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Impact of mutation rate and selection at linked sites on fine-scale DNA variation across the homininae genome

https://doi.org/10.1101/452201
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What this work says

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

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Meiotic recombination favors the spreading of deleterious mutations in human populations
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Divergence and Polymorphism Under the Nearly Neutral Theory of Molecular Evolution
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On the number of segregating sites in genetical models without recombination
inferredcites →https://doi.org/10.1016/j.ajhg.2014.09.008openalex-snapshot
Biased Gene Conversion Skews Allele Frequencies in Human Populations, Increasing the Disease Burden of Recessive Alleles
inferredcites →https://doi.org/10.1016/j.tig.2016.01.004openalex-snapshot
The Limits of Natural Selection in a Nonequilibrium World
inferredcites →https://doi.org/10.1016/s0168-9525(02)02669-0openalex-snapshot
Human SNP variability and mutation rate are higher in regions of high recombination
inferredcites →https://doi.org/10.1017/s0016672300014634openalex-snapshot
The hitch-hiking effect of a favourable gene
inferredcites →https://doi.org/10.1017/s001667230800949xopenalex-snapshot
The effect of linkage on limits to artificial selection
inferredcites →https://doi.org/10.1017/s0016672308009579openalex-snapshot
The hitch-hiking effect of a favourable gene
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A population genetic model for the evolution of synonymous codon usage: patterns and predictions
inferredcites →https://doi.org/10.1038/356519a0openalex-snapshot
Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster
inferredcites →https://doi.org/10.1038/4151022aopenalex-snapshot
Adaptive protein evolution in Drosophila
inferredcites →https://doi.org/10.1038/ejhg.2013.30openalex-snapshot
Meiotic gene-conversion rate and tract length variation in the human genome
inferredcites →https://doi.org/10.1038/hdy.2016.108openalex-snapshot
DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA
inferredcites →https://doi.org/10.1038/nature04107openalex-snapshot
Adaptive evolution of non-coding DNA in Drosophila
inferredcites →https://doi.org/10.1038/nature09525openalex-snapshot
Fine-scale recombination rate differences between sexes, populations and individuals
inferredcites →https://doi.org/10.1038/nature12228openalex-snapshot
Great ape genetic diversity and population history
inferredcites →https://doi.org/10.1038/nature24018openalex-snapshot
Parental influence on human germline de novo mutations in 1,548 trios from Iceland
inferredcites →https://doi.org/10.1038/ncomms10486openalex-snapshot
New observations on maternal age effect on germline de novo mutations
inferredcites →https://doi.org/10.1038/ng.213openalex-snapshot
A common sequence motif associated with recombination hot spots and genome instability in humans
inferredcites →https://doi.org/10.1038/ng.3186openalex-snapshot
No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans
inferredcites →https://doi.org/10.1038/ng.3216openalex-snapshot
Recombination affects accumulation of damaging and disease-associated mutations in human populations
inferredcites →https://doi.org/10.1038/ng.3292openalex-snapshot
Genome-wide patterns and properties of de novo mutations in humans
inferredcites →https://doi.org/10.1038/ng0302-241openalex-snapshot
Unraveling heterochromatin
inferredcites →https://doi.org/10.1038/ng1287openalex-snapshot
Intense and highly localized gene conversion activity in human meiotic crossover hot spots
inferredcites →https://doi.org/10.1038/ng917openalex-snapshot
A high-resolution recombination map of the human genome
inferredcites →https://doi.org/10.1038/nrg1947openalex-snapshot
An evolutionary view of human recombination
inferredcites →https://doi.org/10.1038/nrg3425openalex-snapshot
Genomic signatures of selection at linked sites: unifying the disparity among species
inferredcites →https://doi.org/10.1038/nrg761openalex-snapshot
Resolving the paradox of sex and recombination
inferredcites →https://doi.org/10.1073/pnas.0804933105openalex-snapshot
Sperm cross-over activity in regions of the human genome showing extreme breakdown of marker association
inferredcites →https://doi.org/10.1073/pnas.091427698openalex-snapshot
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes
inferredcites →https://doi.org/10.1073/pnas.1220835110openalex-snapshot
Frequent adaptation and the McDonald–Kreitman test
inferredcites →https://doi.org/10.1073/pnas.1416622112openalex-snapshot
Crossovers are associated with mutation and biased gene conversion at recombination hotspots
inferredcites →https://doi.org/10.1073/pnas.1605660114openalex-snapshot
Evidence that the rate of strong selective sweeps increases with population size in the great apes
inferredcites →https://doi.org/10.1080/00401706.1999.10485954openalex-snapshot
Nonparametric Statistical Methods
inferredcites →https://doi.org/10.1093/gbe/evs027openalex-snapshot
The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes
inferredcites →https://doi.org/10.1093/gbe/evs052openalex-snapshot
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes
inferredcites →https://doi.org/10.1093/genetics/134.4.1289openalex-snapshot
The effect of deleterious mutations on neutral molecular variation.
inferredcites →https://doi.org/10.1093/genetics/155.2.909openalex-snapshot
Genetic Drift in an Infinite Population: The Pseudohitchhiking Model
inferredcites →https://doi.org/10.1093/genetics/159.2.907openalex-snapshot
GC-Content Evolution in Mammalian Genomes: The Biased Gene Conversion Hypothesis
inferredcites →https://doi.org/10.1093/molbev/msp119openalex-snapshot
Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change
inferredcites →https://doi.org/10.1093/molbev/msv331openalex-snapshot
The Time Scale of Recombination Rate Evolution in Great Apes
inferredcites →https://doi.org/10.1093/molbev/msw215openalex-snapshot
Natural Selection in the Great Apes
inferredcites →https://doi.org/10.1093/molbev/msx060openalex-snapshot
Evolution of local mutation rate and its determinants
inferredcites →https://doi.org/10.1093/molbev/msx088openalex-snapshot
Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species
inferredcites →https://doi.org/10.1093/molbev/msy164openalex-snapshot
Nearly Neutral Evolution across the Drosophila melanogaster Genome
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004086openalex-snapshot
Gene Density and Human Nucleotide Polymorphism
inferredcites →https://doi.org/10.1098/rspb.1993.0071openalex-snapshot
Recombination and mammalian genome evolution
inferredcites →https://doi.org/10.1101/287821openalex-snapshot
Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate
inferredcites →https://doi.org/10.1101/427583openalex-snapshot
Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared to mice and Drosophila melanogaster
inferredcites →https://doi.org/10.1101/gr.071548.107openalex-snapshot
No effect of recombination on the efficacy of natural selection in primates
inferredcites →https://doi.org/10.1101/gr.121541.111openalex-snapshot
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
inferredcites →https://doi.org/10.1101/gr.164822.113openalex-snapshot
Genome-wide signals of positive selection in human evolution
inferredcites →https://doi.org/10.1101/gr.185488.114openalex-snapshot
Quantification of GC-biased gene conversion in the human genome
inferredcites →https://doi.org/10.1101/gr.3461105openalex-snapshot
Why do human diversity levels vary at a megabase scale?
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1101/gr.4211905openalex-snapshot
Large-scale recombination rate patterns are conserved among human populations
inferredcites →https://doi.org/10.1103/physreve.71.031907openalex-snapshot
Nonequilibrium model for estimating parameters of deleterious mutations
inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb00188.xopenalex-snapshot
THE ECOLOGY AND GENETICS OF FITNESS IN CHLAMYDOMONAS. XII. REPEATED SEXUAL EPISODES INCREASE RATES OF ADAPTATION TO NOVEL ENVIRONMENTS
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.1117196openalex-snapshot
A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome
inferredcites →https://doi.org/10.1126/science.1183439openalex-snapshot
PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice
inferredcites →https://doi.org/10.1126/science.1216872openalex-snapshot
A Fine-Scale Chimpanzee Genetic Map from Population Sequencing
inferredcites →https://doi.org/10.1126/science.1256442openalex-snapshot
Recombination initiation maps of individual human genomes
inferredcites →https://doi.org/10.1126/science.aau1043openalex-snapshot
Characterizing mutagenic effects of recombination through a sequence-level genetic map
inferredcites →https://doi.org/10.1146/annurev-genom-082908-150001openalex-snapshot
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes
inferredcites →https://doi.org/10.1146/annurev.ecolsys.23.1.263openalex-snapshot
The Nearly Neutral Theory of Molecular Evolution
inferredcites →https://doi.org/10.1186/s40246-015-0043-1openalex-snapshot
Trans-species polymorphism in humans and the great apes is generally maintained by balancing selection that modulates the host immune response
inferredcites →https://doi.org/10.1371/journal.pbio.1002112openalex-snapshot
Natural Selection Constrains Neutral Diversity across A Wide Range of Species
inferredcites →https://doi.org/10.1371/journal.pcbi.1001025openalex-snapshot
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
inferredcites →https://doi.org/10.1371/journal.pgen.1000071openalex-snapshot
The Impact of Recombination on Nucleotide Substitutions in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1000083openalex-snapshot
Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1000471openalex-snapshot
Widespread Genomic Signatures of Natural Selection in Hominid Evolution
inferredcites →https://doi.org/10.1371/journal.pgen.1003684openalex-snapshot
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1004000openalex-snapshot
Loss and Recovery of Genetic Diversity in Adapting Populations of HIV
inferredcites →https://doi.org/10.1371/journal.pgen.1005774openalex-snapshot
Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis
inferredcites →https://doi.org/10.1371/journal.pgen.1006199openalex-snapshot
Determining the Effect of Natural Selection on Linked Neutral Divergence across Species
inferredcites →https://doi.org/10.1371/journal.pgen.1007254openalex-snapshot
Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans
inferredcites →https://doi.org/10.1371/journal.pgen.1008668openalex-snapshot
Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals
inferredcites →https://doi.org/10.1371/journal.pone.0017913openalex-snapshot
Similarity in Recombination Rate Estimates Highly Correlates with Genetic Differentiation in Humans
inferredcites →https://doi.org/10.1534/genetics.106.057570openalex-snapshot
The Distribution of Fitness Effects of New Deleterious Amino Acid Mutations in Humans
inferredcites →https://doi.org/10.1534/genetics.109.112920openalex-snapshot
The Role of Advantageous Mutations in Enhancing the Evolution of a Recombination Modifier
inferredcites →https://doi.org/10.1534/genetics.110.116368openalex-snapshot
Surprising Fitness Consequences of GC-Biased Gene Conversion: I. Mutation Load and Inbreeding Depression
inferredcites →https://doi.org/10.1534/genetics.116.197145openalex-snapshot
Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples
inferredcites →https://doi.org/10.1534/genetics.119.302494openalex-snapshot
Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes
inferredcites →https://doi.org/10.1534/genetics.119.302869openalex-snapshot
From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta’s Slightly Deleterious Model of Molecular Evolution?
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

What points at this work

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

inferred← citeshttps://doi.org/10.1093/gbe/evab064openalex-snapshot
The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes
inferred← citeshttps://doi.org/10.1186/s12864-020-6752-4openalex-snapshot
Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral
inferred← citeshttps://doi.org/10.1534/genetics.119.302494openalex-snapshot
Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes
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