A mitogenomic perspective on the phylogenetic position of the Hapalogenys genus (Acanthopterygii: Perciformes) and the evolutionary origin of Perciformes

Abstract

The Hapalogenys genus was the most controversial and problematic in phylogenetic position of Percoidei. In this study, we rechecked the taxonomic status of Hapalogenys in Percoidei using complete mitochondrial genome data. We purposefully added a new complete mitochondrial sequence from chosen species of Hapalogenys and conducted phylogenetic analyses using a large complete mitochondrial data set. The resultant tree topologies were congruent from partitioned Bayesian and Maximum-likelihood methods. The results indicated that Hapalogenys was distantly related to Haemulidae and could be removed from Haemulidae. The results supported the Hapalogeny was upgraded to a family rank titled Hapalogenyidae, and it should be recognized in a separate family of Hapalogenyidae. A relaxed molecular-clock Bayesian analysis indicated that the divergence times of Perciformes groups had a much older than the available old fossil records. The origin of the common ancestral lineage of Perciformes fish was estimated in the late Jurassic about 149 Myr ago.

Figure 1. Alternative phylogenetic hypotheses between Hapalogenys and Percoidei family.

(A) Parsimony and Neighbor-Joining tree for partial mtDNA cytb gene (Zhu et al., 2006), (B) Minimum-Evolution tree for mtDNA 16s RNA gene (Ren et al., 2007), (C) Neighbor-Joining tree for mtDNA 16s RNA gene (Ren and Zhang, 2007), (D) Neighbor-Joining tree for mtDNA cytb gene (Xu et al., 2010), (E) Bayesian, Maximux-likehood, and Parsimony tree for mtDNA 16s RNA gene (Liang et al., 2012), (F) Bayesian, Maximux-likehood, and Parsimony tree for nuclear TMO-4c4 gene (Liang et al., 2012), (G) Bayesian, Maximux-likehood, and Parsimony tree for mtDNA 16s RNA and nuclear TMO-4c4 gene (Liang et al., 2012), (H) Bayesian and Maximux-likehood tree for mtDNA 16s, COI, and Cytb gene (Tavera et al., 2012).

Figure 2. The majority rule consensus tree of Hapalogenys and related taxa are obtained from partitioned BI, ML analysis of mitochondrial genome dataset.

Numbers near internal branches indicate the ML bootstrap support values (left) and Bayesian posterior probabilities (right), respectively. Support values less than 50% for the node are indicated by a dash.

Figure 3. Posterior distributions of divergence times of Perciformes fishes and related species.

Divergence times were estimated from the partitioned Bayesian analysis using PAML program package. The horizontal bars represent the estimated 95% credibility intervals of the divergence time estimation.