DOI: 10.5061/dryad.280gb5mr2
title: Data from: Phylogeny reconciles classification in Antarctic plunderfishes

description: The resolution of phylogenetic relationships within rapid radiations poses
 a significant challenge in systematic biology. However, the integration of
 genome-scale DNA data with multispecies coalescent-based tree inference
 methods offers a strategy to resolve historically recalcitrant nodes
 within radiations of closely related species. Here, we analyze a dataset
 of over 60,000 loci captured via double digest restriction site-associated
 DNA sequencing (ddRADseq) using both concatenation- and coalescent-based
 approaches to infer the phylogenetic relationships of the Antarctic
 notothenioid lineage Artedidraconinae. Previous studies identify
 artedidraconines as the most rapidly diversifying subclade of
 notothenioids, but evolutionary studies of the clade are stymied by
 pervasive phylogenetic and taxonomic uncertainty. The results of our
 phylogenomic analyses provide clarity to several long-standing challenges
 in the systematics of artedidraconines, including the deep paraphyly of
 Artedidraco. Our findings enable the construction of a classification that
 reflects phylogenetic relationships, including the description of a new
 genus and the resurrection of a classification of Notothenioidei that
 places Artedidraconinae as a subfamily of Harpagiferidae. This work
 provides a phylogenetic perspective for investigations of the tempo and
 mode of diversification in artedidraconines, which is likely to provide
 new insights on the dynamics of the notothenioid adaptive radiation as a
 whole.
description: <strong>IQTREE_min84.phy</strong>
 Input file for Maximum Likelihood-based phylogenetic analysis
 using IQ-TREE. Dataset of concatenated sequences including all ddRAD loci
 shared across 50% (84 of 168) individuals. 
 <strong>IQTREE_min84.tre</strong>
 Consensus tree output from IQ-TREE analysis of IQTREE_min84.phy
 dataset. 
 <strong>IQTREE_min126.phy</strong>
 Input file for Maximum Likelihood-based phylogenetic analysis
 using IQ-TREE. Dataset of concatenated sequences including all ddRAD loci
 shared across 75% (126 of 168) individuals. 
 <strong>IQTREE_min126.tre</strong>
 Consensus tree output from IQ-TREE analysis of IQTREE_min126.phy
 dataset. 
 <strong>IQTREE_min144.phy</strong>
 Input file for Maximum Likelihood-based phylogenetic analysis
 using IQ-TREE. Dataset of concatenated sequences including all ddRAD loci
 shared across 85% (144 of 168) individuals. 
 <strong>IQTREE_min144.tre</strong>
 Consensus tree output from IQ-TREE analysis of IQTREE_min144.phy
 dataset. 
 <strong>meristic_data.csv</strong>
 Table with Standard Length (SL) measurements and counts for all
 five meristic traits for 90 specimens of <em>Artedidraco
 </em>and <em>Neodraco</em>. 
 <strong>tetrad_min84.snps.hdf5</strong>
 Input file for species tree analysis using tetrad (an
 implementation of SVDquartets in ipyrad). Dataset consisting of
 concatenated SNPs from all ddRAD loci shared across 50% (84 of 168)
 individuals. 
 <strong>tetrad_min84.tre</strong>
 Consensus tree output from tetrad analysis of
 tetrad_min84.snps.hdf5 dataset. 
 <strong>tetrad_min126.snps.hdf5</strong>
 Input file for species tree analysis using tetrad (an
 implementation of SVDquartets in ipyrad). Dataset consisting of
 concatenated SNPs from all ddRAD loci shared across 75% (126 of 168)
 individuals. 
 <strong>tetrad_min126.tre</strong>
 Consensus tree output from tetrad analysis of
 tetrad_min126.snps.hdf5 dataset.
 <strong>tetrad_min144.snps.hdf5</strong>
 Input file for species tree analysis using tetrad (an
 implementation of SVDquartets in ipyrad). Dataset consisting of
 concatenated SNPs from all ddRAD loci shared across 85% (144 of 168)
 individuals. 
 <strong>tetrad_min144.tre</strong>
 Consensus tree output from tetrad analysis of
 tetrad_min144.snps.hdf5 dataset.