DOI: 10.5061/dryad.v6726
title: Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape

description: Incorporating genomic data sets into landscape genetic analyses allows for
 powerful insights into population genetics, explicitly geographical
 correlates of selection, and morphological diversification of organisms
 across the geographical template. Here, we utilize an integrative approach
 to examine gene flow and detect selection, and we relate these processes
 to genetic and phenotypic population differentiation across South-East
 Asia in the common sun skink, Eutropis multifasciata. We quantify the
 relative effects of geographic and ecological isolation in this system and
 find elevated genetic differentiation between populations from island
 archipelagos compared to those on the adjacent South-East Asian continent,
 which is consistent with expectations concerning landscape fragmentation
 in island archipelagos. We also identify a pattern of isolation by
 distance, but find no substantial effect of ecological/environmental
 variables on genetic differentiation. To assess whether morphological
 conservatism in skinks may result from stabilizing selection on
 morphological traits, we perform FST–PST comparisons, but observe that
 results are highly dependent on the method of comparison. Taken together,
 this work provides novel insights into the manner by which
 micro-evolutionary processes may impact macro-evolutionary scale
 biodiversity patterns across diverse landscapes, and provide genomewide
 confirmation of classic predictions from biogeographical and landscape
 ecological theory.
description: Allele Frequency
 DataThis file contains
 allele frequency data for each of the 14 populations used in the fst-pst
 analyses. The format of the file format for each population is as follows,
 for each line: locus number, the total number of genes in the population
 for the locus, the number of alleles for the locus, the number of copies
 of each allele in the population.AlleleFrequency.csvBarcodesThis file contains information on the barcode sequence assigned to each individual in our study.StructureThis is a structure formatted file containing genotypic data for each individual used in the study.batch_2structure.strBEDASSLEThis is an R object file that was used to run the BEDASSLE analyses.BootstrapThis R script contains the code for the bootstrapping procedure for obtaining confidence intervals for the global pst data as described in the manuscript.Calculate_FstsThis python script contains the code for calculating global Fst's for each locus as described in the manuscript.Calc_Fsts.pyFastSimCoalThis archive contains the files used to run fastsimcoal2 to obtain the isolation-migration parameter estimates as in the manuscript.Fst_BootstrapThis R script contains the code for calculating bootstrapped confidence intervals for global Fst as described in the manuscript.Fst_boot.RIBDWSThis text file contains the distance matrix information used for testing for isolation by distance using the Isolation by distance web server.Maxent ASCIIThis is the habitat suitability output file from Maxent.multifasciata.ascMorphological DataThis file contains the morphological data used for calculating Psts.MorphData.csvPopulation CoordinatesThis file contains the geographic coordinates (WGS84) for each population used in the landscape genetic analyses.PopulationCoordinates.csv