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in Atta, Yuan, Li, ... et Tornabene, 2022. |
Highlights:
• Phylogenetic analysis of flatfishes uses next-gen dataset with largest taxon sampling to date.
• Rhombosoleidae is found to be in Pleuronectoidea rather than Soleoidea.
• Positions of Poecilopsettidae and Scophthalmidae are dictated by tree-construction method.
• Many relationships in the flatfish tree are unstable due to periods of rapid evolution.
• 8/16 families need thorough analysis; 23/127 genera may not be monophyletic (21 not yet sampled).
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: Phylogenomics, Systematics, Soles, Flounders, Incomplete-lineage-sorting, Target-enrichment
Conclusions:
Our analysis of flatfish systematics using an exon-capture dataset with relatively dense taxon sampling was mostly consistent with the leading phylogenetic hypotheses for the Pleuronectiformes (BHC model) and the Pleuronectidae (Vinnikov et al., 2018). We report a novel position for the family Rhombosoleidae and show extremely poor support for the subfamily Hippoglossinae. Collective inference using sixteen phylogenetic analyses demonstrates the tenuous nature of several flatfish relationships at various evolutionary scales, and how certain relationships are favored by particular methods. By examining our data within the historical context of flatfish systematics we were able to identify several regions where phylogenetic uncertainty is likely to remain and outline groups that should be targeted for further study.
Calder J. Atta, Hao Yuan, Chenhong Li, Dahiana Arcila, Ricardo Betancur-R, Lily C. Hughes, Guillermo Ortí, Luke Tornabene. 2022. Exon-capture Data and Locus Screening provide new insights into the Phylogeny of Flatfishes (Pleuronectoidei). Molecular Phylogenetics and Evolution. 166,107315. DOI: 10.1016/j.ympev.2021.107315
