Data from: Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range ...

• Main Authors: Clucas, Gemma V., Younger, Jane L., Kao, Damian, Rogers, Alex D., Handley, Jonathan, Miller, Gary D., Jouventin, Pierre, Nolan, Paul, Gharbi, Karim, Miller, Karen J., Hart, Tom
• Format: Dataset
• Language: English
• Published: Dryad 2016
• Subjects: genetic homogeneity; BayeScan; King penguin; molecular ecology; Southern Ocean; Aptenodytes patagonicus; SNPs; Antarctic; Antarc*; King Penguins
• Online Access: https://dx.doi.org/10.5061/dryad.7c0q8; https://datadryad.org/stash/dataset/doi:10.5061/dryad.7c0q8

Background: Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion. Results: We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of ... : King penguin filtered SNP datasetking_final_snp_dataset.vcfBayeScan_output_king_penguinsThe output from BayeScan saved as an Excel doc. BayeScan was run on the final dataset of 5154 king penguin SNPs with the prior odds of neutrality set to 5. The columns are in the same order as the standard "yourprefix_fst.txt" output file from BayeScan, but an additional column has been added which maps the input file locus index to the locus index used in the VCF.BayeScan_output.xlsxPython script for filtering .SAM formatted mapping files aligned with BWA memThe filter.py script works on sorted .SAM formatted mapping files from BWA mem alignment. For every pair of mapped forward and reverse reads, it parses out the CIGAR field (column 6 of the SAM file) and the MD tag to calculate the number of insertions, deletions, and mismatches. If a pair of reads have mismatches less than or equal to five and insertion/deletions less than or equal to two, then the pair is kept and printed to linux standard output. SAM header lines ...