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Data for: Parallel recolonisations generate distinct genomic sectors in kelp following high magnitude earthquake disturbance

Citation

Vaux, Felix et al. (2022), Data for: Parallel recolonisations generate distinct genomic sectors in kelp following high magnitude earthquake disturbance, Dryad, Dataset, https://doi.org/10.5061/dryad.jdfn2z3bt

Abstract

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.

Methods

DNA was extracted and purified following the same method described in Peters et al. (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 D. antarctica 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 PstI-HF enzyme, following the GBS protocol described by Elshire et al. (2011), with the same modifications described by Peters et al. (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.

Usage Notes

Sampling, and genotype and loci fasta files
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

Stacks*
Shell files with commands and parameter settings used for each STACKS run.

maps*
Maps used to select individuals and populations in STACKS runs.

excluded_loci*
Lists used to exclude certain loci in STACKS runs.

plink-ld*
Ped and map input files and shell file with settings used by plink to estimate loci in LD.

vcftools-highly-correlated*
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.

vcftools-low-coverage*
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.

R*
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.

Phylogeographic modelling*
Commands and files for conducting phylogeographic model selection in delimitR. Includes observed folded multidimensional site frequency spectrum (mSFS) input file for the Recolonisation dataset.

Demultiplexed reads
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

Raw Illumina reads
Available on request, and we're working to archive all southern bull kelp raw reads on NCBI in the near future.

Further information
See this page: https://sites.google.com/view/evauxlution/data

*Also hosted on GitHub: https://github.com/fvaux/turakirae_d_antarctica_GBS

Funding

Royal Society Te Apārangi, Award: RDF-UOO1803