In concordance with the results of saturation analyses, the complete nucleotide dataset did not distinguish statistically between the competing alternatives of turtles plus archosaurs and turtles plus crocodilians.
However, the alternative topologies proposing turtles as the sister group to other reptiles (including birds), and grouping turtles with squamates (lizards and snakes) received no support from our data.
Conversely, ML and Bayesian phylogenetic reconstructions from the complete nucleotide dataset using a single site-homogeneous GTR + G model for the whole concatenation (BPML = 76; PPBAY = 1.0), and a mixed model partitioned by gene (BPPARTG = 54) tended to support an alternative topology grouping turtles with crocodilians (Table 1).
An alternative hypothesis to the softshell turtles' loss of scutes was put forward by Toni et al. (2007).
Therefore, besides traditional morphological inferences and sequence-based molecular phylogenetic analyses, a third form of data is needed to explore and test the alternative phylogenetic hypotheses of the turtle's placement.
There are 24 topologies on which Parsimov was implemented, resulting from eight alternative hypotheses for the position of turtles within Tetrapoda, each combined with the three alternative topologies of the cryptodire subgroups.
The approximately unbiased (AU) likelihood-based test showed that all proposed alternative hypotheses to the sister group relationship of turtles with archosaurs were rejected based on the amino-acid dataset, irrespective of the model used.
Furthermore, our statistical analyses reject any alternative hypotheses to the sister group relationship of turtles to Archosauria (Table 2), thus advancing the resolution of this long-standing controversial issue of vertebrate evolutionary history.
By making the shorter tow times the required alternative, the EPA intended to minimize any sea turtle casualties as a result of trawlers being allowed to remove the TEDs.
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