C.R.O.P is our weekly journal club for anyone interested in evolution. We meet on Tuesday at 4.15 pm at Theatercafe Filmdose for an open discussion about the weekly paper in a relaxed atmosphere.
Until further notice we will meet in the seminar room on the 3rd floor of the CoMB
Anybody is welcome to join us. The idea is that everyone reads the paper before and we dive directly in without formal presentation of the paper. If you would like to suggest a paper please email Markus.
Summer break
Korfmann, et al, preprint Coalescence and Translation: A Language Model for Population Genetics
Wu et al, preprint Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana
Celebioglu et al, preprint A domestication change at PvMYB26 in common bean sheds light on the origins of Middle American agriculture
Ruffley et al, preprint Selection constraints of plant adaptation can be relaxed by gene editing
Lutz et al, preprint Species-wide gene editing of a flowering regulator reveals hidden phenotypic variation
Razo-Mejia et al, preprint Learning the Shape of Evolutionary Landscapes: Geometric Deep Learning Reveals Hidden Structure in Phenotype-to-Fitness Maps
Chevin and Chauhan, 2025 Evolution of plasticity and character displacement in a fluctuating environment
Almeida-Silva and Van de Peer, preprint Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes
Chen et al, 2025 A single domestication origin of adzuki bean in Japan and the evolution of domestication genes
Gautier et al, 2024 Genomic Reconstruction of the Successful Establishment of a Feralized Bovine Population on the Subantarctic Island of Amsterdam
Kistler et al, 2025 Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation
Jiang et al, 2025 Incorporating genetic load contributes to predicting Arabidopsis thaliana’s response to climate change
Anderson et al, 2025 Adaptation and gene flow are insufficient to rescue a montane plant under climate change
Gompert et al, 2025 Adaptation repeatedly uses complex structural genomic variation
Easter break
Liu et al, 2025 Origin and de novo domestication of sweet orange
Zhang et al, 2025 Transposon proliferation drives genome architecture and regulatory evolution in wild and domesticated peppers
Sedeek et al, preprint Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing
Zhang et al, 2025 Genetic basis of camouflage in an alpine plant and its long-term co-evolution with an insect herbivore
Castellano et al, preprint Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects
Shaw et al, 2025 Global meta-analysis shows action is needed to halt genetic diversity loss
Chevin and Bridle, 2025 Impacts of limits to adaptation on population and community persistence in a changing environment
Cheng et al, 2025 Leveraging a phased pangenome for haplotype design of hybrid potato
Groh et al, 2024 Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories
TRR 341 Seminar
Ramos-Madrigal et al, 2024 The genomic origin of early maize in eastern North America
Burgarella et al, 2024 Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives
Bertolini et al., 2023 Regulatory variation controlling architectural pleiotropy in maize
Guillotin et al., 2023 A pan-grass transcriptome reveals patterns of cellular divergence in crops
Ni et al, 2024 Human-driven evolution of color in a stonefly mimic
Schuh and Morris, preprint Loss of pleiotropic regulatory functions in Tannin1, the sorghum ortholog of Arabidopsis master regulator TTG1
McKenzie et al, preprint A massive community-science flower color dataset reveals convergent evolution of delayed flowering phenology in North American red-flowering plants
TRR 341 seminar
Huang et al, preprint Varying recombination landscapes between individuals are driven by polymorphic transposable elements
Li, preprint The utility of environmental data from traditional varieties for climate-adaptive maize breeding
Short and Streisfeld, preprint The genomic outcomes of hybridization vary over time within a monkeyflower radiation
Long, preprint Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta)
Booker, 2024 The structure of the environment influences the patterns and genetics of local adaptation
Fiscus, et al, preprint Climate, population size, and dispersal influences mutational load across the landscape in Vitis arizonica
Summer break
Landis et al, 2024 Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley
Arca et al, 2023 Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties
Cao et al, 2024 DNA methylation variations underlie lettuce domestication and divergence
Andrade et al, 2024 Selection against domestication alleles in introduced rabbit populations
Ament-Velásquez et al, 2022 The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations
Zhang et al, 2024 Rice’s trajectory from wild to domesticated in East Asia
Smith and Hahn, preprint Selection leads to false inferences of introgression using popular methods
Garner et al, preprint A cis-regulatory point mutation at a R2R3-Myb transcription factor contributes to speciation by reinforcement in Phlox drummondii
Schraiber et al, preprint Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations
Sun et al, 2024 A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce
Lian et al, 2024 A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range
No CROP
Sianta et al, 2024 The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system
TRR 341 seminar
Nocchi et al, preprint Repeated global adaptation across plant species
Easter break
Easter break
He et al, 2024 Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea
He et al, 2024 Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat
Walter et al, 2024 Environmental effects on genetic variance are likely to constrain adaptation in novel environments
Pope et al, 2023 The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator
Kreiner, et al., 2023 Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus
Langmüller, et al., 2023 The genomic distribution of transposable elements is driven by spatially variable purifying selection
Ruffley, et al., preprint Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana
O’Brien, et al., preprint The distribution of fitness effects during adaptive walks using a simple genetic network
Desbiez-Piat, et al., 2023 Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments
Benegas, et al., preprint DNA language models are powerful predictors of genome-wide variant effects
Liu, et al., preprint Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation
Zwaenepoel, et al., preprint Polygenic barriers to gene flow: the role of dominance, haploid selection and heterogeneous genetic architectures
Stitzer et al., preprint Transposable element abundance subtly contributes to lower fitness in maize
Redmond,, et al., preprint Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition
Khaipho-Burch, et al., 2023 Genetic modification can improve crop yields — but stop overselling it
Zeitler, et al., 2023 Purging due to self-fertilization does not prevent accumulation of expansion load
Raingeval et al., preprint Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide
Gu et al., 2023 Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis
Sicard, 2023 Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella
Xiao, 2023 Adaptive and maladaptive introgression in grapevine domestication
Kelly, 2023 The genomic scale of fluctuating selection in a natural plant population
Tenaillon et al., 2023 Crop domestication as a step toward reproductive isolation
Wuest et al., 2023 Single-gene resolution of diversity-driven overyielding in plant genotype mixtures
Fuller et al., 2023 Plant domestication and agricultural ecologies
Belluchi et al., 2023 A pan-genome of 72 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range
Belluchi et al., 2023 Selection and adaptive introgression guided the complex evolutionary history of the European common bean
Simons et al., preprint Simple scaling laws control the genetic architectures of human complex traits
Mueller et al., 2023 The taming of the weed: Developmental plasticity facilitated plant domestication
He et al., preprint Heritable microbiome variation is correlated with source environment in locally adapted maize varieties
Zhao et al., 2023 Population genomics unravels the Holocene history of bread wheat and its relatives
Soudi et al., preprint Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion
Zhong et al., 2022 Hard versus soft selective sweeps during domestication and improvement in soybean
Jensen et al., 2023 Population genetic concerns related to the interpretation of empirical outliers and the neglect of common evolutionary processes
Zhong et al., 2023 Wild progenitors provide a sound baseline model for evolutionary analysis of domesticated crop species
Liang et al., 2023 Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers
Quagliariello et al., 2023 Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture
Shang et al., preprint Drivers of genomic landscapes of differentiation across Populus divergence gradient
James , et al 2022 Replicated Evolution in Plants
Opedal , et al 2022 Evolvability and trait function predict phenotypic divergence of plant populations
Luo , et al 2022 Domestication and selection footprints in Persian walnuts (Juglans regia)
Díaz-Valenzuela, et al preprint The role of non-additive gene action on gene expression variation in plant domestication
Pucker, et al preprint Evolutionary blocks to anthocyanin accumulation and the loss of an anthocyanin carrier protein in betalain-pigmented Caryophyllales
Muleta, et al 2022 The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange
Exposito-Alonso, et al 2022 Genetic diversity loss in the Anthropocene
Lopez-Valdivia, et al 2022 Gradual domestication of root traits in the earliest maize from Tehuacán
Todd, et al 2022 The genomic history and global expansion of domestic donkeys
Vourlaki, et al preprint Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects using Forward Simulations and Polygenic Adaptation
Buckley, et al 2022 Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change
Bieker, et al 2022 Uncovering the genomic basis of an extraordinary plant invasion
Lian, et al 2022 The megabase-scale crossover landscape is largely independent of sequence divergence
Hu, et al preprint Allele-specific expression reveals multiple paths to highland adaptation in maize
Liao, et al 2022 The 3D architecture of the pepper genome and its relationship to function and evolution
Fu, et al 2022 Genome-wide analyses of introgression between two sympatric Asian oak species
Kivikoski, et al preprint Low heritability of crossover rate in wild sticklebacks
No C.R.O.P
Fulgione, et al 2022 Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
Li, et al 2022 CsMYB1 integrates the regulation of trichome development and catechins biosynthesis in tea plant domestication
Liu, et al 2022 A transposon insertion drove the loss of natural seed shattering during foxtail millet domestication
Manuscript in progress (contact Markus for access)
Solares, et al preprint Insights into the domestication of avocado and potential genetic contributors to heterodichogamy
Wohns, et al 2022 A unified genealogy of modern and ancient genomes
no C.R.O.P
Kreiner, et al preprint Rapid adaptation and range expansion in response to agriculture over the last two centuries
Battlay, et al 2021 Pleiotropy drives repeatability in the genetic basis of adaptation
Novo, et al 2022 The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection
Monroe, et al 2022 Mutation bias reflects natural selection in Arabidopsis thaliana
Dahan-Meir, et al preprint The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years
Cai et al 2021 Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits
Monnahan, et al, 2021 Predicting evolutionary change at the DNA level in a natural Mimulus population
Gibson, et al, 2021 Introgression shapes fruit color convergence in invasive Galápagos tomato
Wrightsman, et al, preprint Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks
Naish, et al, 2021 The genetic and epigenetic landscape of the Arabidopsis centromeres
Ye, et al, 2021 Genomic evidence of human selection on Vavilovian mimicry
Grover, et al, preprint Dual domestication, diversity, and differential introgression in Old World cotton diploids
Fuentes et al, 2021 Domestication shapes recombination patterns in tomato
Tittes et al, preprint Not so local: the population genetics of convergent adaptation in maize and teosinte
Morales-Cruz et al, 2021 Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation
Hämälä et al, 2021 Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree
Schaefer et al, 2021 An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
Aguirre-Liguori et al, 2021 The evolutionary genomics of species’ responses to climate change
Sachdeva et al, preprint Genetic load and extinction in peripheral populations: the roles of migration, drift and demographic stochasticity
Katz et al., 2021 Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe
Milla and Osborne, 2021 Crop origins explain variation in global agricultural relevance
Todesco et al, preprint Genetic basis and dual adaptive role of floral pigmentation in sunflowers
Szukala et al, preprint Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)
Ma et al 2021 A chromosome-level Amaranthu cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop
Groen et al preprint Fitness costs and benefits of gene expression plasticity in rice under drought
Berdan et al 2021 Deleterious mutation accumulation and the long-term fate of chromosomal inversions
Chen et al preprint Portrait of a genus: the genetic diversity of Zea
Mabry et al preprint The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)
Burban et al preprint Gene network simulations provide testable predictions for the molecular domestication syndrome
Zhong et al 2021 DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis
Huang et al 2020 Genotype by environment interaction for gene expression in Drosophila melanogaster
MGM2021
Meyer et al 2012 Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops
Crouse et al 2020 Inferring the Allelic Series at QTL in Multiparental Populations
Lovell et al 2021 Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
Liu et al 2021 Genomic basis of geographical adaptation to soil nitrogen in rice
Shirsekar et al preprint Fine-scale Population Structure of North American Arabidopsis thaliana Reveals Multiple Sources of Introduction from Across Eurasia
Migicovsky et al 2021 Genomic consequences of apple improvement
Desbiez-Piat et al preprint Interplay between high-drift and high-selection limits the genetic load in small selfing maize populations
Kistler et al 2020 Archaeological Central American maize genomes suggest ancient gene flow from South America
Pérez-Escobar et al, preprint Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication
James et al, preprint A framework to quantify phenotypic and genotypic parallel evolution
Mooney et al, preprint The impact of identity-by-descent on fitness and disease in natural and domesticated Canid populations
Zhang et al, preprint Evolution of the genetic architecture of local adaptations under genetic rescue is determined by mutational load and polygenicity
Mayer et al, 2020 Discovery of beneficial haplotypes for complex traits in maize landraces
Tusso et al, preprint Experimental evolution of adaptive divergence under varying degrees of gene flow
Zhou et al 2020 Triticum population sequencing provides insights into wheat adaptation
No meeting!
Barton and Keightley
2002 Understanding quantitative genetic variation
No meeting!
Purugganan
2019 Evolutionary Insights into the Nature of Plant
Domestication
Kreiner et al preprint The genetic architecture and genomic context of glyphosate resistance
Le Corre et al. 2020 Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe
Vianna et al. 2020 Genome-wide analyses reveal drivers of penguin diversification
Alonge et al. 2020 Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
Muyle, preprint Investigation Gene body methylation is under selection in Arabidopsis thaliana
Dreissig et al 2020 Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley
Zhang et al 2020 The Impact of Recessive Deleterious Variation on Signals of Adaptive Introgression in Human Populations
Choi and Purugganan preprint Telomere lengths in plants are correlated with flowering time variation
Razifrad et al 2020 Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America
Leder et al 2014 The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability
Voichek and Weigel 2020 Identifying genetic variants underlying phenotypic variation in plants without complete genomes
Gutaker et al. 2020 Genomic history and ecology of the geographic spread of rice
Holiday
Molin et al. 2020 The eccDNA Replicon: A Heritable, Extra-Nuclear Vehicle that Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri
Mathieson and Scally 2020 What is ancestry?
No C.R.O.P.
Vasseur et al. 2020 Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana
Price et al. 2020 In the presence of population structure: From genomics to candidate genes underlying local adaptation
Groen et al. 2020 The strength and pattern of natural selection on gene expression in rice
No C.R.O.P - Carnaval
Albers and McVean 2020 Dating genomic variants and shared ancestry in population-scale sequencing data
Baduel et al. 2019 Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation
Gilbert et al. 2020 Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination
Dreissig et al. 2019 Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley
No C.R.O.P
No C.R.O.P
Lu et al 2019 The prevalence, evolution and chromatin signatures of plant regulatory elements
Ostevik et al preprint Asymmetric gene flow causes cascading reproductive isolation
Wisser et al 2019 The Genomic Basis for Short-Term Evolution of Environmental Adaptation in Maize
Grossen et al preprint Accumulation and purging of deleterious mutations through severe bottlenecks in ibex
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
Todesco et al preprint Massive haplotypes underlie ecotypic differentiation in sunflowers
Holiday - No C.R.O.P
No C.R.O.P
No C.R.O.P
Exposito-Alonso et al 2019 Natural selection on the Arabidopsis thaliana genome in present and future climates
Mattila et al 2019 Impact of demography on linked selection in two outcrossing Brassicaceae species
Yang et al 2019 The genetic architecture of teosinte catalyzed and constrained maize domestication
Christodoulaki et al preprint Distance to trait optimum is a crucial factor determining the genomic signature of polygenic adaptation
Rougemont et al preprint Demographic history, linked selection, and recombination shape the genomic landscape of a broadly distributed Pacific salmon.
Therkildsen et al 2019 Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing
Apuli et al preprint Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen (Populus tremula)
Hermisson and Pennings 2017 Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation
Gutaker et al 2019 The origins and adaptation of European potatoes reconstructed from historical genomes
Moest et al preprint Classic and introgressed selective sweeps shape mimicry loci across a butterfly adaptive radiation
Marin et al preprint Evolutionary inference from QST-FST comparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants
Oziolor et al 2019 Adaptive introgression enables evolutionary rescue from extreme environmental pollution
Holiday
Marand et al 2019 Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice
Stankowski et al preprint Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
We took a little break to set up the lab and find a place
Roessler et al preprint The Genomics of Selfing in Maize (Zea mays ssp. mays): Catching Purging in the Act
Xue et al preprint Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize
Athanasiadis et al preprint Estimating narrow-sense heritability from genome-wide data in admixed populations
Marand et al 2019 Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato
Break
Buffalo and Coop preprint The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data
Mackintosh, et al preprint The determinants of genetic diversity in butterflies - Lewontin’s paradox revisited
Haenel, et al 2018 Meta‐analysis of chromosome‐scale crossover rate variation in eukaryotes and its significance to evolutionary genomics
Yeaman, et al 2018 Quantifying how constraints limit the diversity of viable routes to adaptation
Chen, et al 2019 Allele frequency dynamics in a pedigreed natural population
Albert, et al 2019 Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships
Ashander, et al preprint Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise
Chen, et al 2018 Allele frequency dynamics in a pedigreed natural population
Schwarzkopf, et al preprint Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
Kistler et al 2018 Multiproxy evidence highlights a complex evolutionary legacy of maize in South America
Kreiner et al preprint Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus
Shah et al preprint Extreme genetic signatures of local adaptation during plant colonization
Weng et al 2018 Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana
Mieulet et al. 2018 Unleashing meiotic crossovers in crops
Kelleher et al preprint Inferring the ancestry of everyone
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