Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Horn, Rebekah L.; Narum, Shawn R.

doi:10.1111/mec.16895

Cited by 3 publications

(14 citation statements)

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“…Further, the duplication noted by Thompson et al. (2020) was found to exhibit higher copy numbers in late‐returning fish from each lineage relative to early returning fish (Figure 16, reproduced from Horn & Narum, 2023), suggesting that structural variation in the form of this duplication within the intergenic region between GREB1L and ROCK1 may be a driver of phenotypic differences (Horn & Narum, 2023). These results validate that the GREB1L/intergenic region of Ots28 has phenotypic effects on adult migration timing phenotypes for all lineages of Chinook Salmon in the Columbia River, but the mechanisms of expression on any specific migration phenotypes remain unknown.…”

Section: Chinook Salmon—synthesis Of Patterns Of Genomic Association ...mentioning

confidence: 88%

“… Is there structural variation in the genomic regions of Ots28 and Omy28 that can be verified with advanced sequencing technology? Linkage disequilibrium is extensive within the GREB1L/ROCK1 region for both Chinook Salmon and Steelhead and evidence supports a duplication within this region for Chinook Salmon (Horn & Narum, 2023; Thompson et al., 2020). However, verification of structural variation will require long‐read sequencing that can span these complex sections of the genome as opposed to short‐read sequences that have been applied in previous studies.…”

Section: Further Research Questions For Steelhead and Chinook Salmonmentioning

confidence: 98%

“…(2020) is outlined by a dashed box. For a list of population abbreviations, see table 1 in Horn and Narum (2023).…”

Section: Chinook Salmon—synthesis Of Patterns Of Genomic Association ...mentioning

confidence: 99%

“…Contrast in read depth for the duplication in Ots28 intergenic region sorted by panels for each lineage of Chinook Salmon: left (Coastal = C), middle (interior ocean type = iOT), and right (interior stream type = iST) panels (Horn & Narum, 2023). (a) Late migrating populations of each lineage and (b) early phenotypes of each lineage.…”

Section: Chinook Salmon—synthesis Of Patterns Of Genomic Association ...mentioning

confidence: 99%

“…Chinook Salmon returns over Bonneville Dam (Willis et al, populations that had a gradient of passage timing over Bonneville Dam, with the earliest returning fish from the upper Columbia River and Rapid River, and the latest returning fish from populations in the Salmon River (Hess et al, 2014). The interior stream-type lineage generally had weaker differences in allele frequency within the GREB1L gene region compared with high differences in allele frequency in SNPs through the intergenic region, and the breadth of association in the interior stream-type lineage was estimated to be only ~26 kb of the intergenic region of Ots28 (Figure 15 to high (85%) in the interior stream-type lineage (Table 2, based on allele frequencies from Willis et al, 2021 andHorn et al 2023).…”

Section: Coastal Iot Istmentioning

confidence: 99%

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Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Narum,

Horn,

Willis

et al. 2023

Evolutionary Applications

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With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes of both Chinook Salmon and Steelhead, several subsequent studies have investigated the effect size and distribution of early and late migration alleles among populations in the Columbia River. Here, we synthesize the results of these studies for the major lineages of Chinook Salmon and Steelhead that include highly distinct groups in the interior Columbia River that exhibit atypical life histories from most coastal lineage populations of these two species. Whole‐genome studies with high marker density have provided extensive insight into SNPs most associated with adult migration timing, and suites of markers for each species have been genotyped in large numbers of individuals to further validate phenotypic effects. For Steelhead, the largest phenotypic effect sizes have been observed in the coastal lineage (36% of variation for passage timing at Bonneville Dam; 43% of variation for tributary arrival timing) compared to the inland lineage (7.5% of variation for passage timing at Bonneville Dam; 8.4% of variation for tributary arrival timing) that overwinter in freshwater prior to spawning. For Chinook Salmon, large effect sizes have been observed in all three lineages for multiple adult migration phenotypes (Coastal lineage: percentage of variation of 27.9% for passage timing at Bonneville Dam, 28.7% for arrival timing for spawning; Interior ocean type: percentage of variation of 47.6% for passage timing at Bonneville Dam, 39.6% for tributary arrival timing, 77.9% for arrival timing for spawning; Interior stream type: percentage of variation of 35.3% for passage at Bonneville Dam, 9.8% for tributary arrival timing, 4.7% for arrival timing for spawning). Together, these results have extended our understanding of genetic variation associated with life history diversity in distinct populations of the Columbia River, however, much research remains necessary to determine the causal mechanism for this major effect region on migration timing in these species.

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Section: Chinook Salmon—synthesis Of Patterns Of Genomic Association ...mentioning

confidence: 88%

Section: Further Research Questions For Steelhead and Chinook Salmonmentioning

confidence: 98%

“…(2020) is outlined by a dashed box. For a list of population abbreviations, see table 1 in Horn and Narum (2023).…”

Section: Chinook Salmon—synthesis Of Patterns Of Genomic Association ...mentioning

confidence: 99%

Section: Chinook Salmon—synthesis Of Patterns Of Genomic Association ...mentioning

confidence: 99%

Section: Coastal Iot Istmentioning

confidence: 99%

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Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Narum,

Horn,

Willis

et al. 2023

Evolutionary Applications

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Avian migration clocks in a changing world

Helm,

Liedvogel

2024

J Comp Physiol A

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Avian long-distance migration requires refined programming to orchestrate the birds’ movements on annual temporal and continental spatial scales. Programming is particularly important as long-distance movements typically anticipate future environmental conditions. Hence, migration has long been of particular interest in chronobiology. Captivity studies using a proxy, the shift to nocturnality during migration seasons (i.e., migratory restlessness), have revealed circannual and circadian regulation, as well as an innate sense of direction. Thanks to rapid development of tracking technology, detailed information from free-flying birds, including annual-cycle data and actograms, now allows relating this mechanistic background to behaviour in the wild. Likewise, genomic approaches begin to unravel the many physiological pathways that contribute to migration. Despite these advances, it is still unclear how migration programmes are integrated with specific environmental conditions experienced during the journey. Such knowledge is imminently important as temporal environments undergo rapid anthropogenic modification. Migratory birds as a group are not dealing well with the changes, yet some species show remarkable adjustments at behavioural and genetic levels. Integrated research programmes and interdisciplinary collaborations are needed to understand the range of responses of migratory birds to environmental change, and more broadly, the functioning of timing programmes under natural conditions.

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A major effect locus involved in migration timing is shared by pink and sockeye salmon

Barry,

Tallmon,

Howe

et al. 2024

Preprint

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Migration is an important component of the life cycles of many organisms and differences in migration timing can greatly influence fitness. Variation in migration timing (hereafter referred to as run timing) is found in many salmon species and contributes to the portfolio of life history diversity that is vital for maintaining healthy populations. Pink salmon (Oncorhynchus gorbuscha) are composed of temporally isolated lineages that spawn in even and odd years. Here, we focus on early and late runs of pink salmon in Auke Creek, Alaska, which spawn a few weeks apart in the same ≈50m stretch of stream. We conducted low coverage, whole genome sequencing on pink salmon from the early and late runs of both even and odd lineages to investigate the genetic basis of run timing in this system. Within the even lineage we detected a major effect locus displaying high genetic divergence between early and late run individuals on chromosome 10 of the pink salmon genome. This same locus showed a lower - but still elevated - amount of genetic divergence in the odd lineage. The region of high divergence includes the Leucine Rich Repeat Containing 9 gene (lrrc9), and genetic divergence was substantially reduced outside of this gene. Thelrrc9gene also shows high divergence between two ecotypes of sockeye salmon (Oncorhynchus nerka) that differ in both run timing and spawning habitat. Comparison of thelrrc9gene region in pink and sockeye salmon shows that variation within this gene is associated with run timing in both species. However, the polymorphic sites (i.e, SNPs) and run timing alleles are unique to each species and arose from independent mutations following divergence from a common ancestor. These results demonstrate that adaptation in pink salmon can occur at small temporal scales and that complex traits can be controlled by similar genetic mechanisms in multiple species.

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Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Cited by 3 publications

References 59 publications

Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Avian migration clocks in a changing world

A major effect locus involved in migration timing is shared by pink and sockeye salmon

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