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Stock Structure of Aleutian Island Golden King Crab

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Stock Structure of Aleutian Island Golden King Crab April, 2018 FINAL REPORT Stock Structure of Aleutian Island Golden King Crab Chris Siddon1 and W. Stewart Grant2 1Division of Commercial Fisheries, Alaska Department of Fish and Game, 1255 W. 8th Street, Juneau, AK 99801, USA 2Division of Commercial Fisheries, Alaska Department of Fish and Game, 333 Raspberry Road, Anchorage, AK 99518, USA Grant et al.: Golden king crab population genetics 2 INDEX: Abstract pg. 3 Introduction pg. 4 Objectives pg. 4 Chapter 1 pg. 4 Conclusions pg. 41 Management or Policy Implications pg. 41 Data and Metadata pg. 41 Outreach pg. 41 Acknowledgements pg. 42 Grant et al.: Golden king crab population genetics 3 ABSTRACT: The delineation of population boundaries is a crucial component of the harvest management of wild populations. Here, we report the of a survey of genetic variability among populations of golden king crabs (Lithodes aequispinus) along the Aleutian Islands, in the Bering Sea and southeastern Alaska. These crabs are captured in deep waters with baited pots. An analysis of sequence variability along 643 base pair segment of mitochondrial DNA ND5 gene in 517 crabs revealed no overall departure from neutrality and a total haplotype diversity of h = 0.670 without any geographic trend. An AMOVA detected significant haplotype-frequency differences among populations (FST = 0.344, P <0.0001), which were due to differences between populations on a scale of tens to hundreds of kilometers within regions (FSC = 0.314, P < 0.0001). The analysis of 14 microsatellite loci in 1044 crabs revealed only moderate levels of heterozygosity (HO = 0.605 to 0.692) and allelic richness (AR = 4.07 to 8.00) in populations. Significant allele-frequency differentiation appeared overall 19 samples (FST = 0.002, P = 0.003). This heterogeneity was due to differentiation between Aleutian Island populations as a group and those in southeastern Alaska (FST = 0.003, P = 0.0001). However, no significant differentiation was detected between populations within the two regions. Additional analyses including isolation by distance and STRUCTURE did not detect heterogeneity among populations within either region. These genetic results support the present practice of managing regional Aleutian Island and southeastern Alaska populations separately, but do not support separate management units within the two regions. Nevertheless, harvest management should account for small-scale structure among golden king crab populations. KEY WORDS: Genetic population structure ∙ Fishery management ∙ Mitochondrial DNA ∙ Microsatellite DNA CITATION: Grant W, Siddon C. 2018. Phylogeography and Management of Golden King Crab populations in Alaska. NPRB Project 1526 Final Report. 42 pp. Grant et al.: Golden king crab population genetics 4 INTRODUCTION: The goal of this study was to use mitochondrial (mt) DNA and microsatellite DNA markers to search for genetic differences in Golden King Crab (GKC) across the Aleutian Island archipelago to improve definitions of stock structure in GKC. A particular fisheries management concern is whether GKC populations along the Aleutian Islands need to be split into multiple units for stock assessments. Our null hypothesis is that GKCs along the Aleutians represent a panmictic population. OBJECTIVES: 1) Delineate population production units of golden king crab in Alaska waters with molecular genetic markers. 2) Estimate migration rates between populations of golden king crabs with the spatial distributions of genetic markers. 3) Estimate level of genetic diversity and genetic effective population sizes of golden king crab stocks. All objectives were completed through sample collection and DNA extraction and subsequent analyses. CHAPTER 1: Phylogeography and Management of Golden King Crab populations in Alaska Abstract: The delineation of population boundaries is a crucial component of the harvest management of wild populations. Here, we report the of a survey of genetic variability among populations of golden king crabs (Lithodes aequispinus) along the Aleutian Islands, in the Bering Sea and southeastern Alaska. These crabs are captured in deep waters with baited pots. An analysis of sequence variability along 643 base pair segment of mitochondrial DNA ND5 gene in 517 crabs revealed no overall departure from neutrality and a total haplotype diversity of h = 0.670 without any geographic trend. An AMOVA detected significant haplotype-frequency differences among populations (FST = 0.344, P <0.0001), which were due to differences between populations on a scale of tens to hundreds of kilometers within regions (FSC = 0.314, P < 0.0001). The analysis of 14 microsatellite loci in 1044 crabs revealed only moderate levels of heterozygosity (HO = 0.605 to 0.692) and allelic richness (AR = 4.07 to 8.00) in populations. Significant allele-frequency Grant et al.: Golden king crab population genetics 5 differentiation appeared overall 19 samples (FST = 0.002, P = 0.003). This heterogeneity was due to differentiation between Aleutian Island populations as a group and those in southeastern Alaska (FST = 0.003, P = 0.0001). However, no significant differentiation was detected between populations within the two regions. Additional analyses including isolation by distance and STRUCTURE did not detect heterogeneity among populations within either region. These genetic results support the present practice of managing regional Aleutian Island and southeastern Alaska populations separately, but do not support separate management units within the two regions. Nevertheless, harvest management should account for small-scale structure among golden king crab populations. Introduction: An understanding of population structure in needed to optimize the extent of individuals included in stock assessments (Ward 2006). When the geographic extent of a stock is large and includes small independent populations along with large populations, the smaller populations may be overharvested, leading to the loss of productivity and possibly to the loss of unique genetic diversity. Fishery stocks have largely been identified with morphological and physical tags to measure connectivity between populations and demographic analyses to resolve independent trajectories among populations (e.g. Zheng et al. 1996). Genetic markers can also contribute to defining stocks, but with the recognition that the processes influencing genetic variability generally operate on longer time scales than those producing ecological variability (Waples and Gaggiotti 2006; Waples et al. 2008). When genetic differences are detected between populations, ecological differences are also likely to be present. However, the lack of genetic differentiation between populations may occur even when ecological differences are present. In this study, we used genetic markers to attempt to improve the understanding of stock structure among golden king crab (GKC; Lithodes aequispinus) in Alaska. These crabs inhabit deep coastal waters of the North Pacific from northern British Columbia, throughout the Gulf of Alaska and Bering Sea, along the Aleutian Archipelago, into Russian coastal waters to as far as central Japan (Butler and Hart 1962; Rodin 1970; Hiramoto 1985; Somerton and Otto 1985; Otto and Cummiskey 1985). Populations in the Bering Sea and along the Aleutian Archipelago are jointly managed by the Alaska Department of Fish and Game (ADF&G) and the North Pacific Fishery Management Council (NPFMC), and those in the Gulf of Alaska are managed by Grant et al.: Golden king crab population genetics 6 ADF&G. Catches are limited within regions defined by harvest registration areas and are limited to males. Quotas are determined from size-age profiles that indicate abundance trends and from abundance survey data examined with population models (Zheng et al. 1996). The accuracies of these models, however, depend on correctly defining discrete, more or less self-sustaining populations. The biology of GKC, together with oceanic features of the Aleutian Islands and southeastern Alaska, suggests that populations may be genetically subdivided. The first is that larval development in GKC is lecithotrophic (development without feeding) so that larvae are not tied phytoplankton production in upper waters (Shirley and Zhou 1997; Long and Van Sant 2015). Hence surface ocean currents may not be important in dispersing larvae and connecting populations through gene flow. Additionally, tagging data show that adults do not move long distances, only a few tens of kilometers at most (Blau and Pengilly 1994; Watson and Gish 2000). Effort and catch by the commercial fisheries indicate that GKC occurs in pockets of abundance, suggesting the possibility of isolated subpopulations. Lastly, the topography of the coastline may reinforce isolation between subpopulations. In southeastern Alaska, subpopulations are isolated in deep fjords. In this area, red king crab subpopulations show strong genetic differences between bays (Grant and Cheng 2012). Along the Aleutians, subpopulations may be isolated by deep underwater canyons located between islands (Penguilly 2012). All of these features may contribute to a subdivided population structure. The use of genetic variation in and among populations to inform the management of harvested populations is well established. Genetic markers have been used to resolve population structure Alaskan populations of snow (Albrecht et al. 2014), Tanner crabs (Bunch et al. 1998), and red king crabs (Grant and Cheng 2012; Vulsteck et al. 2013). The results of studies of red king crab (RKC;
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