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Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens

https://doi.org/10.1101/029561
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-319-17157-9_4openalex-snapshot
Variant Calling Using NGS Data in European Aspen (Populus tremula)
inferredcites →https://doi.org/10.1007/s11295-009-0204-2openalex-snapshot
Genetic linkage mapping in aspen (Populus tremula L. and Populus tremuloides Michx.)
inferredcites →https://doi.org/10.1016/j.flora.2011.11.001openalex-snapshot
Photosynthetic characteristics and growth performance of closely related aspen taxa: On the systematic relatedness of the Eurasian Populus tremula and the North American P. tremuloides
inferredcites →https://doi.org/10.1016/j.pbi.2008.02.002openalex-snapshot
Genetic diversity in natural populations: a fundamental component of plant–microbe interactions
inferredcites →https://doi.org/10.1016/j.tig.2006.09.011openalex-snapshot
Molecular evolution of plant immune system genes
inferredcites →https://doi.org/10.1016/s0031-0182(02)00249-3openalex-snapshot
A refined age for the earliest opening of Bering Strait
inferredcites →https://doi.org/10.1016/s0065-2296(02)38033-9openalex-snapshot
The origin and evolution of tertiary relict floras
inferredcites →https://doi.org/10.1016/s1360-1385(98)01327-2openalex-snapshot
The effect of Quaternary climatic changes on plant distribution and evolution
inferredcites →https://doi.org/10.1017/s0016672300014634openalex-snapshot
The hitch-hiking effect of a favourable gene
inferredcites →https://doi.org/10.1038/16446openalex-snapshot
Evidence for an early opening of the Bering Strait
inferredcites →https://doi.org/10.1038/35016000openalex-snapshot
The genetic legacy of the Quaternary ice ages
inferredcites →https://doi.org/10.1038/hdy.2009.151openalex-snapshot
Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species
inferredcites →https://doi.org/10.1038/nature10231openalex-snapshot
Inference of human population history from individual whole-genome sequences
inferredcites →https://doi.org/10.1038/nature11584openalex-snapshot
The genomic landscape of species divergence in Ficedula flycatchers
inferredcites →https://doi.org/10.1038/ncomms2833openalex-snapshot
Genomic islands of divergence are not affected by geography of speciation in sunflowers
inferredcites →https://doi.org/10.1038/ng.3015openalex-snapshot
Inferring human population size and separation history from multiple genome sequences
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nrg1226openalex-snapshot
The power and promise of population genomics: from genotyping to genome typing
inferredcites →https://doi.org/10.1038/nrg2931openalex-snapshot
Forest tree genomics: growing resources and applications
inferredcites →https://doi.org/10.1038/nrg3446openalex-snapshot
Understanding the origin of species with genome-scale data: modelling gene flow
inferredcites →https://doi.org/10.1038/nrg3644openalex-snapshot
Genomics and the origin of species
inferredcites →https://doi.org/10.1073/pnas.0502099102openalex-snapshot
Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis
inferredcites →https://doi.org/10.1073/pnas.0901397106openalex-snapshot
Natural selection in action during speciation
inferredcites →https://doi.org/10.1080/02827581.2011.628949openalex-snapshot
Short-rotation forestry with hybrid aspen ( Populus tremula L.× P. tremuloides Michx.) in Northern Europe
inferredcites →https://doi.org/10.1086/502802openalex-snapshot
A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq322openalex-snapshot
MSMS : a coalescent simulation program including recombination, demographic structure and selection at a single locus
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/btu041openalex-snapshot
ngsTools: methods for population genetics analyses from next-generation sequencing data
inferredcites →https://doi.org/10.1093/genetics/155.3.1405openalex-snapshot
Hitchhiking Under Positive Darwinian Selection
inferredcites →https://doi.org/10.1093/nar/gkq310openalex-snapshot
agriGO: a GO analysis toolkit for the agricultural community
inferredcites →https://doi.org/10.1093/nar/gks540openalex-snapshot
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025953openalex-snapshot
Measures of divergence between populations and the effect of forces that reduce variability
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026248openalex-snapshot
Comparative Evolutionary Analysis of Chalcone Synthase and Alcohol Dehydrogenase Loci in Arabidopsis, Arabis, and Related Genera (Brassicaceae)
inferredcites →https://doi.org/10.1098/rstb.2003.1388openalex-snapshot
Genetic consequences of climatic oscillations in the Quaternary
inferredcites →https://doi.org/10.1098/rstb.2010.0023openalex-snapshot
Speciation genetics: current status and evolving approaches
inferredcites →https://doi.org/10.1098/rstb.2011.0199openalex-snapshot
What can patterns of differentiation across plant genomes tell us about adaptation and speciation?
inferredcites →https://doi.org/10.1098/rstb.2011.0249openalex-snapshot
Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice
inferredcites →https://doi.org/10.1098/rstb.2011.0263openalex-snapshot
Genomic divergence during speciation: causes and consequences
inferredcites →https://doi.org/10.1101/gr.088336.108openalex-snapshot
Darwinian and demographic forces affecting human protein coding genes
inferredcites →https://doi.org/10.1101/gr.196485.115openalex-snapshot
Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
inferredcites →https://doi.org/10.1111/1467-9868.00346openalex-snapshot
A Direct Approach to False Discovery Rates
inferredcites →https://doi.org/10.1111/j.0014-3820.2000.tb00545.xopenalex-snapshot
THE EFFECTS OF SUBDIVISION ON THE GENETIC DIVERGENCE OF POPULATIONS AND SPECIES
inferredcites →https://doi.org/10.1111/j.1365-294x.2004.02164.xopenalex-snapshot
How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03946.xopenalex-snapshot
Divergent selection and heterogeneous genomic divergence
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04532.xopenalex-snapshot
Genomic islands of speciation or genomic islands and speciation?
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
inferredcites →https://doi.org/10.1111/mec.13314openalex-snapshot
Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation
inferredcites →https://doi.org/10.1111/mec.13368openalex-snapshot
Multilocus analysis of nucleotide variation and speciation in three closely related P opulus ( S alicaceae) species
inferredcites →https://doi.org/10.1126/science.1092500openalex-snapshot
The Fine-Scale Structure of Recombination Rate Variation in the Human Genome
inferredcites →https://doi.org/10.1126/science.1128691openalex-snapshot
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
inferredcites →https://doi.org/10.1126/science.1234070openalex-snapshot
Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees
inferredcites →https://doi.org/10.1139/x80-036openalex-snapshot
Flowering phenology of Populustremuloides and P. grandidentata and the potential for hybridization
inferredcites →https://doi.org/10.1146/annurev.ecolsys.16.1.393openalex-snapshot
Gene Flow in Natural Populations
inferredcites →https://doi.org/10.1186/1471-2105-12-231openalex-snapshot
Estimation of allele frequency and association mapping using next-generation sequencing data
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1186/s12870-014-0276-5openalex-snapshot
Populus tremula (European aspen) shows no evidence of sexual dimorphism
inferredcites →https://doi.org/10.1371/journal.pbio.0030285openalex-snapshot
Genomic Islands of Speciation in Anopheles gambiae
inferredcites →https://doi.org/10.1371/journal.pgen.0020064openalex-snapshot
Balancing Selection and Its Effects on Sequences in Nearby Genome Regions
inferredcites →https://doi.org/10.1371/journal.pgen.0020190openalex-snapshot
Population Structure and Eigenanalysis
inferredcites →https://doi.org/10.1371/journal.pgen.1000886openalex-snapshot
Human Population Differentiation Is Strongly Correlated with Local Recombination Rate
inferredcites →https://doi.org/10.1371/journal.pgen.1003519openalex-snapshot
The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit
inferredcites →https://doi.org/10.1371/journal.pgen.1003905openalex-snapshot
Robust Demographic Inference from Genomic and SNP Data
inferredcites →https://doi.org/10.1371/journal.pgen.1004966openalex-snapshot
Genomics of Divergence along a Continuum of Parapatric Population Differentiation
inferredcites →https://doi.org/10.1371/journal.pone.0037558openalex-snapshot
SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pone.0103645openalex-snapshot
Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments
inferredcites →https://doi.org/10.1534/g3.114.015784openalex-snapshot
Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data
inferredcites →https://doi.org/10.1534/genetics.110.118661openalex-snapshot
The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes
inferredcites →https://doi.org/10.1534/genetics.113.154138openalex-snapshot
Estimating Individual Admixture Proportions from Next Generation Sequencing Data
inferredcites →https://doi.org/10.1534/genetics.113.154740openalex-snapshot
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data
inferredcites →https://doi.org/10.2174/157489309787158161openalex-snapshot
A Review of the Primer Approximation Multiplex PCR (PAMP) Technique for Detecting Large Scale Cancer Genomic Lesions
inferredcites →https://doi.org/10.2307/j.ctv1nzfgj7openalex-snapshot
Phylogeography
inferredcites →https://doi.org/10.3732/ajb.91.9.1398openalex-snapshot
Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT‐TRNF region and nuclear rDNA
inferredcites →https://doi.org/10.7312/nei-92038openalex-snapshot
Molecular Evolutionary Genetics

What points at this work

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

inferred← citeshttps://doi.org/10.1111/mec.14083openalex-snapshot
Correlated patterns of genetic diversity and differentiation across an avian family
inferred← citeshttps://doi.org/10.3389/fpls.2018.01912openalex-snapshot
Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects
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