Population Genetic Structure of Atlantic Cod in US Waters

Adrienne Kovach

Cod Population Structure and New England Fisheries Symposium: Furthering Our Understanding by integrating knowledge gained through science and fishing

Overview of Genetic Studies in US & Neighboring Canadian Waters

Studies with Microsatellite Markers & Pan I Western Gulf of Maine, Southern New England & NE Georges Bank

o Wirgin et al. 2007, Kovach et al. 2010Western Georges Bank/Great South Channel – eastern Georges Bank

o Weiss et al. (2005 unpublished report) Georges Bank – Browns Bank

o Lage et al. 2004, Ruzzante et al. 1998

Recent Genomic Studies with SNP markers (single nucleotide polymorphisms)wGoM + Georges Bank – whole genomes (3 chromosomes)

o Barney et al. 2017Western GoM, eastern GoM, NE Georges Bank – SNP (& microsat) markers

o unpublished NOAA report - Kerr, Cadrin, Kovach et alComprehensive US waters & Canadian reference pops – genome-wide SNPs

o Ongoing, preliminary results – Kovach, Therkildsen, Clucas, Louo Ongoing, preliminary results – Puncher, Wang, et al.

Two Kinds of Genetic Variation

Adaptive Variation – associated with a gene and functionunder the influence of natural selection

Neutral Variation – not associated with a gene and functionnot under the influence of natural selection

o Connectivity through adult movements & larval dispersal

o Ecological adaptation to local environmental conditions

Patterns & considerations

• Atlantic cod populations show genetic differences on fine to broad scales, on both sides of Atlantic

• Genetic differentiation can be small –large effective population sizes

• Divergence at adaptive markers is common driven by 4 chromosomeslinked to environment & ecotype

Acknowledgements

Fishing Industry Partners *sample collection & critical knowledge of spawning groundsBill AmaruFrank Blount Carl BouchardJeff CarverDavid GoethelFrank MirarchiChris OdlinIan ParenteProctor Wells

Studies with Microsatellites & Pan I Marker

gene-associated marker (adaptive)

Heterogeneity in western GoMo mixed juvenile collections in Mass Bayo Spring Spawning adults in Ipswich Bay different from all other spawning pops Georges Bank differentiated from southern NE & wGoMConnections btwn wGoM, southern NE, NY Bight (nonspawning)

Consistent with Lage et al. 2004

Population Structure in US Waters – Wirgin et al. 2007

Northern Spring ComplexInshore wGOM – spring spawning

Southern ComplexInshore wGOM winter spawningOffshore wGOMSouthern New England

Georges Bank

o 3 primary spawning complexes o Spatial overlap in wGomo Genetic structure ≠ management units

Temporally stable structure across 5 years

SCNSC

Population Structure in US Waters – Kovach et al. 2010

1) Population Structure was driven by two adaptive markers

2) Differences associated with: temperature, salinity, depth, growth

3) Population structure was not apparent with neutralmarkers only

Western GB (west of Great South Cannel) vs. eastern GB Weiss et al. 2005, unpublished report:

Spawning Adults West of GSC different from eastern GB

Larvae in Shoals and GSC assigned to spawners west of GSC

Consistent with Wirgin et al. 2007; Kovach et al. 2010; Lage et al. 2004 – Chatham/Nantucket vs. eastern GB

Kovach et al. 2010

Working Hypothesis for Population Structure & Identified data gaps

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Motivation for recent studies Using higher resolution genomic methods

Recent & Ongoing Studies with Genome-wide Single Nucleotide Polymorphism (SNP) Markers

Ipswich Bay

Massachusetts Bay

Dec -Jan

April -May

Western Gulf of Maine Spawning Populations

2013-2015 samples

Kerr, Cadrin, Sherwood, Zemeckis, Goethel, Whitener, Clucas, Kovach

o Three Methods (Otoliths, Morphometrics & Genetics) showed differences between Winter & Spring Spawners in wGoM

o Support the hypothesis that winter and spring are distinct ecological units with adaptive life history differences

• 1230 genome-wide SNP markers discriminate winter and spring spawners in both bays

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Ipswich Bay - springMass. Bay - springIpswich Bay - winterMass. Bay - winter

Proportion of correct assignments(SNP dataset)

o Seasonal divergence o Weak fine-scale spatial differences

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Spring Winter

Proportion of correct assignments(SNP dataset)97% 98% Assignment accuracy: 92-96%

o Individuals classified to source populations with high accuracy

n = 24 per group

IP_Spring

MB_Spring

IP_Winter

MB_Winter

CF_May

CF_June

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CF_Mar

CF_Dec

CF_Jan

OtoT1-513

OtoT1-514

OtoT2-513

OtoT2-514

OtoT2-515

Coor

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Coord. 1

• Comparison of Historical & Modern Fishery with Spawning Populationso Shift in population components comprising the

fishery – away from spring-spawning types

Microsatellite & Pan I dataset NOAA Otolith Archive - Stat A: 513,514,5151979-1982; 1989-1992

How does eastern Gulf of Maine Fit into the Picture of Cod Population Structure?

Historical records indicate greater complexity of structure in GoM

Ames 2004

Yong Chen, Anna Henry, Mattie Rodrigue, John Carlucci - UMaineRobin Alden, Ted Ames

Non-spawning fish Sentinel Fishery

How does eastern Gulf of Maine Fit into the Picture of Cod Population Structure?

Georges Bank

Sentinel FisheryeGoM

o Cod in the Sentinel Fishery do not originate from the wGoMo Possible connection to Georges Bank or nearby waters

3128 genome-wide SNP markers

Gemma Clucas et al., manuscript

• Adaptive vs. Neutral Markers

o Differences primarily driven by adaptive markerso On 2 of the 4 chromosomes differentiated in other studies

o Weak neutral differentiation as well.

All 3128 SNP markers 2689 neutral SNP markers (adaptive markers removed)

Georges Bank

Sentinel FisheryeGoM

Georges Bank

Barney et al. 2017 – spring wGoM, winter wGoM, GBgenome-wide SNPs, focus on 3 chromosomes (adaptive)n = 10-11 cod per group (small sample size)

o Differences between Winter & Spring Spawners: “candidate” genes related to temperature-associated physiological differences

o Largest genetic differences overall between Georges Bank and Winter Spawners

Ruzzante et al. 1998, 1999Lage et al. 2004

Prior work suggests connections between Bay of Fundy & Browns Bank, but uncertainty about connections of Bay of Fundy & Browns to GoM & GB

o Missing samples from Bay of Fundy, Browns Bank for comparison…until now...

Broadening the picture to Canadian Waters

Preliminary Results from Ongoing Research

WESTPOPCOD ConsortiumPrincipal InvestigatorsDr. Geneviève Parent Fisheries and Oceans Canada, Maurice-Lamontagne Institute Dr. Yanjun Wang Fisheries and Oceans Canada, St. Andrews Biological Station

Internal collaborators (Fisheries and Oceans Canada)Ryan Martin and Donald ClarkSt. Andrews Biological Station Éric Parent, Dr. Yvan Lambert and Claude Brassard Maurice-Lamontagne Institute

Dr. Rick RideoutNorth West Atlantic Fisheries Center Luc SavoieGulf Fisheries Centre

External CollaboratorsDr. Scott Pavey, Dr. Gregory Neils Puncher (lead researcher),Nathalie Leblanc and Nadine NziroreraUniversity of New Brunswick/Canadian Rivers Institute, Canada Dr. Steve Cadrin and Dr. Douglas ZemeckisUniversity of Massachusetts, USA Dr. Gregory DeCellesMassachusetts Division of Marine Fisheries, USA Dr. Kris VascottoGroundfish Enterprise Allocation Council, Canada Dr. Sherrylynn Rowe Memorial University of Newfoundland, Canada Dr. Arnault Le Bris Fisheries and Marine Institute of Memorial University, Canada

Ongoing Research

Preliminary analysis of samplesfrom the Gulf of Maine

Ongoing Research Gemma Clucas, Adrienne Kovach Nicolas Lou, Nina Therkildsen

7 million genome-wide SNP markers

Zemeckis et al. 2014

• Hypothesized Population Genetic Structure

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Is this model consistent with your knowledge, interpretation, & observations?