DOI: 10.5061/dryad.qrfj6q5t6
title: Evolutionary isolation and ecological stasis in the endangered Comal springs Dryopid beetle (Stygoparnus comalensis)

description: The Comal Springs dryopid beetle (Stygoparnus comalensis) is an
 endangered, subterranean-obligate, long-toed water beetle known only from
 three spring complexes in the Edwards Aquifer region of Texas. Due to
 their small size and reliance on groundwater karst habitats, little is
 known of the biology of these beetles. The aim of this study was to
 investigate evolutionary, ecological and morphological divergence among
 known S. comalensis localities in order to inform conservation management
 plans for this species. We used genotyping-by-sequencing (n = 85), stable
 isotope ($\delta^{15}$N and $\delta^{13}$C) analysis (n = 104), and
 morphometric analysis (n = 80), to describe variation among the three
 known localities and to ask whether ecological or morphological
 differentiation is associated with population genomic
 divergence.  S. comalensis populations are highly structured with
 no evidence of gene flow. Stable isotope ratios and morphology did not
 significantly differ among populations, suggesting that isolation is the
 driver of genetic diversification in S. comalensis. These results indicate
 that isolated populations show great levels of overall genomic divergence,
 while stasis or stabilizing selection has constrained ecological or
 morphological divergence. The three localities where S. comalensis has
 been found should be considered as evolutionarily distinct units based on
 levels of genomic differentiation. Conservation efforts should prioritize
 maintenance of the known localities and continued surveys to discover
 other localities for this endangered beetle.
description: # Evolutionary isolation and ecological stasis in the endangered Comal
 springs Dryopid beetle (Stygoparnus comalensis) Dataset DOI:
 [10.5061/dryad.qrfj6q5t6](10.5061/dryad.qrfj6q5t6) ## Description of the
 data and file structure Files included here contain morphological, stable
 isotope, and population genomics data for Stygoparnus comalensis, the
 blind dryopid beetle. Dryopid_isotopes.csv contains the stable isotope
 data (dC13 and dN15) for all sampled individuals (n = 104). The first
 column codes are: ca = Comal Springs Adult, cl = Comal Springs larva, fa =
 Fern Bank Springs adult, fl = Fern Bank Springs larva, sa = Sessom Springs
 adult. stygoparnus_morph_dryad.csv contains the morphometric data (body
 length, body width). Column "complex" is the spring complex (c =
 Comal Springs, f = Fern Bank Springs, s = Sessom Springs). Column
 "SNPs" identifies individuals that also have SNP genotypes
 (y/n). gprobmean.csv is the matrix of posterior genotype estimates for 85
 salamanders for 52,065 SNP loci indiv_ids.txt contains individual
 information for all genotyped individual samples (n = 85) coords.csv
 contains latitude and longitude for sampling localities
 stygoparnus_isotopes_dryad.R is a script to perform all analyses of
 isotope data and create figures stygoparnus_isotopes_dryad.RData is an
 .RData file with all objects for isotope analyses
 stygoparnus_morph_dryad.R is a script to perform all morphological
 analyses including basic statistical analyses and Redundancy Analysis
 (RDA) to partition genotypic variance by morphology and space.
 Stygoparnus_morph_dryad.RData is an .RData file with all objects for
 morphology analyses ## Sharing/Access information The DNA sequence data
 analysed used to generate the posterior genotype estimates have been
 archived on NCBI’s SRA (PRJNA1243997):
 [https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA1243997](https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA1243997) ### Files and variables #### File: stygoparnus\_isotopes\_dryad.R **Description:** a script to perform all analyses of isotope data and create figures #### File: stygoparnus\_morph\_dryad.R **Description:** a script to perform all morphological analyses including basic statistical analyses and Redundancy Analysis (RDA) to partition genotypic variance by morphology and space. #### File: Dryopid\_isotopes.csv **Description:** contains the stable isotope data (dC13 and dN15) for all sampled individuals (n = 104). The first column codes are: ca = Comal Springs Adult, cl = Comal Springs larva, fa = Fern Bank Springs adult, fl = Fern Bank Springs larva, sa = Sessom Springs adult. ##### Variables * com_stage: ca = Comal Springs Adult, cl = Comal Springs larva, fa = Fern Bank Springs adult, fl = Fern Bank Springs larva, sa = Sessom Springs adult. * id: individual ID * dC13:  carbon isotope data * dN15: nitrogen isotope data #### File: indiv\_ids.txt **Description:** contains individual information for all genotyped individual samples (n = 85) ##### Variables * ind: individual ID using three-letter locality code, \_, three-number ID * pop: three-letter code * taxon: individual ID (three-number) #### File: coords.csv **Description:** contains latitude and longitude for sampling localities (no header) ##### Variables * Spring Island: Spring site * csi: corresponding three-letter locality code * 29.718329:  latitude * -98.131174: longitude #### File: stygoparnus\_isotopes\_dryad.RData **Description:** an .RData file with all objects for isotope analyses #### File: Stygoparnus\_morph\_dryad.RData **Description:** an .RData file with all objects for morphology analyses #### File: gprobmean.csv **Description:** the matrix of posterior genotype estimates for 85 salamanders (rows) for 52,065 SNP loci (cols) ##### Variables * locus0: each col is a locus * locus1: #### File: stygoparnus\_morph\_dryad.csv **Description:** contains the morphometric data (body length, body width). Column "complex" is the spring complex (c = Comal Springs, f = Fern Bank Springs, s = Sessom Springs). Column "SNPs" identifies individuals that also have SNP genotypes (y/n). ##### Variables * complex: spring complex (c = Comal Springs, f = Fern Bank Springs, s = Sessom Springs) * SNPs: y/n indicates if individuals have genotype data for RDA * pop: three-letter locality code * id: individual ID * length(mm): length * width(mm): width ## Code/software R