Comparison of complete mitochondrial DNA control regions among five Asian freshwater turtle species and their phylogenetic relationships

Abstract

ABSTRACT. The complete mitochondrial DNA (mtDNA) control regions (CR), cytochrome b (Cyt b), NADH dehydrogenase subunit 4 (ND4) and cytochrome coxidase subunit I (CO I) genes of four Asian freshwater turtles, Mauremys japonica, Ocadia sinensis, M. mutica, and Annamemys annamensis, were sequenced using universal PCR and long-PCR techniques. Combined with CR sequences of Chinemys reevesii, the composition and structure of CR of the five species were compared and analyzed. Three functional domains (TAS, CD and CSB) in CR and their conserved sequences (TAS, CSB-F, CSB-1, CSB-2, and CSB-3) were identified based on sequence similarity to those of other turtles. At the 3' end of CSB, six type motifs of variable number of tandem repeats (VNTRs) of five species were recognized, in which the TTATATTA motif may be the VNTR motif of the ancestral species of these five turtles. Comparison of nucleotide divergences among Cyt b, ND4, CO I, and CR of 11 turtle species using transitions + transversions and transversions-only methods supported the conclusion that CR evolved 2.6-to 5.7-fold faster than the other mtDNA genes. After excluding VNTRs of CR, molecular phylogenetic trees were constructed with maximum parsimony, maximum likelihood and Bayesian inference methods. The results supported an expanded clade of Mauremys, which included species formerly in Ocadia, Chinemys, Mauremys, and Annamemys; this was also reflected in the results of VNTR analysis.

Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

“…Apart from the general advantages of mitochondrial markers in animal phylogenetic studies, namely their maternal inheritance, lack of recombination, and fast rate of evolution [ 9 , 10 ], several unique qualities make the CR a favoured marker sequence for genetic diversity analyses, in particular, its exceptionally fast evolutionary rate (even in comparison to the rest of the mitochondrial genome [ 11 , 12 ]), polymorphic nature [ 13 ] and presumed selective neutrality as a non-coding region (but see [ 14 , 15 ]). Consequently, this region has been widely used as a genetic marker in phylogenetic studies of various animals including vertebrate classes such as fish (e.g., [ 16 , 17 ]), amphibians [ 18 ], reptiles [ 19 ], birds [ 20 ] and mammals [ 21 , 22 ] as well as numerous invertebrate taxa (e.g., [ 23 – 26 ]. Nevertheless, despite being extremely useful for some species, several factors may hinder the utility of this marker in others.…”

Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka

“…D-loop sequences (∼1000 bp) analyzed in MEGA v6.06 [21] for intraspecific variations revealed 189 variable sites, 51 parsimony informative sites and only 89 conserved sites. Though D-loop is the most variable, fast evolving part of mitochondrial genome [32] , they too possess functional conserved domains preceding VNTR region like TAS, CD (CSB-F) and CSBs (1, 2 and 3) as found in mammals [33] , freshwater turtles of order- Geoemydidae [32] and Trionychidae [34] . These functional sites have been identified in the current data and their intraspecific variations are depicted in Table 3 .…”

A new species of the genus <i>Ocadia</i> (Testudines: Geoemydidae) from the middle Miocene of Tanegashima Island, southwestern Japan and its paleogeographic implications

“…Recent molecular phylogenetic analyses have shown that the genus Ocadia is included in a clade with Chinemys spp. and Mauremys japonica and that these taxa form another more inclusive clade with the remaining living species of Mauremys (Mauremys sensu lato, Honda et al 2002;Barth et al 2004;Feldman and Parham 2004;Spinks et al 2004;Sasaki et al 2006;Jiang et al 2011). However, no synapomorphic morphological character states are known for the two clades (e.g., Honda et al 2002;Hirayama et al 2007).…”

“…In recent molecular phylogenetic studies, this genus has been frequently synonymized with Mauremys along with Chinemys (e.g., Fritz and Havaš 2007;Turtle Taxonomy Working Group 2007;Lovich et al 2011) because O. sinensis, M. japonica and Chinemys spp. form a monophyletic clade and are included in a major, more inclusive clade with the other species of the genus Mauremys sensu stricto (Honda et al 2002;Barth et al 2004;Feldman and Parham 2004;Spinks et al 2004;Sasaki et al 2006;Jiang et al 2011). However, to date, no diagnostic morphological features or synapomorphies are known for the clade embracing O. sinensis, M. japonica, and Chinemys spp.…”