Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data.

ABSTRACT: Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explic

SUBMITTER: Hughes LC 

PROVIDER: S-EPMC6004478 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature