Data from: Phylogeny reconciles classification in Antarctic plunderfishes ...

• Main Authors: Parker, Elyse, Near, Thomas J.
• Format: Dataset
• Language: English
• Published: Dryad 2021
• Subjects: FOS Biological sciences; Southern Ocean; Notothenioidei; multispecies coalescent; Antarctic; The Antarctic; Antarc*
• Online Access: https://dx.doi.org/10.5061/dryad.280gb5mr2; https://datadryad.org/stash/dataset/doi:10.5061/dryad.280gb5mr2

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 ... : IQTREE_min84.phy 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. IQTREE_min84.tre Consensus tree output from IQ-TREE analysis of IQTREE_min84.phy dataset. IQTREE_min126.phy 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. IQTREE_min126.tre Consensus tree output from IQ-TREE analysis of IQTREE_min126.phy dataset. IQTREE_min144.phy 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. IQTREE_min144.tre Consensus tree output from IQ-TREE analysis of IQTREE_min144.phy dataset. meristic_data.csv Table with Standard Length (SL) measurements and counts for all five meristic traits for 90 specimens of Artedidraco and Neodraco. ...