DOI: 10.5061/dryad.v41ns1rw6
title: Data for: Northward range extension for Durvillaea poha bull kelp: response to tectonic disturbance?

description: Data for: Vaux F, Craw D, Fraser CI, Waters JM. (2021). Northward range
 extension for Durvillaea poha bull kelp: response to tectonic disturbance?
 Journal of Phycology. https://doi.org/10.1111/jpy.13179
 Understanding the forces that shape species distributions is increasingly
 important in a fast-changing world. Although major disturbance events can
 adversely affect natural populations, they can also present new
 opportunities, for example by opening up habitat for colonisation by other
 lineages. Following extensive geographic sampling, we use genomic data to
 infer a range extension following disturbance for an ecologically
 important intertidal macroalgal species. Specifically, we genotyped 288
 bull-kelp (Durvillaea) plants from 28 localities across central New
 Zealand. All specimens from the North Island were expected to be D.
 antarctica, but unexpectedly 10 samples from four sites were unexpectedly
 identified as D. poha. Extensive sampling from the northern South Island
 (105 samples at five locations) confirmed the absence of D. poha north of
 the Kaikōura Peninsula. The North Island specimens of D. poha therefore
 reveal a biogeographic disjunction, some 150 km northeast of the nearest
 (South Island) population of this species. Based on strong geographic
 correspondence between these North Island samples and historic
 disturbance, we infer that tectonic upheaval, particularly
 earthquake-generated landslides, likely extirpated local D. antarctica and
 created an opportunity for a northward range expansion event by D. poha.
 Close phylogenomic relationships between this new North Island population
 and South Island samples supports a geologically recent northward
 expansion, rather than a deeper evolutionary origin. These findings
 indicate the potential of large-scale disturbances to facilitate sudden
 biogeographic range expansions, and they emphasise the ability of genomic
 analyses with fine-scale sampling to reveal long-lasting signatures of
 past disturbance, dispersal and colonisation.
description: DNA was extracted and purified following the same method
 described in Peters et al.<i> </i>(2020), except that the new
 Qiagen DNeasy Plant Pro DNA extraction kit replaced the equivalent
 decommissioned Qiagen PowerPlant Pro kit. Samples were used for
 genotyping-by-sequencing (GBS; Elshire et al. 2011). 14 new <i>D.
 poha</i> samples were sequenced across three GBS libraries, which
 contained a total of 340 <i>Durvillaea </i>southern bull-kelp
 samples, plus 61 samples belonging to unrelated taxa. The GBS sequencing
 followed an almost identical method to the previous studies (Parvizi et
 al. 2020, Peters et al. 2020), with size selections varying between 200 –
 500 bp and 200 – 600 bp. stacks 2.53
 (Rochette et al. 2019) was used to demultiplex samples into paired forward
 and reverse reads per individual, call loci, and estimate genotypic
 variation among samples.
description: # north_island_d_poha_GBS # Stacks<br>
 Shell files with commands and parameter settings used for each STACKS
 run. # maps<br> Maps used to select individuals
 and populations in STACKS runs. #
 excluded_loci<br> Lists used to exclude certain loci in STACKS
 runs. # plink-ld<br> Ped and map input files and
 shell file with settings used by plink to estimate loci in LD.
 # vcftools-highly-correlated<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. Includes
 input VCF file (i.e. main filtered dataset). #
 vcftools-low-coverage<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. # R<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. # Sampling, and genotype
 and loci fasta files<br> Supplementary tables, figures, methods and
 results (Appendix S1), full sample details (Appendix S2), COI sequences
 (Appendix S3), GBS files (loci consensus sequences, genotype files,
 phylogenetic alignments, trees) are available here
 on DataDryad.  # Demultiplexed reads<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: PRJNA683976,
 http://www.ncbi.nlm.nih.gov/bioproject/683976 # Raw
 Illumina reads<br> Available on request, and we're working to
 archive all southern bull-kelp raw reads on NCBI in the near
 future. # Further information<br> See this page:
 https://sites.google.com/view/evauxlution/data