DOI: 10.5061/dryad.79cnp5hxm
title: Data from: Population genomic evidence of selection on structural variants in a natural hybrid zone

description: Structural variants (SVs) can promote speciation by directly causing
 reproductive isolation or by suppressing recombination across large
 genomic regions. Whereas examples of each mechanism have been documented,
 systematic tests of the role of SVs in speciation are lacking. Here, we
 take advantage of long-read (Oxford nanopore) whole-genome sequencing and
 a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson
 Hole Lycaeides) to comprehensively evaluate genome-wide patterns of
 introgression for SVs and relate these patterns to hypotheses about
 speciation. We found &gt;100,000 SVs segregating within or between the
 two hybridizing species. SVs and SNPs exhibited similar levels of genetic
 differentiation between species, with the exception of inversions, which
 were more differentiated. We detected credible variation in patterns of
 introgression among SV loci in the hybrid zone, with 562 of 1419
 ancestry-informative SVs exhibiting genomic clines that deviated from null
 expectations based on genome-average ancestry. Overall, hybrids exhibited
 a directional shift towards Jackson Hole Lycaeides ancestry at SV loci,
 consistent with the hypothesis that these loci experienced more selection
 on average than SNP loci. Surprisingly, we found that deletions, rather
 than inversions, showed the highest skew towards excess ancestry from
 Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids
 was also especially pronounced for Z-linked SVs and inversions containing
 many genes. In conclusion, our results show that SVs are ubiquitous and
 suggest that SVs in general, but especially deletions, might
 disproportionately affect hybrid fitness and thus contribute to
 reproductive isolation.
description: This data set includes a new, whole
 genome reference sequence for <em>Lycaeides melissa</em>. We
 used PacBio SMRT sequencing to improve our existing <em>L.
 melissa</em> reference genome, which was assembled from Chicago and
 Hi-C genomic libraries and comprised 24 large scaffolds corresponding to
 the 23 <em>L. melissa</em> linkage groups (22 autosomes and
 the Z sex chromosome, with a all but one chromosome represented by a
 single scaffold). High molecular weight DNA was extracted from a single
 female <em>L. melissa</em>. Following quality control, a HiFi
 library was constructed from purified DNA and sequenced using a PacBio
 Sequell 2 with a 30-hour HiFi SMRT cell. This generated 978,737
 (&gt;Q20) reads with a mean length of 18,683 bps (total length =
 18,286,022,199 &gt;Q20 bps). The BYU DNA Sequencing Center
 bioinformatics team then used these data to improve (extend and replace Ns
 with known bases) our existing genome. Gaps were filled in the assembly
 from Dovetail Genomics using PacBio HiFi reads using TGS-GapCloser v1.0.1.
 Given that the reads were Q20 or higher, the "‑‑ne" (i.e., skip
 error correction) option was used. Other than required parameters (e.g.,
 to provide the input reads and assembly), the only other non-default
 parameter was "‑‑tgstype pb" to specify the read type. Our input
 reference genome comprised 362 Mbps with 56% Ns, whereas after the
 gap-filling process our new reference genome spanned 521 Mbps with only
 6.8% Ns.<br><br>The data set also includes a vcf file with
 structural variant calls for <em>Lycaeides</em>. These
 variants were identified from Oxford nanopore DNA sequence data generated
 with a MinION. Genomic libraries for 37 butterflies were loaded onto R9.4
 flow cells (FLO-Min106, ONT) for sequencing for full 72 hour runs on a
 MinION. This generated an average of 7 GB of sequence data per library,
 with a N50 read length of 1114 to 20,944 bps (mean read length = 9073 bp;
 maximum read length of 342,840 bp). Base calling was performed using the
 ont-guppy algorithm from guppy_basecaller (version 4.2.2). We then used
 guppy_barcoder (version 4.2.2) to demultiplex the nanopore sequence reads
 and subsequently remove the barcode sequences. We used Minimap2 (version
 2.17) to align the nanopore reads to the reference genome, and we used
 Sniffles (version 1.0.12) and SURVIVOR (version 1.03) for structural
 variant calling. We then discarded all structural variants less than 1000
 bp in length.
description: Lmel_dovetailPacBio_genome.fasta = genome assembly for
 <em>Lycaeides melissa</em> in fasta format.
 merged_SURVIVOR_1kbpdist_typesave_new.vcf = structural variant
 file in vcf format.