DOI: 10.5061/dryad.zw3r228g3
title: Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii

description: 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.
description: This data archive contains ecological data and
 genome-by-sequencing (GBS) data collected from Hayden's ringlet
 butterflies, <em>Coenonympha haydenii</em>. 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 <em>C. haydenii </em>butterflies show a preference for
 using grass (<em>Poa pratensis</em>) vs. a sedge
 (<em>Carex hoodii</em>) 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. 
description: # Considerable genetic diversity and structure despite narrow endemism and
 limited ecological specialization in the Hayden's ringlet,
 Coenonympha haydenii ##
 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: 1. 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. 2. 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. 3.
 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. 4. 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. 5.
 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