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Data for: Northward range extension for Durvillaea poha bull kelp: response to tectonic disturbance?

Citation

Vaux, Felix; Craw, Dave; Fraser, Ceridwen I.; Waters, Jonathan M. (2021), Data for: Northward range extension for Durvillaea poha bull kelp: response to tectonic disturbance?, Dryad, Dataset, https://doi.org/10.5061/dryad.v41ns1rw6

Abstract

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 Phycologyhttps://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.

Methods

DNA was extracted and purified following the same method described in Peters et al. (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 D. poha samples were sequenced across three GBS libraries, which contained a total of 340 Durvillaea 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.

Usage Notes

# north_island_d_poha_GBS

# 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. Includes input VCF file (i.e. main filtered dataset).

# 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.

# Sampling, and genotype and loci fasta files
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
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
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

Funding

Royal Society Te Apārangi, Award: Marsden Fund grant (18-UOO-172)

Rutherford

Royal Society Te Apārangi, Award: Rutherford Discovery Fellowship (RDF-UOO1803)

Rutherford