Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes

Abstract

The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.

Sequencing and characterization of the complete mitochondrial genome of Critically Endangered Black Soft-shell Turtle (Nilssonia nigricans)

“…The Cheloniidae species (sea turtle) cladded separately in the ML tree. This phylogenetic analysis combined with all mitochondrial PCGs, is consistent with the previously described phylogeny using partial sequences of mitochondrial and nuclear gene 1,4,13,14,23 . Additionally, further taxon sampling from different taxonomic ranks and their mitogenomics data would be useful to reconcile the phylogenetic and evolutionary relationship of Testudines.…”

“…The genome synteny analysis of turtle mitogenome also depicted the Archosaurian and Diapsid affinity with the sister group of the Archosaurs (Birds and Crocodilians) 18,19 . Furthermore, the gene arrangements in mitogenomes are useful to describe the unusual genomic features and settle phylogenetic hypotheses 20,21,22,23 . So far, the complete mitogenome motifs of N. nigricans is anonymous to the world.…”

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

“…However, to better understand evolutionary relationships and phylogeny within Testudines, datasets representing more taxa and loci are needed (Le et al, ). Comparative mitogenomic data have demonstrated utility in elucidating the phylogenetic relationships of turtles (Kundu, Kumar, Tyagi, et al, ; Li et al, ). The genus Pangshura was erected from Batagur and elevated as a distinct genus through morphological characteristics (Günther, ; Moll, ).…”

The complete mitochondrial genome of Geochelone sulcata

“…The tRNA gene was localized with tRNAscan-SE1.21 software (http://lowelab.ucsc.edu/tRNAscan-SE). The rRNA gene and control region are determined by comparison with other turtles (Lan et al 2015;Li et al 2017). The complete sequence of G. sulcata was submitted to GenBank for accession number KJ489404.…”