Phylogenetic relationships between major clades of turtles are indicated in Fig. 1. The complete phylogeny with all species is presented in Fig. 2. The distribution of confidence values (cv) at nodes is highly skewed in favour of high confidence values (Fig. 3).
Fig. 1. Phylogenetic relationships between turtle major clades. Confidence values are indicated over each branch. Branches supports are in bold when exceeding 0.9.
Our phylogeny shows a clear separation between monophyletic Pleurodira (cv = 1) and Cryptodira (cv = 0.986). In Pleurodira (Fig. 2a), Chelidae forms a clade (cv = 1), which is the sister-group to the Pelomedusoidea, grouping all Pleurodira except Chelidae (cv = 1). The species included in Pelomedusoidea are separated into two monophyletic groups, corresponding to the Podocnemididae (cv = 1) and Pelomedusidae (cv = 1). We observe a clear separation of Chelidae into three clades, corresponding to Chelidinae (cv = 1), Chelodininae (cv = 0.998) and Hydromedusinae, although Hydromedusinae is represented in our study by only one species (Table S2). Chelodininae is the sister-group to all other Chelidae, and Hydromedusa tectifera, the only species of Hydromedusinae in our phylogeny, is sister to Chelidinae. Four pleurodiran genera are found to be polyphyletic (Mesoclemmys, Elseya, Emydura) or paraphyletic (Pelusios). Mesoclemmys hogei is grouped with Phrynops (cv = 0.835), rather than with M. nasutus and M. gibba. Elseya dentata is grouped with Rheodytes leukops (cv = 1) and Elseya purvisi is grouped with Elusor macrurus (cv = 0.929) rather than with the other sampled species of Elseya. Emydura macquarii is grouped with Elseya georgesi and Elseya latisternum (cv = 0.934) rather than with Emydura subglobosa. Pelusios sinuatus is grouped Pelomedusa subrufa (cv = 0.641) rather than with the other sampled species of Pelusios.
Cryptodira is classically organized into five clades (Chelonioidea, Kinosternoidea, Testudinoidea, Trionychia and Chelydroidea, the latter taxon comprising Chelydridae and Platysternidae). Here, Trionychia (cv = 1) is sister to the group formed by all other Cryptodira (cv = 1). The only species from Carettochelyidae, Carettochelys insculpta, is separated from a group including all other Trionychia (cv = 1). The monophyly of Trionychinae (cv = 0.998) and Cyclanorbinae (cv = 1) is also well supported (Table S2, Fig. 2b). All species from the same genus are grouped together.
Trionychia is recovered as the sister group to all remaining clades of cryptodiran turtles which form a tetrapolytomy (Fig. 2b) including: (i) Chelonioidea (cv = 0.999), (ii) Chelydridae (cv = 1), (iii) Kinosternoidea (cv = 1), and (iv) a group formed by Geoemydidae, Testudinidae, Emydidae and Platysternon megacephalum (cv = 1).
In Chelonioidea, there is a clear separation between Cheloniidae (cv = 1) and Dermochelyidae (Table S2, Fig. 2b), as between the two families included in Kinosternoidea, the monotypic Dermatemydidae (Dermatemys mawii) and Kinosternidae (cv = 1). However, Kinosternon appears paraphyletic, as Kinosternon baurii is closer to Sternotherus odoratus (cv = 0.923) than to K. flavescens. The fourth clade is composed of a group formed by Testudinidae and Geoemydidae (cv = 1), and a group formed by Emydidae and Platysternon megacephalum (cv = 0.980). According to the usual taxonomy, Testudinidae, Geoemydidae and Emydidae together form the clade Testudinoidea. This clade is then paraphyletic in our phylogeny due to the inclusion of Platysternon megacephalon as the sister-group to Emydidae (Fig. 2b).
Within the monophyletic Emydidae (cv = 1), Emydinae and Deirochelyinae are both monophyletic (cv = 0.983 and cv = 0.999, respectively; Table S2, Fig. 2b). All species from the same genus are grouped together except for Emys: Emys orbicularis and Emys trinacris are closer to Emydoidea blandingii (cv = 0.863) than to Emys marmorata.
Within the monophyletic Testudinidae (cv = 1), Gopherinae (cv = 0.562) and Testudininae (cv = 1) are monophyletic (Table S2, Fig. 2c). All species from the same genus are grouped together, except for Homopus. Homopus areolatus and Homopus femoralis are close to Psammobates (cv = 0.779), whereas Homopus boulengeri and Homopus signatus are grouped with Chersina angulata (cv = 0.998).
Within the monophyletic Geoemydidae (cv = 0.946), Batagurinae is monophyletic (cv = 0.985) and nested within Geoemydinae, which is thus paraphyletic (Table S2, Fig. 2d). All species from the same genus are grouped together except for Batagur and Kachuga. Batagur affinis and Batagur baska are recovered in a polytomy including Kachuga kachuga (cv = 0.998), whereas Kachuga trivittata is grouped with Callagur borneoensis (cv = 0.987) and Kachuga sylhetensis is grouped with Pangshura (cv = 0.999).