Abstract
In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.
Highlights
MethodsEthics Statement This research was conducted under and approved by UCBerkeley’s Animal Care and Use Committee (protocol #R2790211)
As our method focuses on specific phylogenetic questions, we performed filtering of biased sites twice, once for the turtle question and once for the Lissamphibia question, producing two different sets of alignments
In an effort to remove non-phylogenetic signal in a more targeted way, we develop a new Discriminant Function Analysis (DFA)-based filtering method that attempts to identify sites contributing biased signal based on several data set characteristics known to cause inference problems in certain contexts
Summary
Ethics Statement This research was conducted under and approved by UCBerkeley’s Animal Care and Use Committee (protocol #R2790211). Tissue samples used in this study were obtained from the Museum of Vertebrate Zoology (MVZ), an institution that serves as a specimen and tissue repository for researchers. The MVZ has a strict policy for researchers when depositing specimens and tissues into the museum, requiring local collecting permits and import permits when necessary. Taxon Sampling Our study included sampling for all major vertebrate groups except Tuatara (Sphenodon). Of the 129 taxa included in this study, data were available for 46 taxa from complete genomes or ESTs (GenBank and Ensembl [58]), and the remaining 82 samples were newly sequenced. Available data were skewed heavily towards mammals (36 taxa), and include fish (5 taxa), frog (1 taxon), salamander (1 taxon), lizard (1 taxon), bird (2 taxa), and crocodile (1 taxon).
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