Dryad
Published July 20, 2021 | Version v1
Dataset Open

Data from: Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Creators

  • 1. Yale University
  • 2. University of North Carolina
  • 3. Museum of New Zealand Te Papa Tongarewa
  • 4. Southwest Fisheries Science Center

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.

Notes

Parker_et_al2021_supplement.docx
Supplementary Tables S1-11 and Supplementary Figures S1-S8.

min58.phy 
Dataset of concatenated sequences including all loci shared across 25% (58 of 228) individuals

min116.phy
Dataset of concatenated sequences including all loci shared across 50% (116 of 228) individuals

min174.phy 
Dataset of concatenated sequences including all loci shared across 75% (174 of 228) individuals

noOut_min55.ustr 
Dataset excluding all outgroup taxa and including randomly-sampled unlinked SNPs from loci shared across 25% (55 of 218) individuals analyzed using DAPC

noOut_min110.ustr 
Dataset excluding all outgroup taxa and including randomly-sampled unlinked SNPs from loci shared across 50% (110 of 218) individuals analyzed using DAPC

noOut_min165.ustr 
Dataset excluding all outgroup taxa and including randomly-sampled unlinked SNPs from loci shared across 75% (165 of 218) individuals analyzed using DAPC

noOut_min197.ustr 
Dataset excluding all outgroup taxa and including randomly-sampled unlinked SNPs from loci shared across 90% (197 of 218) individuals analyzed using DAPC

noOut_min195.ustr 
Dataset excluding all outgroup taxa and including randomly-sampled unlinked SNPs from loci shared across 89% (195 of 218) individuals analyzed using STRUCTURE

barsukovi_min61.ustr 
Input file for STRUCTURE including all individuals assigned to "P. barsukovi" cluster in full STRUCTURE analysis and randomly-sampled unlinked SNPs from all loci shared across 96% (61 of 63) individuals

men-alb-mar_min77.ustr 
Input file for STRUCTURE including all individuals assigned to "P. albipinna," "P. marmorata," and "P. mentella" clusters in full STRUCTURE analysis and randomly-sampled unlinked SNPs from all loci shared across 89% (77 of 87) individuals

mentella_min60.ustr 
Input file for STRUCTURE including all individuals assigned to "P. mentella" cluster in full STRUCTURE analysis and randomly-sampled unlinked SNPs from all loci shared across 94% (60 of 64) individuals

scotti_min57.ustr 
Input file for STRUCTURE including all individuals assigned to "P. scotti" cluster in full STRUCTURE analysis and randomly-sampled unlinked SNPs from all loci shared across 96% (57 of 60) individuals

min4_21tax_100loc.seqfile 
Input sequence file for BPP including 1-2 individuals for each of 18 traditionally-defined species of Pogonophryne and 1 putatively new species and 100 randomly-selected loci shared across all 21 individuals

min4_20tax_SNAPP.phy 
Input data file for SNAPP divergence time analysis including 3-4 individuals for each of the 6 Pogonophryne species delimited in this study and all biallelic SNPs shared across 95% of individuals

jaw_data.csv 
Table with all lower jaw length (LJL), head length (HL), and standard length (SL) measurements for calculation of LJL:SL and LJL:HL ratios.

meristic_data.csv
Table with all meristic trait data.

morphometric_data.csv 
Table with all measured linear morphometric characters.

Files

jaw_data.csv

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Additional details

Related works

Is source of
10.5281/zenodo.5083389 (DOI)