A New Turtle Phylogeny


Carettochelys insculpta. JCM Natural History
Turtles (Testudines) form a clade with a distinctive body plan unlike any other living tetrapods. The taxonomy and phylogeny of some turtle clades are stil controversial. Previous studies included only a few species or genera Guillon et al. (2012) used an extensive compilation of DNA sequences from nuclear and mitochondrial genes for more than two thirds of the total number of turtle species to infer a larger more robust phylogeny than had been previously produced.

The resulting phylogeny shows a clear separation between monophyletic Pleurodira and Cryptodira. Within the Pleurodira, Chelidae forms a clade which is the sister-group to the Pelomedusoidea, grouping all Pleurodira except Chelidae. The species included in Pelomedusoidea are separated into two monophyletic groups, corresponding to the Podocnemididae  and Pelomedusidae. They observe a clear separation of Chelidae into three clades, corresponding to Chelidinae, Chelodininae and Hydromedusinae, although Hydromedusinae. 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 were found to be polyphyletic (Mesoclemmys, Elseya, Emydura) or paraphyletic (Pelusios).  Mesoclemmys hogei is grouped with Phrynops, rather than with M. nasutus and M. gibba. Elseya dentata is grouped with Rheodytes leukops and Elseya purvisi is grouped with Elusor macrurus  rather the other sampled species of  Elseya.  Emydura macquarii is grouped with Elseya georgesi and Elseya latisternum rather than with  Emydura subglobosa. Pelusios sinuatus is grouped Pelomedusa subrufa 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 is the sister to the group formed by all other Cryptodira. The only species from Carettochelyidae, Carettochelys insculpta, is separated from a group including all other Trionychia. The monophyly of Trionychinae and Cyclanorbinae is also well supported. 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 including: Chelonioidea, Chelydridae,  Kinosternoidea, and a group formed by Geoemydidae, Testudinidae, Emydidae and Platysternon megacephalum. Within the Chelonioidea, there is a clear separation between Cheloniidae and Dermochelyidae, as between the two families included in Kinosternoidea, the monotypic Dermatemydidae (Dermatemys mawii) and Kinosternidae. However, Kinosternon appears paraphyletic, as Kinosternon baurii is closer to Sternotherus odoratus than to K. flavescens. The fourth clade is composed of a group formed by Testudinidae and  Geoemydidae, and a group formed by Emydidae and Platysternon megacephalum. According to the usual taxonomy, Testudinidae, Geoemydidae and Emydidae together form the clade Testudinoidea. This clade is then paraphyletic in this phylogeny due to the inclusion of  Platysternon megacephalon as the sister-group to Emydidae. Within the monophyletic Emydidae, Emydinae and Deirochelyinae are both monophyletic. All species from the same genus are grouped together except for Emys: Emys orbicularis and Emys trinacris are closer to Emydoidea blandingii  than to Emys marmorata. Within the monophyletic Testudinidae, Gopherinae  and Testudininae are monophyletic. All species from the  same genus are grouped together, except for Homopus. Homopus areolatus and Homopus femoralis are close to Psammobates, whereas Homopus boulengeri and  Homopus signatus are grouped with Chersina angulata. Within the monophyletic Geoemydidae, Batagurinae is monophyletic  and nested within Geoemydinae, which is thus paraphyletic. 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, whereas Kachuga trivittata is grouped with Callagur borneoensis and Kachuga sylhetensis is grouped with Pangshura.

The phylogenetic position of Platysternon megacephalum has long been enigmatic. The first analyses based on morphological characters,  led authors to relate P. megacephalum with Chelydridae (Chelydra serpentina and Macrochelys temminckii). However, some molecular studies found that P. megacephalum was grouped with Testudinoidea (using small nucleolar RNA; , based on 12S, cytB and RAG1). In the phylogeny that Parham et al. (2006) obtained with complete mitochondrial genomes,  P. megacephalum  was included in Testudinoidea as the sister-species to Emydidae. This study finds good support for the same hypothesis.

The entire paper can be found online.

Citation
Jean-Michel Guillon, Loreleï Guéry, Vincent Hulin, Marc Girondot . 2012. A large phylogeny of turtles (Testudines) using molecular data. Contributions to Zoology 81:147-158.