DOI: 10.5061/dryad.vmcvdnczp
title: Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales

description: Understanding how interactions among microevolutionary forces generate
 genetic population structure of exploited species is vital to the
 implementation of management policies that facilitate population
 persistence. Philopatry displayed by many coastal shark species can impact
 gene flow and facilitate selection, and thus has direct implications for
 the spatial scales of management plans. Here, genetic structure of the
 blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker
 approach based on mitochondrial control region sequences and 4,339
 SNP-containing loci generated using ddRAD-Seq. Genetic variation was
 assessed among young-of-the-year sampled in 11 sites in waters of the
 United States in the western North Atlantic Ocean, including the Gulf of
 Mexico. Spatial and environmental analyses detected 68 nuclear loci
 putatively under selection, enabling separate assessments of neutral and
 adaptive genetic structure. Both mitochondrial and neutral SNP data
 indicated three genetically distinct units – the Atlantic, eastern Gulf,
 and western Gulf – that align with regional stocks and suggest regional
 philopatry by males and females. Heterogeneity at loci putatively under
 selection, associated with temperature and salinity, was observed among
 sites within Gulf units, suggesting local adaptation. Furthermore, five
 pairs of siblings were identified in the same site across timescales
 corresponding with female reproductive cycles. This indicates that females
 re-used a site for parturition, which has the potential to facilitate the
 sorting of adaptive variation among neighboring sites. The results
 demonstrate differential impacts of microevolutionary forces at varying
 spatial scales and highlight the importance of conserving essential
 habitats to maintain sources of adaptive variation that may buffer species
 against environmental change.
description: Fin clips were collected from blacktip sharks
 (<em>Carcharhinus limbatus</em>) within or near 11 estuaries
 used for parturition in waters of the United States in the western North
 Atlantic Ocean. A modified version of double digest restriction-site
 associated DNA sequencing (ddRAD-Seq) was used to prepare genomic
 libraries containing 488 young-of-the-year individuals plus technical
 replicates, which were sequenced using 11 lanes of an Illumina HiSeq 4000
 (paired-end 150 bp reads). To map and improve the genotyping efficacy of
 HiSeq data, a separate library consisting of 27 individuals sampled across
 Atlantic and Gulf locations at multiple life-history stages was prepared
 using the same protocol but sequenced on an Illumina MiSeq lane
 (paired-end 300 bp reads). All MiSeq and HiSeq reads
 were quality-trimmed using default parameters in dDocent. dDocent was also
 used to assemble MiSeq reads into a reduced genomic reference. dDocent was
 then used to map HiSeq reads to the MiSeq reference and genotype
 SNPs. SNPs were filtered using VCFtools and R functions
 in a customized workflow. Subsequently, haplotypes were generated by
 collapsing SNPs on the same contig to produce a multi-allelic
 SNP-containing loci dataset. Technical replicates and non-randomly sampled
 kin were then removed. In addition, a 915 bp portion of
 the mitochondrial control region (1070 bp total length) was amplified for
 a subset of individuals.
description: The MiSeq reference, `dDocent` config files, `genepop` file, and
 strata data can be opened and viewed in a text editor. The `.arp` and
 `.ars` files can also be opened and viewed in a text editor but should be
 executed in Arlequin.