introgression can lead to radical differences between gene trees and species histories, even among currently allopatric species with divergent life history adaptations and morphologies. They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations.

Turtles are one of Earth's most instantly recognizable life forms, distinguished for over 200 million years in the fossil record. Even so, key nodes in the phylogeny of turtles remain uncertain. To address this issue, we sequenced >90% of the nuclear recombination activase gene 1 (RAG-1) for 24 species representing all modern turtle families. RAG-1 exhibited negligible saturation and base composition bias, and extensive base composition homogeneity. Most of the relationships suggested by prior phylogenetic analyses were also supported by RAG-1 and, for at least two critical nodes, with a much higher level of support. RAG-1 also indicates that the enigmatic Platysternidae and Chelydridae, often considered sister taxa based on morphological evidence, are not closely related, although their precise phylogenetic placement in the turtle tree is still unresolved. Although RAG-1 is phylogenetically informative, our research revealed fundamental conflicts among analytical methods for estimating phylogenetic hypotheses. Maximum parsimony analyses of RAG-1 alone and in combination with two mitochondrial genes suggest the earliest phylogenetic splits separating into three basal branches, the pig-nosed turtles (Carettochelyidae), the softshell turtles (Trionychidae), and a clade comprising all remaining extant turtles. Maximum likelihood and Bayesian analyses group Carettochelyidae and Trionychidae (=Trionychoidae) in their more traditional location as the sister taxon to all other hidden-necked turtles, collectively forming the Cryptodira. Our research highlights the utility of molecular data in identifying issues of character homology in morphological datasets, while shedding valuable light on the biodiversity of a globally imperiled taxon.

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.

We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously published morphological characters for a complimentary set of 24 species. The combined data set provided complete taxonomic coverage for this globally distributed clade of turtles, with incomplete data for a few taxa. Although our taxonomic sampling is complete, most of the modern taxa are representatives of old and very divergent lineages. Thus, due to biological realities, our sampling consists of one or a few representatives of several ancient lineages across a relatively deep phylogenetic tree. Our analyses of the combined data set converge on a set of well-supported relationships, which is in accord with many aspects of traditional softshell systematics including the monophyly of the Cyclanorbinae and Trionychinae. However, our results conflict with other aspects of current taxonomy and indicate that most of the currently recognized tribes are not monophyletic. We use this strong estimate of the phylogeny of softshell turtles for two purposes: (1) as the basis for a novel rank-free classification, and (2) to retrospectively examine strategies for analyzing highly homoplasious mtDNA data in deep phylogenetic problems where increased taxon sampling is not an option. Weeded and weighted parsimony, and model-based techniques, generally improved the phylogenetic performance of highly homoplasious mtDNA sequences, but no single strategy completely mitigated the problems of associated with these highly homoplasious data. Many deep nodes in the softshell turtle phylogeny were confidently recovered only after the addition of largely nonhomoplasious data from the nuclear intron.

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.

The red-legged frog, Rana aurora, has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red-legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, approximately 400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California.

The painted turtle, Chrysemys picta, is currently recognized as a continentally distributed polytypic species, ranging across North America from southern Canada to extreme northern Mexico. We analyzed variation in the rapidly evolving mitochondrial control region (CR) in 241 turtles from 117 localities across this range to examine whether the painted turtle represents a continentally distributed species based on molecular analysis. We found strong support for the novel hypothesis that C. p. dorsalis is the sister group to all remaining Chrysemys, with the remaining Chrysemys falling into a single, extremely wide-ranging and genetically undifferentiated species. Given our goal of an evolutionarily accurate taxonomy, we propose that two evolutionary lineages be recognized as species within Chrysemys: C. dorsalis (Agassiz 1857) in the southern Mississippi drainage region, and C. picta (Schneider 1783) from the rest of the range of the genus. Neither molecular nor recent morphological analyses argue for the hybrid origin of C. p. marginata as previously proposed. Within C. picta, we find evidence of at least two independent range expansions into previously glaciated regions of North America, one into New England and the other into the upper Midwest. We further find evidence of a massive extinction/recolonization event across the Great Plains/Rocky Mountain region encompassing over half the continental United States. The timing and extent of this colonization is consistent with a recently proposed regional aridification as the Laurentide ice sheets receded approximately 14,000 years ago, and we tentatively propose this paleoclimatological event as a major factor shaping genetic variation in Chrysemys.

We present phylogenetic analyses of both molecular and morphological data for the 23 major lineages of living turtles and seven key fossil taxa. Nearly 1 kilobase of cytochrome b sequence, 325 base pairs of 12S ribosomal DNA, and 115 morphological characters contained similar phylogenetic information, although each provided unique information on different nodes of chelonian history. A character-based combinability test (implemented in PAUP*) and a non-parametric test of taxonomic congruence indicated no strong evidence for heterogeneity among data sets, and we used a combined approach to estimate a final phylogeny of the major lineages of living turtles. This approach resulted in a very well-resolved tree, with only a few of the deep branches within the Cryptodira left as an unresolved polytomy. The addition of six relatively complete fossils chosen to help resolve this basal polytomy provided little added resolution to the tree and resulted in a sharp decline in bootstrap proportions for nodes near the fossils. Branch-length analysis and independent dates from the fossil record suggest that these unresolved nodes may represent a rapid radiation of the major cryptodiran lineages 90-120 million years ago.