DOI: 10.5061/dryad.dv41ns233
title: Data from: Genomics reveals the role of admixture in the evolution of structure among sperm whale populations within the Mediterranean Sea

description: In oceanic ecosystems, the nature of barriers to gene flow, and the
 processes by which populations may become isolated are different from the
 terrestrial environment, and less well understood. In this study, we
 investigate a highly mobile species (the sperm whale, Physeter
 macrocephalus) that is genetically differentiated between an open North
 Atlantic population and the populations in the Mediterranean Sea. We apply
 high-resolution single nucleotide polymorphisms (SNP) analysis to study
 the nature of barriers to gene flow in this system, comparing gene flow
 across the putative boundary into the Mediterranean (Strait of Gibraltar
 and Alboran Sea region) with novel analyses on structuring among sperm
 whale populations within the Mediterranean basin. Our data support a
 recent founding of the Mediterranean, around the time of the last glacial
 maximum, and shows concerted historical demographic profiles in both the
 Atlantic and the Mediterranean. In each region, there is evidence for a
 population decline around the time of the founder event, more extreme
 within the Mediterranean Sea where effective population size is
 substantially lower. While differentiation is strongest at the
 Atlantic/Mediterranean boundary, there is also significant differentiation
 between the Eastern and Western basins of the Mediterranean Sea. We
 propose, however, that the mechanisms are different. While post-founding
 gene flow was reduced between the Mediterranean and Atlantic populations,
 within the Mediterranean an important factor differentiating the basins is
 likely a greater degree of admixture between the Western basin and the
 North Atlantic.
description: Tissue samples were obtained
 during various research projects between 1999 and 2018. DNA
 was extracted both by kit (OMEGA BIOTEK and MN MACHEREY-NAGEL) following
 the manufacturer's protocol, and by the phenol chloroform method
 (after Hoelzel, 1998). Genomic DNA concentration was quantified using the
 Qubit High Sensitivity kit (Thermo Fisher Scientific). We applied the
 ddRADseq methodology (Peterson et al., 2012). Hoelzel,
 A. R. (1998) Molecular analysis of populations; a practical approach.
 Oxford, UK: Oxford University Press. Peterson, B. K., Weber, J. N., Kay, E. H.,
 Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: an
 inexpensive method for de novo SNP discovery and genotyping in model and
 non-model species. PloS one, 7(5), e37135. https://doi.org/10.1371/journal.pone.0037135
description: The two files, .ped and .map
 can be used within the R package <em>SambaR</em>
 (De Jong et al., 2021) in order to do SNP data management and analyses (https://github.com/mennodejong1986/SambaR.git). <strong>DATA FILTERING</strong> Once the dataset is imported, SNPs have to be filtered using the command filterdata(indmiss=0.5,snpmiss=0.05) to generate dataset A and filterdata(indmiss=0.25,snpmiss=0.05) for dataset B. <strong>EXPORT DATA FOR DIFFERENT ANALYSES</strong> input file to run Byesass, Treemix, Admixture, fst in Arlequin can be generated using the command exportsambarfiles()  PCoA, LEA, f4 statistics can be run using the command findstructure() in SambaR de Jong, M. J., de Jong, J. F., Hoelzel, A. R., & Janke, A. (2021). SambaR: An R package for fast, easy, and reproducible population‐genetic analyses of biallelic SNP data sets. Molecular Ecology Resources, 21(4), 1369-1379. https://doi.org/10.1111/1755-0998.13339