Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii
Data files
Mar 08, 2024 version files 1.66 GB
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C_haydenii_data_archive.zip
1.66 GB
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README.md
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Abstract
Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure can reveal signatures of isolation by distance, barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by isolation by distance, isolation by resistance (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping-by-sequencing (GBS) approach coupled with host preference assays, Bayesian modeling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of isolation by resistance and simple isolation by distance, was the major driver of contemporary patterns of differentiation in this narrow endemic species.
README: Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii
https://doi.org/10.5061/dryad.zw3r228g3
Data description and file structure
This data archive contains five directories. Within each directory an additional README.txt file can be found that describes file content and usage details for that particular directory. Information about how data were formatted for analyses and how the individual analyses were conducted can be found in the associated R-script for each analysis. The last section of each R-script displays summary tables and model results and provides explanations regarding the interpretation of these summaries. The five directories included in this archive are as follows:
C_haydenii_EEMS_input_files
This directory contains the input files and parameters necessary to run the program EEMS (Estimated Effective Migration Surfaces) using C. haydenii genetic distance data generated from this project. This program was used to test for isolation by resistance (IBR) across the range of the Hayden's ringlet.
C_haydenii_genetic_distance_analyses
This directory contains the files, scripts, and models necessary to run Bayesian linear models testing the effect of host plant community assemblage, larval herbivory preference, female oviposition preference, and geographic distances on the degree of genetic differentiation (Fst) among populations of Hayden's ringlet butterflies. These models were implemented using Rjags, and were used to test for isolation by distance (IBD) and isolation by environment (IBE) among populations of Hayden's ringlets.
C_haydenii_genomic_data_filtering_scripts
This directory contains custom perl scripts used for cleaning, demultiplexing, filtering, and otherwise manipulating the genomic data and resulting single nucleotide polymorphism (SNP) dataset generated by this project. This directory also contains SNP genotype data for each of the 287 individual Hayden's ringlet butterflies used in this project.
C_haydenii_larval_pref_analyses
This directory contains the files, scripts, and models necessary to fit a hierarchical Bayesian model for larval herbivory preferences at both the species and population level in Hayden's ringlet butterflies. These analyses were also used to test for ecological divergence in larval host plant preference across populations.
C_haydenii_oviposition_pref_analyses
This directory contains the files, scripts, and models necessary to fit a hierarchical Bayesian model for female oviposition preferences at both the species and population level in Hayden's ringlet butterflies. These analyses were also used to test for ecological divergence in female oviposition host plant preference across populations.
Sharing/Access information
Raw sequence data from this project can be found at the NIH National Library of Medicine Sequence Read Archive. The accession number for this archive is:
- PRJNA1036281
Code/Software
Software and packages used to run the scripts in this archive include:
- R (version 4.3.1)
- Stan (version 2.32.2)
- RStan (version 2.32.5)
- jags (version 4.3.1)
- Rjags (version 4-14)
- Geosphere (version 1.5-18)
- Perl
Methods
This data archive contains ecological data and genome-by-sequencing (GBS) data collected from Hayden's ringlet butterflies, Coenonympha haydenii. This archive also contains scripts and Bayesian models used for processing and analyzing these data. Ecological data collected include the following:
- potential larval host plant community assemblage data for 12 sampling sites where Hayden's ringlets are abundant,
- female oviposition preference assay data, and
- larval herbivory preference assay data.
Ecological data were used to assess whether C. haydenii butterflies show a preference for using grass (Poa pratensis) vs. a sedge (Carex hoodii) as a larval host, and whether host preferences varied by population. Single nucleotide polymorphism data were used to estimate the degree of genetic differentiation among populations of Hayden's ringlets sampled, as well as for Bayesian models to assess the degree to which genetic differentiation in this species is associated with host plant community assemblage, female oviposition preference, and larval herbivory preference.