Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon Article Swipe
Tony Kess
,
Sarah J. Lehnert
,
Paul Bentzen
,
Steven Duffy
,
Amber Messmer
,
J. Brian Dempson
,
Jason Newport
,
Chris Whidden
,
Martha J. Robertson
,
Gérald Chaput
,
Cindy Breau
,
Julien April
,
Carole‐Anne Gillis
,
Matthew Kent
,
Cameron M. Nugent
,
Ian Bradbury
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/ece3.11068
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/ece3.11068
Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large‐effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon ( Salmo salar ), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large‐effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans‐Atlantic genomic basis to sea age. Here, we used a large single‐nucleotide polymorphism (SNP) array and low‐coverage whole‐genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large‐effect locus ( vgll3 ) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome‐wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large‐effect genes and molecular pathways despite population‐specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.
Related Topics
Concepts
Biology
Salmo
Parallel evolution
Single-nucleotide polymorphism
Evolutionary biology
Locus (genetics)
SNP
Genetics
Genetic architecture
Genome-wide association study
Quantitative trait locus
Genetic variation
Allele
Gene
Phylogenetics
Genotype
Fishery
Fish <Actinopterygii>
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/ece3.11068
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ece3.11068
- OA Status
- gold
- Cited By
- 6
- References
- 118
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4393989904
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4393989904Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1002/ece3.11068Digital Object Identifier
- Title
-
Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic SalmonWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-04-01Full publication date if available
- Authors
-
Tony Kess, Sarah J. Lehnert, Paul Bentzen, Steven Duffy, Amber Messmer, J. Brian Dempson, Jason Newport, Chris Whidden, Martha J. Robertson, Gérald Chaput, Cindy Breau, Julien April, Carole‐Anne Gillis, Matthew Kent, Cameron M. Nugent, Ian BradburyList of authors in order
- Landing page
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https://doi.org/10.1002/ece3.11068Publisher landing page
- PDF URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ece3.11068Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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-
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ece3.11068Direct OA link when available
- Concepts
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Biology, Salmo, Parallel evolution, Single-nucleotide polymorphism, Evolutionary biology, Locus (genetics), SNP, Genetics, Genetic architecture, Genome-wide association study, Quantitative trait locus, Genetic variation, Allele, Gene, Phylogenetics, Genotype, Fishery, FishTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
6Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 5, 2023: 1Per-year citation counts (last 5 years)
- References (count)
-
118Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.the | 40, 74, 94, 110, 136, 153, 252, 285, 289 |
| abstract_inverted_index.MapK | 239 |
| abstract_inverted_index.age. | 120 |
| abstract_inverted_index.also | 187 |
| abstract_inverted_index.been | 80 |
| abstract_inverted_index.both | 31, 181, 279 |
| abstract_inverted_index.does | 109 |
| abstract_inverted_index.from | 10, 15 |
| abstract_inverted_index.gene | 154 |
| abstract_inverted_index.hard | 18 |
| abstract_inverted_index.life | 64, 292 |
| abstract_inverted_index.loci | 33, 194 |
| abstract_inverted_index.sets | 190 |
| abstract_inverted_index.soft | 20 |
| abstract_inverted_index.that | 42, 175, 230 |
| abstract_inverted_index.this | 176 |
| abstract_inverted_index.used | 123 |
| abstract_inverted_index.well | 53 |
| abstract_inverted_index.were | 231 |
| abstract_inverted_index.with | 87, 158, 196, 227 |
| abstract_inverted_index.(SNP) | 128 |
| abstract_inverted_index.Here, | 121 |
| abstract_inverted_index.North | 101, 144, 204, 259 |
| abstract_inverted_index.Salmo | 71 |
| abstract_inverted_index.These | 274 |
| abstract_inverted_index.among | 199, 234 |
| abstract_inverted_index.array | 129 |
| abstract_inverted_index.based | 179 |
| abstract_inverted_index.basis | 76, 96, 117, 138, 254 |
| abstract_inverted_index.focal | 241 |
| abstract_inverted_index.found | 149, 174 |
| abstract_inverted_index.genes | 265 |
| abstract_inverted_index.large | 125 |
| abstract_inverted_index.level | 157, 287 |
| abstract_inverted_index.loci. | 92 |
| abstract_inverted_index.locus | 161 |
| abstract_inverted_index.often | 3 |
| abstract_inverted_index.rates | 210 |
| abstract_inverted_index.roles | 277 |
| abstract_inverted_index.salar | 72 |
| abstract_inverted_index.sexes | 202 |
| abstract_inverted_index.size. | 27 |
| abstract_inverted_index.trait | 66 |
| abstract_inverted_index.vgll3 | 163 |
| abstract_inverted_index.which | 78 |
| abstract_inverted_index.Salmon | 69, 104, 262 |
| abstract_inverted_index.across | 263 |
| abstract_inverted_index.common | 43 |
| abstract_inverted_index.during | 48 |
| abstract_inverted_index.effect | 26 |
| abstract_inverted_index.extent | 41 |
| abstract_inverted_index.highly | 192 |
| abstract_inverted_index.reveal | 276 |
| abstract_inverted_index.traits | 2 |
| abstract_inverted_index.varied | 178 |
| abstract_inverted_index.within | 100, 203 |
| abstract_inverted_index.Complex | 1 |
| abstract_inverted_index.Despite | 214 |
| abstract_inverted_index.Salmon. | 147 |
| abstract_inverted_index.alleles | 23 |
| abstract_inverted_index.calcium | 237 |
| abstract_inverted_index.complex | 5 |
| abstract_inverted_index.despite | 269 |
| abstract_inverted_index.exhibit | 4 |
| abstract_inverted_index.explore | 135 |
| abstract_inverted_index.genetic | 7, 44, 75, 95, 171 |
| abstract_inverted_index.genomic | 116, 137, 212 |
| abstract_inverted_index.history | 65, 293 |
| abstract_inverted_index.pattern | 177 |
| abstract_inverted_index.region. | 185 |
| abstract_inverted_index.remains | 106 |
| abstract_inverted_index.results | 248 |
| abstract_inverted_index.studied | 81 |
| abstract_inverted_index.studies | 29 |
| abstract_inverted_index.sweeps, | 21 |
| abstract_inverted_index.varying | 25 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.America, | 205 |
| abstract_inverted_index.American | 102, 145, 260 |
| abstract_inverted_index.Atlantic | 68, 85, 103, 146, 261 |
| abstract_inverted_index.European | 84, 168 |
| abstract_inverted_index.However, | 93 |
| abstract_inverted_index.enriched | 233 |
| abstract_inverted_index.findings | 275 |
| abstract_inverted_index.indicate | 249 |
| abstract_inverted_index.parallel | 114 |
| abstract_inverted_index.pathways | 225, 268 |
| abstract_inverted_index.patterns | 36, 271 |
| abstract_inverted_index.repeated | 49, 88, 282 |
| abstract_inverted_index.standing | 16 |
| abstract_inverted_index.unclear, | 107 |
| abstract_inverted_index.utilized | 47 |
| abstract_inverted_index.Together, | 246 |
| abstract_inverted_index.adhesion, | 242 |
| abstract_inverted_index.conserved | 223 |
| abstract_inverted_index.evolution | 14, 290 |
| abstract_inverted_index.implicate | 30 |
| abstract_inverted_index.including | 236 |
| abstract_inverted_index.molecular | 224, 253, 267, 286 |
| abstract_inverted_index.polygenic | 35 |
| abstract_inverted_index.potential | 111 |
| abstract_inverted_index.resulting | 9 |
| abstract_inverted_index.uncovered | 219 |
| abstract_inverted_index.variation | 142 |
| abstract_inverted_index.adaptation | 50, 283 |
| abstract_inverted_index.associated | 195, 226 |
| abstract_inverted_index.geographic | 184 |
| abstract_inverted_index.identified | 166, 188 |
| abstract_inverted_index.indicating | 170, 206 |
| abstract_inverted_index.maturation | 60 |
| abstract_inverted_index.predictive | 193 |
| abstract_inverted_index.previously | 165 |
| abstract_inverted_index.represents | 61 |
| abstract_inverted_index.signaling, | 238, 240 |
| abstract_inverted_index.signaling. | 245 |
| abstract_inverted_index.underlying | 6 |
| abstract_inverted_index.variation, | 17 |
| abstract_inverted_index.variation. | 294 |
| abstract_inverted_index.adaptation, | 38 |
| abstract_inverted_index.combination | 12 |
| abstract_inverted_index.contingency | 280 |
| abstract_inverted_index.extensively | 82 |
| abstract_inverted_index.nonrepeated | 189 |
| abstract_inverted_index.parallelism | 250 |
| abstract_inverted_index.populations | 105, 200 |
| abstract_inverted_index.significant | 63, 150 |
| abstract_inverted_index.understood. | 54 |
| abstract_inverted_index.associations | 151 |
| abstract_inverted_index.comparisons, | 235 |
| abstract_inverted_index.consistently | 232 |
| abstract_inverted_index.parallelism, | 172, 217 |
| abstract_inverted_index.parallelism. | 213 |
| abstract_inverted_index.polygenicity | 207 |
| abstract_inverted_index.polymorphism | 127 |
| abstract_inverted_index.populations, | 86, 169 |
| abstract_inverted_index.resequencing | 133 |
| abstract_inverted_index.underpinning | 37 |
| abstract_inverted_index.Increasingly, | 28 |
| abstract_inverted_index.architectures | 8, 45 |
| abstract_inverted_index.genome‐wide | 216 |
| abstract_inverted_index.polygenicity. | 273 |
| abstract_inverted_index.identification | 89 |
| abstract_inverted_index.large‐effect | 32, 91, 160, 264 |
| abstract_inverted_index.low‐coverage | 131 |
| abstract_inverted_index.whole‐genome | 132 |
| abstract_inverted_index.trans‐Atlantic | 115 |
| abstract_inverted_index.single‐nucleotide | 126 |
| abstract_inverted_index.phosphatidylinositol | 244 |
| abstract_inverted_index.population‐specific | 270 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5010482506 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 16 |
| corresponding_institution_ids | https://openalex.org/I1319689352 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/14 |
| sustainable_development_goals[0].score | 0.8799999952316284 |
| sustainable_development_goals[0].display_name | Life below water |
| citation_normalized_percentile.value | 0.93597782 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |