No abstract

No abstract

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.

No abstract

Aspects of the phylogeny of pleurodiran turtles are contentious, particularly within the Chelidae. Morphological analyses group the long-necked Australasian Chelodina and the longnecked South American Chelus and Hydromedusa into a single clade, suggesting a common derived origin of the long neck and associated habits that predated the separation of Australia from South America. In contrast, published analyses of IZSrRNA and cytochrome b sequences suggest that the long-necked Chelodina are more closely related to the short-necked Australasian genera than to either Chelus or Hydromedusa. This paper adds partial sequences of 16s rRNA and CO1 mitochondria1 genes and partial sequences of the nuclear oncogene c-mos to test a range of previous hypotheses on the phylogenetic relationships among chelid turtles. In total, 1382 nucleotides were available for each of 25 taxa after elimination of ambiguously aligned regions. These taxa included representatives of all the genera of the turtle families Chelidae and Pelomedusidae, the three sub-genera of Phrynops, and recognized sub-generic groups of Elseya and Chelodina. Of the four genes examined, 12s ?-MA was the most informative, followed by c-mos with 16s rRNA and COI the least informative. The molecular data support the currently accepted arrangement for pelomedusid genera, that is, a sister relationship between the African Pelusios and Pelomedusa and a clade comprising the South American Peltoceflhalus and Podocnemis with the Madagascan Eryrnnochelys. However, there is also support for Elymnochebs and Podocnemis as sister taxa to the exclusion of Peltocephalus (bootstrap values of 69-80%) which is at odds with the most commonly accepted arrangement. The South American chelids are monophyletic (76-82%). This clade includes the long-necked Chelus and Hydromedusa, but excludes the Australasian long-necked Chelodina. Furthermore, the South American long-necked chelids are not themselves monophyletic, with 98-100% bootstrap values for the node supporting Chelus and the remaining South American chelids to the exclusion of Hydromedusa. Hence, the hypothesis of a monophyletic grouping of the longnecked genera of South America and Australasia is not supported by the molecular data. Although reciprocal monophyly of the South American and Australasian chelid faunas was the most likely and the most parsimonious arrangement in all but one analysis, bootstrap support for the monophyly of the Australasian chelids was low (52-66%). The South American chelids, Chelodina and the short-necked Australasian chelids form an unresolved trichotomy. The genera Phrynops and Elsga are paraphyletic, leading to a recommendation