DOI: 10.5061/dryad.4f4qrfjc3
title: Data from: Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

description: Application of genetic data to species delimitation often builds
 confidence in delimitations previously hypothesized using morphological,
 ecological, and geographic data and frequently yields recognition of
 previously-undescribed cryptic diversity. However, a recent critique of
 genomic data-based species delimitation approaches is that they have the
 potential to conflate population structure with species diversity,
 resulting in taxonomic oversplitting. The need for an integrative approach
 to species delimitation, in which molecular, morphological, ecological,
 and geographic lines of evidence are evaluated together, is becoming
 increasingly apparent. Here, we integrate phylogenetic, population
 genetic, and coalescent analyses of genome-wide sequence data with
 investigation of variation in multiple morphological traits to delimit
 species within the Antarctic barbeled plunderfishes (Artedidraconidae:
 Pogonophryne). Pogonophryne currently comprises 29 valid species, most of
 which are distinguished solely by variation in ornamentation of the mental
 barbel that projects from the lower jaw, a structure previously shown to
 vary widely within a single species. However, our genomic and phenotypic
 analyses result in a dramatic reduction in the number of distinct species
 recognized within the clade, providing evidence to support the recognition
 of no more than six species. We propose to synonymize 24 of the currently
 recognized species with five species of Pogonophryne. We find genomic and
 phenotypic evidence for a new species of Pogonophryne from specimens
 collected in the Ross Sea. Our findings represent a rare example in which
 application of molecular data provides evidence of taxonomic oversplitting
 on the basis of morphology, clearly demonstrating the utility of an
 integrative species delimitation framework.
description: <b>Parker_et_al2021_supplement.docx</b><br>
 Supplementary Tables S1-11 and Supplementary Figures S1-S8.
 <strong>min58.phy</strong> <br> Dataset of
 concatenated sequences including all loci shared across 25% (58 of 228)
 individuals
 <strong>min116.phy</strong><br> Dataset of
 concatenated sequences including all loci shared across 50% (116 of 228)
 individuals
 <strong>min174.phy </strong><br> Dataset of
 concatenated sequences including all loci shared across 75% (174 of 228)
 individuals
 <strong>noOut_min55.ustr </strong><br> Dataset
 excluding all outgroup taxa and including randomly-sampled unlinked SNPs
 from loci shared across 25% (55 of 218) individuals analyzed using
 DAPC
 <strong>noOut_min110.ustr </strong><br> Dataset
 excluding all outgroup taxa and including randomly-sampled unlinked SNPs
 from loci shared across 50% (110 of 218) individuals analyzed using
 DAPC
 <strong>noOut_min165.ustr </strong><br> Dataset
 excluding all outgroup taxa and including randomly-sampled unlinked SNPs
 from loci shared across 75% (165 of 218) individuals analyzed using
 DAPC
 <strong>noOut_min197.ustr </strong><br> Dataset
 excluding all outgroup taxa and including randomly-sampled unlinked SNPs
 from loci shared across 90% (197 of 218) individuals analyzed using
 DAPC
 <strong>noOut_min195.ustr </strong><br> Dataset
 excluding all outgroup taxa and including randomly-sampled unlinked SNPs
 from loci shared across 89% (195 of 218) individuals analyzed using
 STRUCTURE
 <strong>barsukovi_min61.ustr</strong> <br>
 Input file for STRUCTURE including all individuals assigned to
 “<i>P. barsukovi</i>” cluster in full STRUCTURE analysis and
 randomly-sampled unlinked SNPs from all loci shared across 96% (61 of 63)
 individuals
 <strong>men-alb-mar_min77.ustr</strong> <br>
 Input file for STRUCTURE including all individuals assigned to
 “<i>P. albipinna</i>,” “<i>P. marmorata</i>,” and
 “<i>P. mentella</i>” clusters in full STRUCTURE analysis and
 randomly-sampled unlinked SNPs from all loci shared across 89% (77 of 87)
 individuals
 <strong>mentella_min60.ustr </strong><br> Input
 file for STRUCTURE including all individuals assigned to “<i>P.
 mentella</i>” cluster in full STRUCTURE analysis and
 randomly-sampled unlinked SNPs from all loci shared across 94% (60 of 64)
 individuals
 <strong>scotti_min57.ustr</strong> <br> Input
 file for STRUCTURE including all individuals assigned to “<i>P.
 scotti</i>” cluster in full STRUCTURE analysis and randomly-sampled
 unlinked SNPs from all loci shared across 96% (57 of 60)
 individuals
 <strong>min4_21tax_100loc.seqfile</strong> <br>
 Input sequence file for BPP including 1-2 individuals for each of 18
 traditionally-defined species of <i>Pogonophryne</i> and 1
 putatively new species and 100 randomly-selected loci shared across all 21
 individuals
 <strong>min4_20tax_SNAPP.phy</strong> <br>
 Input data file for SNAPP divergence time analysis including 3-4
 individuals for each of the 6 <i>Pogonophryne</i> species
 delimited in this study and all biallelic SNPs shared across 95% of
 individuals
 <strong>jaw_data.csv</strong> <br> Table with
 all lower jaw length (LJL), head length (HL), and standard length (SL)
 measurements for calculation of LJL:SL and LJL:HL ratios.
 <strong>meristic_data.csv</strong><br> Table
 with all meristic trait data.
 <strong>morphometric_data.csv</strong> <br>
 Table with all measured linear morphometric characters.