DOI: 10.5061/dryad.7c0q8
title: Data from: Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range

description: 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
 kilometers of open-ocean, suggesting migration among islands and
 archipelagos may be common. Our results show that the South Georgia
 population is slightly differentiated from all other colonies and suggest
 that the recently founded Falkland Island colony is likely to have been
 established by migrants from the distant Crozet Islands rather than nearby
 colonies on South Georgia, possibly as a result of density-dependent
 processes. Conclusions: The observed subtle differentiation among king
 penguin colonies must be considered in future conservation planning and
 monitoring of the species, and demographic models that attempt to forecast
 extinction risk in response to large-scale climate change must take into
 account migration. It is possible that migration could buffer king
 penguins against some of the impacts of climate change where colonies
 appear panmictic, although it is unlikely to protect them completely given
 the widespread physical changes projected for their Southern Ocean
 foraging grounds. Overall, large-scale population genetic studies of
 marine predators across the Southern Ocean are revealing more
 interconnection and migration than previously supposed.
description: 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 are ignored by the parser but also printed to standard output for compatible down-stream analysis.filter.py