Resolving the phylogenetic history of the short-necked turtles, genera Elseya and Myuchelys (Testudines: Chelidae) from Australia and New Guinea.

Phylogenetic relationships and taxonomy of the short-necked turtles of the genera Elseya, Myuchelys, and Emydura in Australia and New Guinea have long been debated as a result of conflicting hypotheses supported by different data sets and phylogenetic analyses. To resolve this contentious issue, we analyzed sequences from two mitochondrial genes (cytochrome b and ND4) and one nuclear intron gene (R35) from all species of the genera Elseya, Myuchelys, Emydura, and their relatives. Phylogenetic analyses using three methods (maximum parsimony, maximum likelihood, and Bayesian inference) produce a single, well resolved, and strongly corroborated hypothesis, which provides support for the three genera, with the exception that the genus Myuchelys is paraphyletic - Myuchelys purvisi is the sister taxon to the remaining Elseya, Myuchelys and Emydura. A new genus is proposed for the species Myuchelys purvisi to address this paraphyletic relationship. Time-calibration analysis suggests that diversification of the group in Australia coincides with periods of aridification in the late Eocene and between the mid-Miocene and early Pliocene. Other speciation events occurred during the faunal exchange between Australia and the island of New Guinea during the late Miocene and early Pliocene. Lineages distributed in New Guinea are likely influenced by the complex geologic history of the island, and include cryptic species diversity.

A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes.

Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.

Multiple data sets, high homoplasy, and the phylogeny of softshell turtles (Testudines: Trionychidae).

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.

Phylogenetic hypotheses for the turtle family Geoemydidae.

The turtle family Geoemydidae represents the largest, most diverse, and most poorly understood family of turtles. Little is known about this group, including intrafamilial systematics. The only complete phylogenetic hypothesis for this family positions geoemydids as paraphyletic with respect to tortoises, but this arrangement has not been accepted by many workers. We compiled a 79-taxon mitochondrial and nuclear DNA data set to reconstruct phylogenetic relationships for 65 species and subspecies representing all 23 genera of the Geoemydidae. Maximum parsimony (MP) and maximum-likelihood (ML) analyses and Bayesian analysis produced similar, well-resolved trees. Our analyses identified three main clades comprising the tortoises (Testudinidae), the old-world Geoemydidae, and the South American geoemydid genus Rhinoclemmys. Within Geoemydidae, many nodes were strongly supported, particularly based on Bayesian posterior probabilities of the combined three-gene dataset. We found that adding data for a subset of taxa improved resolution of some deeper nodes in the tree. Several strongly supported groupings within the Geoemydidae demonstrate non-monophyly of some genera and possible interspecific hybrids, and we recommend several taxonomic revisions based on available evidence.

A taxonomic reevaluation of Phrynops (Testudines: Chelidae) with the description of two new genera and a new species of Batrachemys

Relationships among turtle species loosely categorized within the South American genus Phrynops are explored. Three once recognized genera (Batrachemys, Mesoclemmys and Phrynops) that were demoted to subgenera, and then synonymized with Phrynops, are demonstrated to warrant full recognition based on morphometric analysis, skull osteology, and mitochondrial and nuclear gene sequencing. Mesoclemmys is resurrected from the synonymy of Phrynops as a monotypic genus including M. gibba. The genus Rhinemys, previously a synonym of Phrynops, is resurrected for the species R. rufipes. Ranacephala gen. nov. is described to include the species R. hogei. The genus Batrachemys is resurrected from the synonymy of Phrynops and includes B. dahli, B. nasuta, B. raniceps, B. tuberculata, and B. zuliae. The taxon vanderhaegei is placed in Bufocephala gen. nov. The genus Phrynops is redefined to include the taxa P. geoffroanus, P. hilarii, P. tuberosus, and P. williamsi. Cladistic analysis of morphological data supports this taxonomy. A new species of Batrachemys is described from the western Amazon region, and is distinguished by having facial markings in juveniles, a relatively wide head, and a flattened shell. The new species, B. heliostemma sp. nov., is sympatric with and most similar to the recently resurrected form Batrachemys raniceps in the upper Amazonian region of Peru and adjacent Brazil, Ecuador, Venezuela, and Colombia. Lastly, morphometric data from living and museum specimens of all species of Batrachemys are presented.