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Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister-species complex

https://doi.org/10.1101/311464
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Diversifying selection drives parallel evolution of gill raker number and body size along the speciation continuum of European whitefish
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Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations
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Do differences in the activities of carbohydrate metabolism enzymes between Lake Whitefish ecotypes match predictions from transcriptomic studies?
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An Expanded View of Complex Traits: From Polygenic to Omnigenic
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3′ UTRs Are the Primary Regulators of Gene Expression in the C. elegans Germline
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The evolution of gene expression and the transcriptome–phenotype relationship
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Adaptation from standing genetic variation
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A Combinatorial View on Speciation and Adaptive Radiation
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The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations
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Evolutionary changes in cis and trans gene regulation
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The genomic basis of adaptive evolution in threespine sticklebacks
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Fast gapped-read alignment with Bowtie 2
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De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
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The road to modularity
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Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence
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Ecological genomics of local adaptation
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Do assemblages of Coregonus (Teleostei: Salmoniformes) in the Central Alpine region of Europe represent species flocks?
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Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
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Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex
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Uniform Selection as a Diversifying Force in Evolution: Evidence from Drosophila
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Parallel Evolution and Inheritance of Quantitative Traits
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Local Adaptation by Alleles of Small Effect
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The Sequence Alignment/Map format and SAMtools
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The variant call format and VCFtools
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FLASH: fast length adjustment of short reads to improve genome assemblies
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Matrix eQTL: ultra fast eQTL analysis via large matrix operations
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Trimmomatic: a flexible trimmer for Illumina sequence data
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Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches
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Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations
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Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)
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Homologues, Natural Kinds and the Evolution of Modularity
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The Genetic Architecture of Ecological Speciation and the Association with Signatures of Selection in Natural Lake Whitefish (Coregonus sp. Salmonidae) Species Pairs
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Candidate Genes and Adaptive Radiation: Insights from Transcriptional Adaptation to the Limnetic Niche among Coregonine Fishes (Coregonus spp., Salmonidae)
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Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data
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Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome
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Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids
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Detecting gene subnetworks under selection in biological pathways
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Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions
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The probability of genetic parallelism and convergence in natural populations
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On the origin of species: insights from the ecological genomics of lake whitefish
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Convergence in pigmentation at multiple levels: mutations, genes and function
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Genome-wide patterns of divergence during speciation: the lake whitefish case study
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Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
inferredcites →https://doi.org/10.1111/1755-0998.12592openalex-snapshot
pcadapt : an R package to perform genome scans for selection based on principal component analysis
inferredcites →https://doi.org/10.1111/1755-0998.12906openalex-snapshot
Evaluation of redundancy analysis to identify signatures of local adaptation
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THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING
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Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation
inferredcites →https://doi.org/10.1111/evo.12727openalex-snapshot
Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis)
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GENETICALLY BASED PHENOTYPE-ENVIRONMENT ASSOCIATION FOR SWIMMING BEHAVIOR IN LAKE WHITEFISH ECOTYPES (COREGONUS CLUPEAFORMIS MITCHILL)
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Morphological differentiation and resource polymorphism in three sympatric whitefishCoregonus lavaretus(L.) forms in a subarctic lake
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FAST‐TRACK: Integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis)
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Evolutionary history of the European whitefishCoregonus lavaretus(L.) species complex as inferred from mtDNA phylogeography and gill‐raker numbers
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Parallel evolution of ecomorphological traits in the European whitefishCoregonus lavaretus(L.) species complex during postglacial times
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The transcriptomics of life‐history trade‐offs in whitefish species pairs ( Coregonus sp.)
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The genetic differentiation at quantitative trait loci under local adaptation
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Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)
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Parallel evolution of lake whitefish dwarf ecotypes in association with limnological features of their adaptive landscape
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MULTIPLE MODES OF SPECIATION INVOLVED IN THE PARALLEL EVOLUTION OF SYMPATRIC MORPHOTYPES OF LAKE WHITEFISH (COREGONUS CLUPEAFORMIS, SALMONIDAE)
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CONVERGENCE, ADAPTATION, AND CONSTRAINT
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THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER
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The role of gene expression in ecological speciation
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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Model‐based demographic inference of introgression history in European whitefish species pairs'
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Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis)
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The genomic signature of parallel adaptation from shared genetic variation
inferredcites →https://doi.org/10.1111/mec.12796openalex-snapshot
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow
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Do the same genes underlie parallel phenotypic divergence in different L ittorina saxatilis populations?
inferredcites →https://doi.org/10.1111/mec.13596openalex-snapshot
Divergence in gene expression within and between two closely related flycatcher species
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Demographic modelling with whole‐genome data reveals parallel origin of similarPundamiliacichlid species after hybridization
inferredcites →https://doi.org/10.1111/mec.13847openalex-snapshot
Convergence in organ size but not energy metabolism enzyme activities among wild Lake Whitefish (Coregonus clupeaformis) species pairs
inferredcites →https://doi.org/10.1111/mec.14290openalex-snapshot
Speciation as a sieve for ancestral polymorphism
inferredcites →https://doi.org/10.1111/nph.13888openalex-snapshot
Dissection of expression‐quantitative trait locus and allele specificity using a haploid/diploid plant system – insights into compensatory evolution of transcriptional regulation within populations
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The Developmental Role of Agouti in Color Pattern Evolution
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Why are dwarf fish so small? An energetic analysis of polymorphism in lake whitefish (Coregonus clupeaformis)
inferredcites →https://doi.org/10.1139/f94-310openalex-snapshot
Phylogenetic Relationships among Palearctic and Nearctic Whitefish (Coregonussp.) Populations as Revealed by Mitochondrial DNA Variation
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Regulatory Variation Within and Between Species
inferredcites →https://doi.org/10.1186/s12862-016-0732-yopenalex-snapshot
Adaptation and acclimation of traits associated with swimming capacity in Lake Whitefish (coregonus clupeaformis) ecotypes
inferredcites →https://doi.org/10.1186/s12864-016-2709-zopenalex-snapshot
Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database
inferredcites →https://doi.org/10.1186/s12864-017-4368-0openalex-snapshot
Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile
inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1006402openalex-snapshot
Gene co-expression network connectivity is an important determinant of selective constraint
inferredcites →https://doi.org/10.1534/g3.115.019067openalex-snapshot
RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs
inferredcites →https://doi.org/10.1554/04-309openalex-snapshot
THE PROBABILITY OF PARALLEL EVOLUTION
inferredcites →https://doi.org/10.2307/2409706openalex-snapshot
Phylogeographic Structure in Mitochondrial DNA of the Lake Whitefish (Coregonus clupeaformis) and Its Relation to Pleistocene Glaciations
inferredcites →https://doi.org/10.2307/2640895openalex-snapshot
Correlated Trophic Specialization and Genetic Divergence in Sympatric Lake Whitefish Ecotypes (Coregonus clupeaformis): Support for the Ecological Speciation Hypothesis
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Haplotype-based variant detection from short-read sequencing
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Molecular Evolutionary Genetics

What points at this work

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

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inferred← citeshttps://doi.org/10.1101/784231openalex-snapshot
The role of genomic vs. epigenomic variation in shaping patterns of convergent transcriptomic variation across continents in a young species complex
inferred← citeshttps://doi.org/10.1111/1365-2656.14157openalex-snapshot
Alternative splicing in parallel evolution and the evolutionary potential in sticklebacks
inferred← citeshttps://doi.org/10.1111/1755-0998.13483openalex-snapshot
A chromosome‐anchored genome assembly for Lake Trout ( Salvelinus namaycush )
inferred← citeshttps://doi.org/10.1111/eva.12919openalex-snapshot
Genotyping‐by‐sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes
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Model‐based demographic inference of introgression history in European whitefish species pairs'
inferred← citeshttps://doi.org/10.1111/mec.16033openalex-snapshot
Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs
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Network thinking applied to modeling biological evolution
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