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Genome-wide sampling suggests island divergence accompanied by cryptic epigenetic plasticity in Canada lynx

https://doi.org/10.1101/316711
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Selection and drift influence genetic differentiation of insular Canada lynx (Lynx canadensis) on Newfoundland and Cape Breton Island
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WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas
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Epigenetic factors in aging and longevity
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Dispersal promotes high gene flow among Canada lynx populations across mainland North America
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Investigating the genetic and epigenetic basis of big biological questions with the parthenogenetic marbled crayfish: A review and perspectives
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Ecological and genetic spatial structuring in the Canadian lynx
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Conserved role of intragenic DNA methylation in regulating alternative promoters
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Genetic sources of population epigenomic variation
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Functions of DNA methylation: islands, start sites, gene bodies and beyond
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Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells
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Centromere evolution and CpG methylation during vertebrate speciation
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A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions
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No evidence that carotenoid pigments boost either immune or antioxidant defenses in a songbird
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Heritable DNA methylation marks associated with susceptibility to breast cancer
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Maximizing ecological and evolutionary insight in bisulfite sequencing data sets
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Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation
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A new global 1‐km dataset of percentage tree cover derived from remote sensing
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Snow conditions may create an invisible barrier for lynx
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Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation
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Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon
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Methyl-CpG Binding Domain 1 (MBD1) Interacts with the Suv39h1-HP1 Heterochromatic Complex for DNA Methylation-based Transcriptional Repression
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Beta Regression for Modelling Rates and Proportions
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adegenet : a R package for the multivariate analysis of genetic markers
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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
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The variant call format and VCFtools
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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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Redefining CpG islands using hidden Markov models
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Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions
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Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
inferredcites →https://doi.org/10.1101/gr.152538.112openalex-snapshot
Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
inferredcites →https://doi.org/10.1101/gr.228833.117openalex-snapshot
Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
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Widespread evidence for incipient ecological speciation: a meta‐analysis of isolation‐by‐ecology
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The evolution of epigenetically mediated adaptive transgenerational plasticity in a subdivided population
inferredcites →https://doi.org/10.1111/gcb.12526openalex-snapshot
The subtle role of climate change on population genetic structure in Canada lynx
inferredcites →https://doi.org/10.1111/gtc.12440openalex-snapshot
Repetitive DNA methylome analysis by small‐scale and single‐cell shotgun bisulfite sequencing
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Pleistocene and ecological effects on continental‐scale genetic differentiation in the bobcat (Lynx rufus)
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A MORPHOLOGIC AND GENETIC STUDY OF THE ISLAND FOX,UROCYON LITTORALIS
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VEGAN, a package of R functions for community ecology
inferredcites →https://doi.org/10.1111/mec.13436openalex-snapshot
Resource base influences genome‐wide DNA methylation levels in wild baboons (Papio cynocephalus)
inferredcites →https://doi.org/10.1111/mec.13573openalex-snapshot
The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana
inferredcites →https://doi.org/10.1111/mec.13617openalex-snapshot
Epigenetics in ecology and evolution: what we know and what we need to know
inferredcites →https://doi.org/10.1111/mec.14266openalex-snapshot
Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection
inferredcites →https://doi.org/10.1111/mec.14727openalex-snapshot
Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems
inferredcites →https://doi.org/10.1111/mec.14862openalex-snapshot
Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome‐wide sequence data for seven amphibians
inferredcites →https://doi.org/10.1126/science.1063852openalex-snapshot
The Role of DNA Methylation in Mammalian Epigenetics
inferredcites →https://doi.org/10.1126/science.285.5430.1071openalex-snapshot
Common Dynamic Structure of Canada Lynx Populations Within Three Climatic Regions
inferredcites →https://doi.org/10.1139/cjz-2014-0227openalex-snapshot
Isolation of peripheral populations of Canada lynx (Lynx canadensis)
inferredcites →https://doi.org/10.1139/z75-085openalex-snapshot
Differentiation of the Canada lynx, Felis (Lynx) canadensis subsolana, in Newfoundland
inferredcites →https://doi.org/10.1155/2012/698421openalex-snapshot
Environmental Heterogeneity and Phenotypic Divergence: Can Heritable Epigenetic Variation Aid Speciation?
inferredcites →https://doi.org/10.1186/gb-2008-9-5-r79openalex-snapshot
CpG island density and its correlations with genomic features in mammalian genomes
inferredcites →https://doi.org/10.1186/s13059-015-0866-zopenalex-snapshot
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
inferredcites →https://doi.org/10.1186/s13059-016-1090-1openalex-snapshot
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
inferredcites →https://doi.org/10.1186/s13059-016-1127-5openalex-snapshot
Methylome evolution in plants
inferredcites →https://doi.org/10.1242/jcs.011445openalex-snapshot
Tmod3 regulates polarized epithelial cell morphology
inferredcites →https://doi.org/10.1371/journal.pgen.1000695openalex-snapshot
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
inferredcites →https://doi.org/10.1371/journal.pone.0008460openalex-snapshot
The ZEB1 Transcription Factor Is a Novel Repressor of Adiposity in Female Mice
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Data quality of whole genome bisulfite sequencing on Illumina platforms
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A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
inferredcites →https://doi.org/10.1656/045.020.0413openalex-snapshot
Morphological Divergence of Continental and Island Populations of Canada Lynx
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Biogeography and Ecology of the Island of Newfoundland.
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A Morphologic and Genetic Study of the Island Fox, Urocyon littoralis
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HDAC9 Knockout Mice Are Protected From Adipose Tissue Dysfunction and Systemic Metabolic Disease During High-Fat Feeding
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R: A Language and Environment for Statistical Computing
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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
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Ventromedial hypothalamic neurons control a defensive emotion state
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Poppr : an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction
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