DOI: 10.5061/dryad.76hdr7ssw
title: Recent hybrids recapitulate ancient hybrid outcomes

description: Genomic outcomes of hybridization depend on selection and recombination in
 hybrids. Whether these processes have similar effects on hybrid genome
 composition in contemporary hybrid zones versus ancient hybrid lineages is
 unknown. Here we show that patterns of introgression in a contemporary
 hybrid zone in Lycaeides butterflies predict patterns of ancestry in
 geographically adjacent, older hybrid populations. We find a particularly
 striking lack of ancestry from one of the hybridizing taxa, Lycaeides
 melissa, on the Z chromosome in both the old and contemporary hybrids. The
 same pattern of reduced L. melissa ancestry on the Z chromosome is seen in
 two other ancient hybrid lineages. More generally, we find that patterns
 of ancestry in old or ancient hybrids are remarkably predictable from
 contemporary hybrids, which suggests selection and recombination affect
 hybrid genomes in a similar way across disparate time scales and during
 distinct stages of speciation and species breakdown.  
description: We analyzed partial genome sequences from 835
 <em>Lycaeides</em> butterflies from 23 populations in western
 North America. The sequence data from 643 of these butterflies was
 previously described in a study of admixture across the
 <em>Lycaeides</em> species complex (Gompert et al. 2014). Data
 from 192 of the butterflies were generated for the current study, and this
 includes many (but not all) of the Dubois individuals. Specific locations
 (latitude and longitude) and sample sizes for each population are provided
 in the manuscript. DNA sequence data were generated by  on an Illumina
 HiSeq 2500 (100 bp, single-end reads) by the Genome Sequencing and
 Analysis Facility at the University of Texas (Austin, TX).
description: Compressed, archive (tar.gz) files are included for each step in
 the analysis. Each file contains the scripts/code used and a readme file.
 Here we summarize each one: 1. DNA sequence aligment
 and filtering scripts (alignment.tar.gz)
 filterSomeMore.pl = perl script to filter variants<br>
 runbwamem.sh =  bash script to run alignments using bwa mem from
 wrap_qsub_slurm_bwa_mem.pl script<br> runVcfFilter_af.sh = basg
 script to run vcfFilter_af.pl script below on the cluster<br>
 wrap_qsub_slurm_bwa_mem.pl = wrapper perl script to run alignments using
 bwa mem<br> lycaeidesVariantcalling.sh = bash script to do variant
 calling<br> runFilterSomeMore.sh  = bash script to run
 filterSomeMore.pl on the cluster<br> vcfFilter_af.pl = perl script
 to filter variants based on allele frequencies<br>
 wrap_qsub_slurm_sam2bam.pl = wrapper script to convert sam files to bam
 format 2. Variant filtering scripts
 (variantcalling_filtering.tar.gz) filterSomeMore.pl =
 This is a perl script to filter variants  <br> vcf2gl_depth.pl =
 This perl script converts vcf file to genotype likelihood file and filters
 variants based on depth of coverage.<br> vcf2gl_maf.pl = This perl
 script converts vcf file to genotype likelihood file and filters variants
 based on minor allele frequency of SNPs. 3. Genotype
 inference with entropy (entropy.tar.gz)
 forkRunEntropy.pl = perl fork script to run entropy<br>
 gl2genest.pl = perl script to convert genotype likelihood estimates to
 genotype estimates for entopry<br> initq.R  = R command script to
 prepare entropy input files<br> runentropy.sh = run entropy on the
 cluster 4. Ancestry frequency inference
 (popanc.tar.gz) forkrunpopanc.pl = This is a perl
 script to run popanc program  <br> runpopanc_fork.sh = This is a
 bash script to run the perl script on the cluster 5.
 Genomic clines analysis (bgc.tar.gz)<br>  <br> bgc = bgc
 program execution file  <br> estpost_bgc = program execution file to
 calculate posterior estimates<br> forkgenomicclines.pl = perl script
 to run bgc<br> plot_clines_males.R = R script to plot
 clines<br> rungenomicclines_fork.sh = bash script to run bgc on the
 cluster<br> splitPops.pl = perl script to split populations and
 create one file per population 6. Whole genome
 phylogenetic analysis (phylo.tar.gz) phylo.R = whole
 genome phylogentic analyses with R<br> appendWins.pl = processing
 script, adds scaffold and position boundaries to 1000 bp windows<br>
 getWinScafPos.pl = processing script, grabs the first and last position
 and scaffold of the SNPs for each window (works by linkage
 group)<br> mkRunWindows.pl = generates alignments of $win SNPs and
 generates a tree for each alignment<br> catWindowTrees1kb =
 phylogenetic trees for 1 kb windows 7. Genome
 annotation This folder contains working pipeline and
 scripts to do genome annotation.<br> maker_genome_annotation.md =
 describes a pipeline to do genome annotation using MAKER.<br>
 SNP_annotation.md = describes a pipeline to annotation a SNP dataset with
 information from MAKER genome annotation.<br>
 create_snp_annotation.py = is a python script used in SNP annotation (read
 SNP_annotation.md).<br> analysesSnpAnnot_combine.py = is a python
 script used in SNP annotation (read SNP_annotation.md).
 8. Bayesian genomic clines 1.04b
 (bgcdist-tempversion.tar.gz) This is a version of bgc
 that includes a new option to pre-sample hybrid index with alpha and beta
 set to 0.