DOI: 10.5061/dryad.77rf2
title: Data from: Fuzzy boundaries: Color and gene flow patterns among parapatric lineages of the Western shovel-nosed snake and taxonomic implication

description: Accurate delineation of lineage diversity is increasingly important, as
 species distributions are becoming more reduced and threatened. During the
 last century, the subspecies category was often used to denote phenotypic
 variation within a species range and to provide a framework for
 understanding lineage differentiation, often considered incipient
 speciation. While this category has largely fallen into disuse, previously
 recognized subspecies often serve as important units for conservation
 policy and management when other information is lacking. In this study, we
 evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on
 the basis of genetic data and considered how evolutionary processes such
 as gene flow influenced possible incongruence between phenotypic and
 genetic patterns. We used both traditional phylogenetic and Bayesian
 clustering analyses to infer range-wide genetic structure and spatially
 explicit analyses to detect possible boundary locations of lineage
 contact. Multilocus analyses supported three historically isolated groups
 with low to moderate levels of contemporary gene exchange. Genetic data
 did not support phenotypic subspecies as exclusive groups, and we detected
 patterns of discordance in areas where three subspecies are presumed to be
 in contact. Based on genetic and phenotypic evidence, we suggested that
 species-level diversity is underestimated in this group and we proposed
 that two species be recognized, Chionactis occipitalis and C. annulata. In
 addition, we recommend retention of two subspecific designations within C.
 annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts
 in both genetic and phenotypic variation within the species. Our results
 highlight the difficultly in validating taxonomic boundaries within
 lineages that are evolving under a time-dependent, continuous process.
description: # Data from: Fuzzy boundaries: Color and gene flow patterns among
 parapatric lineages of the Western shovel-nosed snake and taxonomic
 implication
 [https://doi.org/10.5061/dryad.77rf2](https://doi.org/10.5061/dryad.77rf2)
 ## Description of the data and file structure We used both traditional
 phylogenetic (nexus file) and Bayesian clustering analyses (genepop file)
 to infer range-wide genetic structure and spatially explicit analyses to
 detect possible boundary locations of lineage contact.  ### Files and
 variables #### File: CHOC\_Microsatellite\_GENEPOP.txt **Description:** 11
 loci (Chionactis 11 loci: PEN160, TRI176, TET1713,
 TRI1164, PEN5400, TRI222, TRI1925, TRI199, TET193, TRI2219, TET1847) #####
 Variables * 4 population grouped by subspecies * pop1 = Chionactis
 occipitalis talpina * pop2 = Chionactis occipitalis occipitalis * pop3
 = Chionactis occipitalis annulata * pop4 = Chionactis occipitalis klauberi
 #### File: CHIONACTIS\_mtDNA\_ND1\_Matrix.nex **Description:** Nexus file
 of mtDNA sequences #### File: TableS1.csv **Description:** Tissue samples
 used in this study along with mtDNA lineage/clade and microsatellite
 cluster assignments, morphology, and locality information. Abbreviations
 and field series abbreviations are as follows: ASU, Arizona State
 University; ATH, Andrew T. Holycross; BEZY, Robert L. Bezy;DAW, Dustin A.
 Wood; DGM, Daniel G. Mulcahy; JESMM, Jesse M. Meik; RDB, Randy Babb; RNF,
 Robert N. Fisher; ROM, Royal Ontario Museum; RWM, Robert W. Murphy; SDSNH
 (SD Field), San Diego Natural History Museum; TCB, Thomas C. Brennan; TRJ,
 Thomas R. Jones; UAZ, University of Arizona; UTA, University of Texas,
 Arlington; all other tissues were obtained from field surveys conducted by
 the San Diego Field Station, US Geological Survey. "n/a" = not
 applicable ##### Variables * Tissue ID * Voucher ID (museum or field ID) *
 Species - following proposed taxonomy from the results of the study *
 mtDNA lineage - details which mtDNA lineage or clade the sample is
 associated with * Microsatellite Cluster - details which cluster the
 sample was assigned to and the posterior probability of that assignment *
 Morphology scaled - whether color pattern and morpological data were taken
 for that specimen. A 'yes' means that a voucher sample was
 obtain and morphology was scored. A 'no' means no voucher
 specimen was available, only a tissue sample was taken. * County, State,
 County (if available), and Locality where the tissue sample was collected
 * Latitude/Longitude - gps coordinates where the sample was taken ####
 File: FigS1\_Mojave\_clade.pdf **Description:** Mojave lineage pruned from
 the full mtDNAphylogeny, shown in the upper left.Numbers at nodesrepresent
 posterior probability support values for individual clades. #### File:
 FigS3\_Colorado\_clade.pdf **Description:** Colorado lineage pruned from
 the fullmtDNA phylogeny, shown in the upper left.Numbers atnodes represent
 posterior probability support values for individualclades. #### File:
 FigS2\_Sonoran\_clade.pdf **Description:** Sonoran lineage pruned from the
 full mtDNAphylogeny, shown in the upper left.Numbers at nodesrepresent
 posterior probability support values for individual clades. #### File:
 FigS5\_Geneland.pdf **Description:** Posterior density of the number of
 clusters(K) from the MCMC analysis of genetic structure acrossArizona
 usingGENELAND. #### File: FigS4\_K\_approximation.pdf
 **Description:** Results from the mean lnP(D|K) scoreagainst the KMAXand
 theDKcriterion of Evanno et al  ## Access information Data was derived
 from the source: See publication