DOI: 10.5061/dryad.9kd51c5dd
title: Genomic population structure of striped bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River

description: Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish
 species that supports fisheries throughout North America and is native to
 the North American Atlantic Coast. Due to long coastal migrations that
 span multiple jurisdictions, a detailed understanding of population
 genomics is required to untangle demographic patterns, understand local
 adaptation, and characterize population movements. This study used 1256
 single nucleotide polymorphism (SNP) loci to investigate genetic structure
 of 477 Striped Bass sampled from 15 locations spanning the North American
 Atlantic coast from the Gulf of St. Lawrence, Canada to the Cape Fear
 River, United States (US). We found striking differences in neutral
 divergence among Canadian sites, which were isolated from each other and
 US populations, compared with US populations that were much less isolated.
 Our SNP dataset was able to assign 99% of Striped Bass back to six
 reporting groups, a 39% improvement over previous genetic markers. Using
 this method, we found (1) evidence of admixture within Saint John River,
 indicating that migrants from the US and from Shubenacadie River
 occasionally spawn in the Saint John River; (2) Striped Bass collected in
 the Mira River, Cape Breton, Canada were found to be of both Miramichi
 River and US origin ; (3) juveniles in the newly restored Kennebec River
 population had small and nonsignificant differences from the Hudson River;
 and (4) tributaries within the Chesapeake Bay showed a mixture of homogeny
 and small differences among each other. This study introduces new
 hypotheses about the dynamic zoogeography of Striped Bass at its northern
 range and has important implications for the local and international
 management of this species.
description: <b><i>Sample
 Collection</i></b> Fin clips and scales were taken
 from Striped Bass from multiple collections (Table 1). Age of sampled
 individuals differed by location. YOY juveniles were individuals less than
 1 year old (&lt;15 cm long). Saint John juveniles were 1–4 years old
 and largely spawned in the year 2013. Ages for Saint John River juveniles
 were obtained from scales. Adults were sexually mature individuals aged 4
 years and older. All adults collected were in spawning condition at time
 of sampling, except for Bras d’Or Lake, Mira River, and Shubenacadie
 River. Shubenacadie origin Striped Bass migrate to the
 Stewiacke-Shubenacadie systems from overwintering sites during the
 sampling period (DFO, 2014; Keyser, Broome, Bradford, Sanderson, &
 Redden, 2016). Adult bass caught during this period are assumed to be of
 Shubenacadie River origin for the purpose of population surveys (DFO,
 2014). Putative Miramichi River origin Striped Bass were included using
 fin clips taken from Striped Bass caught in the Bras d’Or Lake, Cape
 Breton that have previously been examined using microsatellites and found
 to match the Miramichi River population (Bentzen, Mcbride, &
 Paterson, 2014). These samples will hereafter be referred to as Bras
 d’Or–Miramichi individuals.   <b><i>Laboratory</i></b> DNA was isolated using either NucleoMag® 96 Tissue (Machery-Nagel, Düren, Germany) kit on an epMotion 5075t (Cat. 5075000302), or the E.Z.N.A. Tissue DNA Kit (Omega Bio‐Tek, Doraville, CA). Libraries containing 96 individuals each were prepared using a double-digest restriction-site associated DNA sequencing (ddRAD-seq or ddRAD) protocol developed by Poland et al. (2012) and modified as described in LeBlanc et al. (2018). Samples were randomized so that each lane contained individuals from multiple locations and sequenced using Illumina® HiSeq™ 2500 or Illumina® HiSeq™ 4000 (San Diego, U.S.A.) at Génome Québec Innovation Centre.   <b><i>Quality Control and Analysis</i></b> SNPs were demultiplexed and filtered using modified versions of Eric Normandeau’s Stacks workflow scripts, available on github (https://github.com/enorman deau/stacks_workflow, downloaded August 2016). Cutadapt v. 1.13 (Martin, 2011) was used to trim adapters from the raw sequences using a maximum error rate (e) of 0.2 and a minimum read length (m) of 50. FastQC v. 0.11.5 (Babraham Bioinformatics) was used to assess sequence quality before and after. Sequences were then trimmed to a uniform length of 85 bp and demultiplexed using the <i>process radtags</i> module of Stacks v. 1.46 (Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013) using the paired end option –P. BWA version 0.7.15 (Li & Durbin, 2010) was used to align sequences to the Striped Bass genome (BioProject accession number PRJNA266827) using a minimum seed length (k) of 19, a maximum seed occurrence of 55, and no filtering on output alignment score, and otherwise default parameters. The stacks module <i>pstacks</i> identified reference aligned loci with a minimum depth (m) of 4 using the “snp” model type and an alpha of 0.1. Loci were assembled into a catalogue using <i>cstacks</i>, <i>sstacks</i>, and <i>rxstacks</i> with default settings, and unclear or unlikely haplotypes, as well as SNPs with a log likelihood &lt; 45, were pruned from the dataset. Using the <i>populations</i> module, SNPs were further filtered to remove all loci with a stack depth &lt;5, with greater than 20% missing data in any given location, and any loci not amplified in all locations. We examined the output of populations and removed loci with an Fis &lt; -0.3 to eliminate possible paralogs, and used VCFTools 0.1.13 (Danecek et al., 2011) to remove any loci with a minor allele frequency &lt; 0.01, and plink v. 1.90 (Chang et al., 2015) was used to remove loci in linkage disequilibrium with each other.
description: structure_stripedbass_allLoci_noSibs This
 STRUCTURE file contains 1291 RAD-seq derived SNPs detected among 477
 Striped Bass, <em>Morone saxatilis</em>, individuals collected
 from 14 locations. SNPs were called by stacks v1.46, and missing data is
 encoded as '-9'. Parameters are outlined in the methods above
 and in the associated manuscript.<br>
 structure_stripedbass_allLoci_noSibs.str  
 <strong>structure_stripedbass_neutralLoci_noSibs   </strong> This STRUCTURE file contains 1256 putatively neutral RAD-seq derived SNPs detected among 477 Striped Bass, <em>Morone saxatilis</em>, individuals collected from 14 locations. SNPs were called by stacks v1.46, and missing data is encoded as '-9'. Parameters are outlined in the methods above and in the associated manuscript.<br> structure_stripedbass_neutralLoci_noSibs.str    <br>  <br> genepop_stripedbass_allLoci_noSibs.gen This STRUCTURE file contains 1256 putatively neutral RAD-seq derived SNPs detected among 477 Striped Bass, <em>Morone saxatilis</em>, individuals collected from 14 locations. SNPs were called by stacks v1.46, and missing data is encoded as '-9'. Parameters are outlined in the methods above and in the associated manuscript.   batch_1.MiraOnlyNT80.fa This FASTA file contains the full fragment sequences that contain the 1291 SNPs present in other input files. Use the loci_codes.csv file to convert loci names to genomic position   loci_codes.csv    Loci_codes.csv gives the full genome position of all loci. Loci are aligned to assembly GCA_001663605.1 of the Striped Bass genome.   <b>Distances.xlsx</b> Spreadsheet containing approximate distances in kilometres between rivers used in isolation-by-distance calculations.