Science and beer on a Friday afternoon seem to make a good combination. Nobody presents or defends the papers. We assume everyone has read the paper and jump right in to discussion without introduction. This allows for a very informal discussion, and with beer involved even the worst papers are much more manageable. Anyone is welcome to come and anyone can suggest a paper. There is no email list; articles are posted below along with the date.
We meet Fridays at de Vere’s Irish Pub at about 4:15 (on rare occasions when the pub is closed we improvise; email or call to find out the location). Sometimes we’re done at 5 and sometimes not until 6, depending on the paper and the crowd and interest and amount of beer being consumed.
From time to time we also blog our thoughts on the papers we read. One or more of the people present volunteers to write down some of the discussion of each paper. Our hope is that this is useful to authors in clarifying papers when possible (pre-publication) or to others in considering the potential caveats or points of greatest interest (post-publication). Comments on the blog posts are welcome – please email them along.
Below are papers for Oct. 2013 and onward. For 2008-2013 papers see here.
And no, I won’t tell you what R.E.H.A.B. stands for, so don’t ask.
Gilbert and Whitlock 2017 The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large‐effect alleles can allow range expansion
Huang, Gulko & Siepel 2017 Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
Wang et al. 2017 Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication
Charlesworth 2013 Stabilizing Selection, Purifying Selection, and Mutational Bias in Finite Populations
Franssen et al. 2017 Uncovering the genetic signature of quantitative trait evolution with replicated time series data
Hermisson & Pennings 2017 Soft sweeps and beyond: Understanding the patterns and probabilities of selection footprints under rapid adaptation
Brandenburg et al 2017 Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts
Maize meeting – no R.E.H.A.B.
Messer and Petrov 2013 Population genomics of rapid adaptation by soft selective sweeps.
Robillard et al 2016 Experimental evolution reveals hyperparasitic interactions among transposable elements
Watson et al. 2016 Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis
Two papers on enhancers and diversity. If short of time, read Ludwig et al. first.
Wagner et al. 2017 Spatial detection of outlier loci with Moran eigenvector maps (MEM)
Weir and Goudet 2016 A unified characterization of population structure and relatedness.
Puzey et al 2016 Population structure and local selection yield high genomic variation in Mimulus guttatus
PAG - no R.E.H.A.B.
Vidalis et al. 2016 Methylome evolution in plants
No R.E.H.A.B. Happy new year!
No R.E.H.A.B. Happy Festivus!
Barton 2016 How does epistasis influence the response to selection?
Imprialou et al. 2016 Genomic Rearrangements Considered as Quantitative Traits
Klasen et al 2016 A multi-marker association method for genome-wide association studies without the need for population structure correction
No R.E.H.A.B. – Turkey Day!
Moyerbrailean et al. 2016 High-throughput allele-specific expression across 250 environmental conditions
No R.E.H.A.B. - Veteran’s Day
Gould et al. 2016 Pooled Ecotype Sequencing Reveals Candidate Genetic Mechanisms for Adaptive Differentiation and Reproductive Isolation
Phung et al 2015 Natural selection reduces linked neutral divergence between distantly related species
Johnsson Feralisation targets different genomic loci to domestication in the chicken
Fraïsse et al. 2014 Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?
Willing et al. 2016 Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
Schrider et al. 2016 Effects of Linked Selective Sweeps on Demographic Inference and Model Selection
Hughes, Langdale, Kelly 2016 The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize
Groth and Blumenstiel 2016 Horizontal transfer can drive a greater transposable element load in large populations
Venkataram et al 2016 Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast
Uricchio et al. 2016 Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants
Zhang et al. 2016 Recombination rate variation, hitchhiking, and demographic history shape deleterious load in poplar
Fransz et al. 2016 Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana
Fu et al 2016 The genetic history of Ice Age Europe
Sanseverino et al. 2015 Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.
Russel et al 2016 Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation
Lasky et al. 2015 Genome-environment associations in sorghum landraces predict adaptive traits
Sharp & Agrawal 2016 Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum
Arnold et al. 2016 Borrowed alleles and convergence in serpentine adaptation
Bailey et a 2015 The Effect of Selection Environment on the Probability of Parallel Evolution
Zhena and Andolfatto 2012 Methods to Detect Selection on Noncoding DNA
Quadrana et al The Arabidopsis thaliana mobilome and its impact at the species level
1001 Genomes Consortium 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
Cardoso-Moreira et al. 2016 Evidence for the fixation of gene duplications by positive selection in Drosophila
Wales et al Genome sequence of a 5300-year-old maize cob recovered from the Tehuacan Valley provides insights into the early stages of maize domestication
Paccard et al 2016 Quantitative Genetic Architecture at Latitudinal Range Boundaries: Reduced Variation but Higher Trait Independence
Keightley et al 2016 Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster
Exposito-Alonso et al 2016 The rate and effect of de novo mutations in natural populations of Arabidopsis thaliana
Kelley et al 2016 The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana
Roles et al. 2016 Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana
Sanjak et al. 2016 The Genetic Architecture of a Complex Trait is more Sensitive to Genetic Model than Population Growth
Novikova et al. manuscript (see #papers channel on slack for pdf)
He and Knowles 2016 Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions
Lolle et al. 2005 Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis.
Marschall et al. 2016 Computational Pan-Genomics: Status, Promises and Challenges
No R.E.H.A.B. (Maize Meeting!)
Lamichhaney et al. 2012 Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
Keller and Fitzpatrick 2014 Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation
Rausher and Delph 2015 When does understanding phenotypic evolution require identification of the underlying genes?
Gao et al 2015 Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes
Mäki-Tanila and Hill Influence of Gene Interaction on Complex Trait Variation with Multi-Locus Models
Sheehan and Song 2015 Deep learning for population genetic inference
Lamichhaney et al. 2016 Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).
Stephan 2016 Signatures of positive selection: from selective sweeps atindividual loci to subtle allele frequency changes inpolygenic adaptation
Bainard et al. 2012 A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits
Marsden et al. 2015 Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
Steige et al. 2015 The impact of natural selection on the distribution of cis-regulatory variation across the genome of an outcrossing plant
Mascagni et al. 2015 Repetitive DNA and plant domestication: variation in copy number and proximity to genes of LTR-retrotransposons among wild and cultivated sunflower (Helianthus annuus) genotypes.
Remington 2015 Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.
No R.E.H.A.B. for the holidays. But you can get your fill of turkey popgen nonetheless.
Beissinger et al. 2015 Recent demography drives changes in linked selection across the maize genome
van Heerwaarden et al. 2015 Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits
Scheiner et al. 2015 The Genetics of Phenotypic Plasticity. XIV. Coevolution
Chevin and Hospital 2008 (AGAIN!) Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation
Chevin and Hospital 2008 Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation
Raghavan et al. 2015 Genomic evidence for the Pleistocene and recent population history of Native Americans
Skoglund et al. 2015 Genetic evidence for two founding populations of the Americas
Heath and Nuismer 2014 Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies
Lande and Arnold 1983 The measurement of selection on correlated characters
Thornton et al. 2013 Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect
Renaut and Reiseberg 2015 The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops
Kuester et al. 2015 A resurrection experiment finds evidence of both reduced genetic diversity and adaptive evolution in the agricultural weed Ipomoea purpurea
Weis et al. 2015 Hard and soft selection on phenology through seasonal shifts in the general and social environments: A study on plant emergence time
Snir et al. 2015 The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming
Dubin et al. 2015 DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Castellano et al. 2015 Adaptive evolution is substantially impeded by Hill-Robertson interference in Drosophila
Myriad Mutation Models: Three papers on heterozygote impacts on mutation
Yang et al. 2015 Parent–progeny sequencing indicates higher mutation rates in heterozygotes
Hollister et al. 2010 Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants
Tian et al. 2008 Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
Mazet et al. 2015 Demographic inference using genetic data from a single individual: separating population size variation from population structure
Oakley et al 2015 Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana
Monnahan et al. 2015 A genomic selection component analysis characterizes migration-selection balance
Fierst et al. 2015 Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes
Asaf et al. 2015 Obstruction of adaptation in diploids by recessive, strongly deleterious alleles
Mafessoni and Lachman 2015 Selective strolls: fixation and extinction in diploids are slower for weakly selected mutations than for neutral ones
Pease and Hahn 2015 Detection and Polarization of Introgression in a Five-taxon Phylogeny
Wilkes 1977 Hybridization of Maize and Teosinte, in Mexico and Guatemala and the Improvement of Maize
Van der Graf 2015 Rate, spectrum, and evolutionary dynamics of spontaneous epimutations.
Monnahan and Kelly 2015 Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus
Mathieson and McVean 2013 Estimating selection coefficients in spatially structured populations from time series data of allele frequencies
Sheng et al. 2015 Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment
Agren et al. 2014 No evidence that sex and transposable elements drive genome size variation in evening primroses
Douglas et al. 2015 Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
No R.E.H.A.B. Come to the UCDavis Plant Breeding Symposium instead.
Romero et al. SeeDs manuscript (email Jeff for the URL).
Cesar Chavez Day; university closed. No R.E.H.A.B.
Jeffares et al 2015 The genomic and phenotypic diversity of Schizosaccharomyces pombe
NO R.E.H.A.B. – MGC baby!
Bergland et al 2014 Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila
Brown and Levin 2011 Social dilemmas among supergenes: intragenomic sexual conflict and a selfing solution in Oenothera
Huang et al 2014 Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes
Li et al. Methylation manuscript. (printed version available from JRI).
Rodgers-Melnick et al. Recombination manuscript. (printed version available from JRI).
Brandvain et al. 2014 Speciation and Introgression between Mimulus nasutus and Mimulus guttatus
Charlesworth 2015 Causes of natural variation in fitness: Evidence from studies of Drosophila populations
Antonovics 1976 The nature of limits to natural selection.
Wiser et al. 2013 Long-Term Dynamics of Adaptation in Asexual Populations
No R.E.H.A.B., but celebrate the new year in plant genomics by reading up on cotton, including the C-genome species that are 2015 megabases in size.
No R.E.H.A.B., but feel free to get your plant genomics fix by reading up on the Christmas Tree genome
R.E.H.A.B. unexpectedly cancelled due to lab partying (seriously).
Poh et al. 2014 On the prospect of identifying adaptive loci in recently bottlenecked populations
Fu et al. 2014 Characteristics of Neutral and Deleterious Protein-Coding Variation among Individuals and Populations
No REHAB. But that doesn’t meant you can’t get a second helping of turkey genomics should you so desire.
Takuno et al. in prep Independent molecular basis of convergent highland adaptation in maize
Gravel 2014 When is selection effective?
Hough et al. 2014. Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus.
Schiffels & Durbin. Inferring human population size and separation history from multiple genome sequences.
Caicedo et al. 2007. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice
Crawford et al. 2014 Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex
Martin et al 2014. Evaluating the use of ABBA-BABA statistics to locate introgressed loci.
Huber et al. 2014 Keeping it Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana.
Romiguier et al. 2014 Comparative population genomics in animals uncovers the determinants of genetic diversity
Brawand et al. 2014 The genomic substrate for adaptive radiation in African cichlid fish
Spencer et al. 2006 The Influence of Recombination on Human Genetic Diversity
Carneiro et al. 2014 The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit.
Kelley et al. 2014 Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.
Wilson et al. 2014. Soft Selective Sweeps in Complex Demographic Scenarios.
Comeron 2014. Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome
Enard et al. 2014. Genome-wide signals of positive selection in human evolution
Arnegard et al. 2014. Genetics of ecological divergence during speciation
Macadangdang et al. 2014. Evolution of histone 2A for chromatin compaction in eukaryotes
Guenther et al A molecular basis for classic blond hair color in Europeans
No R.E.H.A.B. Watch some fireworks instead!
Ho and Zhang 2014. The Genotype–Phenotype Map of Yeast Complex Traits: Basic Parameters and the Role of Natural Selection
Yeaman 2013. Genomic rearrangements and the evolution of clusters of locally adaptive loci
Chari and Dworkin 2013. The Conditional Nature of Genetic Interactions: The Consequences of Wild-Type Backgrounds on Mutational Interactions in a Genome-Wide Modifier Screen
Balick et al. 2014. Response to a population bottleneck can be used to infer recessive selection
Nadeau et al. 2014. Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato
Soria-Carrasco et al. 2014. Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation
Rogers et al. 2014. Tandem duplications and the limits of natural selection in Drosophila yakuba and Drosophila simulans
Hawkins et al. 2014. Variation in allelic expression associated with a recombination hotspot in Zea mays
Do et al. 2014. No evidence that natural selection has been less effective at removing deleterious mutations in Europeans than in West Africans
Li 2014. Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples.
Nabholz et al. 2014. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima)
JRI’s review (molecol.tex) available in Lab Share folder on Dropbox
NO R.E.H.A.B. Check out the Plant Breeding Symposium instead!
Campos et al. 2014. The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster.
Hirsch et al. 2014. Insights into the maize pan-genome and pan-transcriptome.
Piepho and Möhring 2007. Computing Heritability and Selection Response From Unbalanced Plant Breeding Trials
Cortijo et al. Mapping the Epigenetic Basis of Complex Traits
Peiffer et al. 2014. The genetic architecture of maize height
Cavrak et al. 2014. How a Retrotransposon Exploits the Plant’s Heat Stress Response for Its Activation
Elhaik et al. 2014. The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome
Han et al. 2013. Characterizing bias in population genetic inferences from low coverage sequencing data
Sankararaman et al. 2014. The genomic landscape of Neanderthal ancestry in present-day humans
Nadachowska-Brzyska et al.. Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
Scally et al. 2012. Insights into hominid evolution from the gorilla genome sequence
Chapman et al. 2013. Genomic Divergence during Speciation Driven by Adaptation to Altitude
<CANCELED> – There’s a first time for everything. (Translation: “CANCELLED” for our British and Canadian friends)
Karhunen et al. 2013. Bringing habitat information into statistical tests of local adaptation in quantitative traits: a case study of nine-spined sticklebacks.
Rettelbach et al. 2013. Three modes of adaptive speciation in spatially structured populations
Korneliussen et al. 2013. Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data
Teng et al. 2013. Genome-wide Consequences of Deleting Any Single Gene
No R.E.H.A.B., but to go along with all your TurkeyDay related activities: Seidel et al. 2013. Influence of translocations on eastern wild turkey population genetics in Texas
Thallmann et al. 2012. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs
Kijima and Innan 2013. Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework
Review! Pick up hard copy in 262 Robbins.
Lohmueller 2013. The impact of population demography and selection on the genetic architecture of complex traits
Parker et al. 2013. Genome-wide signatures of convergent evolution in echolocating mammals
Peischl et al. arxiv. On the accumulation of deleterious mutations during range expansions
Ronen et al. 2013. Learning Natural Selection from the Site Frequency Spectrum
Szovenyi et al. 2013. Selection Is No More Efficient in Haploid than in Diploid Life Stages of an Angiosperm and a Moss