DOI: 10.5061/dryad.4tmpg4f6v
title: North Pacific harbor porpoise SNP and microhaplotype genotypes, mitochondrial control region haplotype sequences

description: Harbor porpoises in the North Pacific are found in coastal waters from
 southern California to Japan, but population structure is poorly known
 outside of a few local areas. We used multiplexed amplicon sequencing of
 292 loci and genotyped clusters of SNPs as microhaplotypes (N=271 samples)
 in addition to mtDNA sequence data (N=413 samples), to examine the genetic
 structure from samples collected along the Pacific coast and inland
 waterways from California to southern British Columbia. We confirmed an
 overall pattern of strong isolation-by-distance, suggesting that
 individual dispersal is restricted. We also found evidence of regions
 where genetic differences are larger than expected based on geographic
 distance alone, implying current or historical barriers to gene flow. In
 particular, the southernmost population in California is genetically
 distinct (FST = 0.02 (microhaplotypes); 0.31 (mtDNA)), with both reduced
 genetic variability and high frequency of an otherwise rare mtDNA
 haplotype. At the northern end of our study range, we found significant
 genetic differentiation of samples from the Strait of Georgia, previously
 identified as a potential biogeographic boundary or secondary contact zone
 between harbor porpoise populations. Association of microhaplotypes with
 remotely-sensed environmental variables indicated potential local
 adaptation, especially at the southern end of the species’ range. These
 results inform conservation and management for this nearshore species,
 illustrate the value of genomic methods for detecting patterns of genetic
 structure within a continuously distributed marine species, and highlight
 the power of microhaplotype genotyping for detecting genetic structure in
 harbor porpoises despite reliance on poor-quality samples.
description: Amplicon libraries were prepared following the GT-seq protocol,
 including the optional Exo-SAP pre-treatment of the samples (Campbell et
 al., 2015), and pooled libraries were sequenced on an Illumina NextSeq500
 sequencer, 1x150 bp reads. Custom scripts for processing GT-seq data
 (Campbell et al., 2015) were used to demultiplex the sample files and
 conduct preliminary genotyping. Genotypes were quality checked for
 duplicate samples, percent missing genotypes per locus and sample, and
 percent homozygosity using the <i>strataG</i> package in
 R. Microhaplotypes were generated for all loci using
 the R package <i>MicrohaPlot</i> (Baetscher et al., 2017). The
 <i>MicrohaPlot</i> algorithm inserts N’s for missing sequence
 data at SNPs within haplotypes, so we used a custom R-scripts
 (supplemental materials) to identify SNPs with &gt;10% N’s. The
 identified SNPs were removed from the original vcf file using vcfTools,
 and <i>MicrohaPlot</i> was used to generate new
 microhaplotypes with the remaining variable SNP positions. The unfiltered
 haplotypes were exported for subsequent filtering with custom scripts to
 view and call genotypes. Mitochondiral DNA control
 region haplotype sequences were generated using Sanger dideoxy sequencing
 of PCR products, sequenced in both directions. 
description: Sample ID's, collection location (Latitude, Longitude) and a
 priori geographic stratification are provided in Table S1 of the
 supplemental materials.