Velocity and dominance affect prey capture and microhabitat selection in juvenile Chinook (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>)

Habitat selection is an important phenomenon that may greatly affect individual fitness. Using an artificial stream, we examined the relationship between the percentage of prey captured, reactive distance, dominance, and water velocity for juvenile Chinook Salmon (Oncorhynchus tshawytscha) from the Chena River, Alaska, and tested the fitness-based microhabitat selection model of Grossman et al. (Ecol Freshw Fish 11:2–10, 2002). Recent declines in the abundance of Chinook accentuate our need for habitat selection studies on this species. We conducted three experiments: two with single fish (1st N?=?27, fish SL 58–84 mm, 2nd N?=?14, fish SL 49–56 mm) and one with pairs of dominant and subordinate fish (N?=?10 pairs, 64–96 mm, mean difference in SL?=?7 mm). We placed individual or pairs of fish in an artificial flume and recorded reactive distance and the percent prey capture with individual dead brine shrimp (Artemia spp.) as prey. Prey were presented at 10 cm/s velocity intervals ranging from 10 to 60 cm/s; velocities found in the natural habitat. Mean reactive distance in single fish experiments (henceforth SFE) averaged 33 and 29 cm respectively, and was not related to velocity. We detected a negative, curvilinear relationship between velocity and percent prey capture. Holding velocities for juvenile Chinook were significantly lower than prey capture velocities. The Grossman et al. (Ecol Freshw Fish 11:2–10, 2002) model yielded an optimal focal-point velocity prediction of 35 cm/s for juvenile Chinook, however focal-point velocities occupied by juveniles in the Chena River averaged 12 cm/s. Predicted optimal velocities were present in the Chena River; hence, this discrepancy suggests that other factors such as distraction from drifting debris or predation risk influenced habitat selection. There were no differences in reactive distances or holding velocity/capture velocity relationships for dominant and subordinate fish; however, dominants captured significantly more prey than subordinates. Being subordinate resulted in a decrease of 61% in mean percent prey capture (the difference between what was captured by the fish alone versus the difference with a dominant), whereas the mean cost to fish with dominant rank was a 21% decline between the percentage captured alone versus that with a subordinate.     

Experimental evidence of population-specific marine spatial distributions of Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>

Migratory behavior can be affected by attributes of the animals themselves such as size and growth rate, external factors such as biotic and abiotic features of the environment, and also genetic tendencies. To better understand the role of genetics in the migratory behavior of Chinook salmon, Oncorhynchus tshawytscha, we report the results of an experiment in which two populations (University of Washington (UW) hatchery and Elwha River) and their hybrid offspring were reared at, tagged, and released from a single site, the UW hatchery, at a common size and date. The patterns of recoveries in fisheries differed markedly with respect to spatial distribution and also age of the fish. A larger proportion of the Elwha River fish were recovered in Puget Sound in their first year of marine life than the other groups (40.7% vs. 11.2% for UW and 7.0% for the hybrids). The Elwha River fish also showed a higher proportion of northerly recoveries (21.9%) than UW fish (1.7%), and hybrids showed an intermediate value (8.1%). In contrast, no Elwha River fish were recovered south along the Washington coast compared to 1.3% of the hybrids and 7.7% of the UW fish. The specific mechanisms controlling the migration patterns of the populations remain unclear but the results strongly indicated a genetic influence on distribution patterns.     

Defining marine habitat of juvenile Chinook salmon, <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, and coho salmon, <Emphasis Type="Italic">O. kisutch</Emphasis>, in the northern California Current System

We investigated habitat use by juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) to identify environmental characteristics that may define their optimal marine habitat. We utilized physical and biological data from four cruises in the northern California Current system from Newport, Oregon, to Crescent City, California, in June and August 2000 and 2002. A non-parametric statistical method was used to analyze and select environmental parameters that best defined ocean habitat for each species. Regression trees were generated for all cruises combined to select the most important habitat variables. Chlorophyll a concentration best defined habitat of yearling Chinook salmon, while decapod larvae, salinity, and neuston biovolume defined habitat of yearling coho salmon. Using criteria from the regression tree analysis, GIS maps were produced to show that the habitat of yearling Chinook salmon was widespread over the continental shelf and the habitat of yearling coho salmon was variable and mainly north of Cape Blanco.     

Identification of multiple genetically distinct populations of Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) in a small coastal watershed

Management and restoration planning for Pacific salmon is often characterized by efforts at broad multi-basin scales. However, finer-scale genetic and phenotypic variability may be present within individual basins and can be overlooked in such efforts, even though it may be a critical component for long-term viability. Here, we investigate Chinook salmon (Oncorhynchus tshawytscha) within the Siletz River, a small coastal watershed in Oregon, USA. Adult Chinook salmon were genotyped using neutral microsatellite markers, single nucleotide polymorphisms and “adaptive” loci, associated with temporal variation in migratory behavior in many salmon populations, to investigate genetic diversity based upon both spatial and temporal variation in migratory and reproductive behavior. Results from all three marker types identified two genetically distinct populations in the basin, corresponding to early returning fish that spawn above a waterfall, a spring-run population, and later returning fish spawning below the waterfall, a fall-run population. This finding is an important consideration for management of the species, as spring-run populations generally only have been recognized in large watersheds, and highlights the need to evaluate population structure of salmon within smaller watersheds, and thereby increase the probability of successful conservation of salmon species.     

Vertical self-sorting behavior in juvenile Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>): evidence for family differences and variation in growth and morphology

Life history variation is fundamental to the evolution of Pacific salmon and their persistence under variable conditions. We discovered that Chinook salmon sort themselves into surface- and bottom-oriented groups in tanks within days after exogenous feeding. We hypothesised that this behaviour is correlated with subsequent differences in body morphology and growth (as measured by final length and mass) observed later in life. We found consistent morphological differences between surface and bottom phenotypes. Furthermore, we found that surface and bottom orientation within each group is maintained for at least one year after the phenotypes were separated. These surface and bottom phenotypes are expressed across genetic stocks, brood years, and laboratories and we show that the proportion of surface- and bottom-oriented offspring also differed among families. Importantly, feed delivery location did not affect morphology or growth, and the surface fish were longer than bottom fish at the end of the rearing experiment. The body shape of the former correlates with wild individuals that rear in mainstem habitats and migrate in the fall as subyearlings and the latter resemble those that remain in the upper tributaries and migrate as yearling spring migrants. Our findings suggest that early self-sorting behaviour may have a genetic basis and be correlated with other phenotypic traits that are important indicators for juvenile migration timing.     

Gamete-associated flavobacteria of the oviparous Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) in lakes Michigan and Huron,North America

Flavobacterial diseases, caused by multiple members of the Family Flavobacteriaceae, elicit serious losses in wild and farmed fish around the world. Flavobacteria are known to be transmitted horizontally; however, vertical transmission has been suspected but proven only for one fish-pathogenic flavobacterial species (e.g., Flavobacterium psychrophilum). Herein, we report on the isolation and molecular identification of multiple Flavobacterium and Chryseobacterium taxa from the ovarian fluid and eggs of feral Great Lakes Chinook salmon (Oncorhynchus tshawytscha). Identified egg- and ovarian fluid-associated flavobacteria were either well-known flavobacterial fish pathogens (e.g., F. psychrophilum and F. columnare), most similar to emerging fish-associated flavobacteria (e.g., F. spartansii, F. tructae, F. piscis, C. piscium, C. scophthalmum), or were distinct from all other described Chryseobacterium and Flavobacterium spp., as determined by phylogenetic analyses using neighbor-joining, Bayesian, and Maximum Likelihood methodologies. The gamete-associated flavobacteria fell into three groups (e.g., those that were recovered from the ovarian fluid but not eggs; those that were recovered from the ovarian fluid and eggs; and those that were recovered from eggs but not ovarian fluid), a portion of which were recovered from eggs that were surface disinfected with iodophor at the commonly used dose and duration for egg disinfection. Some gamete-associated flavobacteria were also found in renal, splenic, and neurological tissues. Systemic polymicrobial infections comprised of F. psychrophilum and F. columnare were also detected at nearly an 11% prevalence. This study highlights the potential role that sexual products of female Great Lakes Chinook salmon may play in the transmission of fish-associated flavobacteria.     

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) within a Snake River watershed

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.     

Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>, Walbaum 1792) in the Beagle Channel,Tierra del Fuego: the onset of an invasion

In this paper we provide the first report of the presence of exotic Chinook salmon (Oncorhynchus tshawytscha) in two rivers off the Beagle Channel, Lapataia and Ovando, in southern Tierra del Fuego. We also confirm that successful reproduction occurred in the fall of 2007, as we captured yearlings in freshwater. Scale pattern analyses of adult fish caught were all of the “stream” ecotype, with ages ranging between 3 and 5 (average 4.2 year). Stable isotope analysis of Ovando-Lapataia Chinook population indicates general patterns consistent with those of other populations in the region, but characteristically enriched levels of C indicates a distinct ocean feeding location as compared to Atlantic populations in the Santa Cruz River. Two different haplotypes, one identical to the unique haplotype of the Caterina River population, were found in the Ovando-Lapataia rivers, providing partial evidence for some level of contemporary segregation between these two populations. As an exotic species, Chinook salmon have been able to use the ocean as a waterway to rapidly colonize new habitats both in New Zealand and in several Pacific and Atlantic river basins of continental Patagonia. This record expands the known distribution of this species in Patagonia further south and into the Island of Tierra del Fuego. Its presence in the Beagle Channel creates the conditions for its expansion to a significant collection of new rivers, as well as to adjacent marine areas in and around the Southern Fuegian Channels. Our results provide support to the idea that, in practice, no district of Patagonia is sheltered from the colonization by invasive anadromous Salmonids.     

Juvenile Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) growth in off-channel and main-channel habitats on the Sacramento River,CA using otolith increment widths

Few studies have quantified juvenile salmon growth among different habitats or evaluated the mechanisms controlling salmon growth and survival. We used otolith microstructure to compare daily relative growth rates among main-channel riverine areas, off-channel ponds, and non-natal seasonal tributaries of the Sacramento River, CA. We compared prey availability, prey preference, and stomach fullness between these sites. We observed larger average otolith growth increments, higher prey densities, and warmer water temperatures in both off-channel ponds and non-natal seasonal tributaries compared to the main-channel areas in both 2001 and 2002. Our findings suggest that warmer temperatures and abundant prey in off-channel habitats during Central Valley Chinook salmon rearing periods may lead to higher growth rates, which in turn may improve juvenile survival. Our results suggest that off-channel habitats may be critical habitats to include in conservation and management plans for juvenile salmon.     

New combinations and typifications in <Emphasis Type="Italic">Bistorta</Emphasis>, <Emphasis Type="Italic">Persicaria</Emphasis>, <Emphasis Type="Italic">Polygonum,</Emphasis> and <Emphasis Type="Italic">Rumex</Emphasis> (Polygonaceae)

New combinations are proposed in anticipation of the Polygonaceae treatment in the forthcoming volume of Intermountain Flora: Polygonum kelloggii var. esotericum, P. kelloggii var. watsonii , Rumex densiflorus var. pycnanthus , R. salicifolius var. utahensis, and R. occidentalis var. tomentellus. Typifications are proposed to facilitate ongoing studies in Polygonaceae and to maintain current usage.     

Replication timing of large <Emphasis Type="Italic">Sorex granarius</Emphasis> (<Emphasis Type="Italic">Soricidae</Emphasis>, <Emphasis Type="Italic">Eulipotyphla</Emphasis>) telomeres

Previously, we described the unique feature of telomeric regions in Iberian shrew Sorex granarius: its telomeres have two ranges of size, very small (3.8 kb of telomeric repeats on average) and very large discontinuous telomeres (213 kb) interrupted with 18S rDNA. In this study, we have demonstrated extraordinary replication pattern of S. granarius large telomeres that have not been shown before in other studied mammal. Using the ReD-FISH procedure, we observed prolonged, through S period, large telomere replication. Furthermore, revealed ReD-FISH asymmetric signals were probably caused by partial replication of telomeres within an hour of 5-bromodeoxyuridine treatment due to the large size and special organization. We also found that in contrast to the telomeric halo from primary fibroblasts of bovine, mink, and common shrew, telomere halo of S. granarius consists of multiple loops bundled together, some of which contain rDNA. Here, we suggested several replicons firing possibly stochastic in each large telomere. Finally, we performed the TIF assay to reveal DNA damage responses at the telomeres, and along with TIF in nuclei, we found large bodies of telomeric DNA and ?-H2AX in the cytoplasm and on the surface of fibroblasts. We discuss the possibility of additional origin activation together with recombination-dependent replication pathways, mainly homologous recombination including BIR for replication fork stagnation overcoming and further S. granarius large telomere replication.     

Relationship of winter concealment habitat quality on pool use by juvenile spring Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) in the Grande Ronde River Basin,Oregon USA

Winter concealment habitat quality was assessed and its use by juvenile spring Chinook salmon (Oncorhynchus tshawytscha) quantified in three hatching areas of the Grande Ronde River Basin, Oregon USA. Fish densities were significantly higher in pools with a higher winter concealment habitat index than pools with a lower index. The mean fork length and mean growth rate of fish did not differ between pools with a higher or lower winter concealment habitat index, even though residual fish were significantly larger than fish that emigrated. Biomass–density was significantly higher in pools with a higher winter concealment habitat index than pools with a lower index in all three hatching areas. Biomass–density was positively associated with the amount of cobble substrate (10–24.9 cm/m²) in all three hatching areas, and inversely associated with embeddedness in two of the hatching areas. Results of this study indicate that enhancing winter concealment habitat could improve habitat quality resulting in increased carrying capacity and winter usage by juvenile spring Chinook salmon. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: J. A. Cambray     

<Emphasis Type="Italic">Ty</Emphasis>1<Emphasis Type="Italic">/copia</Emphasis>- and <Emphasis Type="Italic">Ty</Emphasis>3<Emphasis Type="Italic">/gypsy</Emphasis>-like DNA sequences in <Emphasis Type="Italic">Helianthus </Emphasis>species

Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes.     

Determination of Genetic Sex in Chinook Salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) Using the Male-Linked Growth Hormone Pseudogene by Real-Time PCR

This study used a real-time quantitative polymerase chain reaction (qPCR) method based on the growth hormone pseudogene (GHp) in chinook salmon (Oncorhynchus tshawytscha) to determine genetic sex. The GHp is present as a single copy in the genome of the male chinook salmon but is absent in the female, providing a means of using this real-time qPCR method to discriminate genetic sex. Comparisons between genomic DNA samples from 2 geographically distinct populations of chinook salmon (Columbia River, Washington, and Yukon River, Alaska) showed, within each population examined, that the males were clearly differentiated from the females. There were no interpopulation differences between males or females. The advantages of this real-time qPCR method are that it is rapid, is amenable to high sample throughput, and provides an accurate numerical value that allows comparisons between samples by statistical methods.     

<Emphasis Type="Italic">In silico</Emphasis> and <Emphasis Type="Italic">in situ</Emphasis> characterization of the zebrafish (<Emphasis Type="Italic">Danio rerio</Emphasis>) <Emphasis Type="Italic">gnrh3</Emphasis> (sGnRH) gene

Background

Gonadotropin releasing hormone (GnRH) is responsible for stimulation of gonadotropic hormone (GtH) in the hypothalamus-pituitary-gonadal axis (HPG). The regulatory mechanisms responsible for brain specificity make the promoter attractive for in silico analysis and reporter gene studies in zebrafish (Danio rerio).

Results

We have characterized a zebrafish [Trp⁷, Leu⁸] or salmon (s) GnRH variant, gnrh 3. The gene includes a 1.6 Kb upstream regulatory region and displays the conserved structure of 4 exons and 3 introns, as seen in other species. An in silico defined enhancer at -976 in the zebrafish promoter, containing adjacent binding sites for Oct-1, CREB and Sp1, was predicted in 2 mammalian and 5 teleost GnRH promoters. Reporter gene studies confirmed the importance of this enhancer for cell specific expression in zebrafish. Interestingly the promoter of human GnRH-I, known as mammalian GnRH (mGnRH), was shown capable of driving cell specific reporter gene expression in transgenic zebrafish.

Conclusions

The characterized zebrafish Gnrh3 decapeptide exhibits complete homology to the Atlantic salmon (Salmo salar) GnRH-III variant. In silico analysis of mammalian and teleost GnRH promoters revealed a conserved enhancer possessing binding sites for Oct-1, CREB and Sp1. Transgenic and transient reporter gene expression in zebrafish larvae, confirmed the importance of the in silico defined zebrafish enhancer at -976. The capability of the human GnRH-I promoter of directing cell specific reporter gene expression in zebrafish supports orthology between GnRH-I and GnRH-III.

     

Characteristics of the spawning stock of chinook salmon <Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis> from the Apuka River (northeastern Kamchatka)

Biological features of chinook salmon Oncorhynchus tshawytscha from the Apuka River, the largest river of the northeastern Kamchatka inflowing Olyutorskii Bay of the Bering Sea, are studied. Chinook salmon from the Apuka River spend mainly a year in the river before downstream migration to the sea. The fish live in the sea for 1–4 years. The spawning migration of chinook salmon into the Apuka River begins in late May just after ice melting, and it continues until early August. The main part of the spawners enters the river during June. A hypothesis on the occurrence of two seasonal races in the Apuka River is proposed.     

<Emphasis Type="Italic">Quinua</Emphasis> and Relatives (<Emphasis Type="Italic">Chenopodium</Emphasis> sect.<Emphasis Type="Italic">Chenopodium</Emphasis> subsect.<Emphasis Type="Italic">Celluloid</Emphasis>)

Traditionally viewed as an Andean grain crop,Chenopodium quinoa Willd. includes domesticated populations that are not Andean, and Andean populations that are not domesticated. Comparative analysis of leaf morphology and allozyme frequencies have demonstrated that Andean populations, both domesticated(quinua) and free-living(ajara), represent an exceptionally homogeneous unit that is well differentiated from allied domesticates of coastal Chile(quingua) and freeliving populations of the Argentine lowlands(C. hircinum). This pattern of relationships indicates that Andean populations represent a monophyletic crop/weed system that has possibly developed through cyclic differentiation (natural vs. human selection) and introgressive hybridization. Relative levels of variation suggest that this complex originated in the southern Andes, possibly from wild types allied withC. hircinum, with subsequent dispersal north to Colombia and south to the Chilean coast. Coastal populations were apparently isolated from post-dispersal differentiation and homogenization that occurred in the Andes. Other data point toward a center of origin in the northern Andes with secondary centers of genetic diversity subsequently developing in the southern Andes and the plains of Argentina. Comparative linkage of South American taxa, all tetraploid, with North American tetraploids of the subsection will eventually clarify this problem. While the possibility of a direct phyletic connection betweenC. quinoa and the Mexican domesticate(C. berlandieri subsp. nuttalliae,) cannot be excluded, available evidence indicates that the latter represents an autonomous lineage that is associated with the basal tetraploid, C. b. subsp.berlandieri, through var.sinuatum, whereas South American taxa show possible affinities to either var. zschackei or var.berlandieri. An extinct domesticate of eastern North America,C. b. subsp.jonesianum, represents either another instance of independent domestication, possibly from subsp. b. var.zschackei, or a northeastern outlier of subsp.nuttalliae.     

Pedogamy in <Emphasis Type="Italic">Neidium</Emphasis> (<Emphasis Type="Italic">Bacillariophyceae</Emphasis>)

Single (unpaired) vegetative cells of freshwater pennate diatom Neidium cf. ampliatum differentiated into gametangia and produced a single zygote (auxospore) via a pedogamic process. The gametic nuclei fused after auxospore expansion had begun. The auxospore expanded in parallel to the apical axis of the gametangium.