Molecular phylogeny of African hinge-back tortoises (Kinixys): implications for phylogeography and taxonomy (Testudines: Testudinidae)

Abstract

We examine the phylogeography, phylogeny and taxonomy of hinge‐back tortoises using a comprehensive sampling of all currently recognized Kinixys species and subspecies and sequence data of three mitochondrial DNA fragments (2273 bp: 12S rRNA, ND4 + adjacent DNA coding for tRNAs, cytb) and three nuclear loci (2569 bp: C‐mos, ODC, R35). Combined and individual analyses of the two data sets using Bayesian and Maximum Likelihood methods suggest that the savannah species of Kinixys are paraphyletic with respect to the rainforest species K. homeana and K. erosa, and that the rainforest species may be derived from a savannah‐living ancestor. The previously recognized savannah species K. belliana was a conglomerate of three deeply divergent clades that we treat here as distinct species. We restrict the name K. belliana (Gray, 1830) to hinge‐back tortoises ranging from Angola to Burundi, while five‐clawed hinge‐back tortoises from the northernmost part of the formerly recognized range of K. belliana, together with four‐clawed tortoises from West Africa, are assigned to the species K. nogueyi (Lataste, 1886). These two species are allied to K. spekii, whereas Southeast African and Malagasy hinge‐back tortoises formerly lumped together with K. belliana represent the distinct species K. zombensis Hewitt, 1931, which is sister to K. lobatsiana. The latter two species together constitute the sister group of the rainforest species K. homeana and K. erosa. Mitochondrial data suggest that K. natalensis has a basal phylogenetic position in a clade embracing K. belliana sensu stricto, K. nogueyi and K. spekii, while nuclear data and the two data sets combined favour a sister group relationship of K. natalensis to all other hinge‐back tortoises. Phylogeographic structure is present in all wide‐ranging species and correlates in K. homeana and K. erosa with the Dahomey Gap and former rainforest refugia. The Malagasy population of K. zombensis is weakly differentiated from its South African conspecifics and further sampling is needed to determine whether there is support for the subspecific distinctness of Malagasy tortoises.

Complex phylogeography in Rhinoclemmys melanosterna: conflicting mitochondrial and nuclear evidence suggests past hybridization (Testudines: Geoemydidae)

“…In several species of turtles and tortoises, insertions of mtDNA in the nuclear genome (numts) are known to occur, specifically numts derived from the cyt b gene (Fritz et al , 2012cWiens et al 2010;Kindler et al 2012). However, base frequencies of our sequences as well as their ratios of synonymous and non-synonymous substitutions corresponded to the expectations for mtDNA.…”

“…Several recent studies have used uncorrected p distances of the mitochondrial cyt b gene as a tool for species delimitation in chelonians (Vargas-Ramírez et al 2010;Praschag et al 2011;Fritz et al 2012b, c;Kindler et al 2012;Liebing et al 2012), similar to the barcoding approach (e.g., Hebert et al 2003). When this method is applied to Rhinoclemmys, we see that R. melanosterna, R. diademata, R. funerea and R. punctularia differ by sequence divergences of 0.51% to 3.20%.…”

<strong>A revision of African helmeted terrapins (Testudines: Pelomedusidae: <em>Pelomedusa</em>), with descriptions of six new species</strong>

“…Vargas-Ramírez et al 2010Praschag et al 2011;Fritz et al 2012a, b;Kindler et al 2012;Iverson et al 2013;Todd et al 2014). Important insights of these studies were that there is a wide range of divergence values among congeneric species, and that there is no general threshold of sequence divergence that 'axiomatically' indicates distinct species (see also Shen et al 2013).…”

“…Vargas-Ramírez et al 2010Praschag et al 2011;Fritz et al 2012a, b;Kindler et al 2012). In the present study, divergences among Pelomedusa lineages are compared to those of the 17 species of African hinged terrapins (Pelusios), which represent the genus most closely related to Pelomedusa.…”

<span style="font-size: small;"><span style="font-family: 'Times New Roman'; font-size: small;">Order Testudines: 2013 update. In: Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013)</span></span>

“…7. Species count includes now Kinixys nogueyi and K. zombensis, formerly subspecies of K. belliana (Kindler et al 2012). The synonymy of Chelonoidis chilensis, C. donosobarrosi and C. petersi was confirmed (Fritz et al 2012b).…”