Science and a beverage on a Friday afternoon are a good combination. R.E.H.A.B. is intended to be a low-key venue for people to get discuss papers and become familiar with a broader literature. Nobody presents or defends the papers. We assume everyone has read the paper (but you are welcome to come and listen and chat even if you haven’t!). We start by asking each person’s thoughts and questions about the paper, then jump right in to discussion. This allows for a very informal discussion, and with a beverage and friendly colleagues 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 Pizza and Pints at 3:30pm.
To be aware of any last-minute changes, please email Jeff to be added to the Slack channel.
Below are papers for Oct. 2013 and onward. For 2008-2013 papers see here.
We’re proud of the growing list of journal clubs modelled on R.E.H.A.B., including C.A.M.P., E.H.R.A.B., (Re)views, esfoyaza, Q.U.I.T., p.r.o.s.t., frydomics, and C.R.O.P.
And no, I won’t tell you what R.E.H.A.B. stands for, so don’t ask.
Li et al 2024 A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice
Harris 2007 (See Slack for Chapter PDF) Agriculture, Cultivation and Domestication: Exploring the Conceptual Framework of Early Food Production
No REHAB - Turkey Preservation Day
Deletre et al 2021 Kinship networks of seed exchange shape spatial patterns of plant virus diversity
Milesi et al 2024 Resilience of genetic diversity in forest trees over the Quaternary
With additional reading here
BAPG
Rainegeval et al 2024 Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide
Huang et al. preprint Varying recombination landscapes between individuals are driven by polymorphic transposable elements
No R.E.H.A.B.
Baduel et al. preprint Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature
Holland-Lulewicz et al. 2024 The initial spread of peaches across eastern North America was structured by Indigenous communities and ecologies
Akbari et al. 2024 Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation
Bolognini et al. 2024 Recurrent evolution and selection shape structural diversity at the amylase locus.
Eroglu et al. 2024 Noncanonical inheritance of phenotypic information by protein amyloids.
Lin et al 2023 The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge
Ritchey et al 2022 “The wind that shakes the barley: the role of East Asian cuisines on barley grain size”
No R.E.H.A.B.
Lasky et al 2024 Estimating scale-specific and localized spatial patterns in allele frequency
Tataru et al preprint Fluctuating selection in a Monkeyflower hybrid zone
Zhang et al 2024Rice’s trajectory from wild to domesticated in East Asia
Usui & Angert 2024 Range expansion is both slower and more variable with rapid evolution across a spatial gradient in temperature
Liu et al. 2024 Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
Jian et al. 2023 Forces driving transposable element load variation during Arabidopsis range expansion Get access
Marsh and Johri preprint Biases in ARG-based inference of historical population size in populations experiencing selection
Nocchi et al preprint Repeated global adaptation across plant species
Spiedel et al preprint High-resolution genomic ancestry reveals mobility in early medieval Europe
no R.E.H.A.B.
de la Fuente Castro et al 2024 The genomic and cultural diversity of the Inka Qhapaq hucha ceremony in Chile and Argentina
No R.E.H.A.B.
Lanaud et al 2024 A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches
No R.E.H.A.B.
Long et al 2024 Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta)
No R.E.H.A.B. – Maize meeting!
Pironon, Ondo, et. al. The global distribution of plants used by humans
Pope et al . 2023 The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator
No R.E.H.A.B.
Löytynoja 2022 Thousands of human mutation clusters are explained by short-range template switching
Lind et al preprint How useful is genomic data for predicting maladaptation to future climate?
Delmore et al 2023 Structural genomic variation and migratory behavior in a wild songbird
Gautier et al 2023 Genomic reconstruction of the successful establishment of a feralized bovine population on the subantarctic island of Amsterdam
no REHAB
Happy New Year’s!
No REHAB
Zhang et al 2023 The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids
Rivera-Rodríguez et al 2023 Genomic diversity and population structure of teosinte (Zea spp.) and its conservation implications
Nigenda-Morales et al 2023 The genomic footprint of whaling and isolation in fin whale populations
Gobble gobble gobble gobble gobble gobble
Diop et al 2023 Ethnolinguistic and genetic diversity of fonio (Digitaria exilis) in Senegal
Veteran’s Day - no REHAB
Igolkina et al 2023 Historical Routes for Diversification of Domesticated Chickpea Inferred from Landrace Genomics
Lang et al 2022 Century-long timelines of herbarium genomes predict plant stomatal response to climate change
Castillo et al 2023 Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails
No REHAB
Gordon et al. 2023 Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
Bontrager et al. 2020 Climate warming weakens local adaptation
No REHAB – lab event
Pope et al. 2023 The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator
No REHAB - lab trip!
Engelhorn et al. 2023 Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites
Mueller et al. 2023 The taming of the weed: Developmental plasticity facilitated plant domestication
Jorgensen et al. 2022 Genetic adaptations to potato starch digestionin the Peruvian Andes
Berube et al preprint Teosinte Pollen Drive guides maize domestication and evolution by RNAi
Benegas et al preprint DNA language models are powerful zero-shot predictors of genome-wide variant effects
Hohenlohe et al. 2010 Using population genomics to detect selection in natural populations: key concpets and methodological considerations (Topic: detecting selection)
No REHAB
Peter 2016 Admixture, Population Structure, and F-Statistics (Topic: inferring population structure)
Battey, Ralph, and Kern 2020 Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data (Topic: assumptions of population structure)
Hayward and Sella 2022 Polygenic adaptation after a sudden change in environment (Topic: polygenic adaptation)
No REHAB
Mather 2020 A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data (Topic: applications of coalescence theory)
Sethupathy and Hanenhali 2008 A tutorial of the poisson random field model in population penetics (Topic: diffusion theory)
Torres et al. 2020 The temporal dynamics of background selection in nonequilibrium populations (Topic: linked selection)
Kelly 2022 The genomic scale of fluctuating selection in a natural plant population
No R.E.H.A.B. – visiting our awesome undergraduate researchers presenting at the URSCA Conference
Muir et al. 2015 The Limited Contribution of Reciprocal Gene Loss to Increased Speciation Rates Following Whole-Genome Duplication.
Silva and Van de Peer preprint Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms
Dong et al. 2023 Dual domestications and origin of traits in grapevine evolution
Gonçalves-Dias preprint Evolutionary rescue through gene flow despite genetic incompatibilities shaped diversity of the pseudo-cereal grain amaranth
No R.E.H.A.B. – maize meeting!
Bénitière et al. preprint Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans
Soudi et al. preprint Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion
Rodrigues et al. preprint Shared evolutionary processes shape landscapes of genomic variation in the great apes
Matheson and Masel preprint Unlinked background selection reduces neutral diversity more than linked background selection
Barbeiri et al. 2022 A global analysis of matches and mismatches between human genetic and linguistic histories
Opedal et al. 2022 Evolvability and trait function predict phenotypic divergence of plant populations
Milesi et al. preprint Synchronous effective population size changes and genetic stability of forest trees through glacial cycles
Bohutinska et al. preprint Repeated adaptation to whole genome duplication in outcrossing Arabidopsis is mediated by mosaic adaptive haplotypes
Chturvedi et al. 2022 Local adaptation of life-history traits within urban populations of Arabidopsis thaliana
Schmitz et al. preprint Local adaptation of life-history traits within urban populations of Arabidopsis thaliana
Hibbins & Hahn 2022 The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes
No R.E.H.A.B. – harvest!
Todd et al. 2022 The genomic history and global expansion of domestic donkeys
No R.E.H.A.B. – corn maze! Email if you’d like to join!
Le et al, preprint 1,000 ancient genomes uncover 10,000 years of natural selection in Europe
Bieker et al. 2022 Uncovering the genomic basis of an extraordinary plant invasion
Le et al, preprint 1,000 ancient genomes uncover 10,000 years of natural selection in Europe
Liu and Zhang 2022 Is the Mutation Rate Lower in Genomic Regions of Stronger Selective Constraints?
Lotterhos preprint Does the paradigm of genotype-environment associations need to be re-assessed? The paradox of adaptive phenotypic clines with non-clinal patterns in causal alleles
Postponed
Moreno-Villena et al. 2022 Spatial resolution of an integrated C4+CAM photosynthetic metabolism
Widen et al. preprint Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities
Barnes, Rordíguez-Zapata, Juárez-Núñez et al. 2022 An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time
Gloss et al. 2022 Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
Wu et al. 2022 Allelochemicals targeted to balance competing selections in African agroecosystems
Cai et al. 2022 Transposable element insertion: a hidden major source ofdomesticated phenotypic variation inBrassica rapa
Berdan et al. 2022 Mutation accumulation opposes polymorphism: supergenes and the curious case of balanced lethals
Weide et al. 2022 A new functional ecological model reveals the nature of early plant management in southwest Asia
Atmore et al. preprint Serial depletion of Baltic herring since the Viking Age revealed by ancient DNA and population genomics
No R.E.H.A.B – PEQG!
Padilla-Iglesias et al. 2022 Population interconnectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers
Franco et al. preprintA Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies
Mostafavi et al. preprint Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery
Thornton 2019 Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation Under Gaussian Stabilizing Selection and Additive Effects on a Single Trait
Láruson et a l. 2022 Seeing the forest for the trees: Assessing genetic offset predictions from gradient forest
Postponed, see May 6
Zuin et al. 2022 Nonlinear control of transcription through enhancer–promoter interactions
Napier et al. 2022 A generalist–specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range
Lasky et al. preprint Wavelet characterization of spatial pattern in allele frequency
Wuitchik et al. 2022 Evolution of thermal physiology alters the projected range of threespine stickleback under climate change
University holiday, no R.E.H.A.B.
White et al. 2022 Experimental evolution of local adaptation under unidimensional and multidimensional selection
Haupt & Schmid preprint Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions
Kreiner et al. 2022 Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations
McGlothlin et al. preprint Conservation and Convergence of Genetic Architecture in the Adaptive Radiation of Anolis Lizards
Cooke et al. 2020 Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts
Murphy et al. preprint Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding elements
van der Zee et al. 2022 Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata)
Saleh et al. 2022 Genome-wide evolutionary response of European oaks during the Anthropocene
Dahan-Meir preprint The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years
Ho et al. Engines of change: Transposable element mutation rates are high and variable within Daphnia magna.
Exposito-Alonso et al preprint Quantifying the scale of genetic diversity extinction in the Anthropocene.
Matheson et al. preprint Haldane’s cost of selection imposes a mild constraint on adaptation, with a high proportion of deaths in A. thaliana being selective
Zongker et al. preprint Turkey or chicken? A perennial Thanksgiving debate. (No REHAB)
Jaegle et al. preprint Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity.
Johri et al preprint Statistical inference in population genomics.
Kulbaba et al. preprint Chasing the fitness optimum: temporal variation in the genetic and environmental expression of life-history traits for a perennial plant
Ye et al. 2019 Genomic evidence of human selection on Vavilovian mimicry
No R.E.H.A.B. – RI-lab fest for Gates, Tittes, Fairbanks, Solares et al. and annual corn maize!
Ojeda-Granado et al. preprint Dietary, Cultural and Pathogens-related Selective Pressures Shaped Differential Adaptive Evolution Among Native Mexican Populations
Battlay et al preprint Pleiotropy drives repeatability in the genetic basis of adaptation
Grieshop et al. preprint Dominance reversals, antagonistic pleiotropy, and the maintenance of genetic variation
Howe et al. preprint Within-sibship GWAS improve estimates of direct genetic effects
AND
Paige Harden 2018 Why Progressives Should Embrace the Genetics of Education
Brown and Kelly preprint Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations
Domínguez et al. 2020 The impact of transposable elements on tomato diversity
Aguirre-Liguori et al. 2021 The evolutionary genomics of species’ responses to climate change
Gibson et al. 2021 Introgression shapes fruit color convergence in invasive Galápagos tomato
Todesco et al, preprint Genetic basis and dual adaptive role of floral pigmentation in sunflowers
Szukala et al Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae).
Moutinho et al, 2021 Testing the adaptive walk model of gene evolution.
Tittes et al. DRAFT (PDF on Slack, or request access by email). The population genetics of local adaptation and convergence in maize landrace and its wild relative teosinte.
Brown & Kelly, 2021 Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations
Blavet et al. 2021 Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution
Kistler et al. 2020 Archaeological Central American maize genomes suggest ancient gene flow from South America
Yamaguchi & Otto, 2020 Insights from Fisher’s geometric model on the likelihood of speciation under different histories of environmental change
Booker et al. 2021 Selective sweeps influence diversity over large regions of the mouse genome
Kirch et al. 2021 Ancient and modern stickleback genomes reveal the demographic constraints on adaptation
Milla & Osborne 2021 Crop origins explain variation in global agricultural relevance
Burban et al. 2021 Gene network simulations provide testable predictions for the molecular domestication syndrome
Hejase et al. 2020 Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps
Cancelled
Rudman et al. preprint Direct observation of adaptive tracking on ecological timescales in Drosophila
Kling and Ackerly Global wind patterns shape genetic differentiation, asymmetric gene flow, and genetic diversity in trees
Gupta et al. preprint Inter-chromosomal linkage disequilibrium and linked fitness cost loci influence the evolution of nontarget site herbicide resistance in an agricultural weed
No R.E.H.A.B.
Bergström, Franz et al. 2020 Origins and genetic legacy of prehistoric dogs
Shahzad et al 2021 Gene body methylation mediates epigenetic inheritance of plant traits.
Meng et al. 20201 Predicting transcriptional responses to cold stress across plant species
Buffalo preprint Why do species get a thin slice of π? Revisiting Lewontin’s Paradox of Variation
Soni et al. preprint A new test suggests that balancing selection maintains hundreds of non-synonymous polymorphisms in the human genome
Lovell et al. 2021 Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
Hufnagel et al. 2021 Evidence for Multiple Teosinte Hybrid Zones in Central Mexico
Wei et al. 2021 A quantitative genomics map of rice provides genetic insights and guides breeding
Nelson et al. preprint Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)
Schluter et al. 2021 Fitness maps to a large-effect locus in introduced stickleback populations
Wos et al. 2020 Parallelism in gene expression between foothill and alpine ecotypes in Arabidopsis arenosa
Domb et al. 2020 DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation
Göktay et al. 2020 A new catalogue of structural variants in 1301 A. thaliana lines from Africa, Eurasia and North America reveals a signature of balancing at defense response genes
Desbiez-Piat et al. preprint Interplay between high-drift and high-selection limits the genetic load in small selfing maize populations
Bergero et al. 2019 Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms
Mérel et al. preprint The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions
Gordon et al. 2020 Rapid Changes in the Sex Linkage of Male Coloration in Introduced Guppy Populations
No R.E.H.A.B.
No R.E.H.A.B.
Crouse et al. 2020 Inferring the Allelic Series at QTL in Multiparental Populations
Batstone et al. 2020 et al. Experimental evolution makes microbes more cooperative with their local host genotype
Geiler-Samerotte et al. 2020 Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping
Wyler et al. 2020 Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon
Corre et al. 2020 Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe
Spencer et al. 2006 The Influence of Recombination on Human Genetic Diversity
Bourgeois et al. 2018 Genome‐wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon
Franco et al. preprint A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies
Ahrens et al. Spatial, climate, and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra
Kreiner et al. preprint The genetic architecture and genomic context of glyphosate resistance
Liu et al. 2020 Pan-Genome of Wild and Cultivated Soybeans
Wang et al. Automatic Inference of Demographic Parameters Using Generative Adversarial Networks
James et al. A framework to quantify phenotypic and genotypic parallel evolution
Kon et al. The Genetic Basis of Morphological Diversity in Domesticated Goldfish
Exposito-Alonso et al. preprint Non-additive polygenic models improve predictions of fitness traits in three eukaryote model species
Manuscript Review (check slack or email JRI for docs)
Choi & Purugganan preprint Telomere lengths in plants are correlated with flowering time variation
Boukas et al. preprint Purifying selection acts on germline methylation to modify the CpG mutation rate at promoters
Monnahan et al. 2020 Predicting evolutionary change at the DNA level in a natural Mimulus population
Fang et al. 2020 Genetic basis of kernel nutritional traits during maize domestication and improvement
DeWitt et al. Joint nonparametric coalescent inference of mutation spectrum history and demography
Hämälä and Tiffin Biased Gene Conversion Constrains Adaptation in Arabidopsis thaliana
Shah et al. Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan
Kyriazis, Wayne, and Lohmueller High genetic diversity can contribute to extinction in small populations
Ralph et al. 2020 Efficiently summarizing relationships in large samples: a general duality between statistics of genealogies and genomes
Baduel et al. 2019 Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation
Monroe et al. manuscript Is mutation rate variation across the Arabidopsis thaliana genome adaptive? (email/slack JRI for copy)
MacPherson et al. preprint Parental population range expansion before secondary contact promotes heterosis
Kiefer et al. 2019 Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation
Voichek Weigel 2020 Identifying genetic variants underlying phenotypic variation in plants without complete genomes
Thompson 2020 Experimental hybridization studies suggest that pleiotropic alleles commonly underlie adaptive divergence between natural populations
Hamlin et a l. 2020 Assessing biological factors affecting postspeciation introgression
Khromov and Morozov preprint Widespread selection against deleterious mutations in the Drosophila genome
Quadrana et al. 2019 Transposition favors the generation of large effect mutations that may facilitate rapid adaption
Corbett-Detig et al. 2020 Phenotypic convergence is not mirrored at the protein level in a lizard adaptive radiation
Lesaffre and Billiard preprint On deleterious mutations in perennials: inbreeding depression, mutation load and life-history evolution
Durvasula and Sankararaman 2020 Recovering signals of ghost archaic introgression in African populations
Lee et al 2017 On the post-glacial spread of human commensal Arabidopsis thaliana
Chen et al 2020 Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
Aguirre-Liguori et al. 2019 Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize.
Brown and Kelly 2019 Severe inbreeding depression is predicted by the “rare allele load” in Mimulus guttatus
Battey et al. preprint Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data
Xu et al. manuscript Adaptive evolution of DNA methylation reshaped gene regulation in maize
Wisser et al. 2019 The Genomic Basis for Short-Term Evolution of Environmental Adaptation in Maize
Fitzpatrick et al. 2020 Genomic and Fitness Consequences of Genetic Rescue in Wild Populations
Johri 2019 Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection.
Bierne 2010 The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population
Adams et al. preprint Slow recovery from inbreeding depression generated by the complex genetic architecture of segregating deleterious mutations comment
Bellis et al. preprint Genomics of sorghum local adaptation to a parasitic plant
McClintock 1984 The Significance of Responses of the Genome to Challenge
Zhao et al. 2019 Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil
Hayward and Sella preprint Polygenic adaptation after a sudden change in environment
Schwarzkopf et al. preprint Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
Todesco et al. preprint Massive haplotypes underlie ecotypic differentiation in sunflowers
Muyle et al. preprint Gene capture by transposable elements leads to epigenetic conflict
Samuk et al. preprint Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura
Rojas-Barrera et al. 2019 Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties
Gutaker et al. preprint Genomic history and ecology of the geographic spread of rice
Hämälä et al. 2019 Gene expression modularity reveals footprints of polygenic adaptation in Theobroma cacao
Booker et al. preprint Global adaptation confounds the search for local adaptation
No R.E.H.A.B.
Galloway et al. preprint A few stickleback suffice for the transport of alleles to new lakes
Rougemont et al. preprint Demographic history, linked selection, and recombination shape the genomic landscape of a broadly distributed Pacific salmon
Stankowski et al. 2019 Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Yan et al. 2019 Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize
Dunning et al. 2019 Lateral transfers of large DNA fragments spread functional genes among grasses
Xu et al. 2019 Evolutionary Metabolomics Identifies Substantial Metabolic Divergence between Maize and its Wild Ancestor, Teosinte
No R.E.H.A.B.
Uricchio 2019 Evolutionary perspectives on polygenic selection, missing heritability, and GWAS
Bradburd and Ralph preprint Spatial Population Genetics: It’s About Time
Hämälä and Savolainen 2019 Genomic patterns of local adaptation under gene flow in Arabidopsis lyrata
Wang et al. 2019 The architecture of intra-organism mutation rate variation in plants
Lowry et al. 2019 QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient
Yang et al. 2019 Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement
Harris 2015 Evidence for recent, population-specific evolution of the human mutation rate
Verta and Jones 2019 Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks
MS in development email Jeff for link or find on Slack
Vasseur et al. 2019 Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana
Wang et al. 2019 Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean
Berg et al. 2019 Reduced signal for polygenic adaptation of height in UK Biobank
Fustier et al. preprint Genomic footprints of local adaptation along elevation gradients associate with present phenotypic variation in teosintes
Wainschtein et al. preprint Recovery of trait heritability from whole genome sequence data
Yang et al. 2019 The genetic architecture of teosinte catalyzed and constrained maize domestication
Monnahan et al 2019 Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa
Liu et al. 2019 Biological relevance of computationally predicted pathogenicity of noncoding variants
Maize Genetics Conference
Owens and Samuk preprint Adaptive introgression during environmental change can weaken reproductive isolation
Mee and Yeaman preprint Unpacking conditional neutrality: genomic signatures of selection on conditionally beneficial and conditionally deleterious mutations
Esnault et al. 2019 Transposable element insertions in fission yeast drive adaptation to environmental stress
Uricchio et al. 2019 An evolutionary compass for detecting signals of polygenic selection and mutational bias
Petr et al. 2019 Limits of long-term selection against Neandertal introgression
Lee et al. preprint Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2/3 islands located in euchromatic genome
Ferrero-Serrano et al. 2019 Phenotypic and genome-wide association with the local environment of Arabidopsis
Weng et al. 2018 Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana
Martin et al., preprint Recombination rate variation shapes barriers to introgression across butterfly genomes
Zhou et al., preprint Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)
Happy Holidays, no R.E.H.A.B.
Happy Holidays, no R.E.H.A.B.
Tenaillon et al, preprint Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network
Kelleher et al, preprint Inferring the ancestry of everyone
Ruby et al, 2018 Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating
No R.E.H.A.B., but in honor of Thanksgiving you can read about the origin of your favorite side dish, sweet potato
more eLife review! email Jeff for link or find on Slack
Lin et al. 2018 Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen
Special Seminar – no R.E.H.A.B.
Fugère and Hendry, 2018 Human influences on the strength of phenotypic selection
Tavares et al. 2018 Selection and gene flow shape genomic islands that control floral guides
Yang et al. 2018 Kin recognition in rice (Oryza sativa) lines
Albers and McVean, preprint Dating genomic variants and shared ancestry in population-scale sequencing data
eLife review email Jeff for link
Bellon et al., 2018 Evolutionary and food supply implications of ongoing maize domestication by Mexican campesinos
Zuellig et al., 2018 A two‐locus hybrid incompatibility is widespread, polymorphic, and active in natural populations of Mimulus
Crown et al., 2018 Local inversion heterozygosity alters recombination throughout the genome
Fuller et al. 2018 Ancestral polymorphisms explain the role of chromosomal inversions in speciation
Simon et al. 2018 Coadapted genomes and selection on hybrids: Fisher’s geometric model explains a variety of empirical patterns
Ashander et al. preprint Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise
Stankowski et al. preprint The tempo of linked selection: Rapid emergence of a heterogeneous genomic landscape during a radiation of monkeyflowers
Jay et al. 2018 Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion
Marques et al. 2018 Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation
McGlothlin et al. 2018 Adaptive radiation along a deeply conserved genetic line of least resistance in Anolis lizards
Parada and Charlesworth preprint The effects on neutral variability of recurrent selective sweeps and background selection
Constable and Kokko 2018 The rate of facultative sex governs the number of expected mating type
Smith et al., preprint A domestication history of dynamic adaptation and genomic deterioration in sorghum
Zou, et al., 2017 Adaptation of Arabidopsis thaliana to the Yangtze River basin
Fisher, 1918 The correlation between relatives on the supposition of Mendelian inheritance
Barghi et al. preprint Polygenic adaptation fuels genetic redundancy in Drosophila
Flagel et al. preprint A synthesis of mapping experiments reveals extensive genomic structural diversity in the Mimulus guttatus species complex
Corbett-Detig et al. manuscript (email for pdf) Bulk Pollen Sequencing Reveals Rapid Evolution of Segregation Distortion In The Male Germline of Arabidopsis Hybrids
Raynes et al. 2018 Sign of selection on mutation rate modifiers depends on population size
Kelly 2018 The amount of nitrogen used for photosynthesis modulates molecular evolution in plants
Kern and Hahn 2018 The neutral theory in light of natural selection
Note: REHAB at 3pm at 3rd and U
Schumer
et al. 2018 Natural selection interacts with recombination to shape
the evolution of hybrid genomes
Zeng et al. 2018 Signatures of negative selection in the genetic architecture of human
Gage et al. preprint Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding [commentary]
Yeaman et al. preprint Quantifying how constraints limit the diversity of viable routes to adaptation
MGC – no R.E.H.A.B.
MGC – no R.E.H.A.B.
Booker and Keightley preprint Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome comment
Filiault et al. preprint The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history
di Iulio et al. 2018 The human noncoding genome defined by genetic diversity
Willi et al. 2018 Accumulation of mutational load at the edges of a species range.
Huang et al. 2018 ZmCCT9 enhances maize adaptation to higher latitudes
Kong et al. 2018 The nature of nurture: Effects of parental genotypes
Ørsted et al. 2017 Environmental variation partitioned into separate heritable components
Hayward et al. 2017 Evidence for Selection-by-Environment but Not Genotype-by-Environment Interactions for Fitness-Related Traits in a Wild Mammal Population
Borges et al. 2018 Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis
No R.E.H.A.B. (lab at Plant and Animal Genome conference)
Patwa & Wahl 2008 The fixation probability of beneficial mutations
Murray et al. 2017 Natural selection shaped the rise and fall of passenger pigeon genomic diversity
Comeron 2017 Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies
Gienapp et al. 2017 Genomic Quantitative Genetics to Study Evolution in the Wild
…and a special thanks to John Burke for making me owe Matt Hufford a beer.
No R.E.H.A.B., but in honor of Thanksgiving you can bone up on your statistics by learning about Turkey’s test.
Zan and Carlborg preprint Explorations of the polygenic genetic architecture of flowering time in the worldwide Arabidopsis thaliana population
Bosse et al. 2017 Recent natural selection causes adaptive evolution of an avian polygenic trait
Schrider & Kern preprint Machine Learning for Population Genetics: A New Paradigm
Osada et al. 2017 Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster
Lotterhos et al. preprint Modular environmental pleiotropy of genes involved in local adaptation to climate despite physical linkage
Forsythe et al preprint Epistatic interactions drive biased gene retention in the face of massive nuclear introgression
Salojärvi et al. 2017 Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.
Huber et al preprint Gene expression drives the evolution of dominance
Jain and Stephan 2017 Modes of rapid polygenic adaptation
Gage et al. 2017 The effect of artificial selection on phenotypic plasticity in maize (email or see lab Slack for paper)
Oka et al. 2017 Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
R.E.H.A.B. joint paper review. (email or see lab Slack for paper)
Zhang and Gao 2017 Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species
González-Martínez4 et al. 2017 Range Expansion Compromises Adaptive Evolution in an Outcrossing Plant
Hübner et al. 2017 The Cultivated Sunflower Pan Genome Provides Insights on the Contribution of Introgressions to Breeding of Modern Varieties
No R.E.H.A.B.
Zan et al. 2017 Artificial selection response due to polygenic adaptation from a multi-locus, multi-allelic genetic architecture
Sohail et al 2017 Negative selection in humans and fruit flies involves synergistic epistasis
Chen et al. 2017 Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species
Hurst and Randerson 2000 Dosage, Deletions and Dominance: Simple Models of the Evolution of Gene Expression
Vijay et al. 2017 Genome-wide patterns of variation in genetic diversity are shared among populations, species and higher order taxa
Gould et al. preprint The Gene Regulatory Landscape of Local Adaptation
Zeng et al. preprint Widespread signatures of negative selection in the genetic architecture of human complex traits
Simons et al. 2017 A model for the genetic architecture of quantitative traits under stabilizing selection
Walter et al. preprint Evolution of genetic variance during adaptive radiation
Lee et al. 2017 Young inversion with multiple linked QTLs under selection in a hybrid zone
Corbett-Detig et al. 2015 Natural Selection Constrains Neutral Diversity across A Wide Range of Species
AND
Coop 2016 preprint Does linked selection explain the narrow range of genetic diversity across species?
Durvasula et al. 2017 African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana
Gilbert et al. 2017 Local Adaptation Interacts with Expansion Load during Range Expansion: Maladaptation Reduces Expansion Load
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 preprint 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.
1) Ludwig
et al. 2000 Evidence for stabilizing selection in a eukaryotic
enhancer element
2) Alexandre et
al preprint Regulatory DNA in A. thaliana can tolerate high levels
of sequence divergence
Wagner et al. 2017 Spatial detection of outlier loci with Moran eigenvector maps (MEM)
Weir and Goudet preprint 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. preprint 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 preprint 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
AND
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. 2016 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 preprint 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. preprint 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. preprint 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 preprint 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. preprint 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
AND
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. preprint 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. preprint 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 preprint 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. preprint Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment
Fishman and Kelly 2015 Centromere–associated meiotic drive and female fitness variation in Mimulus
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. preprint 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 preprint 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. preprint Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex
Martin et al preprint. 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
Special double genome delux! Myburg et al. 2014. The genome of Eucalyptus grandis and Schmutz et al. 2014 A reference genome for common bean and genome-wide analysis of dual domestications
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. preprint. 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.
\emph{Also see slides}
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