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Genomic population structure of striped bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River

Citation

LeBlanc, Nathalie et al. (2020), Genomic population structure of striped bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River, Dryad, Dataset, https://doi.org/10.5061/dryad.9kd51c5dd

Abstract

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.

Methods

Sample Collection

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 (<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.

 

Laboratory

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.

 

Quality Control and Analysis

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 process radtags 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 pstacks 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 cstacks, sstacks, and rxstacks with default settings, and unclear or unlikely haplotypes, as well as SNPs with a log likelihood < 45, were pruned from the dataset. Using the populations module, SNPs were further filtered to remove all loci with a stack depth <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 < -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 < 0.01, and plink v. 1.90 (Chang et al., 2015) was used to remove loci in linkage disequilibrium with each other.

Usage Notes

structure_stripedbass_allLoci_noSibs

This STRUCTURE file contains 1291 RAD-seq derived SNPs detected among 477 Striped Bass, Morone saxatilis, 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.
structure_stripedbass_allLoci_noSibs.str

 

structure_stripedbass_neutralLoci_noSibs   

This STRUCTURE file contains 1256 putatively neutral RAD-seq derived SNPs detected among 477 Striped Bass, Morone saxatilis, 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.
structure_stripedbass_neutralLoci_noSibs.str   


 
genepop_stripedbass_allLoci_noSibs.gen

This STRUCTURE file contains 1256 putatively neutral RAD-seq derived SNPs detected among 477 Striped Bass, Morone saxatilis, 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.

 

Distances.xlsx

Spreadsheet containing approximate distances in kilometres between rivers used in isolation-by-distance calculations.

Funding

Canada Research Chairs

Massachusetts Division of Marine Fisheries

Natural Sciences and Engineering Research Council of Canada

New Brunswick Innovation Foundation

U.S. Fish and Wildlife Service, Sportfish Restoration Program, Award: F-57-R-24

University of New Brunswick

Massachusetts Division of Marine Fisheries

U.S. Fish and Wildlife Service, Sportfish Restoration Program, Award: F-57-R-24