Mitogenomic Evolution and Interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The First Evidence Toward Resolution of Higher-Level Relationships of the World’s Largest Freshwater Fish Clade Based on 59 Whole Mitogenome Sequences

Abstract

Fishes of the order Cypriniformes are almost completely restricted to freshwater bodies and number > 3400 species placed in 5 families, each with poorly defined subfamilies and/or tribes. The present study represents the first attempt toward resolution of the higher-level relationships of the world's largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from 53 cypriniforms (including 46 newly determined sequences) plus 6 outgroups. Unambiguously aligned, concatenated mt genome sequences (14,563 bp) were divided into 5 partitions (first, second, and third codon positions of the protein-coding genes, rRNA genes, and tRNA genes), and partitioned Bayesian analyses were conducted, with protein-coding genes being treated in 3 different manners (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]; third codon positions excluded). The resultant phylogenies strongly supported monophyly of the Cypriniformes as well as that of the families Cyprinidae, Catostomidae, and a clade comprising Balitoridae + Cobitidae, with the 2 latter loach families being reciprocally paraphyletic. Although all of the data sets yielded nearly identical tree topologies with regard to the shallower relationships, deeper relationships among the 4 major clades (the above 3 major clades plus Gyrinocheilidae, represented by a single species Gyrinocheilus aymonieri in this study), were incongruent depending on the data sets. Treatment of the rapidly saturated third codon-position transitions appeared to be a source of such incongruities, and we advocate that RY-coding, which takes only transversions into account, effectively removes this likely "noise" from the data set and avoids the apparent lack of signal by retaining all available positions in the data set.

Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

“…More recently, several new morphological and molecular analyses have been published with greatly enhanced character and taxon sampling, as well as more sophisticated analyses, tests, and diverse outgroup representation. Saitoh et al (2006) described six major clades based on whole mitochondrial (mt) genome sequences from 33 species of Cyprinidae and resolved two reciprocally monophyletic groups congruent with the results recognized by Cavender and Coburn (1992) (Fig. 1C).…”

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

“…The close phylogenetic relationship between goldfish and zebrafish (Saitoh et al, 2003, 2006) suggest that the well‐established molecular techniques, as well as mutant, morphant, and gene expression patterns, catalogued in The Zebrafish Model Organism Database (Bradford et al, 2011), can be directly applied to goldfish research (Mabee et al, 2007; Schlling and Webb, 2007; Tsai et al, 2013). Moreover, it was recently confirmed that these two teleost species are similar in terms of embryological development (Tsai et al, 2013).…”

Comparative mapping for bighead carp (Aristichthys nobilis) against model and non-model fishes provides insights into the genomic evolution of cyprinids

“…A second-generation genetic linkage map with 659 microsatellites has recently been constructed for bighead carp (Zhu et al 2014), and it provides an essential tool to perform comparative genome mapping for bighead carp against model and non-model fishes, particularly those in the Cyprinidae of the Cypriniform. Cyprinidae is the largest family of the freshwater fishes in the world, and molecular systematics and phylogenetic relationships among members of this family have been studied through mitochondrial DNA and gene sequences (Saitoh et al 2006;Wang et al 2007Wang et al , 2012b. However, similarity and evolutionary relationships among cyprinid fishes have not been studied based on genetic information throughout the entire genomes.…”