Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Abstract

ABSTRACT. Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.

Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

“…Hungarian red deer joined to the semi-domesticated red deer of New Zealand with a bootstrap value of 100%, and clustered to tarim red deer (C. e. yarkandensis) forming a western clade of red deer. Other Cervus elaphus subspecies, which were Asian ecotypes, formed a second, eastern clade; which is consistent with previous reports [2,7,12,15,20,37].…”

“…All supra-generic taxa described in previous studies [7,[34][35]37] are highly supported, i.e. the subfamily Cervinae with two tribes Cervini and Muntiacini, and the subfamily Capreolinae with three tribes Alceini, Odocoileini and Capreolini.…”

“…The high-throughput approach for sequencing was useful for obtaining the whole mitochondrial genome of red deer, so this method could be used broadly among animal taxa. Based on our phylogenetic results using whole mitochondrial genomes, family Cervidae is divided into two subfamilies, Cervinae and Capreolinae, which are also called subfamilies Plesiometacarpalia and Telemetacarpalia [5,7,22,34,37]. The two subfamilies contain five tribes, and four of these, Cervini, Muntiacini, Odocoileinae, and Capreolini, are well determined by the phylogenetic trees of family Cervidae.…”

“…The phylogenetic tree showed not only the phylogeny of the whole family but also the monophyly of tribes, such as Muntiacini. The phylogenetic tree suggested classification information within species, for example, the division of Cervus elaphus into two clades: a western clade with C. e. hippelaphus and C. e. yarkandensis, and an eastern clade with C. e. xanthopygus, C. e. alxaicus and C. e. songaricus, which were Asian ecotypes [2,7,15,20,37].…”

“…3. Following previous research [5,7,37], we selected three time constraints for fossil calibration: the first was the oldest fossil of Cervidae (20 ± 2 mya), the second one was Table 1 Species and accession numbers of mitochondrial genome sequences used in this study Species Accession number…”