Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

Abstract

Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci.

Terrestrial feeding in aquatic turtles: environment-dependent feeding behavior modulation and the evolution of terrestrial feeding in Emydidae

“…In this study, phylogenetic signal was tested for in all primary kinematic variables and significant kinematic PCs for both terrestrial and aquatic bites (note that the PC scores do not represent the results of a phylogenetically informed PCA) (Revell, 2009). A phylogeny of emydid turtles [ fig.3 in Wiens et al (Wiens et al, 2009)] was used to describe the relationships among this study's six focal taxa, and species' mean scores (see above for calculation) were used as input. Scores for aquatic and terrestrial bites were treated as separate variables in these analyses; given that 10 primary kinematic variables and four PC variables were used, a total of 28 analyses were conducted.…”

“…a total of 28 variables). Again, the phylogeny of Wiens et al (Wiens et al, 2009) was used; means and variances at the tips were calculated from the original species mean data. Simulations were conducted as follows.…”

To name or not to name: Criteria to promote economy of change in Linnaean classification schemes

“…Fritz et al (2011) used a similar rationale to advocate the use of three distinct turtle genera, Emys, Actinemys, and Emydoidea. The concerned species had previously been merged in a single, inclusive genus Emys (Spinks & Shaffer 2009), but the monophyly of such an inclusive Emys was contradicted by a subset of possible gene trees (Wiens et al 2010) and the respective clade stability thus compromised.…”

Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

“…To identify potential contaminants, sequences from each gene can be initially analyzed using MP and/or subjected to a BLAST search against the National Center for Biotechnology Information database (http://www.ncbi.nlm.nih.gov). If different species have identical sequences, contamination may have occurred [40].…”