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Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon

https://doi.org/10.1101/351338
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Outgoing claims: the papers this work cites, builds on, or argues with.

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The Atlantic Salmon
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Chromosome Morphology
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Quantitative trait loci for precocious parr maturation, early smoltification, and adult maturation in double-backcrossed trans-Atlantic salmon (Salmo salar)
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Genetic mixed stock analysis of an interceptory Atlantic salmon fishery in the Northwest Atlantic
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Phylogenetic analysis: models and estimation procedures
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Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon
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Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species
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Continent of origin of Atlantic salmon (Salmo salar L.) at West Greenland
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Distribution and biological characteristics of Atlantic salmon (Salmo salar) at Greenland based on the analysis of historical tag recoveries
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Phylogeography of 3 North Atlantic Wolffish species (Anarhichas spp.) with Phylogenetic Relationships within the Family Anarhichadidae
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SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes
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PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R
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Chromosomal Hybrid Zones in Eutherian Mammals
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Range-wide parallel climate-associated genomic clines in Atlantic salmon
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A hybrid zone comprising staggered chromosomal clines in the house mouse ( Mus musculus domesticus )
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‘Good genes as heterozygosity’: the major histocompatibility complex and mate choice in Atlantic salmon ( Salmo salar )
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Atlantic salmon eggs favour sperm in competition that have similar major histocompatibility alleles
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qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots
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Genomic scans for selective sweeps using SNP data
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pcadapt : an R package to perform genome scans for selection based on principal component analysis
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CRYPTIC CHOICE OF CONSPECIFIC SPERM CONTROLLED BY THE IMPACT OF OVARIAN FLUID ON SPERM SWIMMING BEHAVIOR
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Genome-wide tests for introgression between cactophilicDrosophilaimplicate a role of inversions during speciation
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PHYLOGEOGRAPHY AND HISTORICAL ECOLOGY OF THE NORTH ATLANTIC INTERTIDAL
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Some genetic consequences of ice ages, and their role in divergence and speciation
inferredcites →https://doi.org/10.1111/j.1365-294x.2004.02395.xopenalex-snapshot
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Hybridization and speciation
inferredcites →https://doi.org/10.1111/j.1471-8286.2005.01155.xopenalex-snapshot
genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
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Cytological studies in Atlantic salmon from Canada, in hybrids between Atlantic salmon from Canada and Sweden and in hybrids between Atlantic salmon and sea trout
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Morphological and phylogenetic evidence for hybridization and introgression in a sea star secondary contact zone
inferredcites →https://doi.org/10.1111/mec.12972openalex-snapshot
Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci
inferredcites →https://doi.org/10.1111/mec.13074openalex-snapshot
Chromosome inversions, adaptive cassettes and the evolution of species' ranges
inferredcites →https://doi.org/10.1111/mec.13395openalex-snapshot
Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction‐site associated DNA sequencing for the resolution of complex spatial structure
inferredcites →https://doi.org/10.1111/mec.13701openalex-snapshot
Genome‐wide set of SNP s reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate
inferredcites →https://doi.org/10.1111/mec.14442openalex-snapshot
Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic
inferredcites →https://doi.org/10.1139/cjfas-2013-0240openalex-snapshot
Landscape structure and climatic variation determine Atlantic salmon genetic connectivity in the Northwest Atlantic
inferredcites →https://doi.org/10.1139/f91-105openalex-snapshot
Discrimination between Atlantic Salmon (Salmo salar) of North American and European Origin using Restriction Analyses of Mitochondrial DNA
inferredcites →https://doi.org/10.1139/g59-023openalex-snapshot
CHROMOSOME STUDIES ON THREE CANADIAN POPULATIONS OF ATLANTIC SALMON, SALMO SALAR L
inferredcites →https://doi.org/10.1139/g68-108openalex-snapshot
CHROMOSOMAL POLYMORPHISM IN NORTH AMERICAN LANDLOCKED SALMO SALAR
inferredcites →https://doi.org/10.1146/annurev.es.18.110187.002421openalex-snapshot
INTRASPECIFIC PHYLOGEOGRAPHY: The Mitochondrial DNA Bridge Between Population Genetics and Systematics
inferredcites →https://doi.org/10.1186/1471-2164-12-615openalex-snapshot
A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns
inferredcites →https://doi.org/10.1186/1471-2164-13-432openalex-snapshot
Chromosomal differences between European and North American Atlantic salmon discovered by linkage mapping and supported by fluorescence in situ hybridization analysis
inferredcites →https://doi.org/10.1353/hub.2012.a493568openalex-snapshot
PCAdmix: Principal Components-Based Assignment of Ancestry Along Each Chromosome in Individuals with Admixed Ancestry from Two or More Populations
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ParallelStructure: A R Package to Distribute Parallel Runs of the Population Genetics Program STRUCTURE on Multi-Core Computers
inferredcites →https://doi.org/10.1534/genetics.117.300093openalex-snapshot
Significant Synteny and Colocalization of Ecologically Relevant Quantitative Trait Loci Within and Across Species of Salmonid Fishes
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Atlantic Salmon (Salmo salar) Chromosomes and Speciation
inferredcites →https://doi.org/10.2307/2410309openalex-snapshot
Hybrid Zones and the Evolutionary Process.
inferredcites →https://doi.org/10.3389/fgene.2014.00001openalex-snapshot
Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ece3.5258openalex-snapshot
Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway
inferred← citeshttps://doi.org/10.1101/2024.07.22.604627openalex-snapshot
Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions
inferred← citeshttps://doi.org/10.1111/1755-0998.13256openalex-snapshot
Chromosome‐level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water
inferred← citeshttps://doi.org/10.1111/mec.14965openalex-snapshot
Chromosomal fusion and life history‐associated genomic variation contribute to within‐river local adaptation of Atlantic salmon
inferred← citeshttps://doi.org/10.1139/gen-2024-0180openalex-snapshot
The evolution of genomic organization through chromosomal rearrangements in Arctic charr (Salvelinus alpinus)
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