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The role of genomic vs. epigenomic variation in shaping patterns of convergent transcriptomic variation across continents in a young species complex

https://doi.org/10.1101/784231
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Adaptation from standing genetic variation
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Fast gapped-read alignment with Bowtie 2
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Epigenetic programming by maternal behavior
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A study of fluctuating asymmetry in hybrids of dwarf and normal lake whitefish ecotypes (Coregonus clupeaformis) from different glacial races
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Do assemblages of Coregonus (Teleostei: Salmoniformes) in the Central Alpine region of Europe represent species flocks?
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Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes
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Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon
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Ecological Speciation
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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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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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CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data
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A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
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The geography of introgression in a patchy environment and the thorn in the side of ecological speciation
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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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Gene Expression Divergence and Hybrid Misexpression between Lake Whitefish Species Pairs (Coregonus spp. Salmonidae)
inferredcites →https://doi.org/10.1093/molbev/msx154openalex-snapshot
Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome
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The human liver‐specific proteome defined by transcriptomics and antibody‐based profiling
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Rapid parallel adaptive radiations from a single hybridogenic ancestral population
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The probability of genetic parallelism and convergence in natural populations
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Persistent and plastic effects of temperature on DNA methylation across the genome of threespine stickleback (Gasterosteus aculeatus)
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On the origin of species: insights from the ecological genomics of lake whitefish
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Convergence in form and function overcomes non-parallel evolutionary histories in a Holarctic fish
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Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister-species complex
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Genome-wide repressive capacity of promoter DNA methylation is revealed through epigenomic manipulation
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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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Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis)
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Polygenic evolution drives species divergence and climate adaptation in corals
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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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Evolutionary history of the European whitefishCoregonus lavaretus(L.) species complex as inferred from mtDNA phylogeography and gill‐raker numbers
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Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformisMitchill) ecotypes
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The transcriptomics of life‐history trade‐offs in whitefish species pairs ( Coregonus sp.)
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The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
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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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The genetic basis of intrinsic and extrinsic post-zygotic reproductive isolation jointly promoting speciation in the lake whitefish species complex ( Coregonus clupeaformis )
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Role of epibenthic resource opportunities in the parallel evolution of lake whitefish species pairs (Coregonus sp.)
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Hybridization and speciation
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ALLOPATRIC ORIGIN OF SYMPATRIC POPULATIONS OF LAKE WHITEFISH (COREGONUS CLUPEAFORMIS) AS REVEALED BY MITOCHONDRIAL-DNA RESTRICTION ANALYSIS
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PHYLOGEOGRAPHIC STRUCTURE IN MITOCHONDRIAL DNA OF THE LAKE WHITEFISH (COREGONUS CLUPEAFORMIS) AND ITS RELATION TO PLEISTOCENE GLACIATIONS
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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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CORRELATED TROPHIC SPECIALIZATION AND GENETIC DIVERGENCE IN SYMPATRIC LAKE WHITEFISH ECOTYPES (COREGONUS CLUPEAFORMIS): SUPPORT FOR THE ECOLOGICAL SPECIATION HYPOTHESIS
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Epigenetics in natural animal populations
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Model‐based demographic inference of introgression history in European whitefish species pairs'
inferredcites →https://doi.org/10.1111/mec.13436openalex-snapshot
Resource base influences genome‐wide DNA methylation levels in wild baboons (Papio cynocephalus)
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Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification
inferredcites →https://doi.org/10.1111/mec.15140openalex-snapshot
What drives phenotypic divergence among coral clonemates of Acropora palmata ?
inferredcites →https://doi.org/10.1111/mec.15226openalex-snapshot
Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex
inferredcites →https://doi.org/10.1126/science.1086887openalex-snapshot
Heterochromatin and Epigenetic Control of Gene Expression
inferredcites →https://doi.org/10.1126/science.1200684openalex-snapshot
The Developmental Role of Agouti in Color Pattern Evolution
inferredcites →https://doi.org/10.1126/science.1233749openalex-snapshot
Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module
inferredcites →https://doi.org/10.1126/science.1260419openalex-snapshot
Tissue-based map of the human proteome
inferredcites →https://doi.org/10.1139/cjfas-58-2-394openalex-snapshot
Why are dwarf fish so small? An energetic analysis of polymorphism in lake whitefish (Coregonus clupeaformis)
inferredcites →https://doi.org/10.1139/f00-252openalex-snapshot
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
inferredcites →https://doi.org/10.1146/annurev.genom.9.081307.164445openalex-snapshot
Transgenerational Epigenetic Effects
inferredcites →https://doi.org/10.1186/1471-2164-14-774openalex-snapshot
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
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Polymorphism in regulatory gene sequences.
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/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13148-016-0295-1openalex-snapshot
Mendelian inheritance of trimodal CpG methylation sites suggests distal cis-acting genetic effects
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Optical mapping in plant comparative genomics
inferredcites →https://doi.org/10.1371/journal.pbio.0020109openalex-snapshot
The Genetic Architecture of Parallel Armor Plate Reduction in Threespine Sticklebacks
inferredcites →https://doi.org/10.1371/journal.pgen.1007005openalex-snapshot
The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases
inferredcites →https://doi.org/10.1371/journal.pgen.1007796openalex-snapshot
Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution
inferredcites →https://doi.org/10.1371/journal.pmed.1000055openalex-snapshot
Multiple Origins and Regional Dispersal of Resistant dhps in African Plasmodium falciparum Malaria
inferredcites →https://doi.org/10.1371/journal.pone.0150002openalex-snapshot
CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon
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Cutadapt removes adapter sequences from high-throughput sequencing reads
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/10.1534/g3.118.200127openalex-snapshot
Comparison of the Relative Potential for Epigenetic and Genetic Variation To Contribute to Trait Stability
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Genome-Wide Variation of Cytosine Modifications Between European and African Populations and the Implications for Complex Traits
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Multiple microarray platforms utilized for hepatic gene expression profiling of GH transgenic coho salmon with and without ration restriction
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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
inferredcites →https://doi.org/10.32614/cran.package.veganopenalex-snapshot
vegan: Community Ecology Package
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.7554/elife.05255openalex-snapshot
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
inferredcites →https://doi.org/10.7554/elife.05290openalex-snapshot
A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA
inferredcites →https://doi.org/10.7554/elife.43785openalex-snapshot
Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

What points at this work

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

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Epigenetic effects associated with salmonid supplementation and domestication
inferred← citeshttps://doi.org/10.1111/eva.13235openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/eva.13267openalex-snapshot
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inferred← citeshttps://doi.org/10.1126/sciadv.adh8990openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s12915-025-02176-0openalex-snapshot
The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback
inferred← citeshttps://doi.org/10.70675/51661937zcaeaz45fbz8b20z00070b39557eopenalex-snapshot
Determinants and relative weight of genetic and epigenetic variation in the resistance of the oyster Crassostrea gigas to the Pacific Oyster Mortality Syndrome
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