Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei)

Calder J Atta; Hao Yuan; Chenhong Li; Dahiana Arcila; Ricardo Betancur-R; Lily C Hughes; Guillermo Ortí; Luke Tornabene

doi:10.1016/j.ympev.2021.107315

Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei)

Mol Phylogenet Evol. 2022 Jan:166:107315. doi: 10.1016/j.ympev.2021.107315. Epub 2021 Sep 16.

Authors

Calder J Atta¹, Hao Yuan², Chenhong Li², Dahiana Arcila³, Ricardo Betancur-R³, Lily C Hughes⁴, Guillermo Ortí⁵, Luke Tornabene⁶

Affiliations

¹ School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA. Electronic address: calderatta@gmail.com.
² Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China.
³ Sam Noble Oklahoma Museum of Natural History, The University of Oklahoma, Norman, OK 73072, USA; Department of Biology, The University of Oklahoma, Norman, OK 73072, USA.
⁴ Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA.
⁵ National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA.
⁶ School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA.

PMID: 34537325
DOI: 10.1016/j.ympev.2021.107315

Abstract

There is an extensive collection of literature on the taxonomy and phylogenetics of flatfishes (Pleuronectiformes) that extends over two centuries, but consensus on many of their evolutionary relationships remains elusive. Phylogenetic uncertainty stems from highly divergent results derived from morphological and genetic characters, and between various molecular datasets. Deciphering relationships is complicated by rapid diversification early in the Pleuronectiformes tree and an abundance of studies that incompletely and inconsistently sample taxa and genetic markers. We present phylogenies based on a genome-wide dataset (4,434 nuclear markers via exon-capture) and wide taxon sampling (86 species spanning 12 of 16 families) of the largest flatfish suborder (Pleuronectoidei). Nine different subsets of the data and two tree construction approaches (eighteen phylogenies in total) are remarkably consistent with other recent molecular phylogenies, and show strong support for the monophyly of all families included except Pleuronectidae. Analyses resolved a novel phylogenetic hypothesis for the family Rhombosoleidae as being within the Pleuronectoidea rather than the Soleoidea, and failed to support the subfamily Hippoglossinae as a monophyletic group. Our results were corroborated with evidence from previous phylogenetic studies to outline regions of persistent phylogenetic uncertainty and identify groups in need of further phylogenetic inference.

Keywords: Flounders; Incomplete-lineage-sorting; Phylogenomics; Soles; Systematics; Target-enrichment.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Biological Evolution
Exons
Flatfishes* / genetics
Genome
Humans
Phylogeny

Associated data

Dryad/10.5061/dryad.d51c5b036