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

Wei T, Sun Y, Zhang B, Wang R, Xu T - PLoS ONE (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China.

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.

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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).
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pone-0103011-g001: 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).

Mentions: There has been some dispute in the literature as to genus Hapalogenys and whether it should be treated as separate families [4]–[6]. At the morphological level, the research of Hapalogenys is poorly understood, and its accurate taxomomic status remains ambiguity. Meanwhile, some evaluations of the classification and phylogeny of Hapalogenys have investigated the evolution of the complex genus. Different molecular markers, such as nuclear TMO-4c4 gene or mitochondrial genes (12s, 16s rRNA, COI and Cytb) have been used for evaluating phylogenetic relationships within the Hapalogenys. Some molecular examples of solving relationships of Hapalogenys include studies by Zhu et al. (2006), Ren et al. (2007), Ren and Zhang (2007), Liang et al. (2010), Xu et al. (2010), and Tavera et al. (2012) (Fig. 1) [6]–[11]. Each of these studies has provided valuable information for phylogenetic relationships of Hapalogenys fish. Zhu et al. (2006) proposed Hapalogenys belong to Haemulidae family, and it had a close genetic relationship with Plectorhynchus. However, later, Ren et al (2007) and Ren and Zhang’s (2007) results suggested the genus Hapalogenys was removed from the family Haemulidae according to their molecular findings. In 2010, Xu et al. advised that Hapalogenys had surpassed the genetic differentiation level with other Haemulidae species. However, it was still belong to Percoidea for the genetic distance and phylogenetic analysis. Liang et al. (2012) and Tavera et al. (2012) suggested Hapalogenys could potentially be removed from the Haemulidae family. The proposed hypotheses based on the short sequences were contradictory and controversial due to different analytical methods and datasets. The phylogeny of the Hapalogenys has never been studied by using a longer mitogenomic dataset and a robust phylogenetic tree with appropriate representation species. Recently, it has been demonstrated that the complete mitochondrial genomes can offer sufficient resolution for constructing a robust phylogeney and estimating divergence time events compared with single gene sequences or segments [12], [13]. Therefore, to make a further toward the comprehension for Hapalogenys phylogeny, it was appropriate to address these questions from a longer mitogenomic perspective.


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

Wei T, Sun Y, Zhang B, Wang R, Xu T - PLoS ONE (2014)

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).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4117523&req=5

pone-0103011-g001: 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).
Mentions: There has been some dispute in the literature as to genus Hapalogenys and whether it should be treated as separate families [4]–[6]. At the morphological level, the research of Hapalogenys is poorly understood, and its accurate taxomomic status remains ambiguity. Meanwhile, some evaluations of the classification and phylogeny of Hapalogenys have investigated the evolution of the complex genus. Different molecular markers, such as nuclear TMO-4c4 gene or mitochondrial genes (12s, 16s rRNA, COI and Cytb) have been used for evaluating phylogenetic relationships within the Hapalogenys. Some molecular examples of solving relationships of Hapalogenys include studies by Zhu et al. (2006), Ren et al. (2007), Ren and Zhang (2007), Liang et al. (2010), Xu et al. (2010), and Tavera et al. (2012) (Fig. 1) [6]–[11]. Each of these studies has provided valuable information for phylogenetic relationships of Hapalogenys fish. Zhu et al. (2006) proposed Hapalogenys belong to Haemulidae family, and it had a close genetic relationship with Plectorhynchus. However, later, Ren et al (2007) and Ren and Zhang’s (2007) results suggested the genus Hapalogenys was removed from the family Haemulidae according to their molecular findings. In 2010, Xu et al. advised that Hapalogenys had surpassed the genetic differentiation level with other Haemulidae species. However, it was still belong to Percoidea for the genetic distance and phylogenetic analysis. Liang et al. (2012) and Tavera et al. (2012) suggested Hapalogenys could potentially be removed from the Haemulidae family. The proposed hypotheses based on the short sequences were contradictory and controversial due to different analytical methods and datasets. The phylogeny of the Hapalogenys has never been studied by using a longer mitogenomic dataset and a robust phylogenetic tree with appropriate representation species. Recently, it has been demonstrated that the complete mitochondrial genomes can offer sufficient resolution for constructing a robust phylogeney and estimating divergence time events compared with single gene sequences or segments [12], [13]. Therefore, to make a further toward the comprehension for Hapalogenys phylogeny, it was appropriate to address these questions from a longer mitogenomic perspective.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, China.

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.

Show MeSH