title: New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset.
abstract: Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates.
authors.affiliation: North Carolina Museum of Natural Sciences, Raleigh, NC, USA. Electronic address: alex.dornburg@naturalsciences.org.
authors.forename: Alex
authors.initials: A
authors.lastname: Dornburg
authors.affiliation: Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Biostatistics, Yale University, New Haven, CT 06510, USA.
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Townsend
authors.affiliation: North Carolina Museum of Natural Sciences, Raleigh, NC, USA.
authors.forename: Willa
authors.initials: W
authors.lastname: Brooks
authors.affiliation: Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Spriggs
authors.affiliation: Marine Biology Department, Texas A&M University at Galveston, Galveston, TX 77554, USA.
authors.forename: Ron I
authors.initials: RI
authors.lastname: Eytan
authors.affiliation: Florida Atlantic University, Wilkes Honors College, Jupiter, FL 33458, USA; Florida Atlantic University, Harbor Branch Oceanographic Institution, Fort Pierce, FL 34946, USA.
authors.forename: Jon A
authors.initials: JA
authors.lastname: Moore
authors.affiliation: Department of Evolution & Ecology, University of California, Davis, CA 95616, USA.
authors.forename: Peter C
authors.initials: PC
authors.lastname: Wainwright
authors.affiliation: Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Lemmon
authors.affiliation: Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Near
mesh_terms: D000596:Amino Acids / Q000235:genetics; D000818:Animals; D001482:Base Composition / Q000235:genetics; D030541:Databases, Genetic; D005399:Fishes / Q000145:classification* / Q000235:genetics*; D023281:Genomics; D006824:Hybridization, Genetic; D016013:Likelihood Functions; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D000596:Amino Acids; D009711:Nucleotides
keywords: Anchored phylogenomics; Beryciformes; Codon bias; GC3; Homoplasy; Hybrid enrichment; Nucleotide saturation