Comparative genome mapping between Chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (O. mykiss) based on homologous microsatellite loci.

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Comparative genome mapping between Chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (O. mykiss) based on homologous microsatellite loci.

G3 (Bethesda). 2013 Dec;3(12):2281-8

Authors: Naish KA, Phillips RB, Brieuc MS, Newton LR, Elz AE, Park LK

Abstract
Comparative genome mapping can rapidly facilitate the transfer of DNA sequence information from a well-characterized species to one that is less described. Chromosome arm numbers are conserved between members of the teleost family Salmonidae, order Salmoniformes, permitting rapid alignment of large syntenic blocks of DNA between members of the group. However, extensive Robertsonian rearrangements after an ancestral whole-genome duplication event has resulted in different chromosome numbers across Salmonid taxa. In anticipation of the rapid application of genomic data across members of the Pacific salmon genus Oncorhynchus, we mapped the genome of Chinook salmon (O. tshawytscha) by using 361 microsatellite loci and compared linkage groups to those already derived for a well-characterized species rainbow trout (O. mykiss). The Chinook salmon female map length was 1526 cM, the male map 733 cM, and the consensus map between the two sexes was 2206 cM. The average female to male recombination ratio was 5.43 (range 1-42.8 across all pairwise marker comparisons). We detected 34 linkage groups that corresponded with all chromosome arms mapped with homologous loci in rainbow trout and inferred that 16 represented metacentric chromosomes and 18 represented acrocentric chromosomes. Up to 13 chromosomes were conserved between the two species, suggesting that their structure precedes the divergence between Chinook salmon and rainbow trout. However, marker order differed in one of these linkage groups. The remaining linkage group structures reflected independent Robertsonian chromosomal arrangements, possibly after divergence. The putative linkage group homologies presented here are expected to facilitate future DNA sequencing efforts in Chinook salmon.

PMID: 24170738 [PubMed – indexed for MEDLINE]

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Relationship between effective population size, inbreeding and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild.

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Relationship between effective population size, inbreeding and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild.

Mol Ecol. 2013 Mar;22(5):1295-309

Authors: Naish KA, Seamons TR, Dauer MB, Hauser L, Quinn TP

Abstract
Inbreeding is of concern in supportive breeding programmes in Pacific salmonids, Oncorhynchus spp, where the number of breeding adults is limited by rearing space or poor survival to adulthood, and large numbers are released to supplement wild stocks and fisheries. We reconstructed the pedigree of 6602 migratory hatchery steelhead (Oncorhynchus mykiss) over four generations, to determine the incidence and fitness consequences of inbreeding in a northwest USA programme. The hatchery maintained an effective population size, Ñ(e) = 107.9 from F(0) to F(2), despite an increasing census size (N), which resulted in a decreasing N(e)/N ratio (0.35 in F(0) to 0.08 in F(2)). The reduced ratio was attributed to a small broodstock size, nonrandom transfers and high variance in reproductive success (particularly in males). We observed accumulation of inbreeding from the founder generation (in F(4), percentage individuals with inbreeding coefficients Δf > 0 = 15.7%). Generalized linear mixed models showed that body length and weight decreased significantly with increasing Δf, and inbred fish returned later to spawn in a model that included father identity. However, there was no significant correlation between Δf and age at return, female fecundity or gonad weight. Similarly, there was no relationship between Δf and reproductive success of F(2) and F(3) individuals, which might be explained by the fact that reproductive success is partially controlled by hatchery mating protocols. This study is one of the first to show that small changes in inbreeding coefficient can affect some fitness-related traits in a monitored population propagated and released to the wild.

PMID: 23379933 [PubMed – indexed for MEDLINE]

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Temporal variation in selection on body length and date of return in a wild population of coho salmon, Oncorhynchus kisutch.

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Temporal variation in selection on body length and date of return in a wild population of coho salmon, Oncorhynchus kisutch.

BMC Evol Biol. 2012;12:116

Authors: Kodama M, Hard JJ, Naish KA

Abstract
BACKGROUND: A number of studies have measured selection in nature to understand how populations adapt to their environment; however, the temporal dynamics of selection are rarely investigated. The aim of this study was to assess the temporal variation in selection by comparing the mode, direction and strength of selection on fitness-related traits between two cohorts of coho salmon (Oncorhynchus kisutch). Specifically, we quantified individual reproductive success and examined selection on date of return and body length in a wild population at Big Beef Creek, Washington (USA).
RESULTS: Reproductive success and the mode, direction and strength of selection on date of return and body length differed between two cohorts sampled in 2006 and 2007. Adults of the first brood year had greater success over those of the second. In 2006, disruptive selection favored early and late returning individuals in 2-year-old males, and earlier returning 3-year-old males had higher fitness. No evidence of selection on date of return was detected in females. In 2007, selection on date of return was not observed in males of either age class, but stabilizing selection on date of return was observed in females. No selection on body length was detected in males of both age classes in 2006, and large size was associated with higher fitness in females. In 2007, selection favored larger size in 3-year-old males and intermediate size in females. Correlational selection between date of return and body length was observed only in 2-year-old males in 2006.
CONCLUSIONS: We found evidence of selection on body length and date of return to the spawning ground, both of which are important fitness-related traits in salmonid species, but this selection varied over time. Fluctuation in the mode, direction and strength of selection between two cohorts was likely to be due to factors such as changes in precipitation, occurrence of catastrophic events (flooding), the proportion of younger- versus older-maturing males, sex ratio and densities of spawners.

PMID: 22805481 [PubMed – indexed for MEDLINE]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/22805481?dopt=Abstract

Relationship between effective population size, inbreeding and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild.

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Relationship between effective population size, inbreeding and adult fitness-related traits in a steelhead (Oncorhynchus mykiss) population released in the wild.

Mol Ecol. 2013 Feb 4;

Authors: Naish KA, Seamons TR, Dauer MB, Hauser L, Quinn TP

Abstract
Inbreeding is of concern in supportive breeding programmes in Pacific salmonids, Oncorhynchus spp, where the number of breeding adults is limited by rearing space or poor survival to adulthood, and large numbers are released to supplement wild stocks and fisheries. We reconstructed the pedigree of 6602 migratory hatchery steelhead (Oncorhynchus mykiss) over four generations, to determine the incidence and fitness consequences of inbreeding in a northwest USA programme. The hatchery maintained an effective population size, N˜e = 107.9 from F(0) to F(2) , despite an increasing census size (N), which resulted in a decreasing N(e) /N ratio (0.35 in F(0) to 0.08 in F(2) ). The reduced ratio was attributed to a small broodstock size, nonrandom transfers and high variance in reproductive success (particularly in males). We observed accumulation of inbreeding from the founder generation (in F(4) , percentage individuals with inbreeding coefficients Δf > 0 = 15.7%). Generalized linear mixed models showed that body length and weight decreased significantly with increasing Δf, and inbred fish returned later to spawn in a model that included father identity. However, there was no significant correlation between Δf and age at return, female fecundity or gonad weight. Similarly, there was no relationship between Δf and reproductive success of F(2) and F(3) individuals, which might be explained by the fact that reproductive success is partially controlled by hatchery mating protocols. This study is one of the first to show that small changes in inbreeding coefficient can affect some fitness-related traits in a monitored population propagated and released to the wild.

PMID: 23379933 [PubMed – as supplied by publisher]

via pubmed: school of aquatic an… http://www.ncbi.nlm.nih.gov/PubMed/23379933?dopt=Abstract

Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?

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Can interbreeding of wild and artificially propagated animals be prevented by using broodstock selected for a divergent life history?

Evol Appl. 2012 Nov;5(7):705-19

Authors: Seamons TR, Hauser L, Naish KA, Quinn TP

Abstract
TWO STRATEGIES HAVE BEEN PROPOSED TO AVOID NEGATIVE GENETIC EFFECTS OF ARTIFICIALLY PROPAGATED INDIVIDUALS ON WILD POPULATIONS: (i) integration of wild and captive populations to minimize domestication selection and (ii) segregation of released individuals from the wild population to minimize interbreeding. We tested the efficacy of the strategy of segregation by divergent life history in a steelhead trout, Oncorhynchus mykiss, system, where hatchery fish were selected to spawn months earlier than the indigenous wild population. The proportion of wild ancestry smolts and adults declined by 10-20% over the three generations since the hatchery program began. Up to 80% of the naturally produced steelhead in any given year were hatchery/wild hybrids. Regression model selection analysis showed that the proportion of hatchery ancestry smolts was lower in years when stream discharge was high, suggesting a negative effect of flow on reproductive success of early-spawning hatchery fish. Furthermore, proportions of hybrid smolts and adults were higher in years when the number of naturally spawning hatchery-produced adults was higher. Divergent life history failed to prevent interbreeding when physical isolation was ineffective, an inadequacy that is likely to prevail in many other situations.

PMID: 23144657 [PubMed – in process]

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