4.8 Article

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

Publisher

NATL ACAD SCIENCES
DOI: 10.1073/pnas.1719358115

Keywords

phylogenomics; divergence times; bony fish; paralogy; tree of life

Funding

  1. National Natural Science Foundation of China [31370047]
  2. Shenzen Special Program for Strategic Emerging Industries [JSGG20170412153411369]
  3. Biomedical Research Council of Singapore
  4. A*STAR
  5. US National Science Foundation [DEB-147184, DEB-1541491, DEB-1457426, DEB-1541554]
  6. The Smithsonian Institution (GGI-SIBG Awards Program)
  7. Harlan Endowment
  8. Direct For Biological Sciences
  9. Division Of Environmental Biology [1457426, 1457184] Funding Source: National Science Foundation
  10. Division Of Environmental Biology
  11. Direct For Biological Sciences [1541552] Funding Source: National Science Foundation

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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. Genomescale 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 explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.

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