C.R.O.P is our weekly journal club for anyone interested in evolution. We meet on Tuesday at 4.00 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 4th floor of the Biocenter

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.


Tuesday July 23

Arca et al, 2023 Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties

Tuesday July 16

Cao et al, 2024 DNA methylation variations underlie lettuce domestication and divergence

Tuesday July 9

Andrade et al, 2024 Selection against domestication alleles in introduced rabbit populations

Tuesday July 2

Ament-Velásquez et al, 2022 The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations


Tuesday June 25

Zhang et al, 2024 Rice’s trajectory from wild to domesticated in East Asia

Tuesday June 18

Smith and Hahn, preprint Selection leads to false inferences of introgression using popular methods


Tuesday May 28

Garner et al, preprint A cis-regulatory point mutation at a R2R3-Myb transcription factor contributes to speciation by reinforcement in Phlox drummondii

Tuesday May 21

Schraiber et al, preprint Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

Tuesday May 14

Sun et al, 2024 A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce

Tuesday May 7

Lian et al, 2024 A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range


Tuesday April 30


Tuesday April 23

Sianta et al, 2024 The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system

Tuesday April 16

TRR 341 seminar

Tuesday April 9

Nocchi et al, preprint Repeated global adaptation across plant species

Tuesday April 2

Easter break


Tuesday March 26

Easter break

Tuesday March 19

He et al, 2024 Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea

Tuesday March 12

He et al, 2024 Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

Tuesday March 5

Walter et al, 2024 Environmental effects on genetic variance are likely to constrain adaptation in novel environments


Tuesday February 20

Pope et al, 2023 The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator

Thursday February 1

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


Thursday January 25

Langmüller, et al., 2023 The genomic distribution of transposable elements is driven by spatially variable purifying selection



Thursday December 7

Ruffley, et al., preprint Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana


Thursday November 30

O’Brien, et al., preprint The distribution of fitness effects during adaptive walks using a simple genetic network

Thursday November 23

Desbiez-Piat, et al., 2023 Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments

Thursday November 16

Benegas, et al., preprint DNA language models are powerful predictors of genome-wide variant effects

Thursday November 9

Liu, et al., preprint Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

Thursday November 2

Zwaenepoel, et al., preprint Polygenic barriers to gene flow: the role of dominance, haploid selection and heterogeneous genetic architectures


Thursday October 26

Stitzer et al., preprint Transposable element abundance subtly contributes to lower fitness in maize

Thursday October 19

Redmond,, et al., preprint Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition

Thursday October 12

Khaipho-Burch, et al., 2023 Genetic modification can improve crop yields — but stop overselling it

Thursday October 5

Zeitler, et al., 2023 Purging due to self-fertilization does not prevent accumulation of expansion load


Thursday September 21

Raingeval et al., preprint Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide

Thursday September 14

Gu et al., 2023 Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis


Thursday August 24

Sicard, 2023 Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella


Thursday July 20

Xiao, 2023 Adaptive and maladaptive introgression in grapevine domestication

Thursday July 13

Kelly, 2023 The genomic scale of fluctuating selection in a natural plant population

Thursday July 6

Tenaillon et al., 2023 Crop domestication as a step toward reproductive isolation


Thursday June 22

Wuest et al., 2023 Single-gene resolution of diversity-driven overyielding in plant genotype mixtures

Thursday June 15

Fuller et al., 2023 Plant domestication and agricultural ecologies

Thursday June 1

Belluchi et al., 2023 A pan-genome of 72 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range


Thursday May 25

Belluchi et al., 2023 Selection and adaptive introgression guided the complex evolutionary history of the European common bean

Thursday May 4

Simons et al., preprint Simple scaling laws control the genetic architectures of human complex traits


Thursday April 27

Mueller et al., 2023 The taming of the weed: Developmental plasticity facilitated plant domestication

Thursday April 20

He et al., preprint Heritable microbiome variation is correlated with source environment in locally adapted maize varieties


Thursday March 30

Zhao et al., 2023 Population genomics unravels the Holocene history of bread wheat and its relatives

Thursday March 23

Soudi et al., preprint Repeatability of adaptation in sunflowers: genomic regions harbouring inversions also drive adaptation in species lacking an inversion

Thursday March 16

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


Thursday February 23

Liang et al., 2023 Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers

Thursday February 9

Quagliariello et al., 2023 Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

Thursday February 2

Shang et al., preprint Drivers of genomic landscapes of differentiation across Populus divergence gradient


Thursday January 26

James , et al 2022 Replicated Evolution in Plants

Thursday January 19

Opedal , et al 2022 Evolvability and trait function predict phenotypic divergence of plant populations

Thursday January 12

Luo , et al 2022 Domestication and selection footprints in Persian walnuts (Juglans regia)



Thursday November 24

Díaz-Valenzuela, et al preprint The role of non-additive gene action on gene expression variation in plant domestication

Thursday November 17

Pucker, et al preprint Evolutionary blocks to anthocyanin accumulation and the loss of an anthocyanin carrier protein in betalain-pigmented Caryophyllales


Thursday October 13

Muleta, et al 2022 The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange

Thursday October 6

Exposito-Alonso, et al 2022 Genetic diversity loss in the Anthropocene


Thursday September 29

Lopez-Valdivia, et al 2022 Gradual domestication of root traits in the earliest maize from Tehuacán

Thursday September 22

Todd, et al 2022 The genomic history and global expansion of domestic donkeys

Thursday September 15

Vourlaki, et al preprint Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects using Forward Simulations and Polygenic Adaptation

Thursday September 8

Buckley, et al 2022 Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change

Thursday September 1

Bieker, et al 2022 Uncovering the genomic basis of an extraordinary plant invasion


Thursday August 25

Lian, et al 2022 The megabase-scale crossover landscape is largely independent of sequence divergence


Thursday July 28

Hu, et al preprint Allele-specific expression reveals multiple paths to highland adaptation in maize


Thursday June 23

Liao, et al 2022 The 3D architecture of the pepper genome and its relationship to function and evolution

Thursday June 9

Fu, et al 2022 Genome-wide analyses of introgression between two sympatric Asian oak species

Thursday June 2

Kivikoski, et al preprint Low heritability of crossover rate in wild sticklebacks


Thursday May 12

No C.R.O.P

Thursday May 5

Fulgione, et al 2022 Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages


Thursday April 28

Li, et al 2022 CsMYB1 integrates the regulation of trichome development and catechins biosynthesis in tea plant domestication

Thursday April 21

Liu, et al 2022 A transposon insertion drove the loss of natural seed shattering during foxtail millet domestication

Thursday April 14

Manuscript in progress (contact Markus for access)

Thursday April 7

Solares, et al preprint Insights into the domestication of avocado and potential genetic contributors to heterodichogamy


Thursday March 17

Wohns, et al 2022 A unified genealogy of modern and ancient genomes

Thursday March 10

no C.R.O.P

Thursday March 3

Kreiner, et al preprint Rapid adaptation and range expansion in response to agriculture over the last two centuries


Thursday February 17

Battlay, et al 2021 Pleiotropy drives repeatability in the genetic basis of adaptation

Thursday February 10

Novo, et al 2022 The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection

Thursday February 3

Monroe, et al 2022 Mutation bias reflects natural selection in Arabidopsis thaliana


Thursday January 27

Dahan-Meir, et al preprint The genetic structure of a wild wheat population has remained associated with microhabitats over 36 years

Thursday January 13

Cai et al 2021 Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits



Thursday December 9

Monnahan, et al, 2021 Predicting evolutionary change at the DNA level in a natural Mimulus population

Thursday December 2

Gibson, et al, 2021 Introgression shapes fruit color convergence in invasive Galápagos tomato


Thursday November 25

Wrightsman, et al, preprint Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

Thursday November 18

Naish, et al, 2021 The genetic and epigenetic landscape of the Arabidopsis centromeres

Thursday November 4

Ye, et al, 2021 Genomic evidence of human selection on Vavilovian mimicry


Thursday October 28

Grover, et al, preprint Dual domestication, diversity, and differential introgression in Old World cotton diploids

Thursday October 21

Fuentes et al, 2021 Domestication shapes recombination patterns in tomato

Thursday October 7

Tittes et al, preprint Not so local: the population genetics of convergent adaptation in maize and teosinte


Thursday September 30

Morales-Cruz et al, 2021 Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation

Thursday September 9

Hämälä et al, 2021 Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree

Thursday September 2

Schaefer et al, 2021 An ancestral recombination graph of human, Neanderthal, and Denisovan genomes


Thursday August 26

Aguirre-Liguori et al, 2021 The evolutionary genomics of species’ responses to climate change

Thursday August 19

Sachdeva et al, preprint Genetic load and extinction in peripheral populations: the roles of migration, drift and demographic stochasticity

Thursday August 12

Katz et al., 2021 Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe

Thursday August 5

Milla and Osborne, 2021 Crop origins explain variation in global agricultural relevance


Thursday July 29

Todesco et al, preprint Genetic basis and dual adaptive role of floral pigmentation in sunflowers

Thursday July 22

Szukala et al, preprint Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)


Thursday May 27

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

Thursday May 20

Groen et al preprint Fitness costs and benefits of gene expression plasticity in rice under drought

Thursday May 6

Berdan et al 2021 Deleterious mutation accumulation and the long-term fate of chromosomal inversions


Thursday April 29

Chen et al preprint Portrait of a genus: the genetic diversity of Zea

Thursday April 15

Mabry et al preprint The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

Thursday April 8

Burban et al preprint Gene network simulations provide testable predictions for the molecular domestication syndrome


Thursday March 25

Zhong et al 2021 DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis

Thursday March 18

Huang et al 2020 Genotype by environment interaction for gene expression in Drosophila melanogaster

Thursday March 11


Thursday March 4

Meyer et al 2012 Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops


Thursday Febraury 25

Crouse et al 2020 Inferring the Allelic Series at QTL in Multiparental Populations

Thursday Febraury 18

Lovell et al 2021 Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Thursday Febraury 11

Liu et al 2021 Genomic basis of geographical adaptation to soil nitrogen in rice

Thursday Febraury 4

Shirsekar et al preprint Fine-scale Population Structure of North American Arabidopsis thaliana Reveals Multiple Sources of Introduction from Across Eurasia


Thursday January 28

Migicovsky et al 2021 Genomic consequences of apple improvement

Thursday January 21

Desbiez-Piat et al preprint Interplay between high-drift and high-selection limits the genetic load in small selfing maize populations

Thursday January 14

Kistler et al 2020 Archaeological Central American maize genomes suggest ancient gene flow from South America



Thursday December 10

Pérez-Escobar et al, preprint Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

Thursday December 3

James et al, preprint A framework to quantify phenotypic and genotypic parallel evolution


Thursday November 26

Mooney et al, preprint The impact of identity-by-descent on fitness and disease in natural and domesticated Canid populations

Thursday November 19

Zhang et al, preprint Evolution of the genetic architecture of local adaptations under genetic rescue is determined by mutational load and polygenicity

Thursday November 12

Mayer et al, 2020 Discovery of beneficial haplotypes for complex traits in maize landraces

Thursday November 5

Tusso et al, preprint Experimental evolution of adaptive divergence under varying degrees of gene flow


Thursday October 29

Zhou et al 2020 Triticum population sequencing provides insights into wheat adaptation

Thursday October 22

No meeting!
Barton and Keightley 2002 Understanding quantitative genetic variation

Thursday October 15

No meeting!
Purugganan 2019 Evolutionary Insights into the Nature of Plant Domestication

Thursday October 8

Kreiner et al preprint The genetic architecture and genomic context of glyphosate resistance

Thursday October 1

Le Corre et al. 2020 Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe


Thursday September 24

Vianna et al. 2020 Genome-wide analyses reveal drivers of penguin diversification

Thursday September 17

Alonge et al. 2020 Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Thursday September 10

Muyle, preprint Investigation Gene body methylation is under selection in Arabidopsis thaliana

Thursday September 3

Dreissig et al 2020 Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley


Thursday July 16

Zhang et al 2020 The Impact of Recessive Deleterious Variation on Signals of Adaptive Introgression in Human Populations

Thursday July 9

Choi and Purugganan preprint Telomere lengths in plants are correlated with flowering time variation

Thursday July 2

Razifrad et al 2020 Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America


Thursday June 18

Leder et al 2014 The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability

Thursday June 4

Voichek and Weigel 2020 Identifying genetic variants underlying phenotypic variation in plants without complete genomes


Thursday May 28

Gutaker et al. 2020 Genomic history and ecology of the geographic spread of rice

Thursday May 21


Thursday May 14

Molin et al. 2020 The eccDNA Replicon: A Heritable, Extra-Nuclear Vehicle that Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri

Thursday May 7

Mathieson and Scally 2020 What is ancestry?


Thursday March 19

No C.R.O.P.

Thursday March 12

Vasseur et al. 2020 Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

Thursday March 5

Price et al. 2020 In the presence of population structure: From genomics to candidate genes underlying local adaptation


Thursday February 27

Groen et al. 2020 The strength and pattern of natural selection on gene expression in rice

Thursday February 20

No C.R.O.P - Carnaval

Thursday February 12

Albers and McVean 2020 Dating genomic variants and shared ancestry in population-scale sequencing data

Thursday February 6

Baduel et al. 2019 Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation


Thursday January 30

Gilbert et al. 2020 Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination



Thursday December 12

Dreissig et al. 2019 Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

Thursday December 5

No C.R.O.P


Thursday November 28

No C.R.O.P

Thursday November 21

Lu et al 2019 The prevalence, evolution and chromatin signatures of plant regulatory elements

Thursday November 14

Ostevik et al preprint Asymmetric gene flow causes cascading reproductive isolation

Thursday November 7

Wisser et al 2019 The Genomic Basis for Short-Term Evolution of Environmental Adaptation in Maize


Thursday October 31

Grossen et al preprint Accumulation and purging of deleterious mutations through severe bottlenecks in ibex

Thursday October 24

Samuk et al preprint Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura

Thursday October 17

Rojas-Barrera et al 2019 Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties

Thursday October 10

Todesco et al preprint Massive haplotypes underlie ecotypic differentiation in sunflowers

Thursday October 3

Holiday - No C.R.O.P


Thursday September 26

No C.R.O.P

Thursday September 19

No C.R.O.P

Thursday September 12

Exposito-Alonso et al 2019 Natural selection on the Arabidopsis thaliana genome in present and future climates

Thursday September 5

Mattila et al 2019 Impact of demography on linked selection in two outcrossing Brassicaceae species


Thursday August 29

Yang et al 2019 The genetic architecture of teosinte catalyzed and constrained maize domestication

Thursday August 22

Christodoulaki et al preprint Distance to trait optimum is a crucial factor determining the genomic signature of polygenic adaptation

Thursday August 15

Rougemont et al preprint Demographic history, linked selection, and recombination shape the genomic landscape of a broadly distributed Pacific salmon.

Thursday August 8

Therkildsen et al 2019 Contrasting genomic shifts underlie parallel phenotypic evolution in response to fishing

Thursday August 1

Apuli et al preprint Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen (Populus tremula)


Thursday July 25

Hermisson and Pennings 2017 Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation

Thursday July 18

Gutaker et al 2019 The origins and adaptation of European potatoes reconstructed from historical genomes

Thursday July 11

Moest et al preprint Classic and introgressed selective sweeps shape mimicry loci across a butterfly adaptive radiation

Thursday July 4

Marin et al preprint Evolutionary inference from QST-FST comparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants


Thursday June 27

Oziolor et al 2019 Adaptive introgression enables evolutionary rescue from extreme environmental pollution

Thursday June 20


Thursday June 13

Marand et al 2019 Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice

Thursday June 6

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


Thursday April 18

Roessler et al preprint The Genomics of Selfing in Maize (Zea mays ssp. mays): Catching Purging in the Act

Thursday April 4

Xue et al preprint Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize


Thursday March 28

Athanasiadis et al preprint Estimating narrow-sense heritability from genome-wide data in admixed populations

Thursday March 21

Marand et al 2019 Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato

Thursday March 14


Thursday March 7

Buffalo and Coop preprint The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data


Thursday February 28

Mackintosh, et al preprint The determinants of genetic diversity in butterflies - Lewontin’s paradox revisited

Thursday February 21

Haenel, et al 2018 Meta‐analysis of chromosome‐scale crossover rate variation in eukaryotes and its significance to evolutionary genomics

Thursday February 14

Yeaman, et al 2018 Quantifying how constraints limit the diversity of viable routes to adaptation

Thursday February 7

Chen, et al 2019 Allele frequency dynamics in a pedigreed natural population


Thursday January 31

Albert, et al 2019 Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships

Thursday January 24

Ashander, et al preprint Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise

Thursday January 17

Chen, et al 2018 Allele frequency dynamics in a pedigreed natural population

Thursday January 10

Schwarzkopf, et al preprint Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

Thursday January 3

Kistler et al 2018 Multiproxy evidence highlights a complex evolutionary legacy of maize in South America



Thursday December 27

Kreiner et al preprint Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

Thursday December 20

Shah et al preprint Extreme genetic signatures of local adaptation during plant colonization

Thursday December 13

Weng et al 2018 Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

Thursday December 6

Mieulet et al. 2018 Unleashing meiotic crossovers in crops


Thursday November 29

Kelleher et al preprint Inferring the ancestry of everyone

© Markus Stetter 2020 Impressum