DOI: 10.5061/dryad.jdfn2z3bt
title: Data for: Parallel recolonisations generate distinct genomic sectors in kelp following high magnitude earthquake disturbance

description: Large-scale disturbance events have the potential to drastically reshape
 biodiversity patterns. Notably, newly vacant habitat space cleared by
 disturbance can be colonised by multiple lineages, which can lead to the
 evolution of distinct spatial ‘sectors’ of genetic diversity within a
 species. We test for disturbance-driven sectoring of genetic diversity in
 intertidal southern bull kelp, Durvillaea antarctica (Chamisso) Hariot
 following the high-magnitude 1855 Wairarapa earthquake in New Zealand.
 Specifically, we use genotyping-by-sequencing (GBS) to analyse fine-scale
 population structure across the uplift zone to assess the fit of
 alternative recolonisaton models. Our analysis reveals that specimens from
 the uplift zone carry genomic signatures distinct from populations in
 other regions, consistent with recolonisation after the 1855 earthquake.
 Crucially, our analysis identifies two parapatric spatial-genomic sectors
 of D. antarctica at Turakirae Head, which experienced the most dramatic
 uplift. We infer that bull kelp in the Wellington region survived moderate
 uplift and recolonised the devastated Turakirae Head coastline through two
 parallel, eastward recolonisation events. By identifying multiple
 parapatric genotypic sectors within a recently recolonised coastal region,
 the current study confirms that competing lineage expansions can generate
 striking spatial structuring of genetic diversity, even in highly
 dispersive taxa.
description: DNA was extracted and purified following the same method
 described in Peters <i>et al. </i>(2020), except that we used
 the updated Qiagen DNeasy Plant Pro DNA extraction kit. The kit protocol
 was followed, except that the lysis step was extended to 24 hours, and
 immediately after lysis, samples were treated with 100 µl isopropanol and
 incubated at 65°C for 30 minutes, vortexing every 15 minutes. Three new
 GBS libraries including 185 <i>D. antarctica </i>samples were
 used for this study (Supplementary Table 1; Appendix A). We also used GBS
 data for four samples sequenced within a previous study (Peters et al.,
 2020), bringing the total number of analysed individuals to 189
 (Supplementary Table 1; Appendix A). DNA was digested using the
 <i>PstI-HF </i>enzyme, following the GBS protocol described by
 Elshire <i>et al. </i>(2011), with the same modifications
 described by Peters <i>et al.</i> (2020). The size selection
 varied between 200 – 500 bp and 200 – 600 bp (Supplementary Table 1). The
 four libraries were sequenced on four separate runs using mid output flow
 cells on the Illumina NextSeq 500 platform (75 bp paired-end;
 Supplementary Table 1). stacks 2.53
 (Rochette, Rivera-Colón, & Catchen, 2019) was used to demultiplex
 samples into paired forward and reverse reads per individual, using inline
 barcodes and call variant loci.
description: <strong>Sampling, and genotype and loci fasta
 files</strong><br>Full sample details (Appendix A),
 supplementary methods, tables, and figures (Appendix B), GBS files (loci
 consensus sequences, genotype files, phylogenetic alignments, trees, and
 all commands and files provided on GitHub) are available in this DataDryad
 repository. Appendices A and B are also hosted with the main text: https://doi.org/10.1111/mec.16535 <strong>Stacks</strong>*<br>Shell files with commands and parameter settings used for each STACKS run. <strong>maps</strong>*<br>Maps used to select individuals and populations in STACKS runs. <strong>excluded_loci</strong>*<br>Lists used to exclude certain loci in STACKS runs. <strong>plink-ld</strong>*<br>Ped and map input files and shell file with settings used by plink to estimate loci in LD. <strong>vcftools-highly-correlated</strong>*<br>Shell file with commands and the recoded VCF files used to estimate highly correlated loci (additional filtering step for alternative filtered dataset). Text file lists loci added for alternative dataset excluded loci list. <strong>vcftools-low-coverage</strong>*<br>Shell file with commands and the recoded VCF files used to estimate low coverage genotypes and loci (first filtering step). Text file lists loci added for first list of excluded loci. <strong>R</strong>*<br>R files for running loci filtering (e.g. loci coverage depth outliers) and population genetic analyses (e.g. adegenet, LEA). I recommmend viewing original source GitHub pages and tutorials noted in each R file credits. Includes example R project and geno files for LEA analyses. <strong>Phylogeographic modelling</strong>*<br>Commands and files for conducting phylogeographic model selection in delimitR. Includes observed folded multidimensional site frequency spectrum (mSFS) input file for the Recolonisation dataset. <strong>Demultiplexed reads</strong><br>Demultiplexed forward and reverse DNA sequence reads for the southern bull-kelp sequenced in this study are openly available on the NCBI sequence read archive (SRA) under: PRJNA769149, http://www.ncbi.nlm.nih.gov/bioproject/PRJNA769149 <strong>Raw Illumina reads</strong><br>Available on request, and we're working to archive all southern bull kelp raw reads on NCBI in the near future. <strong>Further information</strong><br>See this page: https://sites.google.com/view/evauxlution/data *Also hosted on GitHub: https://github.com/fvaux/turakirae_d_antarctica_GBS