Evolutionary isolation and ecological stasis in the endangered Comal springs Dryopid beetle (Stygoparnus comalensis)
Data files
May 29, 2025 version files 123.72 MB
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coords.csv
242 B
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Dryopid_isotopes.csv
2.39 KB
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gprobmean.csv
59.25 MB
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indiv_ids.txt
1.37 KB
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README.md
4.43 KB
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stygoparnus_isotopes_dryad.R
33.50 KB
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stygoparnus_isotopes_dryad.RData
7.92 MB
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stygoparnus_morph_dryad.csv
2.24 KB
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stygoparnus_morph_dryad.R
8.49 KB
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Stygoparnus_morph_dryad.RData
56.50 MB
Abstract
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.
Dataset DOI: 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
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