We used genetic techniques to identify gadids (cods) to species in the Pacific Arctic during a time of substantial physical change in the marine ecosystem between 2012 and 2019. The dominant fish species in the Chukchi Sea is Arctic Cod (Boreogadus saida); however, other gadids such as Saffron Cod (Eleginus gracilis), Pacific Cod (Gadus macrocephalus) and Walleye Pollock (Gadus chalcogrammus) have been observed. Two aims in this study were to evaluate the accuracy of at sea morphological identification (which can be difficult for juveniles) with genetic species identification and to document potential variation in species composition and distribution of gadids in the Pacific Arctic in response to changing environmental conditions. Microsatellite and mtDNA genetic results revealed that most B. saida collected in the Chukchi Sea in 2012 and 2013 were correctly identified at sea. Conversely, genetic results from samples collected in 2017 and 2019 revealed a large number of G. chalcogrammus and some G. macrocephalus and E. gracilis that were initially identified at sea as B. saida. The majority of misidentification occurred between B. saida and G. chalcogrammus. This study indicates a northward shift of G. chalcogrammus and B. saida during warmer conditions. In addition, juvenile Polar Cod (A. glacialis), which is not typically found in the Chukchi Sea and was not identified at sea, was genetically detected on 3 hauls on the northern Chukchi Shelf, outside of its documented distribution. Accurate species identification, especially during a time of changing marine landscapes, is not only important for survey abundance estimates but for downstream analyses as well. This emphasizes the value of implementing strategies for correct identification of the gadid species to better capture and monitor responses to varying and likely changing conditions. Our results provide strong evidence of distributional shifts and range expansions of gadid species in the Arctic, which may be the result of changing climactic conditions.

Walter et al. (1) and Safina (2) raise numerous concerns regarding our study (3). Specifically, they question our conclusions that (i) a majority of spawning occurs outside the Gulf of Mexico, (ii) western North Atlantic bluefin tuna mature earlier than currently estimated, and (iii) additional spawning locations and younger age at maturity mean that the western Atlantic bluefin tuna are less vulnerable to anthropogenic impacts, including exploitation.

Atlantic bluefin tuna are a symbol of both the conflict between preservationist and utilitarian views of top ocean predators, and the struggle to reach international consensus on the management of migratory species. Currently, Atlantic bluefin tuna are managed as an early-maturing eastern stock, which spawns in the Mediterranean Sea, and a late-maturing western stock, which spawns in the Gulf of Mexico. However, electronic tagging studies show that many bluefin tuna, assumed to be of a mature size, do not visit either spawning ground during the spawning season. Whether these fish are spawning in an alternate location, skip-spawning, or not spawning until an older age affects how vulnerable this species is to anthropogenic stressors including exploitation. We use larval collections to demonstrate a bluefin tuna spawning ground in the Slope Sea, between the Gulf Stream and northeast United States continental shelf. We contend that western Atlantic bluefin tuna have a differential spawning migration, with larger individuals spawning in the Gulf of Mexico, and smaller individuals spawning in the Slope Sea. The current life history model, which assumes only Gulf of Mexico spawning, overestimates age at maturity for the western stock. Furthermore, individual tuna occupy both the Slope Sea and Mediterranean Sea in separate years, contrary to the prevailing view that individuals exhibit complete spawning-site fidelity. Overall, this complexity of spawning migrations questions whether there is complete independence in the dynamics of eastern and western Atlantic bluefin tuna and leads to lower estimates of the vulnerability of this species to exploitation and other anthropogenic stressors.

Summary Genetic tools are commonly used for conservation and management of at‐risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. We previously reported a signature of positive selection in the mitochondrial‐encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co‐evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5‐based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. We used RAD‐based next‐generation sequencing and identified a nuclear‐encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it.

A genetic analysis of samples from the Chinook salmon (Oncorhynchus tshawytscha) bycatch of the 2014 Bering Sea-Aleutian Island (BSAI) trawl fishery for walleye pollock (Gadus chalcogrammus) was undertaken to determine the overall stock composition of the bycatch. Samples were genotyped for 43 single nucleotide polymorphism (SNP) DNA markers and results were estimated using the Alaska Department of Fish and Game (ADF&G) SNP baseline. In 2014, genetic samples from the Bering Sea were collected using a systematic random sampling protocol where one out of every 10 Chinook salmon encountered was sampled. Based on the analysis of 1,385 Chinook salmon bycatch samples collected throughout the 2014 BSAI walleye pollock trawl fishery, Coastal Western Alaska stocks dominated the sample set (49%) with smaller contributions from North Alaska Peninsula (18%), British Columbia (14%), and West Coast U.S. (WA/OR/CA) (7%) stocks. Analysis of temporal groupings within the pollock “A” and “B” seasons revealed changes in stock composition during the course of the year with lower contributions of Coastal Western Alaska, North Alaska Peninsula and Yukon stocks and higher contributions of West Coast U.S. (WA/OR/CA), British Columbia, NW Gulf of Alaska and Coastal Southeast Alaska stocks during the “B” season.

The systematic status of North Pacific sand lances (genus Ammodytes) was assessed from mitochondrial DNA (cytochrome oxidase c subunit 1) sequence data and morphological data to identify the number of species in the North Pacific Ocean and its fringing seas. Although only 2 species, Ammodytes hexapterus and A. personatus, have been considered valid in the region, haplotype networks and trees constructed with maximum parsimony and genetic distance (neighbor-joining) methods revealed 4 highly divergent monophyletic clades that clearly represent 4 species of Ammodytes in the North Pacific region. On the basis of our material and comparisons with sequence data reported in online databases, A. personatus is found throughout the eastern North Pacific Ocean, Gulf of Alaska, Aleutian Islands, and the eastern Bering Sea where it co-occurs with a northwestern Arctic species, A. hexapterus, that is found throughout the North American Arctic from Hudson Bay, Canada, in the east, through the Beaufort and Chukchi seas, into the northern and western Bering Sea, and to the southern Sea of Okhotsk in the Soya Strait off Hokkaido, Japan. Two other species reside in waters around Japan: A. japonicus throughout the Sea of Japan and the Seto Inland Sea and a new species in the Sea of Japan and the North Pacific Ocean off northern Honshu. We designate neotypes for A. hexapterus and A. personatus because of the absence of type material and the close similarity of these 2 species. Ammodytes ale utensis is a junior synonym of A. japonicus, and A. alascanus is a junior synonym of A. personatus.

Red king crab, Paralithodes camtschaticus Tilesius, 1815, an economically and culturally important species in the state of Alaska, experienced drastic reductions in abundance over large portions of their Alaskan range by 1980. Abundance of crabs in some of the most important historical fishing areas have failed to rebound, some even in the absence of fishing, highlighting the need for additional research to infer genetic structure and reproductive biology of the species that can then be used to inform management efforts. Red king crab samples were collected from eleven locations throughout Alaska (n = 845), of these, six locations were sampled at least one generation apart. Results of this study suggest moderate rates of gene flow within the Gulf of Alaska/Western Alaska region. Levels of genetic differentiation among populations within Southeast Alaska were higher than seen elsewhere, and there was strong evidence of multiple distinct populations. Red king crab in Bristol Bay and in two areas in Southeast Alaska show signs of recent population bottlenecks and shifts in allele frequencies not observed in previous studies that used less polymorphic genetic markers. In addition to population genetic structure analyses, 24 female red king crab and their broods were collected for purposes of inferring mating system. 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 region and suggest that finer-scale management may be beneficial in Southeast Alaska.

The subsistence fishery for Chinook salmon in the Kuskokwim Management Area is one of the largest and most significant in Alaska. Low returns in recent years have yielded shortfalls in escapements basin-wide and resulted in fishing restrictions, which directly affect local communities. Sustained productivity of salmon relies on maintenance of genetic diversity through informed management of the resource. We investigated the genetic diversity of Chinook salmon from the Kuskokwim River using two types of genetic markers, microsatellites and single nucleotide polymorphisms, to understand the population structure. Analysis of genetic data found evidence of significant structure among these Chinook salmon populations. However, much of the diversity was associated with two populations in the upper drainage.

Understanding stock and age-specific seasonal migrations of Pacific salmon during ocean residence is essential to both the conservation and management of this important resource. Based upon 11 microsatellites assayed on 265 individuals collected aboard international research surveys during winter 2009, we found substantial differences in the age-specific origin of chum salmon (Oncorhynchus keta) in the North Pacific Ocean. Overall, Asian stocks dominated the collections, however, ocean age 1 fish were primarily of Japanese origin and ocean age 2–3+ fish were predominantly of Russian origin. These results suggest that cohorts of chum salmon stocks migrate nonrandomly in the North Pacific Ocean and adjacent seas.

α‐Actinins are actin‐binding proteins that can be broadly divided into Ca2+‐sensitive cytoskeletal and Ca2+‐insensitive sarcomeric isoforms. To date, little is known about functional differences between the isoforms due to their indistinguishable activities in most in vitro assays. To identify functional differences in vivo between sarcomeric isoforms, we employed computational and molecular approaches to characterize the zebrafish (Danio rerio) genome, which contains orthologoues of each human α‐actinin gene, including duplicated copies of actn3. Each isoform exhibits a distinct and unique pattern of gene expression as assessed by mRNA in situ hybridization, largely sharing similar expression profiles as seen in humans. The spatial conservation of expression of these genes from lower invertebrates to humans suggests that regulation and subsequent functions of these genes are conserved during evolution. Morpholino‐based knockdown of the sarcomeric isoform, actn2, leads to skeletal muscle, cardiac, and ocular defects evident over the first week of development. Remarkably, despite the high degree of sequence conservation between actn2 and actn3, the phenotypes of α‐actinin‐2 deficient zebrafish can be rescued by overexpression of α‐actinin‐2 but not by α‐actinin‐3 mRNAs from zebrafish or human. These data provide functional evidence that the primary sequences of α‐actinin‐2 and α‐actinin‐3 evolved differences to optimize their functions.—Gupta, V., Discenza, M., Guyon, J. R., Kunkel, L. M., Beggs, A. H. α‐Actinin‐2 deficiency results in sarcomeric defects in zebrafish that cannot be rescued by α‐actinin‐3 revealing functional differences between sarcomeric isoforms. FASEB J. 26, 1892‐1908 (2012). www.fasebj.org

Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although F(ST) values were low, a neighbor-joining tree based on genetic distance, homogeneity, and F(ST) values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later-an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.

A genetic analysis of samples from the chum salmon (Oncorhynchus keta) bycatch of the 2008 Bering Sea walleye pollock (Theragra chalcogramma) trawl fishery was undertaken to determine the overall stock composition of the sample set. Samples were genotyped for eleven microsatellite markers and results were estimated using the current chum salmon microsatellite baseline. In 2008, genetic samples were collected opportunistically as part of a special project, but sample biases have the potential to affect stock composition analysis results. Consequently, stock composition estimates apply to the sample set and may not represent the entire chum salmon bycatch. Based on the analysis of 629 chum salmon bycatch samples collected throughout the 2008 Bering Sea trawl fishery, North Asian (27%), East Asian (35%), and Eastern Gulf of Alaska/Pacific Northwest (24%) stocks dominated the sample set, with smaller contributions from western Alaska (7%) and Upper/Middle Yukon River (6%) stocks. The estimates for the 2008 chum salmon bycatch sample set were similar to the 2005, 2006, 2007, and 2009 chum salmon bycatch estimates, suggesting consistency of the regional stock contributions across years. Analysis of temporal groupings within the groundfish “B” season revealed changes in stock composition during the course of the season with decreasing contribution of Eastern Gulf of Alaska/Pacific Northwest stocks over time, but leaves unanswered whether these changes are due to temporal or spatial differences in the sample set.

Two known zebrafish dystrophin mutants, sapje and sapje-like (sap(c/100)), represent excellent small-animal models of human muscular dystrophy. Using these dystrophin-null zebrafish, we have screened the Prestwick chemical library for small molecules that modulate the muscle phenotype in these fish. With a quick and easy birefringence assay, we have identified seven small molecules that influence muscle pathology in dystrophin-null zebrafish without restoration of dystrophin expression. Three of seven candidate chemicals restored normal birefringence and increased survival of dystrophin-null fish. One chemical, aminophylline, which is known to be a nonselective phosphodiesterase (PDE) inhibitor, had the greatest ability to restore normal muscle structure and up-regulate the cAMP-dependent PKA pathway in treated dystrophin-deficient fish. Moreover, other PDE inhibitors also reduced the percentage of affected sapje fish. The identification of compounds, especially PDE inhibitors, that moderate the muscle phenotype in these dystrophin-null zebrafish validates the screening protocol described here and may lead to candidate molecules to be used as therapeutic interventions in human muscular dystrophy.

Introduction: Over the past 10 years, the use of zebrafish for scientific research in the area of muscle development has increased dramatically. Although several protocols exist for the isolation of adult myoblast progenitors from larger fish, no standardized protocol exists for the isolation of myogenic progenitors from adult zebrafish muscle. Methods: Using a variant of a mammalian myoblast isolation protocol, zebrafish muscle progenitors have been isolated from the total dorsal myotome. These zebrafish myoblast progenitors can be cultured for several passages and then differentiated into multinucleated, mature myotubes. Results: Transcriptome analysis of these cells during myogenic differentiation revealed a strong downregulation of pluripotency genes, while, conversely, showing an upregulation of myogenic signaling and structural genes. Conclusions: Together these studies provide a simple, yet detailed method for the isolation and culture of myogenic progenitors from adult zebrafish, while further promoting their therapeutic potential for the study of muscle disease and drug screening. Muscle Nerve, 2011

Farley, E. V., Starovoytov, A., Naydenko, S., Heintz, R., Trudel, M., Guthrie, C., Eisner, L., Guyon, J. R. 2011. Implications of a warming eastern Bering Sea for Bristol Bay sockeye salmon. – ICES Journal of Marine Science, 68: 1138–1146.Overwinter survival of Pacific salmon (Oncorhynchus sp.) is believed to be a function of size and energetic status they gain during their first summer at sea. We test this notion for Bristol Bay sockeye salmon (O. nerka), utilizing data from large-scale fisheries and oceanographic surveys conducted during mid-August to September 2002–2008 and from February to March 2009. The new data presented in this paper demonstrate size-selective mortality for Bristol Bay sockeye salmon between autumn and their first winter at sea. Differences in the seasonal energetic signatures for lipid and protein suggest that these fish are not starving, but instead the larger fish caught during winter apparently are utilizing energy stores to minimize predation. Energetic status of juvenile sockeye salmon was also strongly related to marine survival indices and years with lower energetic status apparently are a function of density-dependent processes associated with high abundance of juvenile sockeye salmon. Based on new information regarding eastern Bering Sea ecosystem productivity under a climate-warming scenario, we hypothesize that sustained increases in spring and summer sea temperatures may negatively affect energetic status of juvenile sockeye salmon, potentially resulting in increased overwinter mortality.