Figure 1.
Alternative hypotheses in the vertebrate phylogeny.
Uncertainties in the vertebrate phylogeny examined in this study. (A) The five alternative hypotheses for the placement of turtles within amniotes 1) turtles as basal amniotes, 2) turtles as basal sauropsids, 3) turtle-lepidosaur sister group, 4) turtle-archosaur sister group, and 5) turtle-crocodilian sister group. (B) monophyletic and (C) paraphyletic alternative hypotheses for lissamphibian (extant amphibians) relationships.
Figure 2.
Phylogenetic results from individual gene analyses.
(A) The phylogenetic position of turtles within amniotes when all major groups were present and (B) when no crocodilians were present. (C) The relationships between major lissamphibian groups. The “other” category includes topologies that do not match any of the previously proposed hypotheses, usually with a major amniote group being paraphyletic.
Table 1.
Summary of phylogenetic results from different datasets.
Figure 3.
Flow diagram of data filtering method.
Steps of the new statistical methodology to identify and filter out sites that contain putative non-phylogenetic signal (i.e. biased sites). Analyses pertaining to the phylogenetic position of turtles are used in this example.
Figure 4.
Consensus vertebrate phylogeny.
Consensus phylogeny from datasets with the 10% most putatively biased sites removed. (A) Turtles are either the sister group to Crocodilians or Archosauria. (B) Lissamphibia: salamanders (Caudata) and caecilians (Gymnophiona) are sister groups, and this group is either the sister group to frogs (Procera hypothesis) or Amniota (rendering Lissamphibia paraphyletic). RAxML bootstrap values are at nodes, with “*” representing support ≥95.
Table 2.
Phylogenetic results from filtered datasets.