Only one MPT of 5483 steps (Fig. 2A) was obtained analyzing the concatenated data matrix of molecular data including five genes (12S RNA, 16S RNA, cytochrome b, RAG-1, and intron of the fingerprint protein R35). The molecular partition retrieved as monophyletic the major groups of crown turtles: Chelidae and Pelomedusoides for Pleurodira and Trionychia, Kinosternoidea, Testudinidae + Geoemydidae, Chelydridae, Chelonioidea, and Emydidae for Cryptodira. Almost all of these clades are well supported by Jackknife values (>80 %); however, no Jackknife values were recovered for the internal branches, except for the branch dividing Pleurodira and Cryptodira. The analysis depicts Kinosternoidea and Trionychia as the successive adjacent groups of Pleurodira showing that the molecular signal is responsible for the close affinities of Pleurodira and Trionychia in the total evidence analysis (see below).
The separate analyses of each of the analyzed genes are summarized in Fig. 2B-F. Given that the most striking differences in the results of the present analyses are the affinities of Pleurodira, one of the two major groups of living turtles, I will focus on the adjacent groups of Pleurodira. The phylogenetic analyses of the sequences of cytochrome b (one MPT of 2061 steps; Fig. 2B), 12S RNA (two MPTs of 644 steps; strict consensus in Fig. 2C), and RAG-1 (one MPT of 927 steps; Fig. 2D) show that the adjacent group of Pleurodira is Trionychia, followed by the group Kinosternoidea. The results of these three genes generally resemble the topology obtained with that of the concatenated data matrix of all the molecules (Fig. 2A), except for the position of Emydidae that is closer to Kinosternoidea and/or Trionychia (Fig. 2B-D) than in the analysis of the five genes.
On the other hand, the topologies obtained in the analyses of the sequences of 16S RNA and the intron fingerprint protein R35 are slightly different. The result of the sequence 16S RNA (one MPT of 838 steps) shows Kinosternoidea as the adjacent group of Pleurodira, however, the Jackknife values are very low (Fig. 2E). The later result could be affected by the scarce sequence information on trionychians and kinosternoids that are represented in this analysis by only one species each. The result obtained for analysis of the intron of the fingerprint protein 35 (two MPTs of 972 steps) shows that the interrelationships among Cryptodira are not resolved and therefore there is no clear signal to test which of the cryptodiran groups is closer to Pleurodira (Fig. 2F)