Molecular phylogeny of the softshell turtle genus Nilssonia revisited, with first records of N. formosa for China and wild-living N. nigricans for Bangladesh

Abstract

Based on 2354 bp of mitochondrial DNA (12S rRNA, ND4, cyt b) and 2573 bp of nuclear DNA (C-mos, ODC, R35), we re-examine the phylogenetic relationships of Nilssonia species. Individual and combined analyses of mitochondrial and nuclear DNA using Maximum Likelihood and Bayesian approaches confirm the monophyly of the genus. While mitochondrial data alone could not resolve the phylogenetic position of N. formosa, nuclear data support a sister group relationship of N. formosa and the remaining Nilssonia species. Combined analyses of mitochondrial and nuclear DNA suggest the following branching pattern, with N. formosa as the sister taxon of the remaining species: N. formosa + ((N. gangetica + N. leithii) + (N. hurum + N. nigricans)). Among the samples we studied is the first record of N. formosa for Yunnan, China, and the first record of wild-living N. nigricans for Bangladesh. In N. gangetica, each of the studied major river basins harbours a genetically distinct population, suggesting that at least three distinct management units should be distinguished: (1) Brahmaputra River; (2) Indus and Ganges Rivers plus Ganges Delta; and (3) Mahanadi River.

Phylogeography of the Asian softshell turtle Amyda cartilaginea (BODDAERT, 1770): evidence for a species complex

“…Then, the sequences of the respective samples were placed in clade B in a basal polytomy together with the well-supported clade 2 (trees not shown). In addition, N. formosa constituted in the trees based on mtDNA and nDNA, with high support, the sister taxon of the remaining Nilssonia species (see also lieBinG et al 2012). Otherwise the trees resulting from the merged mtDNA and nDNA sequences were identical to the trees based on mtDNA alone, and support values showed only negligible differences.…”

“…For the present study, 19 fresh blood or tissue samples of Amyda cartilaginea plus 14 tissue samples from historical museum specimens were used (Table S1). For fresh material, three mitochondrial and three nuclear DNA fragments were chosen, which have been successfully used in softshell turtles for phylogenetic and phylogeographic purposes (Weisrock & janzen 2000;enGstroM et al 2002enGstroM et al , 2004PraschaG et al 2007PraschaG et al , 2011McGauGh et al 2008;fritz et al 2010;lieBinG et al 2012;le et al 2014 ), namely, part of the 12S ribosomal RNA gene (12S rRNA or 12S), the complete cytochrome b gene (cyt b) plus adjacent DNA coding for tRNA-Thr, part of the 3' half of the NADH dehydrogenase subunit 4 gene (ND4) plus adjacent DNA coding for tRNAs, part of the gene coding for oocyte maturation factor Mos (Cmos), part of the gene coding for ornithine decarboxylase (ODC), and part of intron 1 of the orphan G protein-coupled receptor gene R35 (R35). For PCR and sequencing of the 12S, ND4, Cmos, ODC and R35 fragments of fresh samples, the same primer pairs were applied as in lieBinG et al (2012).…”

“…While this has allowed a pioneering assessment of the phylogenetic relationships (Meylan 1987), the rarity of material of many taxa hampered a detailed understanding of the species diversity. Thus, it is not surprising that several studies using molecular genetic approaches have gained a much refined understanding of trionychid taxonomy (Weisrock & janzen 2000;enGstroM et al 2002enGstroM et al , 2004PraschaG et al 2007PraschaG et al , 2011McGauGh et al 2008;fritz et al 2010;lieBinG et al 2012;le et al 2014) and resulted in the recognition of six additional species (Chitra chitra, C. vandijki, Lissemys ceylonensis, Pelodiscus axenaria, P. maackii, P. parviformis;enGstroM et al 2002;Mccord & Pritchard 2003;fritz et al 2010;PraschaG et al 2011; and two additional subspecies (Chitra chitra javanensis, Lissemys punctata vittata;enGstroM et al 2002;Mccord & Pritchard 2003;Pra-schaG et al 2011) compared to previous morphologybased assessments (WeBB 1982;Meylan 1987). However, molecular studies have not yet been conducted for the majority of trionychid species, so that the existence of further distinct, but currently unrecognized, taxa is most likely.…”