title: Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii).
abstract: The actinopterygians comprise nearly one-half of all extant vertebrate species and are very important for human well-being. However, the phylogenetic relationships among certain groups within the actinopterygians are still uncertain, and debates about these relationships have continued for a long time. Along with the progress achieved in sequencing technologies, phylogenetic analyses based on multi-gene sequences, termed phylogenomic approaches, are becoming increasingly common and often result in well-resolved and highly supported phylogenetic hypotheses. Based on the transcriptome sequences generated in this study and the extensive expression data currently available from public databases, we obtained alignments of 274 orthologue groups for 26 scientifically and commercially important actinopterygians, representing 17 out of 44 orders within the class Actinopterygii. Using these alignments and probabilistic methods, we recovered relationships between basal actinopterygians and teleosts, among teleosts within protacanthopterygians and related lineages, and also within acanthomorphs. These relationships were recovered with high confidence.
authors.affiliation: The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
authors.forename: Ming
authors.initials: M
authors.lastname: Zou
authors.forename: Baocheng
authors.initials: B
authors.lastname: Guo
authors.forename: Wenjing
authors.initials: W
authors.lastname: Tao
authors.forename: Gloria
authors.initials: G
authors.lastname: Arratia
authors.forename: Shunping
authors.initials: S
authors.lastname: He
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005399:Fishes / Q000235:genetics*; D016013:Likelihood Functions; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D059467:Transcriptome