scholarly journals Genomic changes associated with reproductive and migratory ecotypes in sockeye salmon (Oncorhynchus nerka)

2017 ◽  
Author(s):  
Andrew J Veale ◽  
Michael A Russello
Keyword(s):  
Life History ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Multiple Comparisons ◽  
Nucleotide Polymorphisms ◽  
Life History Variation ◽  
Genomic Changes ◽  
Outlier Loci ◽  
Patterns And Processes ◽  
Genomic Regions

AbstractMechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms (SNPs), 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Eighty-six of these outliers were present in multiple comparisons, with thirty-three detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser and Snake). We also detected several islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The SNPs and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.

Physiological and Growth Differences in Three Stocks of Underyearling Sockeye Salmon (Oncorhynchus nerka) on Early Entry into Seawater

1994 ◽  
Vol 51 (4) ◽  
pp. 974-980 ◽  
Author(s):  
Stanley D. Rice ◽  
Robert E. Thomas ◽  
Adam Moles
Keyword(s):  
Life History ◽  
Sockeye Salmon ◽  
Salt Water ◽  
Oncorhynchus Nerka ◽  
Early Life History ◽  
Life History Strategies ◽  
Growth Differences ◽  
The Impact ◽  
Lake Type ◽  
River Type

We compared the impact of exposure to seawater on three sockeye salmon (Oncorhynchus nerka) stocks: one that normally migrates to sea as underyearlings (sea-type) and two with the more common life history strategies of 1 (river-type) or 2 (lake-type) yr of freshwater residence prior to seaward migration. Innate differences in survival, ability to regulate tissue chlorides, and oxygen consumption when first introduced into salt water were more evident in April and May when fish were less than 50 mm in length. In fish longer than 50 mm, the only significant differences among the stocks were in saltwater growth. Between June and August, sea-type fish showed faster growth than river-type fish which in turn grew faster than lake-type fish. When introduced into salt water in October, virtually no growth occurred in any stock, regardless of fish size. River-type and lake-type sockeye, which normally overwinter 1 and 2 yr, respectively, in freshwater, can be reared in seawater if underyearlings are raised to a length of 50 mm before release into salt water, similar to the normal life history of sea-type underyearlings. Early life history appears to be influenced more by habitat than by genetics.

scholarly journals Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

2014 ◽  
Vol 281 (1783) ◽  
pp. 20140012 ◽  
Author(s):  
Devon E. Pearse ◽  
Michael R. Miller ◽  
Alicia Abadía-Cardoso ◽  
John Carlos Garza
Keyword(s):  
Life History ◽  
Rainbow Trout ◽  
Parallel Evolution ◽  
Genomic Region ◽  
Life History Strategies ◽  
Strong Linkage Disequilibrium ◽  
Rapid Adaptation ◽  
Life History Variation ◽  
Standing Variation ◽  
Genomic Regions

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss . Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

AN INVESTIGATION OF THE LIFE HISTORY AND PROPAGATION OF THE SOCKEYE SALMON (ONCORHYNCHUS NERKA) AT CULTUS LAKE, BRITISH COLUMBIA: No. 4. THE LIFE HISTORY CYCLE OF THE 1925 YEAR CLASS WITH NATURAL PROPAGATION

1933 ◽  
Vol 8 (1) ◽  
pp. 345-355
Author(s):  
R. E. FOERSTER
Keyword(s):  
British Columbia ◽  
Life History ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Spawning Areas

Eggs spawned naturally by 3,883 females in 1925 were estimated as amounting to 17,470,000. Approximately 12,500 fry (0.07% of eggs) migrated to sea in 1926, 183,272 yearlings (1.05%) in 1927, and 1,722 two-year-olds (0.01%) in 1928, making 1.13% in all. Returning fish consisted of no three-year (32 group), 4,463 four-year (42 group), and 1,112 five-year fish (no 52 group, all being of the 53 group). None of the fish was reported returning to other spawning areas.

scholarly journals Genetic coupling of life-history and aerobic performance in juvenile Atlantic salmon

2021 ◽  
Author(s):  
Jenni M. Prokkola ◽  
Eirik R Åsheim ◽  
Sergey Morozov ◽  
Paul Bangura ◽  
Jaakko Erkinaro ◽  
...  
Keyword(s):  
Life History ◽  
Atlantic Salmon ◽  
Metabolic Rate ◽  
Aerobic Performance ◽  
Age At Maturity ◽  
Life History Variation ◽  
Early Maturation ◽  
Genomic Regions ◽  
Late Maturation

1. The physiological underpinnings of life history adaptations in ectotherms are not well understood. Theories suggest energy metabolism influences life history variation via modulation of resource acquisition. However, the genetic basis of this relation and its dependence on ecological conditions, such as food availability, have rarely been characterized, despite being critical to predicting the responses of populations to environmental changes. 2. The Atlantic salmon (Salmo salar) is an emerging wild model species for addressing these questions; strong genetic determination of age-at-maturity at two unlinked genomic regions (vgll3 and six6) enables the use of complex experimental designs and tests of hypotheses on the physiological and genetic basis of life-history trait variation. 3. In this study, we crossed salmon to obtain individuals with all combinations of late and early maturation genotypes for vgll3 and six6 within full-sib families. Using more than 250 juveniles in common garden conditions, we tested (i) whether metabolic phenotypes (i.e., standard and maximum metabolic rates, and absolute aerobic scope) were correlated with the age-at-maturity genotypes and (ii) if high vs. low food availability modulated the relationship. 4. We found that salmon with vgll3 early maturation genotype had a higher aerobic scope and maximum metabolic rate, but not standard metabolic rate, compared to salmon with vgll3 late maturation genotype. This suggests that physiological or structural pathways regulating maximum oxygen supply or demand are potentially important for the determination of age-at-maturity in Atlantic salmon. 5. Vgll3 and six6 exhibited physiological epistasis, whereby maximum metabolic rate significantly decreased when late maturation genotypes were present concurrently in both loci compared to other genotype combinations. 6. The growth of the feed restricted group decreased substantially compared to the high food group. However, the effects of life-history genomic regions were similar in both feeding regimes, indicating a lack of genotype-by-environment interactions. 7. Our results indicate that aerobic performance of juvenile salmon may affect their age-at-maturity. The results may help to better understand the mechanistic basis of life-history variation, and the metabolic constrains on life-history evolution.

A comparison of polymorphism of genetic markers and population sample sizes required for mixed-stock analysis of sockeye salmon (Oncorhynchus nerka) in British Columbia

2011 ◽  
Vol 68 (3) ◽  
pp. 550-562 ◽  
Author(s):  
Terry D. Beacham ◽  
B. McIntosh ◽  
C. G. Wallace
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Population Sample ◽  
Identification Accuracy ◽  
Stock Identification ◽  
Nucleotide Polymorphisms ◽  
Sample Sizes ◽  
Genetic Stock ◽  
Baseline Sample

We evaluated two questions: (i) do microsatellites require larger population baseline sample sizes than single nucleotide polymorphisms (SNPs) to allow the accuracy provided by the microsatellites in genetic stock identification (GSI) applications to be expressed, and (ii) do less genetically distinct populations require larger population baseline sample sizes than more distinct populations to improve population-specific accuracy in GSI applications? Forty-six SNP loci were surveyed in 40 populations of sockeye salmon ( Oncorhynchus nerka ) over 16 regions from southern and central British Columbia and were split into two groups: the top 23 SNPs evaluated for stock identification for British Columbia sockeye salmon and the poorest 23 nuclear SNPs. Fourteen microsatellites were surveyed and split into two groups, with loci from the top 7 loci for stock identification accuracy assembled in one group, and the remaining 7 microsatellites assigned to a second group. SNPs and microsatellites with lower stock identification power required larger population sample sizes to allow expression of stock identification potential. To achieve the same level of population-specific accuracy, SNPs required fewer individuals to be sampled in a population than did microsatellites. Less genetically distinct populations required larger population sample sizes to achieve a given level of accuracy in estimated stock compositions.

scholarly journals Putting the ‘bio’ into bioinformatics

2009 ◽  
Vol 5 (3) ◽  
pp. 391-393 ◽  
Author(s):  
Lindell Bromham
Keyword(s):  
Stochastic Process ◽  
Life History ◽  
Molecular Evolution ◽  
Selection Pressure ◽  
Molecular Data ◽  
Special Issue ◽  
Genomic Change ◽  
Genomic Changes ◽  
Patterns And Processes ◽  
Underlying Processes

Bioinformatic analyses have grown rapidly in sophistication and efficiency to accommodate the vast increase in available data. One of the major challenges has been to incorporate the growing appreciation of the complexity of molecular evolution into new analytical methods. As the reliance on molecular data in biology and medicine increases, we need to be confident that these methods adequately reflect the underlying processes of genome change. This special issue focuses on the way that patterns and processes of molecular evolution are influenced by features of populations of whole organisms, such as selection pressure, population size and life history. The advantage of this approach to molecular evolution is that it views genomic change not simply as a biochemical or stochastic process, but as the result of a complex series of interactions that shape the kinds of genomic changes that can and do happen.

Sign in / Sign up

Export Citation Format

Share Document