DOI: 10.5061/dryad.8sq3vg5
title: Data from: Integrative ichthyological species delimitation in the Greenthroat Darter complex (Percidae: Etheostomatinae)

description: Species delimitation is fundamental to deciphering the mechanisms that
 generate and maintain biodiversity. Alpha taxonomy historically relied on
 expert knowledge to describe new species using phenotypic and
 biogeographic evidence, which has the appearance of investigator
 subjectivity. In contrast, DNA‐based methods using the multispecies
 coalescent model (MSC) promise a more objective approach to describing
 biodiversity. However, recent criticisms suggest that under some
 conditions the MSC may over‐split lineages, identifying species that do
 not reflect biological reality. Here, we reconcile these approaches using
 empirical data for the Greenthroat Darter complex (Etheostoma lepidum), a
 small freshwater fish species with a disjunct distribution in Texas and
 New Mexico, USA. We demonstrate that MSC methods recognizes all nine
 sampled populations as distinct species, sometimes splitting specimens
 from a single locality into multiple species. However, environmental,
 phenotypic and biogeographic evidence do not corroborate the nine species
 supported by the MSC. Instead, collective evidence indicates
 that E. lepidum is comprised of just three species that
 are consistent with the molecular phylogeny: Etheostoma
 lepidum (Greenthroat Darter) in rivers draining the eastern
 Edwards Plateau, Etheostoma cf. lepidum (Texas
 Darter) in the Concho and San Saba rivers and
 Etheostoma cf. lepidum (Pecos Darter) in the
 Pecos River. The Pecos Darter is likely highly imperiled due to its
 localized distribution and reliance on vanishing spring‐fed stream
 habitats. The impending biodiversity crisis makes integrative and swift
 species delimitation more necessary than ever. Our study exemplifies how
 classic taxonomic expertise combined with molecular phylogenetics can
 produce a more robust description of threatened biodiversity.
description: <strong>DNA alignments</strong>
 Alignments for 1 mtDNA gene cytochrome b (cytb) and 13 nuclear
 loci: the first intron of the S7 ribosomal protein and protein coding
 exons ENC1, Glyt, ptr, RAG1 exon 3, SH3PX3, Sidkey, sreb2, tbr1, UBE3A,
 UBE3A-like, zic1, and ZNF503. (alignments.zip)
 <strong>RADSeq concatenated
 alignment</strong> Concatenated alignment of
 5,336 RADseq loci. Data from MacGuigan and Near (2019).
 (Elepidum_RADSeq.phy) <strong>RADSeq unlinked
 SNPs</strong> Concatenated alignment of 4,707
 unlinked (1 per locus) RADseq SNPs. Data from MacGuigan and Near (2019).
 (Elepidum_RADSeq_unlinkedSNPs.phy)
 <strong>Meristic Dataset</strong>
 Dataset of meristic traits for Etheostoma lepidum. See text for
 description of traits (Elep_meristicsFINAL.csv)
 <strong>Morphometric TPS File</strong>
 Original TPS file (Elep.tps), unbent TPS using 5 lateral line
 landmarks (Elep_unbend_5LM.tps), specimen data (photoData_final.txt), and
 sliding landmark data for geomorph (sliders.txt).
 <strong>Environmental Dataset</strong>
 Environmental dataset for Etheostoma lepidum historic localities.
 See text for description of variables.
 (Elep_allLocs_finalGeoref_noDups_envData.csv)
 <strong>Tree Files</strong> Tree
 files produced by various phylogenetic analyses. See text for
 details.