A Newly Isolated Family of Short Interspersed Repetitive Elements (Sines) in Coregonid Fishes (Whitefish) with Sequences That Are Almost Identical to Those of the Smai Family of Repeats: Possible Evidence for the Horizontal Transfer of Sines

The SmaI family of repeats is present only in the chum salmon and the pink salmon, and it is not present in five other species in the same genus or in other species in closely related genera. In the present study, we showed that another short interspersed repetitive elements (SINEs) family, which is almost identical to the SmaI family, is present in all fishes in the subfamily Coregoninae, being regarded as the most primitive salmonids. This new family of SINEs was designated the SmaI-cor family (SmaI family of repeats in coregonids). The consensus sequence of the SmaI-cor family was found to be 98.6% homologous to that of the SmaI family. Accordingly, it is difficult to explain the high degree of homology between these two families of SINEs by any mechanism other than the horizontal transfer of SINEs. The estimates of the rate of neutral mutation of nuclear genes, comparing chum salmon and European whitefish, confirmed this possibility. Our results strongly suggest that a member(s) of the SmaI-cor family might have been transferred horizontally from one coregonid species to a common ancestor of chum and pink salmon or to these two species independently, to allow subsequent amplification of the SmaI family in their respective genomes.     

Characterization of species-specifically amplified SINEs in three salmonid species—Chum salmon,pink salmon,and kokanee: The local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus

Short interspersed repetitive elements (SINEs), known as theHpaI family, are present in the genomes of all salmonid species (Kido et al.,Proc. Natl. Acad. Sci. USA 1991, 88: 2326–2330). Recently, we showed that the retropositional efficiency of the SINE family in the lineage of chum salmon is extraordinarily high in comparison with that in other salmonid lineages (Takasaki et al.,Proc. Natl. Acad. Sci. USA 1994, 91: 10153–10157). To investigate the reason for this high efficiency, we searched for members of theHpaI SINE family that have been amplified species-specifically in pink salmon. Since the efficiency of the species-specific amplification in pink salmon is not high and since other members of the same subfamily of SINEs were also amplified species-specifically in pink salmon, the actual sequence of this subfamily might not be the cause of the high retropositional efficiency of SINEs in chum salmon. Rather, it appears that a highly dominant source gene for the subfamily may have been newly created by retroposition, and some aspect of the local environment around the site of retroposition may have been responsible for the creation of this dominant source gene in chum salmon. Furthermore, a total of 11 sequences ofHpaI SINEs that have been amplified species-specifically in three salmon lineages was compiled and characterized. Judging from the distribution of members of the same-sequence subfamily of SINEs in different lineages and from the distribution of the different-sequence subfamilies in the same lineage, we have concluded that multiple dispersed loci are responsible for the amplification of SINEs. We also discuss the additional possibility of horizontal transmission of SINEs between species. The availability of the sets of primers used for the detection of the species-specific amplifications of the SINEs provides a convenient and reliable method for identification of these salmonid species.     

Details of Retropositional Genome Dynamics That Provide a Rationale for a Generic Division: The Distinct Branching of All the Pacific Salmon and Trout (Oncorhynchus) from the Atlantic Salmon and Trout (Salmo)

Salmonid species contain numerous short interspersed repetitive elements (SINEs), known collectively as the HpaI family, in their genomes. Amplification and successive integration of individual SINEs into the genomes have occurred during the evolution of salmonids. We reported previously a strategy for determining the phylogenetic relationships among the Pacific salmonids in which these SINEs were used as temporal landmarks of evolution. Here, we provide evidence for extensive genomic rearrangements that involved retropositions and deletions in a common ancestor of all the Pacific salmon and trout. Our results provide genetic support for the recent phylogenetic reassignment of steelhead and related species from the genus Salmo to the genus Oncorhynchus. Several other informative loci identified by insertions of HpaI SINEs have been isolated, and previously proposed branching orders of the Oncorhynchus species have been confirmed. The authenticity of our phylogenetic tree is supported both by the isolation of more than two informative loci per branching point and by the congruence of all our data, which suggest that the period between succesive speciations was sufficiently long for each SINE that had been amplified in the original species to become fixed in all individuals of that species.     

Wild and hatchery reproduction of pink and chum salmon and their catches in the Sakhalin-Kuril region,Russia

In the Sakhalin-Kuril region hatchery culture of pink and chum salmon is of great importance compared to other regions of the Russian Far East. During the last 30 years the number of hatcheries increased two-fold, and significant advances were made in hatchery technologies. As a result, chum salmon capture in regions where hatcheries operate (southwestern and eastern Sakhalin coasts, and Iturup Island) was 9 times as high during 2006–2010 than during 1986–1990, whereas wild chum salmon harvest markedly declined. Recent dynamics in pink salmon catch appear to track trends in natural spawning in monitored index rivers, suggesting natural-origin pink salmon play a dominant role in supporting the commercial fishery. It remains uncertain as to whether hatcheries have substantially supplemented commercial catch of pink salmon in this region, and I recommend continued research (including implementing mass marking and recovery programs) before decisions are made regarding increasing pink salmon hatchery production. Location of hatcheries in spawning river basins poses problems for structuring a management system that treats hatchery and wild populations separately. Debate continues regarding the existence and importance of density-dependent processes operating in the ocean environment and the role hatcheries play in these processes. Loss of critical spawning habitat for chum salmon in the Sakhalin-Kuril region has lead to significant declines in their abundance. I conclude by recommending increases in releases of hatchery chum salmon numbers in the region to help recover depressed wild populations and provide greater commercial fishing benefits in the region.     

Differential rejection of salmon lice by pink and chum salmon: disease consequences and expression of proinflammatory genes

The consequences of high (735 copepodids fish-1) and low (243 copepodids fish-1) level exposures of size-matched juvenile pink and chum salmon to Lepeophtheirus salmonis copepodids were examined. At both levels of exposure the prevalence and abundance of L. salmonis was significantly higher on chum salmon. In addition, the weight of exposed chum salmon following the high exposure was significantly less than that of unexposed chum salmon. At both exposures, the haematocrit of exposed chum salmon was significantly less than that of unexposed chum. Neither weight nor haematocrit of pink salmon was affected by exposures at these levels. Despite the presence of microscopic inflammatory lesions associated with attachment of L. salmonis on the epithelium of gill and fin of both salmon species, there were no mortalities following either exposure. A transient cortisol response was observed in chum salmon 21 d after low exposure. An earlier and quantitatively higher expression of the proinflammatory genes interleukin-8 (IL-8), tumour necrosis factor alpha-1 (TNFalpha-1) and interleukin-1beta (IL-1beta) in fin and head kidney of pink salmon suggested a mechanism of more rapid louse rejection in this species. Together, these observations indicate a relatively enhanced innate resistance to L. salmonis in the juvenile pink salmon compared with the juvenile chum salmon.     

Sex ratio control in pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) populations: the possible causes and mechanisms of changes in the sex ratio

Long-term changes in the sex ratio have been studied in pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) populations of Kamchatka and Sakhalin. It has been demonstrated that these changes are an adaptation to population dynamics: an increase in the population size is accompanied by a shift towards a higher proportion of males; a decrease in population size, by a shift towards a higher proportion of females. The correspondence between morphological and molecular characters in populations of the two species has been analyzed in order to determine the mechanism of sex ratio control. In some pink salmon and chum salmon populations, there is a discrepancy between sex identifications based on morphological characters and molecular markers. This discrepancy is assumed to be accounted for by sex inversion mechanisms, which may be population- or region-specific. In two cases, it has been found that the sex ratio discrepancy in populations is related to the numbers of fish in subsequent generations. These findings suggest that sex inversion may be related to population size control.     

Comparative anatomy of the dorsal hump in mature Pacific salmon

Mature male Pacific salmon (Genus Oncorhynchus ) demonstrate prominent morphological changes, such as the development of a dorsal hump. The degree of dorsal hump formation depends on the species in Pacific salmon. It is generally accepted that mature males of sockeye (O. nerka ) and pink (O. gorbuscha ) salmon develop most pronounced dorsal humps. The internal structure of the dorsal hump in pink salmon has been confirmed in detail. In this study, the dorsal hump morphologies were analyzed in four Pacific salmon species inhabiting Japan, masu (O. masou ), sockeye, chum (O. keta ), and pink salmon. The internal structure of the dorsal humps also depended on the species; sockeye and pink salmon showed conspicuous development of connective tissue and growth of bone tissues in the dorsal tissues. Masu and chum salmon exhibited less‐pronounced increases in connective tissues and bone growth. Hyaluronic acid was clearly detected in dorsal hump connective tissue by histochemistry, except for in masu salmon. The lipid content in dorsal hump connective tissue was richer in masu and chum salmon than in sockeye and pink salmon. These results revealed that the patterns of dorsal hump formation differed among species, and especially sockeye and pink salmon develop pronounced dorsal humps through both increases in the amount of connective tissue and the growth of bone tissues. In contrast, masu and chum salmon develop their dorsal humps by the growth of bone tissues, rather than the development of connective tissue.     

Differential expression of the pro-inflammatory cytokines IL-1beta-1, TNFalpha-1 and IL-8 in vaccinated pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon juveniles

Laboratory-reared pink and chum salmon juveniles (approximately 2g) received an intraperitoneal injection with a commercial, unadjuvanted Aeromonas salmonicida bacterin or sterile saline. Relative to elongation factor-1A, expression levels of genes encoding the proinflammatory cytokines interleukin-1beta-1 (IL-1beta), tumour necrosis factor-alpha-1 (TNFalpha) and interleukin-8 (IL-8) in pools of kidney and liver were examined 6- and 24-h after injection. Expression of IL-1beta was significantly elevated in pink and chum salmon by 6-h, and declined in pink salmon but not in chum salmon by 24-h. Similarly, expression of TNFalpha was significantly elevated in both species at 6h and only in chum salmon after 24-h. Expression of IL-8 was significantly elevated in both species at 6- and 24-h after injection. Expression of the three proinflammatory cytokine genes differed between salmon species both in the timing and magnitude of their expression. The significance of these differences with respect to immune function in these fish requires further research.     

Annual changes in the population size of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae) on high-seas Pacific Salmon (Oncorhynchus spp.), and relationship to host abundance

The population size of the salmon louse, Lepeophtheirus salmonis, was monitored annually in the summers of 1991–1997 by examining six species of Pacific salmon (Oncorhynchus spp.) caught by surface long-lines in oceanic offshore waters of the North Pacific Ocean and Bering Sea. The annual copepod population size on all salmonids caught was estimated by combining the calculated number of copepods carrying on each salmonid species. The copepod population fluctuated markedly from year to year, which resulted largely from marked annual changes in abundance of pink salmon (O. gorbuscha). Since pink salmon were most frequently and heavily infected and since their abundance changed every year, the copepod population was high in the years when this salmonid species was abundant, but low when it was rare. On the contrary, chum salmon (O. keta) did not show high prevalence and intensity of infection, but the annual abundance of this host species was consistently high, i.e. chum salmon carried many copepods every year. Copepods on other salmonid species (sockeye salmon O. nerka, coho salmon O. kisutch, chinook salmon O. tshawytscha, and steelhead trout O. mykiss) constantly formed a small percentage of the total copepod population. Both chum and pink salmon are the most important hosts in terms of their substantial contribution to support the copepod population, but the importance as hosts of each species is definitely different between the species. Chum salmon is a stable important host supporting the copepod population at a relatively high level every year, while the number of copepods on pink salmon annually exhibits marked fluctuations, and this salmonid species is regarded as an unstable important host.     

Sex ratio control in pink salmon (<Emphasis Type="Italic">Oncorhynchus gorbuscha</Emphasis> and chum salmon (<Emphasis Type="Italic">O. keta</Emphasis>) populations: The possible causes and mechanisms of changes in the sex ratio

Long-term changes in the sex ratio have been studied in pink salmon (Oncorhynchus gorbuscha and chum salmon (O. keta) populations of Kamchatka and Sakhalin. It has been demonstrated that these changes are an adaptation to population dynamics: an increase in the population size is accompanied by a shift towards a higher proportion of males; a decrease in population size, by a shift towards a higher proportion of females. The correspondence between morphological and molecular characters in populations of the two species has been analyzed in order to determine the mechanism of sex ratio control. In some pink salmon and chum salmon populations, there is a discrepancy between sex identifications based on morphological characters and molecular markers. This discrepancy is assumed to be accounted for by sex inversion mechanisms, which may be population-or region-specific. In two cases, it has been found that the sex ratio discrepancy in populations is related to the numbers of fish in subsequent generations. These findings suggest that sex inversion may be related to population size control.     

Genetic Variation and Differentiation among Populations of Chum Salmon Oncorhynchus ketaWalbaum from Southern Russian Far East

Allozyme variation of populations of chum salmon Oncorhynchus ketafrom southern Russian Far East was examined. Of 55 loci screened, 31 were polymorphic. Within-population variation accounted for most of the allele diversity; F _STaveraged over loci was 0.052. Linkage disequilibrium was found in less than 5% of locus pairs in the chum population examined. Analysis of within- and among-population variance components of linkage disequilibrium using D-statistics (Ohta, 1982) showed that most genetic variation was distributed among populations.     

Perspectives on wild and hatchery salmon interactions at sea,potential climate effects on Japanese chum salmon,and the need for sustainable salmon fishery management reform in Japan

Pacific salmon (Oncorhynchus spp.) play an important role as a keystone species and provider of ecosystem services in the North Pacific ecosystem. We review our studies on recent production trends, marine carrying capacity, climate effects and biological interactions between wild and hatchery origin populations of Pacific salmon in the open sea, with a particular focus on Japanese chum salmon (O. keta). Salmon catch data indicates that the abundance of Pacific salmon increased since the 1976/77 ocean regime shift. Chum and pink salmon (O. gorbuscha) maintained high abundances with a sharp increase in hatchery-released populations since the late 1980s. Since the 1990s, the biomass contribution of hatchery returns to the total catch amounts to 50% for chum salmon, more than 10% for pink salmon, and less than 10% for sockeye salmon (O. nerka). We show evidence of density-dependence of growth and survival at sea and how it might vary across spatial scales, and we provide some new information on foraging plasticity that may offer new insight into competitive interactions. The marine carrying capacity of these three species is synchronized with long-term patterns in climate change. At the present time, global warming has positively affected growth and survival of Hokkaido populations of chum salmon. In the future, however, global warming may decrease the marine carrying capacity and the area of suitable habitat for chum salmon in the North Pacific Ocean. We outline future challenges for salmon sustainable conservation management in Japan, and recommend fishery management reform to sustain the hatchery-supported salmon fishery while conserving natural spawning populations.     

Preferences of invasive Ponto-Caspian and native European gammarids for zebra mussel (<Emphasis Type="Italic">Dreissena polymorpha</Emphasis>, Bivalvia) shell habitat

The migratory behavior and swimming patterns of anadromous upstream migratory fish have been poorly described in the Shibetsu River in eastern Hokkaido, Japan. In this 2004 study, we used electromyogram (EMG) transmitters and depth/ temperature (DT) loggers to compare the upstream migratory behavior of adult male chum salmon (Oncorhynchus keta) and pink salmon (O. gorbuscha) in the canalized and reconstructed segments of the Shibetsu River, where a part of canalized section was preliminary reconstructed meander to restore a more natural section. The EMG transmitter and DT logger were externally attached to the left side of the body, below the front edge of the dorsal fin. Fish of both species often migrated along the riverbanks and near the bottom of the water column, sometimes engaged in holding behavior, which was defined as cessation of swimming during their upstream migration for 5 minutes. Modal swimming depth calculated by DT loggers for chum salmon (0.2–0.4 m) was shallower than pink salmon (0.6–0.8 m). Further, modal swimming speeds measured by calibrated EMG for chum salmon (0.2–0.4 BL s⁻¹) were slower than pink salmon (1.2–1.4 BL s⁻¹). Pink salmon swam faster as well as in relatively deeper than chum salmon, suggesting that they expend more energy than chum salmon in the reconstructed segment. Based on these results, it seemed likely that the upstream migration behavior of chum and pink salmon was different with species-specific strategies.     

微卫星标记对黑龙江流域大麻哈鱼遗传多样性的研究

采用 12个微卫星标记 ,对中国 3个大麻哈鱼洄游群体 (乌苏里江、黑龙江和绥芬河 )的遗传多样性进行了检测。计算出各个种群的基因杂合度、遗传多样性和各个座位的多态信息含量。结果表明 ,3个大麻哈鱼洄游种群的平均基因杂合度分别为 :0 .6 732、0 5 995、0 .6 917,种群遗传多样性分别为 0 .70 82、0 .6 5 11、0 .76 16。这些结果表明大麻哈鱼遗传多样性还比较丰富 ,其资源的恢复具有良好的前景 ,说明当前中国大麻哈鱼资源数量下降并非由遗传因素引起 ,主要原因可能是由于过度捕捞和水域环境污染等人为因素造成。人工增殖放流为恢复中国大麻哈鱼资源起到了重要作用 ,但目前大麻哈鱼的小种群极易产生遗传瓶颈的现状也应引起人们高度重视     

Salmon species, density and watershed size predict magnitude of marine enrichment in riparian food webs

Resource subsidies across habitat boundaries can structure recipient communities and food webs. In the northern Pacific region, bears Ursus spp. foraging on anadromous salmon Oncorhynchus spp. provide a key link between marine and terrestrial ecosystems, with salmon density, fish size and watershed size as potential predictors of the magnitude of marine subsidy to terrestrial habitats. We use nitrogen and carbon stable isotopes to provide an assessment of the patterns of marine‐enrichment in riparian plants (11 species, 4 guilds) and litter invertebrates (4 guilds) sampled from 27 watersheds in coastal British Columbia, Canada. Watersheds occurred in three geographical regions (Vancouver Island, mainland midcoast and Haida Gwaii) and varied in size, and in biomass (kg m^?1 of spawning length) and species of salmon (chum O. keta, pink O. gorbuscha and coho O. kisutch). δ¹⁵N values in all plant species and invertebrate guilds were positively predicted by total salmon biomass (kg m^?1) and negatively predicted by watershed size. We observed replicated parallel slopes among plant species and invertebrate guilds across the gradient in salmon biomass, with differences in means hypothesized to be due to plant fractionation and animal trophic position. As such, we derived a watershed δ¹⁵N‐index averaged across guilds, and using an information theoretic approach we find that the biomass of chum salmon is a much stronger predictor of the δ¹⁵N‐index than either pink or coho salmon, or the sum biomass of all species. The top linear model contained chum biomass and watershed size. Chum salmon biomass independently predicted δ¹⁵N‐index variation in all three regions of British Columbia. Chum salmon are larger than pink or coho and provide an energetic reward for bears that facilitates carcass transfer, tissue selective foraging, and nutrient distribution by insect scavengers. Analyses of biodiversity and habitat data across many watersheds moves towards a long‐term goal in fisheries ecology to better integrate ecosystem values in salmon conservation.     

Adaptive strategies and life history characteristics in a warming climate: Salmon in the Arctic?

In the warming Arctic, aquatic habitats are in flux and salmon are exploring their options. Adult Pacific salmon, including sockeye (Oncorhynchus nerka), coho (O. kisutch), Chinook (O. tshawytscha), pink (O. gorbuscha) and chum (O. keta) have been captured throughout the Arctic. Pink and chum salmon are the most common species found in the Arctic today. These species are less dependent on freshwater habitats as juveniles and grow quickly in marine habitats. Putative spawning populations are rare in the North American Arctic and limited to pink salmon in drainages north of Point Hope, Alaska, chum salmon spawning rivers draining to the northwestern Beaufort Sea, and small populations of chum and pink salmon in Canada’s Mackenzie River. Pacific salmon have colonized several large river basins draining to the Kara, Laptev and East Siberian seas in the Russian Arctic. These populations probably developed from hatchery supplementation efforts in the 1960’s. Hundreds of populations of Arctic Atlantic salmon (Salmo salar) are found in Russia, Norway and Finland. Atlantic salmon have extended their range eastward as far as the Kara Sea in central Russian. A small native population of Atlantic salmon is found in Canada’s Ungava Bay. The northern tip of Quebec seems to be an Atlantic salmon migration barrier for other North American stocks. Compatibility between life history requirements and ecological conditions are prerequisite for salmon colonizing Arctic habitats. Broad-scale predictive models of climate change in the Arctic give little information about feedback processes contributing to local conditions, especially in freshwater systems. This paper reviews the recent history of salmon in the Arctic and explores various patterns of climate change that may influence range expansions and future sustainability of salmon in Arctic habitats. A summary of the research needs that will allow informed expectation of further Arctic colonization by salmon is given.     

Isolation, primary structure, and biological and immunological properties of pink and chum salmon insulins

1. Insulins have been isolated from islet tissue of pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon. The primary structure of chum and pink salmon insulins was found to be identical. Compared to the amino acid sequence of human insulin, the salmon insulins under study differed at 14 positions. 2. Biological activity of pink salmon insulin was 83% of that of standard porcine insulin. 3. The immunological properties of fish insulins were investigated in specific radioimmunoassay (RIA) systems, based on porcine and pink salmon insulins. 4. A significant difference in the antigenic determinants of these fish and mammalian hormones was revealed.     

Identification of the sex chromosome pair in chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha)

Fluorescence in situ hybridization (FISH) using a probe to the male-specific GH-Y (growth hormone pseudogene) was used to identify the Y chromosome in the karyotypes of chum salmon (Oncorhynchus keta) and pink salmon (Oncorhynchus gorbuscha). The sex chromosome pair is a small acrocentric chromosome pair in chum salmon and the smallest metacentric chromosome pair in pink salmon. Both of these chromosome pairs are morphologically different from the sex chromosome pairs in chinook salmon (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch). The 5S rRNA genes are on multiple chromosome pairs including the sex chromosome pair in chum salmon, but at the centromeres of two autosomal metacentric pairs in pink salmon. The sex chromosome pairs and the chromosomal locations of the 5S rDNA appear to be different in all five of the North American Pacific salmon species and rainbow trout. The implications of these results for evolution of sex chromosomes in salmonids are discussed.     

Trophic ecology of Pacific salmon (<Emphasis Type="Italic">Oncorhynchus</Emphasis> spp.) in the ocean: a synthesis of stable isotope research

Increasing interest in the marine trophic dynamics of Pacific salmon has been motivated by the recognition of their sensitivity to changing climate and to the competitive effects of hatchery fish on wild stocks. It has become more common to use stable isotopes to supplement traditional diet studies of salmon in the ocean; however, there have been no integrated syntheses of these data to determine whether stable isotope analyses support the existing conventional wisdom of feeding strategies of the Pacific salmon. We performed a meta-analysis of stable isotope data to examine the extent of trophic partitioning among five species of Pacific salmon during their marine lives. Pink, sockeye, and chum salmon showed very high overlap in resource use and there was no consistent evidence for chum relying on alternative food webs dominated by gelatinous zooplankton. δ¹⁵N showed that Chinook and coho salmon fed at trophic levels higher than the other three species. In addition, these two species were distinctly enriched in ¹³C, suggesting more extensive use of coastal food webs compared to the more depleted (pelagic) signatures of pink, sockeye, and chum salmon. This paper presents the first synthesis of stable isotope work on Pacific salmon and provides δ¹⁵N and δ¹³C values applicable to research on the fate of the marine derived nutrients these organisms transport to freshwater and riparian ecosystems.