Detox Journal Club

Each week, the DETOX journal club meets to discuss the latest papers in evolutionary genetics and plant/animal breeding. After a week of doing science for work, we can all benefit from the chance to detoxify our systems by talking over a paper in a fun, no-pressure setting. Papers cover all aspects of evolutionary genetics and breeding, giving us the chance to stay up-to-date on the literature in our own and related fields.

Regular attendance isn't mandatory, just come when you can and/or when the paper interests you. Attendees do not need to be members or affiliates of any particular division or group, just scientists at any stage of their careers who are interested in the topics and papers we'll discuss.

We meet on Wednesday afternoons at 16:30 at Monro’s Park, in the Göttingen City Center. If you'd like email reminders, please ask Dilek Mut ( to add you to the email list.

Email paper nominations to Tim (, and he'll work them into the schedule below.

Detox schedule in reverse-chronological order:

December 4

Zhang et. al. 2019 . The genetic basis of inbreeding depression in potato

November 27

Detox canceled to encourage attendance of DNPW colloquium. Prof. Neugart will present at 16:15 in room L01.

November 20

Monnahan et al. 2015. Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus

November 13

Detox canceled to encourage attendance of DNPW colloquium. Tim will present at 16:15 in room L01.

November 6

Cordell, 2002. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans

October 30

Detox canceled to encourage attendance of DNPW colloquium. Prof. Rostas will present at 16:15 in room L01.

October 23

Kerin et al. 2019. Gene-environment interactions using a Bayesian whole genome regression model

October 16

Turner-Hissong et al. Evolutionary insights into plant breeding.

October 9

Detox cancelled due to Eucarpia conference in Munich.

October 2

Lowry et al. 2019  QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

September 25
Gage et al. 2018 Selection Signatures Underlying Dramatic Male Inflorescence Transformation During Modern Hybrid Maize Breeding

September 18

Yang et al. 2019 Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

September 11

Uricchio 2019 Evolutionary perspectives on polygenic selection, missing heritability, and GWAS

September 4

Voss-Fels et al. 2019 Breeding improves wheat productivity under contrasting agrochemical input levels


Detox Hiatus: 2018- July 2019

Detox will be taking a break while it relocates from Missouri, USA to Göttingen, Germany. If you are at MU, check out the DataPhiles group instead! Info here: DataPhiles!

February 2018

February 22 Detox Extravaganza/Tim Send off

To celebrate Tim's last Detox in Columbia, we'll spend an hour discussing each of the following three papers at three different locations. We'll start at Craft Beer Cellar an hour earlier than usual, at 4:00, to discuss citrus domestication (paper #1). At 5:00 we'll grab food at Seol Taco before heading to Gunter Hans to talk about erd-GWAS (paper #2). At 6:00 we'll go to The Understudy where we'll discuss a classic that demonstrated the power of PCA (paper #3).

Wu et al. 2018 Genomics of the origin and evolution of Citrus
Lin et al. 2017 Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS
Novembre et al. 2008 Genes mirror geography within Europe

February 15

Pitchers et al. 2017 The power of a multivariate approach to genome-wide association studies: an example with Drosophila melanogaster wing shape Dr. Dworkin will give a DBS seminar on Feb 20!

February 8

Instead of Detox, consider attending the MU Plant Research Symposium

February 1

Mathew et al. Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population

January 2018

January 25

Tilk et al High accuracy haplotype-derived allele frequencies from ultra-low coverage pool-seq samples

January 18

Zhao and Begun Genomics of parallel adaptation at two timescales in Drosophila

January 11

Zhao and Begun Genomics of parallel adaptation at two timescales in Drosophila Canceled due to hazardous weather

January 4

Cornejo et al Genomic insights into the domestication of the chocolate tree, Theobroma cacao L.

December 2017

December 28

Like the rest of the University, Detox will be closed this week. Happy new year!

December 21

Senn 2011 Francis Galton and regression to the mean

December 14

Schrider and Kern, 2017 Machine Learning for Population Genetics: A New Paradigm

December 7

Falconer 1992 Early Selection Experiments

November 2017

November 30

Gage et al 2017 The effect of artificial selection on phenotypic plasticity in maize

November 16 #TBT

Falconer 1992 Early Selection Experiments

November 9

Santos et al. Taxon-restricted genes at the origin of a novel trait allowing access to a new environment

November 2

Bosse et al. Recent natural selection causes adaptive evolution of an avian polygenic trait

October 2017

October 26

Chari et al. Compensatory evolution via cryptic genetic variation: Distinct trajectories to phenotypic and fitness recovery

October 19

Yang et al. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize We're going to Lucky's Market again this week. Soon we'll vote on the regular destination. Location:

October 12

NoaLiscovitch-Brauer et al. Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods We're going to give Lucky's Market a try this week. Instead of Craft Beer Cellar, we'll meet at Lucky's. Location:

October 5

Goiffon et al. Improving Response in Genomic Selection with a Population-Based Selection Strategy: Optimal Population Value Selection

September 2017

September 28

Edwards et al. Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

September 21

Bromham et al. Exploring the Relationships between Mutation Rates, Life History, Genome Size, Environment, and Species Richness in Flowering Plants

September 14

Alguillon et al. Deconstructing isolation-by-distance: The genomic consequences of limited dispersal

September 7

No Detox - Go to the Tomato festival!

August 2017

August 31

Guerrero et al. Pervasive antagonistic interactions among hybrid incompatibility loci

August 24

Swarts et al. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

August 17

Noble et al. Polygenicity and epistasis underlie fitness-proximal traits in the Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel

August 10

Cheng et al. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

August 3

Venkat et al Multinucleotide mutations cause false inferences of positive selection

July 2017

July 27

Grauer An upper limit on the functional fraction of the human genomeXs

July 20

Monnahan and Kelly The Genomic Architecture of Flowering Time Varies Across Space and Time in Mimulus guttatus

July 13

Fleming et al. Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure

July 6

Boyle et al. An Expanded View of Complex Traits: From Polygenic to Omnigenic

June 2017

June 29

Zhou et al. The Evolutionary Genomics of Grape (Vitis vinifera ssp. vinifera) Domestication

June 22

Liu et al. Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies

June 15

Han et al. Clustering of 770,000 genomes reveals post-colonial population structure of North America

June 8

Malinski et al. Whole Genome Sequences Of Malawi Cichlids Reveal Multiple Radiations Interconnected By Gene Flow

June 1

Sauvage et al. Domestication rewired gene expression and nucleotide diversity patterns in tomato

May 2017

May 25

Chan et al. The Complex Genetic Architecture of the Metabolome

May 18

Barber and Elde Escape from bacterial iron piracy through rapid evolution of transferrin

May 11

Shen et al. Contentious relationships in phylogenomic studies can be driven by a handful of genes

May 4

Huang et al. Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

April 2017

April 27

Zhang et al. Genetic Basis of Melanin Pigmentation in Butterfly Wings

April 20

Thalmann et al. The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A In honor of my new backyard chicks, which include one of the type described here

April 13

Forsberg and Carlborg On The Relationship Between Epistasis And Genetic Variance-Heterogeneity

April 6

Porto et al. Evolution of the Genotype-to-Phenotype Map and the Cost of Pleiotropy in Mammals

March 2017

March 30

Graves et al. Genomics of Parallel Experimental Evolution in Drosophila

March 23

Burke et al. Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae

March 16

Forsberg et al. Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast

March 9

Josephs et al. What can genome-wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?

March 2

Imprialou et al. Genomic Rearrangements Considered as Quantitative Traits

February 2017

February 23 This discussion will be in anticipation of Ruth Shaw's BioSci seminar the following Tuesday, February 28

Shaw and Shaw Quantitative genetic study of the adaptive process

February 16

Nam et al. Evidence that the rate of strong selective sweeps increases with population size in the great apes

February 9

Lillie et al. Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens

February 2

Instead of Detox, go to the MU Pioneer Plant Science Symposium!

January 2017

January 26

Siddiq et al, 2016 Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster

January 19

Brzyski et al, 2017 Controlling the Rate of GWAS False Discoveries

January 12

No Detox

January 5

No Detox

December 2016

December 29

No Detox -- You should be writing!

December 22

No Detox -- Read on your own

December 15

No Detox -- Good luck on finals!

December 8

Sicard et al, 2016 Standing genetic variation in a tissue-specific enhancer underlies selfing-syndrome evolution in Capsella

December 1

Yang et al, 2016 Incomplete dominance of deleterious alleles contribute substantially to trait variation and heterosis in maize

November 2016

Thursday, November 24, 2016

Thanksgiving. Discuss a good paper with non-scientist family and friends!

Thursday, November 17, 2016

Gould et al Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation

Thursday, November 10, 2016

Natarajan et al Predictable convergence in hemoglobin function has unpredictable molecular underpinnings

Thursday, November 3, 2016

Petkova et al Visualizing spatial population structure with estimated effective migration surfaces

October 2016

Thursday, October 27, 2016

Yang et alCommon SNPs explain a large proportion of the heritability for human height

Thursday, October 20, 2016

Bosse et al Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs

Thursday, Octoberr 13, 2016

Johnsson et al Feralisation targets different genomic loci to domestication in the chicken

Thursday, October 6, 2016

Zhao et al. Breeding signature of combining ability improvement revealed by a genomic variation map from recurrent selection population in Brassica napus

September 2016

Thursday, September 29, 2016

Rougemont et al. Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Thursday, September 22, 2016

Abdollahi-Arpanahi et al. Differential contribution of genomic regions to marked genetic variation and prediction of quantitative traits in broiler chickens

Thursday, September 15, 2016, We'll have an important visitor, Sarah Turner from the University of Wisconsin, participating in this Detox

Josephs and Wright On the Trail of Linked Selection

Thursday, September 8, 2016, this will be good reading before John Kelly's IPG seminar on September 12

Kelly et al. The Genomic Signal of Partial Sweeps in Mimulus guttatus

Thursday, September 1, 2016

Martin and Orgogozo The Loci of Repeated Evolution: A Catalog of Genetic Hotspots of Phenotypic Variation

August 2016

Thursday, August 25, 2016

Schrider et al. Effects of linked selective sweeps on demographic inference and model selection

Thursday, August 18, 2016

Lamichhaney et al. A beak size locus in Darwin’s finches facilitated character displacement during a drought

Thursday, August 11, 2016

Schrider et al. Effects of linked selective sweeps on demographic inference and model selection

Thursday, August 4, 2016

Lan et al. Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

July 2016

Thursday, July 28, 2016

Fuchsberger et al. The genetic architecture of type 2 diabetes

Thursday, July 21, 2016

Boyko et al. A Simple Genetic Architecture Underlies Morphological Variation in Dogs

Thursday, July 14, 2016

Battagin et al. Effect of manipulating recombination rates on response to selection in livestock breeding programs

NOTE FOR JULY 14: We will try meeting at Gunter Hans (7 Hitt Street) for a change of pace

Thursday, July 7, 2016

Merotto et al. Evolutionary and social consequences of introgression of NON-transgenic herbicide resistance from rice to weedy rice in Brazil

June 2016

Thursday, June 30, 2016

Mitteroecker et al. Multivariate Analysis of Genotype–Phenotype Association

Thursday, June 23, 2016

Tian et al. The Dissection of Expression Quantitative Trait Locus Hotspots

Thursday, June 16, 2016

Sadhu et al. CRISPR-directed mitotic recombination enables genetic mapping without crosses

Thursday, June 9, 2016

Dittmar et al. Factors influencing the effect size distribution of adaptive substitutions

Thursday, June 2, 2016

Gallaher et al. Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies

May 2016

Thursday, May 26, 2016

Detox cancelled due to conflict with IPG Symposium.

Thursday, May 19, 2016

Field et al. Detection of human adaptation during the past 2,000 years

Thursday, May 12, 2016

Barrett and Hoekstra Molecular spandrels: tests of adaptation at the genetic level

Thursday, May 5, 2016

McManus et al. Population Genetic Analysis of the DARC Locus (Duffy) Reveals Adaptation from Standing Variation Associated with Malaria Resistance in Humans

April 2016

Thursday, April 28, 2016

Wang et al. Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

Thursday, April 21, 2016

Allaby et al. Surprisingly low limits of selection in plant domestication

Thursday, April 14, 2016

Boitard et al. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

Thursday, April 7, 2016

Sheehan and Song Deep learning for population genetic inference

March 2016

Thursday, March 31, 2016

Pavlidis et al. A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

Thursday, March 24, 2016

Zhang et al. Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-dose Ultraviolet Radiation in High-altitude Environments

Thursday, March 17, 2016

Lamichhaney et al. Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

Thursday, March 10, 2016 ( Requested by Libby )

Huang et al. Epistasis dominates the genetic architecture of Drosophila quantitative traits

Thursday, March 3, 2016

MacLeod et al. Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

February 2016

Thursday, February 25, 2016

Swinnen et al. Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement

Thursday, February 18, 2016

Davies et al. Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice

Thursday, February 11, 2016

Cubillos et al. High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population

Thursday, February 4, 2016

Rausher and Delph Commentary: When does understanding phenotypic evolution require identificationof the underlying genes?

January 2016

Thursday, January 28

Decker et al. A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits

Thursday, January 21, 2016

Marsden et al. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

Thursday, January 14, 2016

Henn, et al. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

Thursday, January 7, 2016

No Detox -- Winter Holiday

December 2015

Thursday, December 31, 2015

No Detox -- Winter Holiday

Thursday, December 24, 2015

No Detox -- Winter Holiday

Thursday, December 17, 2015

Sellis et al. Empirical evidence for heterozygote advantage in adapting diploid populations of Saccharomyces cerevisiae

Thursday, December 10, 2015

Exome Aggregation Consortium et al. Analysis of protein-coding genetic variation in 60,706 humans

Thursday, December 3, 2015

Lamichhaney et al. Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

November 2015

Thursday, November 26, 2015

No DETOX -- Thanksgiving

Thursday, November 19, 2015 (5pm Start)

Monnahan et al. Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus

Thursday, November 12, 2015

Mikheyev et al., 2015  Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite