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Data from: Genomics detects population structure within and between ocean basins in a circumpolar seabird: the white-chinned petrel

Citation

Rexer-Huber, Kalinka et al. (2020), Data from: Genomics detects population structure within and between ocean basins in a circumpolar seabird: the white-chinned petrel, Dryad, Dataset, https://doi.org/10.5061/dryad.v9s4mw6qd

Abstract

The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (Procellaria aequinoctialis) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and 1st domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.

Methods

Rexer-Huber_WCP_cytb.fasta is haplotypes of the mitochondrial cytochrome b haplotypes (~1200 bp) for white-chinned petrels, produced via Sanger sequencing on an ABI 3730xl DNA analyser.

Rexer-Huber_cytb_haplotype-sample_table.xlsx links haplotype names to the original petrel samples.

Rexer-Huber_WCP_CR1D.fasta is haplotypes of the first domain of the mitochondrial control region (~559 bp) for white-chinned petrels, produced by Sanger sequencing on an ABI 3730xl DNA analyser. Haplotypes are named according to sample and location of origin.

File Rexer-Huber_GBS_s_4_fastq.txt.gz is the raw reads produced by genotyping-by-sequencing. Genomic DNA was digested with PstI and MspI. Size selection to 193-500 bp. Library sequenced on Illumina HiSeq2500 using single-end reads, with 101 cycles in high-output mode (v4 chemistry).

Rexer-Huber_GBS_barcodes.txt is the barcodes.

Further datasets are stored on the Molecular Ecology website as Supporting Data files with the publication. These are: Supp Data A WCP outliers.xlsx (outputs from outlier analyses), Supp Data B WCP fulmar map.xlsx (loci mapped to the northern fulmar genome), and Supp Data C WCP outliers combined genepop.txt (outlier loci for GenePop analyses).

Usage Notes

A ReadMe is provided to identify datasets, define abbreviations, and describe related datasets stored elsewhere.

Rexer-Huber_cytb_haplotype-sample_table.xlsx links cytochrome b haplotype names to the original petrel samples.

Throughout, abbreviations for sampling location are: ANT Antipodes; CAM Campbell; AKL Auckland; SG South Georgia; FK Falkland Islands; CRO Crozet; MAR Marion; KER Kerguelen; AIO haplotype ocurring across more than one Atlantic-Indian Ocean island.