Spatio-temporal population genetic structure and mating system of red king crab (Paralithodes camtschaticus) in Alaska

Thesis (M.S.) University of Alaska Fairbanks, 2011Population genetic data can be used to make inferences about the Population structure and mating system and inform management decisions of overharvested species such as red king crab (Paralithodes camtschaticus) in Alaska. Red king crab tissue and hemolymph samples were collected from 11 geographically distinct locations from Norton Sound through Southeast Alaska (n = 845). At six locations, two collections were taken at least one generation apart. Heterogeneity of allele frequencies over time was detected in three of the six locations examined, which suggested signs of recent population bottlenecks. An overall Fst = 0.025 (P <0.00 1) suggested moderate genetic differentiation among red king crab collections. A two-region model of spatial differentiation in which collections from Southeast Alaska diverge from those in the Gulf of Alaska and Westen Alaska was supported by pairwise Fst Values, homogeneity tests, Bayesian clustering, and discriminant analysis of principal components. However, spatial analysis of molecular variance suggests some finer-scale structuring within regions and greater differentiation occurs among collections within Southeast Alaska than among the rest of the collections. In addition to population genetic structure analyses, 24 female red king crab and their broods were collected from the Bering Sea. Ovigerous females and 20 offspring per brood were genotyped in order to determine whether multiple mating of a female occurred. There was no evidence of multiple paternity in any brood. The results of this study support continued management of distinct geographic groups within the Gulf of Alaska/Western Alaska/Western Alaska region and suggest that finer-scale management may be beneficial in Southeast Alaska.Introduction -- History of the fishery -- Population genetic structure -- Mating system -- Objectives -- Materials and methods -- Sample collection -- Microsatellite analysis -- Genetic diversity and population genetic structure -- Effective population size and population bottlenecks -- Mating system -- Results -- Genetic diversity -- Temporal population structure -- Spatial population structure -- Effective population size and population bottlenecks -- Mating system -- Discussion -- Genetic diversity and population structure -- Mating system -- General conclusions and management recommendations -- References -- Appendix

Environmental DNA for the enumeration and management of Pacific salmon

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near‐daily, flow‐corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher‐resolution stream‐flow data, at‐least‐daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults

Otolith shape variability and associated body growth differences in giant grenadier, Albatrossia pectoralis.

Fish stocks can be defined by differences in their distribution, life history, and genetics. Managing fish based on stock structure is integral to successful management of a species because fishing may affect stocks disproportionately. Genetic and environmental differences can affect the shape and growth of otoliths and these differences may be indicative of stock structure. To investigate the potential for speciation or stock structure in giant grenadier, Albatrossia pectoralis, we quantified the shape of female giant grenadier otoliths and compared body growth rates for fish with three otolith shapes; shape types were classified visually by an experienced giant grenadier age reader, and were not defined by known distribution or life history differences. We found extreme variation in otolith shape among individuals; however, the shapes were a gradation and not clearly defined into three groups. The two more extreme shapes, visually defined as "hatchet" and "comb", were discernable based on principal component analyses of elliptical Fourier descriptors, and the "mixed" shape overlapped both of the extreme shapes. Fish with hatchet-shaped otoliths grew faster than fish with comb-shaped otoliths. A genetic test (cytochrome c oxidase 1 used by the Fish Barcode of Life Initiative) showed almost no variability among samples, indicating that the samples were all from one species. The lack of young specimens makes it difficult to link otolith shape and growth difference to life history. In addition, shape could not be correlated with adult movement patterns because giant grenadiers experience 100% mortality after capture and, therefore, cannot be tagged and released. Despite these limitations, the link between body growth and otolith shape indicates measurable differences that deserve more study

Alternative life‐history strategy contributions to effective population size in a naturally spawning salmon population

Abstract Alternative life‐history tactics are predicted to affect within‐population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (Ne) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males (“jacks”) to Ne in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single‐nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (Nb). Jack contribution to Nb was assessed by comparing values of Nb calculated with and without jacks and their offspring. Over a range of Nb values (108–406), the average jack contribution to Nb from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence Nb/N. The linkage disequilibrium Ne estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence Nb and Ne and can make a substantial contribution to population dynamics and conservation of threatened stocks

King_RSOS_Submission_READ_Me.pdf from Reproductive success of jack and full-size males in a wild coho salmon population

Despite the wealth of research on Pacific salmon Oncorhynchus spp. life histories there is limited understanding of the lifetime reproductive success of males that spend less time at sea and mature at a smaller size (jacks) than full-size males. Over half of returning male spawners can be jacks in some populations, so it is crucial to understand their contribution to population productivity. We quantified adult-to-adult reproductive success (RS) of jacks and their relative reproductive success (RRS) compared to full-size males in a wild population of Coho Salmon in the Auke Creek watershed, Juneau, AK. We used genetic data from nearly all individuals (approx. 8,000) returning to spawn over a decade (2009–2019) to conduct parentage analysis and calculate individual RS. The average adult-to-adult RS of jacks (mean = 0.7 & s.e. = 0.1) was less than that of full-size males (mean = 1.1 & s.e. = 0.1). Jack RRS was consistently below 1.0 but ranged widely (0.23 to 0.96). Despite their lower average success, jacks contributed substantially to the population by siring 23% of the total returning adult offspring (1.033 of 4.456) produced between 2009 and 2015. Our results imply that jacks can affect evolutionary and population dynamics, and are relevant to the conservation and management of Pacific salmon

King_RSOS_data.zip from Reproductive success of jack and full-size males in a wild coho salmon population

Despite the wealth of research on Pacific salmon Oncorhynchus spp. life histories there is limited understanding of the lifetime reproductive success of males that spend less time at sea and mature at a smaller size (jacks) than full-size males. Over half of returning male spawners can be jacks in some populations, so it is crucial to understand their contribution to population productivity. We quantified adult-to-adult reproductive success (RS) of jacks and their relative reproductive success (RRS) compared to full-size males in a wild population of Coho Salmon in the Auke Creek watershed, Juneau, AK. We used genetic data from nearly all individuals (approx. 8,000) returning to spawn over a decade (2009–2019) to conduct parentage analysis and calculate individual RS. The average adult-to-adult RS of jacks (mean = 0.7 & s.e. = 0.1) was less than that of full-size males (mean = 1.1 & s.e. = 0.1). Jack RRS was consistently below 1.0 but ranged widely (0.23 to 0.96). Despite their lower average success, jacks contributed substantially to the population by siring 23% of the total returning adult offspring (1.033 of 4.456) produced between 2009 and 2015. Our results imply that jacks can affect evolutionary and population dynamics, and are relevant to the conservation and management of Pacific salmon

King_RSOS_table_and_figure_captions.docx from Reproductive success of jack and full-size males in a wild coho salmon population

Despite the wealth of research on Pacific salmon Oncorhynchus spp. life histories there is limited understanding of the lifetime reproductive success of males that spend less time at sea and mature at a smaller size (jacks) than full-size males. Over half of returning male spawners can be jacks in some populations, so it is crucial to understand their contribution to population productivity. We quantified adult-to-adult reproductive success (RS) of jacks and their relative reproductive success (RRS) compared to full-size males in a wild population of Coho Salmon in the Auke Creek watershed, Juneau, AK. We used genetic data from nearly all individuals (approx. 8,000) returning to spawn over a decade (2009–2019) to conduct parentage analysis and calculate individual RS. The average adult-to-adult RS of jacks (mean = 0.7 & s.e. = 0.1) was less than that of full-size males (mean = 1.1 & s.e. = 0.1). Jack RRS was consistently below 1.0 but ranged widely (0.23 to 0.96). Despite their lower average success, jacks contributed substantially to the population by siring 23% of the total returning adult offspring (1.033 of 4.456) produced between 2009 and 2015. Our results imply that jacks can affect evolutionary and population dynamics, and are relevant to the conservation and management of Pacific salmon

Total number (N), average age, and age range (in parenthesis) of giant grenadier by sampling station and year.

<p>Samples were either collected in the central Gulf of Alaska (CGOA), eastern Gulf of Alaska (EGOA), and the eastern Bering Sea (EBS). NA indicates that an age range is not applicable because there was one sample.</p

2014_2015_2016_Auke_qPCR-master

R code and data files to replicate the analyses in Levi, T., Allen, J.M., Bell, D., Joyce, J., Russell, J.R., Tallmon, D.A., Vulstek, S.C., Yang, C.Y., Yu, D.W. 2018. Environmental DNA for the enumeration and management of Pacific salmon. Molecular Ecology Resources. doi:10.1111/1755-0998.1298

King_RSOS_Supplementary_Material.docx from Reproductive success of jack and full-size males in a wild coho salmon population

Despite the wealth of research on Pacific salmon Oncorhynchus spp. life histories there is limited understanding of the lifetime reproductive success of males that spend less time at sea and mature at a smaller size (jacks) than full-size males. Over half of returning male spawners can be jacks in some populations, so it is crucial to understand their contribution to population productivity. We quantified adult-to-adult reproductive success (RS) of jacks and their relative reproductive success (RRS) compared to full-size males in a wild population of Coho Salmon in the Auke Creek watershed, Juneau, AK. We used genetic data from nearly all individuals (approx. 8,000) returning to spawn over a decade (2009–2019) to conduct parentage analysis and calculate individual RS. The average adult-to-adult RS of jacks (mean = 0.7 & s.e. = 0.1) was less than that of full-size males (mean = 1.1 & s.e. = 0.1). Jack RRS was consistently below 1.0 but ranged widely (0.23 to 0.96). Despite their lower average success, jacks contributed substantially to the population by siring 23% of the total returning adult offspring (1.033 of 4.456) produced between 2009 and 2015. Our results imply that jacks can affect evolutionary and population dynamics, and are relevant to the conservation and management of Pacific salmon