The Salmon Smai Family of Short Interspersed Repetitive Elements (Sines): Interspecific and Intraspecific Variation of the Insertion of Sines in the Genomes of Chum and Pink Salmon

The genomes of chum salmon and pink salmon contain a family of short interspersed repetitive elements (SINEs), designated the salmon SmaI family. It is restricted to these two species, a distribution that suggests that this SINE family might have been generated in their common ancestor. When insertions of the SmaI SINEs at 10 orthologous loci of these species were analyzed, however, it was found that there were no shared insertion sites between chum and pink salmon. Furthermore, at six loci where SmaI SINEs have been species-specifically inserted in chum salmon, insertions of SINEs were polymorphic among populations of chum salmon. By contrast, at four loci where SmaI SINEs had been species-specifically inserted in pink salmon, the SINEs were fixed among all populations of pink salmon. The interspecific and intraspecific variation of the SmaI SINEs cannot be explained by the assumption that the SmaI family was amplified in a common ancestor of these two species. To interpret these observations, we propose several possible models, including introgression and the horizontal transfer of SINEs from pink salmon to chum salmon during evolution.     

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.     

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.     

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.     

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.     

The abundance and distribution of Lepeophtheirus salmonis (Copepoda: Caligidae) on pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon in coastal British Columbia

In total, 23,750 specimens of the salmon louse, Lepeophtheirus salmonis, were collected from 3,907 juvenile pink and 3,941 chum salmon caught within the Broughton Archipelago during a 2-yr survey. The prevalence on pink salmon was significantly higher than on chum salmon in 2004 (62.3% and 58.6%, respectively) and in 2005 (26.4% and 23.1%, respectively). The mean abundance on chum salmon was significantly higher than on pink salmon in 2004 (7.0 +/- 0.3 and 2.8 +/- 0.2, respectively), whereas in 2005 the mean abundance did not differ between species (0.6 +/- 0.1 and 0.5 +/- 0.0, respectively). The mean intensity on chum salmon was significantly higher than on pink salmon in 2004 (12.0 +/- 0.4 and 4.5 +/- 0.2, respectively) and in 2005 (2.5 +/- 0.2 and 1.7 +/- 0.1, respectively). The prevalence, intensity, and abundance of L. salmonis were significantly higher on salmon belonging to both host species in 2004 compared with 2005. In both years, a majority of pink and chum salmon had 2 or fewer lice. In general, a decline in abundance of L. salmonis over the 3 collection periods in each year coincided with an increased percentage of motile developmental stages. The abundance was lowest on fish collected from zones in which the seawater surface salinity was also lowest. Seawater surface temperature was higher and salinity was lower in 2004 compared with 2005. The spatial and temporal trends in the abundance of L. salmonis in relation to host size, infestation rates, and seawater salinity and temperature, evident in both years, must be considered in future studies assessing the role of farmed salmon in the epizootiology of this parasite on juvenile salmon in this area.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

Evidence for competitive dominance of Pink salmon (<Emphasis Type="Italic">Oncorhynchus gorbuscha</Emphasis>) over other Salmonids in the North Pacific Ocean

Relatively little is known about fish species interactions in offshore areas of the world’s oceans because adequate experimental controls are typically unavailable in such vast areas. However, pink salmon (Oncorhynchus gorbuscha) are numerous and have an alternating-year pattern of abundance that provides a natural experimental control to test for interspecific competition in the North Pacific Ocean and Bering Sea. Since a number of studies have recently examined pink salmon interactions with other salmon, we reviewed them in an effort to describe patterns of interaction over broad regions of the ocean. Research consistently indicated that pink salmon significantly altered prey abundance of other salmon species (e.g., zooplankton, squid), leading to altered diet, reduced total prey consumption and growth, delayed maturation, and reduced survival, depending on species and locale. Reduced survival was observed in chum salmon (O. keta) and Chinook salmon (O. tshawytscha) originating from Puget Sound and in Bristol Bay sockeye salmon (O. nerka). Growth of pink salmon was not measurably affected by other salmon species, but their growth was sometimes inversely related to their own abundance. In all marine studies, pink salmon affected other species through exploitation of prey resources rather than interference. Interspecific competition was observed in nearshore and offshore waters of the North Pacific Ocean and Bering Sea, and one study documented competition between species originating from different continents. Climate change had variable effects on competition. In the North Pacific Ocean, competition was observed before and after the ocean regime shift in 1977 that significantly altered abundances of many marine species, whereas a study in the Pacific Northwest reported a shift from predation- to competition-based mortality in response to the 1982/1983 El Nino. Key traits of pink salmon that influenced competition with other salmonids included great abundance, high consumption rates and rapid growth, degree of diet overlap or consumption of lower trophic level prey, and early migration timing into the ocean. The consistent pattern of findings from multiple regions of the ocean provides evidence that interspecific competition can significantly influence salmon population dynamics and that pink salmon may be the dominant competitor among salmon in marine waters.     

A genetic analysis of early development in pink (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) at three different temperatures

A factorial mating design was employed in which five males were mated to each of five females in each of two stocks for both pink and chum salmon. The resulting embryos and alevins were incubated at constant water temperatures of 4, 8, and 16 degrees C for pink salmon and 3, 8, and 15 degrees C for chum salmon. Variation among families in alevin and fry survival rates, hatching, button-up time, length, and weight was the least at 8 degrees C. Heritability of traits directly correlated with fitness, such as survival rates and button-up time, was low at all temperatures (h2 less than or equal to 0.25). Maternal effects could account for a substantial portion of the variation in alevin and fry size characters. Nonadditive genetic variance accounted for more of the variation in fry size characters than in those of alevins. Negative genetic correlations were observed between embryo survival and subsequent alevin size and between hatching time and subsequent alevin and fry size. Genotype-temperature interactions could underlie a substantial amount of phenotypic variation in the developmental characters examined for both 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.     

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.     

Self-sustaining populations, population sinks or aggregates of strays: chum (Oncorhynchus keta) and Chinook salmon (Oncorhynchus tshawytscha) in the Wood River system, Alaska

Small populations can provide insights into ecological and evolutionary aspects of species distributions over space and time. In the Wood River system in Alaska, USA, small aggregates of Chinook (Oncorhynchus tshawytscha) and chum salmon (O. keta) spawn in an area dominated by sockeye salmon (O. nerka). Our objective was to determine whether these Chinook and chum salmon are reproductively isolated, self-sustaining populations, population sinks that produce returning adults but receive immigration, or strays from other systems that do not produce returning adults. DNA samples collected from adult chum salmon from 16 streams and Chinook salmon from four streams in the Wood River system over 3 years were compared to samples from large populations in the nearby Nushagak River system, a likely source of strays. For both species, microsatellite markers indicated no significant genetic differentiation between the two systems. Simulations of microsatellite data in a large source and a smaller sink population suggested that considerable immigration would be required to counteract the diverging effects of genetic drift and produce genetic distances as small as those observed, considering the small census sizes of the two species in the Wood River system. Thus, the Wood River system likely receives substantial immigration from neighbouring watersheds, such as the Nushagak River system, which supports highly productive runs. Although no data on population productivity in the Wood River system exist, our results suggest source-sink dynamics for the two species, a finding relevant to other systems where salmonid population sizes are limited by habitat factors.     

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.