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 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.

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes*

“…Favored trees inferred by recent phylogenomic analyses of contentious clades of Otophysa. Two studies (Arcila et al and Hughes et al ) support the MC hypothesis (monophyletic Characiformes) based on GGI and maximum likelihood (ML) analysis of the concatenated amino acid sequences (also by other results based on species‐tree analyses, see figure 1 of Arcila et al and figure of Hughes et al ). In contrast, Chakrabarty et al () and Dai et al () support the NMC hypothesis (non‐monophyletic Characiformes) based on ML and species‐tree analyses of DNA sequences (they did not conduct GGI analyses).…”

“…; Hughes et al. ) have proposed that characoids and citharinoids are sister taxa supporting a monophyletic order Characiformes (MC hereafter), whereas the other two (Chakrabarty et al. ; Dai et al.…”

“…; Hughes et al. ), Dai et al. () date the split between the African Phenacogrammus (Characiformes) and the South American Apteronotus (Gymnotiformes) at just 28 Ma.…”

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

“…Note that the temporal divergence of our target fish orders (Gymnotiformes, Characiformes and Siluriformes) is well over 100 my old (Arcila et al, ; Betancur‐R et al., ). There is also a potential for paralogous locus assembly (Mastretta‐Yanes et al, ; Verdu et al, ), a problem that is exacerbated in fishes due to multiple rounds of whole genome duplications (Hughes et al, ). By contrast, data missingness is not likely to pose a large effect on our analyses of sequence capture data given that we successfully assembled ~92% of the ~one thousand target loci across both populations and species.…”

Staging and normal table of postembryonic development of the clownfish (Amphiprion ocellaris)

“…Its phylogenetic position (exemplified by A. ocellaris and the damselfish Stegastes partitus, whose genomes have been sequenced) is shown in Figure . It illustrates how it is nested in the late radiation of the Perciformes, cichlids being the closest classical fish model . Pomacentrids have developed fascinating innovations that can provide fertile ground for evo‐devo studies.…”