title: Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis.
abstract: Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.
authors.affiliation: Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan. Electronic address: microceb@hotmail.com.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lavoué
authors.affiliation: Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto 606-8502, Japan.
authors.forename: Kouji
authors.initials: K
authors.lastname: Nakayama
authors.affiliation: Centre for Sustainable Tropical Fisheries and Aquaculture, School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia.
authors.forename: Dean R
authors.initials: DR
authors.lastname: Jerry
authors.affiliation: Atmosphere Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Yamanoue
authors.affiliation: Faculty of Agriculture, Kinki University, 3327-204 Naka-machi, Nara 631-8505, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Yagishita
authors.affiliation: Research Center of Sub-tropical Fisheries, Seikai National Fisheries Research Institute, Fisheries Research Agency, Fukai-Ota 148-446, Ishigaki, Okinawa 907-0451, Japan.
authors.forename: Nobuaki
authors.initials: N
authors.lastname: Suzuki
authors.affiliation: Atmosphere Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan.
authors.forename: Mutsumi
authors.initials: M
authors.lastname: Nishida
authors.affiliation: Department of Zoology, Natural History Museum & Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Miya
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics*; D019143:Evolution, Molecular; D050259:Genes, Mitochondrial; D054629:Genome, Mitochondrial; D010471:Perches / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
keywords: Evolution; Fish; Mitogenome; Phylogenomics; Phylogeny; Simultaneous analysis