Multiple Data Sets, High Homoplasy, and the Phylogeny of Softshell Turtles (Testudines: Trionychidae)

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.

The Roles of Taxonomy and Systematics in Bat Conservation

“…However, these tools must be used with caution, as not every new mitochondrial clade warrants recognition as a distinct species-some genes are known to be hypervariable and poor indicators of species limits (Engstrom et al 2004;Lohse 2009;Galtier et al 2009). The phylogenetic signal for hybridizing species may look very similar to incomplete lineage sorting (e.g., both phenomena would result in non-monophyletic trees) and therefore requires more genetic data and stricter quantitative assessments of genetic data to test different evolutionary scenarios (Maddison 1997;Yu et al 2012).…”

Phylogenetic incongruence in the Drosophila melanogaster species group

“…Following Engstrom et al (2004), for each locus, the uncorrected distance (p) between each pair of species was plotted against the maximum likelihood corrected distance (ML). A positive relationship is expected for unsaturated data, while saturated data plateau at higher levels of divergence.…”

Soft-shelled turtles (Trionychidae) from the Cenomanian of Uzbekistan

“…1 based on the presence of seven or fewer neurals . It is important to note that although Meylan's (1987) cladistic analysis recovered a monophyletic Trionychini, subsequent phylogenetic analyses have not (Engstrom et al, 2004;Joyce and Lyson, 2010).…”