Tim King, US DOI, USGS Barbara Lubinski, US DOI, USGS Tim Sheehan, US DOC, NOAA Fisheries Dave Reddin, CA, DFO

Determining the continent-of-origin and regionof-origin for Atlantic salmon collected at West Greenland from 1995-2010: A review of the findings and a look at what the future holds for molecular genetic methods of mixed-fishery assessment (in 15 minutes?) Tim King, US DOI, USGS Barbara Lubinski, US DOI, USGS Tim Sheehan, US DOC, NOAA Fisheries Dave Reddin, CA, DFO

Determining the continent-of-origin and regionof-origin for Atlantic salmon collected at West Greenland from 1995-2010: A review of the findings and a look at what the future holds for molecular genetic methods of mixed-fishery assessment Tim King, US DOI, USGS Barbara Lubinski, US DOI, USGS Tim Sheehan, US DOC, NOAA Fisheries Dave Reddin, CA, DFO

Presentation Objectives Briefly review the phylogeographic patterns observed among Atlantic salmon populations from mtdna and ndna Discuss the results of west Greenland mixed-fishery analysis at two scales: continent-of-origin (COO) & region-of-origin (ROO) Compare the results of individual assignment (IA) with mixedstock (MSA) analyses Test the temporal robustness and allele frequency stability of the Atlantic salmon baseline database at assigning populations represented in the West Greenland mixed-fishery to COO

Metric Tons Historic Commercial Atlantic Salmon Fishery at Greenland (1960-2003) 3,000 Catch Quota 2,500 2,000 1,500 1,000 500 0 1960 1963 1966 1969 1972 1975 1978 1981 1984 1987 1990 1993 1996 1999 2002 Year

mtdna Control Region (CR) Haplotype Networks A, G, I, J, K CR more variable in western Atlantic populations I ND1 haplotypes also observed in these populations by Verspoor et al. 1999 and Nilsson et al. 2001. I I A B A, C B, C, E, I, J A, B, C, D, E, F G D A F C B E H I J K I

Western Atlantic NJ Tree - D a Distance Range-wide Perspective from 11 microsatellite DNA loci Eastern Atlantic/Baltic

Summary of Phylogeographic/Population Studies Over 5,000 Atlantic salmon have been genotyped at 12 microsatellite loci Western Atlantic populations of salmon are genetically distinct from Eastern Atlantic populations. Microsatellite DNA results confirm findings from mtdna and other nuclear markers (e.g., alloyzmes, mini-satellite DNA) Wild salmon in Maine are genetically distinct from Canadian salmon Genetic divergence exists among populations of wild salmon in Maine rivers and among Canadian Provinces; similar patterns exist among eastern Atlantic populations (3 major regions) Independent management complicated by the fact that Eastern and Western Atlantic populations share some foraging range (e.g., West and East Greenland, Faroe Islands).

GSI of Mixed Fisheries Microsatellite DNA allows clear delineation of continent-of-origin for Atlantic salmon harvested in the Greenland mixed-fishery. What about the mtdna haplotype variation that suggests incomplete separation between eastern and western Atlantic salmon?

1 Multidimensional Scaling (1-D a ) SP-2 FR-1 SP-4 SP-3 NB-1 NB-3 NB-4 0 SC-1 IR-1 SC-2 IR-2 EN-1 QB-2 NS-1 NF-3 QB-1 NF-1 ME-6 LA-1 LA-2 NO-2 NO-1 IC-1 FI-1 RU-2 Kachkovka RU-1 Pecha IC-2 NF-2 Bristol Cove NF-7 NF-6 Ouananiche Beck NF-5 Trepassey ME-1 ME-2 ME-3 ME-4 ME-5 ME-7 ME-8 ME-9 ME-10 ME-11 ME-12-1 - 2-1 0 1 2

ME MEL NB NS QB NF LB IC NO FN SC IR SP Total Assignment Tests - COO Population ME 571 5 36 9 1 12 5 - - - - - - 639 MEL 1 90 - - - 1 - - - - - - - 92 NB 8-76 7 23 5 3 - - - - - - 122 NS 5 1 8 88 6 2 - - - - - - - 110 QB - - 25 5 89 1 2 - - - - - - 122 NF 5-7 5 4 71 1 - - - - - - 93 LB - 2 6 1 2 2 32 - - - - - - 45 IC - - - - - - - 95 1 - - - - 96 NO - - - - - - - - 99-2 - - 101 FN - - - - - - - - - 61 - - - 61 SC - - - - - - - - - - 38 8 7 53 IR - - - - - - - 1 - - 11 48 4 64 SP - - - - - - - - 7-5 4 68 84 Percent correctly assigned to region 89.4 97.8 62.3 80 73 76.3 71.1 99 98 100 71.7 75 81 91.2

North American Continent of Origin - Baseline 70.00 60.00 50.00 40.00 30.00 20.00 10.00 00.00 00.00 10.00 20.00 30.00 40.00 50.00 60.00 70.00 European

West Greenland Fishery Since 1995, over 12,500 salmon have been sampled for scale and genetic analysis during the Fall fishery. 0A 1A 1B Qeqertarsuaq Ilulissat Sisimiut Sarfannguaq Collections have ranged from Sisimiut (NW) to Qaqortoq (S). 1C Kangaamiut Maniitsoq Atammik Genetics used to verify scale results. Thus, the need for individual-based assignment. 0B 1D Nuuk Qeqertarsuatsiaat Paamiut Salmon were genotyped at 4-11 loci for continent-oforigin (COO) assignment. 2G 1E 1F Arsuk - Kangilinnguit Qassimiut Narsaq Qaqortoq

Continental Composition of West Greenland Catch 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% North American European

Assignment to COO 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 European North American 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 European North American

Individual Assignment (Geneclass) Individual Assignment and Mixed-Stock Assignment of West Greenland Atlantic Salmon to Continent-of-Origin 1.00 r = 0.98; t = 6.95; p < 0.0001 0.75 0.50 0.25 0.00 0.02 0.24 0.47 0.70 0.93 Mixed-Stock Allocation (ONCOR)

Individual Assignment Robustness West Greenland Atlantic Salmon to Continent-of-Origin Year Eastern Atlantic Ratio Western Atlantic Ratio 1997 2.3 2.9 2000 2.1 3.0 2001 2.2 3.0 2002 2.3 3.0 2003 2.3 3.0 2004 2.2 2.9 2005 2.3 2.9 2006 2.3 2.9 2007 2.3 3.0 2008 2.3 3.0 2009 2.3 2.9 2010 2.4 2.9

Summary of COO Assignments 1995-2010 Over 12,500 Atlantic salmon sampled from the West Greenland mixed-fishery have been genotyped Majority of the catch consisted of fish from the western Atlantic although spatial differences exist in the make-up of the fishery IA and MSA results are highly correlated (at COO) The proportions of the fishery appear to be temporally stable throughout the sampled areas Baseline is robust a decade after establishment

D i m e n s i o n 2 ROO - Multidimensional Scaling (1 - D a ) Western Atlantic Eastern Atlantic/Baltic 2 2 NS1 1 1 0-1 QB2 LB2 QB1 LB1 NB1 NB2 NF2 NF1 ME 1 4 3 2 NS2 MEL2 MEL1 D i m e n s i o n 2 0-1 FN1 IC1 IC2 NO2 NO1 SC1 SC2 IR2 IR1 SP4 SP3 SP2-2 -2-1 0 1 2 Dimension 1-2 -2-1 0 1 2 Dimension 1

ME MEL NB NS QB NF LB IC NO FN SC IR SP Total Assignment Tests - ROO Population ME 571 5 36 9 1 12 5 - - - - - - 639 MEL 1 90 - - - 1 - - - - - - - 92 NB 8-76 7 23 5 3 - - - - - - 122 NS 5 1 8 88 6 2 - - - - - - - 110 QB - - 25 5 89 1 2 - - - - - - 122 NF 5-7 5 4 71 1 - - - - - - 93 LB - 2 6 1 2 2 32 - - - - - - 45 IC - - - - - - - 95 1 - - - - 96 NO - - - - - - - - 99-2 - - 101 FN - - - - - - - - - 61 - - - 61 SC - - - - - - - - - - 38 8 7 53 IR - - - - - - - 1 - - 11 48 4 64 SP - - - - - - - - 7-5 4 68 84 Percent correctly assigned to region 89.4 97.8 62.3 80 73 76.3 71.1 99 98 100 71.7 75 81 91.2

Summary of ROO Assignments Mixed-Stock Analysis Gauthier-Ouellet, M, M Dionne, F Caron, TL King, and L. Bernatchez. 2009. Spatiotemporal dynamics of the Atlantic salmon (Salmo salar) Greenland Fishery inferred from mixed-stock analysis. Canadian Journal of Fisheries and Aquatic Sciences 66:2040-2051. Individual Assignment Sheehan, TF, CM Legault, TL King, and AP Spidle. 2010. Probabilistic-based genetic assignment model: assignments to subcontinent of origin of the West Greenland Atlantic salmon harvest. ICES Journal of Marine Science 67:537-550.

Other Molecular Approaches for COO Several loci have been shown to exhibit high resolution of COO: SS1 SSOSL438* SsaD486 Ssa202* SsaA86 Ssa289* SsaA119 SsaA124 SSOSL311* Combination - microsatellite locus (SS1) & mtdna RFLP (ND 1) See Gilbey J. et al. 2005. Novel DNA markers for rapid, accurate and costeffective discrimination of continental origin of Atlantic salmon (Salmo salar L.). ICES. Emerging molecular techniques - Single Nucleotide Polymorphisms (SNPs) Massively parallel (or next generation) sequencing

Acknowledgements NOAA Fisheries and USGS provided funding for the research The following provide tissue or DNA KNAPK Tom Cross Albert Pendas Eric Verspoor John Taggart Andrew Ferguson Jose Sanchez Prado Fiona O Flynn John Bailey G.W. Friars T. Rex Porter Gil Farmer Terry Goff Trevor Goff Doug Aitkin Tony Mills Spurgeon Lloy Staff from the Greenland Nature Institute Participants in the West Greenland Program Aquatic Ecology Branch Leetown Science Center Biological Resources Division

Continent of Origin PGA Methods Sub-continent of Origin US Partitioning EUR NA CAN US PN CT MK DPS OTH 1. COO assignment 2. Binomial assignment for unsampled individuals 3. Binomial assignment via standardized probabilities 4. Misclassification adjustment 5. Binomial assignment for unsampled individuals 6. Multinomial assignment via adult returns 7. Adjust migration M (10 months)

ROO Summary PGA Model We have developed and applied a method to estimate sub-coo partitioning of catch Probabilistic approach incorporates the uncertainty of fine-scale genetic assignments and sampling Provides estimated US take at West Greenland Results Among fish identified as being of western Atlantic origin, the majority of the catch originates from Canada Within the US, the majority of the catch comes from the Penobscot The effect of the West Greenland harvest on individual US stocks varies annually Even a relatively small harvest could have significant impacts on stocks experiencing periods of low abundance