Mitochondrial DNA variation and genetic population structure of chum salmon Oncorhynchus keta around the Pacific Rim

A survey of mtDNA variation among populations of chum salmon Oncorhynchus keta around the Pacific Rim revealed four large population groups: Rim of the Sea of Japan, the Rim of the Okhotsk Sea and West Bering Sea, North‐west Alaska and Gulf of Alaska. The observed population structure appears to reflect isolation by distance with limited gene flow between regions and larger amounts of gene flow between populations within these four regions.     

The Long-Term Dynamics of Sablefish (Anoplopoma fimbria) Stocks in the Western Bering Sea and Prospects for their Commercial Exploitation

Russian Journal of Marine Biology - The dynamics of sablefish stocks and fishery in the Bering Sea, the Gulf of Alaska, and off the Aleutian Islands are considered based on the data of bottom and...     

Sperm whale depredation of sablefish longline gear in the northeast Pacific Ocean

Interactions between marine mammals and fisheries include competition for prey (catch), marine mammal entanglement in fishing gear, and catch removal off fishing gear (depredation). We estimated the magnitude of sperm whale depredation on a major North Pacific longline fishery (sablefish) using data collected during annual longline surveys. Sperm whale depredation occurs while the longline gear is off‐bottom during retrieval. Sperm whales were observed on 16% of longline survey sampling days, mostly (95% of sightings) over the continental slope. Sightings were most common in the central and eastern Gulf of Alaska (98% of sightings), occasional in the western Gulf of Alaska and Aleutian Islands, and absent in the Bering Sea. Longline survey catches were commonly preyed upon when sperm whales were present (65% of sightings), as evidenced by damaged fish. Neither sperm whale presence (P = 0.71) nor depredation rate (P = 0.78) increased significantly from 1998 to 2004. Longline survey catch rates were about 2% less at locations where depredation was observed, but the effect was not significant (P = 0.34). Estimated sperm whale depredation was <1% of the annual sablefish longline fishery catch off Alaska during 1998 to 2004.     

Population genetic structure of northern Dolly Varden char <Emphasis Type="Italic">Salvelinus malma malma</Emphasis> in Asia and North America

The level of genetic differentiation of northern Dolly Varden char Salvelinus malma malma from Asia and North America was evaluated using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D-loop) obtained by means of PCR-RFLP analysis. For S. m. malma, the mean values of haplo-type and nucleotide diversity were 0.5261 ± 0.00388 and 0.001558, respectively. The mean estimate of the population nucleotide divergence constituted 0.055%. It was demonstrated that S. m. malma on the most part of the species range examined (drainages of the Beaufort Sea, Chukotka Sea, Bering Sea, and the Sea of Okhotsk) was characterized by the population genetic structure with the low level of genetic differentiation and divergence. At the same time, populations from the Pacific Ocean Gulf of Alaska demonstrated marked genetic differentiation, supported by the high pairwise G4ST values (from 0.4198 to 0.5211) and nucleotide divergence estimates (mean divergence, 0.129%), from Asian and North American populations. Analysis of molecular variance (AMOVA) showed that most of the mtDNA variation in S. m. malma fell in the intrapopulation component (72.5%). At the same time, the differences between the populations (21.1%) and between the regions (6.4%) made lower contribution to the total variation.     

Fine-scale population genetic structure in Alaskan Pacific halibut (<Emphasis Type="Italic">Hippoglossus stenolepis</Emphasis>)

Pacific halibut collected in the Aleutian Islands, Bering Sea and Gulf of Alaska were used to test the hypothesis of genetic panmixia for this species in Alaskan marine waters. Nine microsatellite loci and sequence data from the mitochondrial (mtDNA) control region were analyzed. Eighteen unique mtDNA haplotypes were found with no evidence of geographic population structure. Using nine microsatellite loci, significant heterogeneity was detected between Aleutian Island Pacific halibut and fish from the other two regions (F _ST range = 0.007–0.008). Significant F _ST values represent the first genetic evidence of divergent groups of halibut in the central and western Aleutian Archipelago. No significant genetic differences were found between Pacific halibut in the Gulf of Alaska and the Bering Sea leading to questions about factors contributing to separation of Aleutian halibut. Previous studies have reported Aleutian oceanographic conditions at deep inter-island passes leading to ecological discontinuity and unique community structure east and west of Aleutian passes. Aleutian Pacific halibut genetic structure may result from oceanographic transport mechanisms acting as partial barriers to gene flow with fish from other Alaskan waters.     

Mitochondrial DNA Diversity in Three Populations of the Giant Tiger Shrimp Penaeus monodon

Mitochondrial DNA restriction fragment length polymorphism (mtDNA-RFLP) was utilized for determination of genetic variation and population structure in Penaeus monodon collected from Satun (the Andaman Sea) and Surat and Trat (the Gulf of Thailand). Twenty-eight composite haplotypes were generated from 52 restriction profiles of P. monodon mtDNA digested with 11 restriction endonucleases. The size of the entire P. monodon mitochondrial genome was estimated to be 15.913 ± 0.177 kb. The average haplotype diversity in P. monodon was 0.864, whereas the mean nucleotide diversity within populations was 2.51%, 2.22%, and 1.91% for Satun, Trat, and Surat, respectively. Geographic heterogeneity analysis indicated population differentiation between P. monodon from the Andaman Sea and P. monodon from the Gulf of Thailand (p < .0001). On the basis of the high genetic diversity level of P. monodon in Thailand, the Satun and Trat P. monodon populations from the west and east of the pennisula were selected to be founder stocks in our selective breeding program. Received February 23, 1998; accepted September 30, 1998.     

A comparison of the maturation and growth of female flathead sole in the central Gulf of Alaska and south‐eastern Bering Sea

Female flathead sole Hippoglossoides elassodon maturity appears not to be area dependent since the total length ( L _T) at which 50% were mature ( L _T50) was similar for the central Gulf of Alaska (333 mm) and south‐eastern Bering Sea (320 mm) areas. Likewise the age at which 50% were mature ( A ₅₀) was similar in the south‐eastern Bering Sea (9·7 years) and central Gulf of Alaska (8·7 years). The timing of female flathead sole spawning may also be similar between areas. Batch or serial spawning was indicated for flathead sole. Female flathead sole grew at a similar rate in both the Gulf of Alaska and Bering Sea. In contrast, males grew faster in the Bering Sea than in the Gulf of Alaska. Males grew more slowly than females in both areas after 5 years of age, and reached a smaller maximum L _T. The growth of both sexes was similar during 1993 and 1996 in the Gulf of Alaska.     

Micro-evolutionary processes in sablefish Anoplopoma fimbria,based on polymorphism of the two sites of mitochondrial DNA

Sablefish Anoplopoma fimbria is a deep-sea fish, endemic to the North Pacific Ocean, with continuous range from southern California to the central part of Honshu Island, including the Bering and Okhotsk Seas. It is an important commercial species and a promising object for aquaculture [1, 2]. Compared to the eastern part of the range [3, 4] the population structure of sablefish in Asian waters is poorly studied. It is believed that sablefish goes to the Bering Sea and Pacific waters of Kamchatka and the Kuril Islands from the northeastern Pacific, and Asian waters are its eviction zone [5]. Other authors suggest that replenishment of sablefish off the eastern Kamchatka and the Kuril Islands is not only due to migration of the adult fish from the Bering Sea along the continental slope, but also due to the drift of yearlings by Aleutian current over the American coast [6].     

Early larvae of <Emphasis Type="Italic">Zesticelus profundorum</Emphasis> (family Cottidae) identified using DNA barcoding

Early larvae of Flabby Sculpin, Zesticelus profundorum, are described using DNA barcoding methods to identify specimens collected in the Gulf of Alaska and Bering Sea. Based on the low myomere count, distribution of larvae, and vertebral counts in adults, we selected Zesticelus profundorum and Sebastolobus macrochir as good potential candidates for genetic comparison. We used DNA samples from voucher specimens of each candidate taxon to identify species-specific sequences. An exact match in sequence data allowed us to positively identify these larvae as Zesticelus profundorum, a rare deepwater species of the family Cottidae.     

Mitochondrial DNA Variation in Northwestern Bering Sea Walleye Pollock, Theragra chalcogramma (Pallas)

Genetic variability of the highly valuable gadid species, walleye pollock, Theragra chalcogramma (Pallas 1811), from five spatially separated northwestern Bering Sea areas (Ozernoi Bay, Olutorskyi Bay, Koryak shelf, Navarin region, and Anadyr Gulf) was investigated. Haplotype diversity within the samples ranged from 0.8788±0.0393 to 0.9436±0.0162. Nucleotide diversity within the samples ranged from 0.0108 to 0.0127. Nucleotide diversity among the regional collections ranged from 0% to 0.18%. Walleye pollock from the Anadyr Gulf appeared genetically separate from the other four samples in a clustering of genetic distances. Total heterogeneity among all five samples was significant, while there was no heterogeneity among the four samples excluding that from the Anadyr Gulf. Pair-wise comparisons using tests for heterogeneity and F_st supported the dendrogram of genetic distances in that only the collection from the Anadyr Gulf was significantly different from the others. The observed pattern of genetic differentiation among walleye pollock from the northwestern Bering Sea presumably emerged as a result of a population of the species subdividing in the northernmost part of its geographic range, though further analysis is needed to verify this supposition.     

First record of the decapod-egg predator Ovicides paralithodis (Nemertea,Carcinonemertidae) from the snow crab Chionoecetes opilio (Decapoda,Brachyura)

The carcinonemertid monostiliferan Ovicides paralithodis Kajihara and Kuris, 2013 was originally described as an egg predator of the red-king crab Paralithodes camtschaticus (Tilesius, 1815) in the Sea of Okhotsk, the Bering Sea, and the Gulf of Alaska. In the present study, several carcinonemertid specimens were obtained from the egg mass of the snow crab Chionoecetes opilio (O. Fabricius, 1788) in the Sea of Japan. Partial sequences of the mitochondrial cytochrome c oxidase subunit I gene (COI) determined from two specimens of the carcinonemertid were identical with a barcode sequence from the holotype of O. paralithodis, indicating that the host range of the species covers at least the two decapod species, P. camtschaticus and C. opilio.     

Trans‐Pacific and trans‐Arctic pathways of the intertidal macroalga Fucus distichus L. reveal multiple glacial refugia and colonizations from the North Pacific to the North Atlantic

Aim We examined the phylogeography of the cold‐temperate macroalgal species Fucus distichus L., a key foundation species in rocky intertidal shores and the only Fucus species to occur naturally in both the North Pacific and the North Atlantic. Location North Pacific and North Atlantic oceans (42° to 77° N). Methods We genotyped individuals from 23 populations for a mitochondrial DNA (mtDNA) intergenic spacer (IGS) (n = 608) and the cytochrome c oxidase subunit I (COI) region (n = 276), as well as for six nuclear microsatellite loci (n = 592). Phylogeographic structure and connectivity were assessed using population genetic and phylogenetic network analyses. Results IGS mtDNA haplotype diversity was highest in the North Pacific, and divergence between Pacific haplotypes was much older than that of the single cluster of Atlantic haplotypes. Two ancestral Pacific IGS/COI clusters led to a widespread Atlantic cluster. High mtDNA and microsatellite diversities were observed in Prince William Sound, Alaska, 11 years after severe disturbance by the 1989 Exxon Valdez oil spill. Main conclusions At least two colonizations occurred from the older North Pacific populations to the North Atlantic between the opening of the Bering Strait and the onset of the Last Glacial Maximum. One colonization event was from the Japanese Archipelago/eastern Aleutians, and a second was from the Alaskan mainland around the Gulf of Alaska. Japanese populations probably arose from a single recolonization event from the eastern Aleutian Islands before the North Pacific–North Atlantic colonization. In the North Atlantic, the Last Glacial Maximum forced the species into at least two known glacial refugia: the Nova Scotia/Newfoundland (Canada) region and Andøya (northern Norway). The presence of two private haplotypes in the central Atlantic suggests the possibility of colonization from other refugia that are now too warm to support F. distichus. With the continuing decline in Arctic ice cover as a result of global climate change, renewed contact between North Pacific and North Atlantic populations of Fucus species is expected.     

Genetic Heterogeneity of the Giant Tiger Shrimp (Penaeus monodon) in Thailand Revealed by RAPD and Mitochondrial DNA RFLP Analyses

Genetic diversity of the giant tiger shrimp (Penaeus monodon) collected from 5 areas, Chumphon and Trat (Gulf of Thailand), and Phangnga, Satun, and Trang (Andaman Sea), was examined by randomly amplified polymorphic DNA (RAPD) and mitochondrial DNA (16S ribosomal DNA and an intergenic COI-COII) polymorphism. A total of 53 polymorphic fragments from UBC299, UBC273, and UBC268 was consistently scored across all samples. From the respective primers 26, 32, and 30 genotypes were generated. A 260-bp RAPD fragment generated by the primer UBC268 was specifically observed in 95.8% of Trat P. monodon, suggesting that this RAPD could be used as a marker for comparing phenotypic performance of P. monodon from Trat and other geographic samples. In addition, 37 mtDNA composite haplotypes were observed from restriction analysis of the same P. monodon samples. High haplotype diversity (0.855) and nucleotide diversity (3.328%) of Thai P. monodon were observed. Population differentiation of P. monodon between the Andaman Sea and Gulf of Thailand was clearly illustrated by both techniques (P < .0001). Nevertheless, contradictory results on patterns of differentiation were observed between P. monodon within the Gulf of Thailand. Analysis of nuclear DNA polymorphism (RAPD) indicated a genetically significant difference between Chumphon and Trat (P < .0001), whereas mtDNA polymorphism did not show differentiation between these samples (P= .0497). Under the presumption of selective neutrality of these markers, biased female gene flow between Trat and Chumphon P. monodon may exist and be responsible for an anomalous differentiation pattern between these geographic samples. Received October 11, 2000; accepted March 5, 2001.     

Systematic review of the genus <Emphasis Type="Italic">Bothrocara</Emphasis> Bean 1890 (Teleostei: Zoarcidae)

The systematics of the eelpout genus Bothrocara Bean 1890 is reviewed on the basis of 941 specimens. Eight mostly eurybathic, demersal species are recognized, distributed mainly along the continental slopes of the North and South Pacific oceans, with one species entering the South Atlantic. Distributions are: B. brunneum ranges from the Sea of Okhotsk to the Gulf of Panama at depths of 199–1,829 m; B. elongatum ranges from the Gulf of Panama to Chile at depths of 720–1,866 m; B. hollandi ranges from the Sea of Japan to the southeastern Bering Sea at depths of 150–1,980 m; B. molle ranges from the western Bering Sea to the South Atlantic at depths of 106–2,688 m; B. nyx is known only from the eastern Bering Sea at depths of 790–1,508 m; B. pusillum ranges from the northern Bering Sea to British Columbia, Canada, at depths of 55–642 m; B. tanakae is found along the northern coasts of Honshu and Hokkaido islands, Japan, at depths of 274–892 m; B. zestum ranges from the Izu Islands, Japan, and central Honshu, Japan, to the Gulf of Alaska at depths of 199–1,620 m (an unidentifiable specimen from off Taiwan may be B. zestum). The species are distinguished from one another mainly on the basis of head pore patterns, gill raker morphology, coloration and various meristic and morphometric values. A determination key to the species is provided.     

Population genetic structure of northern Dolly Varden char Salvelinus malma malma in Asia and North America

The level of genetic differentiation of northern Dolly Varden char Salvelinus malma malma from Asia and North America was evaluated using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained by means of PCR-RFLP analysis. For S. m. malma, the mean values of haplotype and nucleotide diversity were 0.5261 +/- 0.00388 and 0.001558, respectively. The mean estimate of the population nucleotide divergence constituted 0.055%. It was demonstrated that S. m. malma on the most part of the species range examined (drainages of the Beaufort Sea, Chukotka Sea, Bering Sea, and the Sea of Okhotsk) was characterized by the population genetic structure with the low level of genetic differentiation and divergence. At the same time, populations from the Pacific Ocean Gulf of Alaska demonstrated marked genetic differentiation, supported by the high pairwise phi(ST) values (from 0.4198 to 0.5211) and nucleotide divergence estimates (mean divergence, 0.129%), from Asian and North American populations. Nested analysis of molecular variance (AMOVA) showed that most of the mtDNA variation in S. m. malma fell in the intrapopulation component (72.5%). At the same time, the differences between the populations (21.1%) and between the regions (6.4%) made lower contribution to the total variation.     

Genetic and morphological evidence for cryptic diversity in the <Emphasis Type="Italic">Careproctus rastrinus</Emphasis> species complex (Liparidae) of the North Pacific

The molecular phylogeny of the Careproctus rastrinus species complex is presented on the basis of sequence variations in the 16S rRNA and cytochrome b genes (1,447 base pairs) of mitochondrial DNA using specimens collected from across the North Pacific and its marginal seas, including the Sea of Japan, the Pacific coast of Japan, the Sea of Okhotsk, the Bering Sea, the Gulf of Alaska, and the Arctic Ocean. Gene flow and migration between geographic regions is apparently strictly restricted in the C. rastrinus species complex, as this phylogeny revealed nine genetically diverged groups in the C. rastrinus species complex, most of which corresponded well with major geographic regions. Most of the groups were different in terms of morphological characters. Five nominal species have been considered to be members of the complex and have been variously recognized as being valid or as synonyms of C. rastrinus, but the present genetic and morphological differences suggested that the C. rastrinus species complex represents far more divergence. Such cryptic diversity of the C. rastrinus species complex defined by geographic regions may be related to their low dispersal ability, because they bear large demersal eggs. The genetic divergence suggested that colder climates from the late Pliocene and the isolation of marginal seas during the Pleistocene may have driven the divergence of the C. rastrinus species complex.     

Female maturity,reproductive potential,relative distribution,and growth compared between arrowtooth flounder (Atheresthes stomias) and Kamchatka flounder (A. evermanni) indicating concerns for management

Arrowtooth flounder (Atheresthes stomias) and Kamchatka flounder (A. evermanni), major piscivorous predators in the eastern Bering Sea and Aleutian Islands, are morphologically similar. Consequently the two species have been managed together as a species complex using the length‐ and age‐at‐maturity derived from Gulf of Alaska arrowtooth flounder, which had been the only available maturity estimates. However, there could be serious management consequences if the two species matured at significantly different ages and fork lengths. Therefore, this study was conducted during 2007 and 2008 to determine if there were significant differences in maturation between the two species. Significant differences in size and age of female maturation and growth were found. The age and length of 50% maturity (A_50,L_50, respectively) for arrowtooth flounder females is 7.6 years of age and 480 mm in body length. In comparison, A_50,L₅₀ of Kamchatka flounder females is 10.1 years of age and 550 mm, meaning that Kamchatka flounder has a significantly lower reproductive potential than arrowtooth flounder. The large difference in reproductive potential indicates that managing the two species together as a species complex using the reproductive characteristics of arrowtooth flounder, was not conservative for Kamchatka flounder. This study also determined that arrowtooth flounder maturation was consistent between the Gulf of Alaska and eastern Bering Sea populations.     

Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure

The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.