DOI: 10.5061/dryad.5qfttdz2w
title: Confronting sources of systematic error to resolve historically contentious relationships: a case study using gadiform fishes (Teleostei, Paracanthopterygii, Gadiformes)

description: Reliable estimation of phylogeny is central to avoid inaccuracy in
 downstream macroevolutionary inferences. However, limitations exist in the
 implementation of concatenated and summary coalescent approaches, and
 Bayesian and full coalescent inference methods may not yet be feasible for
 computation of phylogeny using complicated models and large datasets.
 Here, we explored methodological (e.g., optimality criteria, character
 sampling, model selection) and biological (e.g., heterotachy, branch
 length heterogeneity) sources of systematic error that can result in
 biased or incorrect parameter estimates when reconstructing phylogeny by
 using the gadiform fishes as a model clade. Gadiformes include some of the
 most economically important fishes in the world (e.g., Cods, Hakes, and
 Rattails). Despite many attempts, a robust higher-level phylogenetic
 framework was lacking due to limited character and taxonomic sampling,
 particularly from several species-poor families that have been
 recalcitrant to phylogenetic placement. We compiled the first phylogenomic
 dataset, including 14,208 loci (&gt;2.8 M bp) from 58 species
 representing all recognized gadiform families, to infer a time-calibrated
 phylogeny for the group. Data were generated with a gene-capture approach
 targeting coding DNA sequences from single-copy protein-coding genes.
 Species-tree and concatenated maximum-likelihood analyses resolved all
 family-level relationships within Gadiformes. While there were a few
 differences between topologies produced by the DNA and the amino acid
 datasets, most of the historically unresolved relationships among gadiform
 lineages were consistently well resolved with high support in our analyses
 regardless of the methodological and biological approaches used. However,
 at deeper levels, we observed inconsistency in branch support estimates
 between bootstrap and gene and site coefficient factors (gCF, sCF).
 Despite numerous short internodes, all relationships received unequivocal
 bootstrap support while gCF and sCF had very little support, reflecting
 hidden conflict across loci. Most of the gene-tree and species-tree
 discordance in our study is a result of short divergence times, and
 consequent lack of informative characters at deep levels, rather than
 incomplete lineage sorting (ILS). We use this phylogeny to establish a new
 higher-level classification of Gadiformes as a way of clarifying the
 evolutionary diversification of the order. We recognize 17 families in
 five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei,
 and Macrouroidei (including two subclades). A time-calibrated analysis
 using 15 fossil taxa suggests that Gadiformes evolved ~79.5 million years
 ago (Ma) in the late Cretaceous, but that most extant lineages diverged
 after the Cretaceous-Paleogene (K-Pg) mass extinction (66 Ma). Our results
 reiterate the importance of examining phylogenomic analyses for evidence
 of systematic error that can emerge as a result of unsuitable modeling of
 biological factors and/or methodological issues, even when datasets are
 large and yield high support for phylogenetic relationships.
description: We compiled the first phylogenomic dataset, including 14,208 loci (&gt;2.8 M bp) from
 58 species representing all recognized gadiform families, to infer a
 time-calibrated phylogeny for the group. Data were generated
 with a gene-capture approach targeting coding DNA sequences from
 single-copy protein-coding genes. Species-tree and concatenated
 maximum-likelihood analyses resolved all family-level relationships within
 Gadiformes.