DOI: 10.5061/dryad.87ht5v0
title: Data from: The predictability of genomic changes underlying a recent host shift in Melissa blue butterflies

description: Despite accumulating evidence that evolution can be predictable, studies
 quantifying the predictability of evolution remain rare. Here, we measured
 the predictability of genome-wide evolutionary changes associated with a
 recent host shift in the Melissa blue butterfly (Lycaeides melissa). We
 asked whether and to what extent genome-wide patterns of evolutionary
 change in nature could be predicted (1) by comparisons among instances of
 repeated evolution, and (2) from SNP $\times$ performance associations in
 a lab experiment. We delineated the genetic loci (SNPs) most strongly
 associated with host use in two L. melissa lineages that colonized
 alfalfa. Whereas most SNPs were strongly associated with host use in none
 or one of these lineages, we detected a ~two-fold excess of SNPs
 associated with host use in both lineages. Similarly, we found that
 host-associated SNPs in nature could also be partially predicted from SNP
 $\times$ performance (survival and weight) associations in a lab rearing
 experiment. But the extent of overlap, and thus degree of predictability,
 was somewhat reduced. Although we were able to predict (to a modest
 extent) the SNPs most strongly associated with host use in nature (in
 terms of parallelism and from the experiment), we had little to no ability
 to predict the direction of evolutionary change during the colonization of
 alfalfa. Our results show that different aspects of evolution associated
 with recent adaptation can be more or less predictable, and highlight how
 stochastic and deterministic processes interact to drive patterns of
 genome-wide evolutionary change
description: Ancestral reconstruction
 of host useThe files in this
 compressed directory are for the ancestral reconstruction of host use,
 including determining posterior probabilities for number of transitions
 from native feeding to Medicago sativa feeding. The R script also
 specifies the plotting of the ancestral state reconstruction
 tree.ancState.tar.gzVariant callingThese are scripts we used for SNP variant calling. The locuslist provides a list of specific SNPs which were called for this analysis. We used samtools for variant calling.variancalling.tar.gzTreemix analysisThis compressed directory contains the files we used to conduct the treemix analysis. This includes scripts and infiles. A readme.txt file is included providing additional details.treemix.tar.gzSex chromosome analysisThis compressed directory contains the infiles and R script for the analysis to determine if SNPs associated with parallelism between melissa-east and melissa-west populations are present on the sex chromosome. A readme.txt file is included with additional details.sexChrom.tar.gzBAYPASS data and scriptsThis compressed directory contains the infiles, outfiles, and scripts for the BAYPASS analyses used to delineate host-associated SNPs and to test for parallelism. A readme.txt file is included with additional details about each file in the directory.baypass.tar.gzPredicting SNP-host use association from an experimentThis compressed directory contains multiple R scripts and text files to implement the tests for overlap and sign coincidence between SNP-host use association in nature and SNP-performance association from a larval rearing experiment. A readme.txt file is included with additional details about each file.expComp.tar.gzPredicting genetic differenitation from an experimentThis compressed directory contains an R script and text files to implement the tests for overlap and sign coincidence between genetic differentiation between focal populations and SNP-performance association from a larval rearing experiment. A readme file is included with additional details about each file.fstanalysis.tar.gz