Disclaimer: The content on this website may not be accurate as the domain is not with its previous owner. For updated and accurate content, kindly refer to rilab.ucdavis.edu


The Ross-Ibarra lab website has moved to rilab.ucdavis.edu. This domain is currently available for purchase.


Science and beer on a Friday afternoon seem to make a good combination. Nobody presents or defends the papers. We assume everyone has read the paper and jump right in to discussion without introduction. This allows for a very informal discussion, and with beer involved even the worst papers are much more manageable. Anyone is welcome to come and anyone can suggest a paper. There is no email list; articles are posted below along with the date. We meet Fridays in the Tropical Room (2346) in Storer Hall at 3:30pm. Jeff will provide some beer, but more is always welcome!

From time to time we also blog our thoughts on the papers we read. One or more of the people present volunteers to write down some of the discussion of each paper. Our hope is that this is useful to authors in clarifying papers when possible (pre-publication) or to others in considering the potential caveats or points of greatest interest (post-publication). Comments on the blog posts are welcome – please email them along.

Below are papers for Oct. 2013 and onward. For 2008-2013 papers see here.

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.



Friday August 17

Stankowski et al. 2019 Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

Friday August 9

Yan et al. 2019 Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize

Friday August 2

Dunning et al. 2019 Lateral transfers of large DNA fragments spread functional genes among grasses


Friday July 26

Xu et al. 2019 Evolutionary Metabolomics Identifies Substantial Metabolic Divergence between Maize and its Wild Ancestor, Teosinte

Friday July 19

No R.E.H.A.B.

Friday July 12

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

Friday July 5

Bradburd and Ralph preprint Spatial Population Genetics: It’s About Time


Friday June 28

Hämälä and Savolainen 2019 Genomic patterns of local adaptation under gene flow in Arabidopsis lyrata

Friday June 21

Wang et al. 2019 The architecture of intra-organism mutation rate variation in plants

Friday June 14

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

Friday June 7

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


Friday May 31

Harris 2015 Evidence for recent, population-specific evolution of the human mutation rate

Friday May 24

Verta and Jones 2019 Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

Friday May 17

MS in development email Jeff for link or find on Slack

Friday May 10

Vasseur et al. 2019 Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

Friday May 3

Wang et al. 2019 Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean


Friday April 26

Berg et al. 2019 Reduced signal for polygenic adaptation of height in UK Biobank

Friday April 19

Fustier et al. preprint Genomic footprints of local adaptation along elevation gradients associate with present phenotypic variation in teosintes

Friday April 12

Wainschtein et al. preprint Recovery of trait heritability from whole genome sequence data

Friday April 5

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


Friday Mar 29

Monnahan et al 2019 Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

Friday Mar 22

Liu et al. 2019 Biological relevance of computationally predicted pathogenicity of noncoding variants

Friday Mar 15

Maize Genetics Conference

Friday Mar 8

Owens and Samuk preprint Adaptive introgression during environmental change can weaken reproductive isolation

Friday Mar 1

Mee and Yeaman preprint Unpacking conditional neutrality: genomic signatures of selection on conditionally beneficial and conditionally deleterious mutations


Friday Feb 22

Esnault et al. 2019 Transposable element insertions in fission yeast drive adaptation to environmental stress

Friday Feb 15

Uricchio et al. 2019 An evolutionary compass for detecting signals of polygenic selection and mutational bias

Friday Feb 8

Petr et al. 2019 Limits of long-term selection against Neandertal introgression


Friday Feb 1

Lee et al. preprint Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2/3 islands located in euchromatic genome


Friday Jan 25

Ferrero-Serrano et al. 2019 Phenotypic and genome-wide association with the local environment of Arabidopsis

Friday Jan 18

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

Friday Jan 11

Martin et al., preprint Recombination rate variation shapes barriers to introgression across butterfly genomes

Friday Jan 4

Zhou et al., preprint Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)



Friday December 28

Happy Holidays, no R.E.H.A.B.

Friday December 21

Happy Holidays, no R.E.H.A.B.

Friday December 14

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

Friday December 7

Kelleher et al, preprint Inferring the ancestry of everyone


Friday November 30

Ruby et al, 2018 Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating

Friday November 23

No R.E.H.A.B., but in honor of Thanksgiving you can read about the origin of your favorite side dish, sweet potato

Friday November 16

more eLife review! email Jeff for link or find on Slack

Friday November 9

Lin et al. 2018 Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Friday November 2

Special Seminar – no R.E.H.A.B.


Friday October 26

Fugère and Hendry, 2018 Human influences on the strength of phenotypic selection

Friday October 19

Tavares et al. 2018 Selection and gene flow shape genomic islands that control floral guides

Friday October 12

Yang et al. 2018 Kin recognition in rice (Oryza sativa) lines

Friday October 5

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


Friday September 28

eLife review email Jeff for link

Friday September 21

Bellon et al., 2018 Evolutionary and food supply implications of ongoing maize domestication by Mexican campesinos

Friday September 14

Zuellig et al., 2018 A two‐locus hybrid incompatibility is widespread, polymorphic, and active in natural populations of Mimulus

Friday September 7

Crown et al., 2018 Local inversion heterozygosity alters recombination throughout the genome


Friday August 31

Fuller et al. 2018 Ancestral polymorphisms explain the role of chromosomal inversions in speciation

Friday August 24

Simon et al. 2018 Coadapted genomes and selection on hybrids: Fisher’s geometric model explains a variety of empirical patterns

Friday August 17

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

Friday August 10

Stankowski et al. preprint The tempo of linked selection: Rapid emergence of a heterogeneous genomic landscape during a radiation of monkeyflowers

Friday August 3

Jay et al. 2018 Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion


Friday July 27

Marques et al. 2018 Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation

Friday July 20

McGlothlin et al. 2018 Adaptive radiation along a deeply conserved genetic line of least resistance in Anolis lizards

Friday July 13

Parada and Charlesworth preprint The effects on neutral variability of recurrent selective sweeps and background selection

Friday July 6

Constable and Kokko 2018 The rate of facultative sex governs the number of expected mating type


Friday June 29

Smith et al., preprint A domestication history of dynamic adaptation and genomic deterioration in sorghum

Friday June 22

Zou, et al., 2017 Adaptation of Arabidopsis thaliana to the Yangtze River basin

Friday June 15

Fisher, 1918 The correlation between relatives on the supposition of Mendelian inheritance

Friday June 8

Barghi et al. preprint Polygenic adaptation fuels genetic redundancy in Drosophila

Friday June 1

Flagel et al. preprint A synthesis of mapping experiments reveals extensive genomic structural diversity in the Mimulus guttatus species complex


Friday May 25

Corbett-Detig et al. manuscript (email for pdf) Bulk Pollen Sequencing Reveals Rapid Evolution of Segregation Distortion In The Male Germline of Arabidopsis Hybrids

Friday May 18

Raynes et al. 2018 Sign of selection on mutation rate modifiers depends on population size

Friday May 11

Kelly 2018 The amount of nitrogen used for photosynthesis modulates molecular evolution in plants

Friday May 4

Kern and Hahn 2018 The neutral theory in light of natural selection


Friday Apr. 27

Note: REHAB at 3pm at 3rd and U Schumer et al. 2018 Natural selection interacts with recombination to shape the evolution of hybrid genomes

Friday Apr. 20

Zeng et al. 2018 Signatures of negative selection in the genetic architecture of human

Friday Apr. 13

Gage et al. preprint Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding [commentary]

Friday Apr. 6

Yeaman et al. preprint Quantifying how constraints limit the diversity of viable routes to adaptation


Friday Mar. 30

MGC – no R.E.H.A.B.

Friday Mar. 23

MGC – no R.E.H.A.B.

Friday Mar. 16

Booker and Keightley preprint Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome

Friday Mar. 9

Filiault et al. preprint The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history

Friday Mar. 2

di Iulio et al. 2018 The human noncoding genome defined by genetic diversity


Friday Feb. 23

Willi et al. 2018 Accumulation of mutational load at the edges of a species range.

Friday Feb. 16

Huang et al. 2018 ZmCCT9 enhances maize adaptation to higher latitudes

Friday Feb. 9

Kong et al. 2018 The nature of nurture: Effects of parental genotypes

Friday Feb. 2

Ørsted et al. 2017 Environmental variation partitioned into separate heritable components


Friday Jan. 26

Hayward et al. 2017 Evidence for Selection-by-Environment but Not Genotype-by-Environment Interactions for Fitness-Related Traits in a Wild Mammal Population

Friday Jan. 19

Borges et al. 2018 Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

Friday Jan. 12

No R.E.H.A.B. (lab at Plant and Animal Genome conference)

Friday Jan. 5

Patwa & Wahl 2008 The fixation probability of beneficial mutations



Dec. 22, 29 No R.E.H.A.B. – Happy Holidays!
Friday Dec. 15

Murray et al. 2017 Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Friday Dec. 8

Comeron 2017 Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies

Friday Dec. 1

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.


Friday Nov 24

No R.E.H.A.B., but in honor of Thanksgiving you can bone up on your statistics by learning about Turkey’s test.

Friday Nov 17

Zan and Carlborg preprint Explorations of the polygenic genetic architecture of flowering time in the worldwide Arabidopsis thaliana population

Friday Nov 10

Bosse et al. 2017 Recent natural selection causes adaptive evolution of an avian polygenic trait

Friday Nov 3

Schrider & Kern preprint Machine Learning for Population Genetics: A New Paradigm


Friday Oct 27

Osada et al. 2017 Cis- and Trans-regulatory Effects on Gene Expression in a Natural Population of Drosophila melanogaster

Friday Oct 20

Lotterhos et al. preprint Modular environmental pleiotropy of genes involved in local adaptation to climate despite physical linkage

Friday Oct 13

Forsythe et al preprint Epistatic interactions drive biased gene retention in the face of massive nuclear introgression

Friday Oct 6

Salojärvi et al. 2017 Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.


Friday Sept 29

Huber et al preprint Gene expression drives the evolution of dominance

Friday Sept 22

Jain and Stephan 2017 Modes of rapid polygenic adaptation

Friday Sept 15

Gage et al. 2017 The effect of artificial selection on phenotypic plasticity in maize (email or see lab Slack for paper)

Friday Sept 8

Oka et al. 2017 Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

Friday Sept 1

R.E.H.A.B. joint paper review. (email or see lab Slack for paper)


Friday Aug 25

Zhang and Gao 2017 Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species

Friday Aug 18

González-Martínez4 et al. 2017 Range Expansion Compromises Adaptive Evolution in an Outcrossing Plant

Friday Aug 11

Hübner et al. 2017 The Cultivated Sunflower Pan Genome Provides Insights on the Contribution of Introgressions to Breeding of Modern Varieties

Friday Aug 4

No R.E.H.A.B.


Friday July 28

Zan et al. 2017 Artificial selection response due to polygenic adaptation from a multi-locus, multi-allelic genetic architecture

Friday July 21

Sohail et al 2017 Negative selection in humans and fruit flies involves synergistic epistasis

Friday July 14

Chen et al. 2017 Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species

Friday July 7

Hurst and Randerson 2000 Dosage, Deletions and Dominance: Simple Models of the Evolution of Gene Expression


Friday June 30

Vijay et al. 2017 Genome-wide patterns of variation in genetic diversity are shared among populations, species and higher order taxa

Friday June 23

Gould et al. preprint The Gene Regulatory Landscape of Local Adaptation

Friday June 16

Zeng et al. preprint Widespread signatures of negative selection in the genetic architecture of human complex traits

Friday June 9

Simons et al. 2017 A model for the genetic architecture of quantitative traits under stabilizing selection

Friday June 2

Walter et al. preprint Evolution of genetic variance during adaptive radiation


Friday May 26

Lee et al. 2017 Young inversion with multiple linked QTLs under selection in a hybrid zone

Friday May 19

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?

Friday May 12

Durvasula et al. 2017 African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Friday May 5

Gilbert et al. 2017 Local Adaptation Interacts with Expansion Load during Range Expansion: Maladaptation Reduces Expansion Load


Friday April 28

Gilbert and Whitlock 2017 The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large‐effect alleles can allow range expansion

Friday April 21

Huang, Gulko & Siepel 2017 Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

Friday April 14

Wang et al. 2017 Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

Friday April 7

Charlesworth 2013 Stabilizing Selection, Purifying Selection, and Mutational Bias in Finite Populations


Friday March 31

Franssen et al. 2017 Uncovering the genetic signature of quantitative trait evolution with replicated time series data

Friday March 24

Hermisson & Pennings preprint Soft sweeps and beyond: Understanding the patterns and probabilities of selection footprints under rapid adaptation

Friday March 17

Brandenburg et al 2017 Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

Friday March 10

Maize meeting – no R.E.H.A.B.

Friday March 3

Messer and Petrov 2013 Population genomics of rapid adaptation by soft selective sweeps.

February 2017

Friday Feb. 24

Robillard et al 2016 Experimental evolution reveals hyperparasitic interactions among transposable elements

Friday Feb. 17

Watson et al. 2016 Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis

Friday Feb. 10

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

Friday Feb. 3

Wagner et al. 2017 Spatial detection of outlier loci with Moran eigenvector maps (MEM)

January 2017

Friday Jan 27

Weir and Goudet preprint A unified characterization of population structure and relatedness.

Friday Jan 20

Puzey et al 2016 Population structure and local selection yield high genomic variation in Mimulus guttatus

Friday Jan 13

PAG – no R.E.H.A.B.

Friday Jan 6

Vidalis et al. 2016 Methylome evolution in plants


December 2016

Friday Dec. 30

No R.E.H.A.B. Happy new year!

Friday Dec. 23

No R.E.H.A.B. Happy Festivus!

Friday Dec. 16

Barton 2016 How does epistasis influence the response to selection?

Friday Dec. 9

Imprialou et al. preprint Genomic Rearrangements Considered as Quantitative Traits

Friday Dec 2

Klasen et al 2016 A multi-marker association method for genome-wide association studies without the need for population structure correction

November 2016

Friday Nov 25

No R.E.H.A.B. – Turkey Day!

Friday Nov 18

Moyerbrailean et al. 2016 High-throughput allele-specific expression across 250 environmental conditions

Friday Nov 11

No R.E.H.A.B. – Veteran’s Day

Friday Nov 4

Gould et al. 2016 Pooled Ecotype Sequencing Reveals Candidate Genetic Mechanisms for Adaptive Differentiation and Reproductive Isolation

October 2016

Friday Oct 28

Phung et al preprint Natural selection reduces linked neutral divergence between distantly related species

Friday Oct 21

Johnsson Feralisation targets different genomic loci to domestication in the chicken

Friday Oct 14

Fraïsse et al. 2014 Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

Friday Oct 7

Willing et al. 2016 Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

September 2016

Friday Sept 30

Schrider et al. 2016 Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Friday Sept 23

Hughes, Langdale, Kelly 2016 The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

Friday Sept 16

Groth and Blumenstiel 2016 Horizontal transfer can drive a greater transposable element load in large populations

Friday Sept 9

Venkataram et al 2016 Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

Friday Sept 2

Uricchio et al. 2016 Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

August 2016

Friday Aug 26

Zhang et al. 2016 Recombination rate variation, hitchhiking, and demographic history shape deleterious load in poplar

Friday Aug 19

Fransz et al. 2016 Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

Friday August 12

Fu et al 2016 The genetic history of Ice Age Europe

Friday Aug 5

Sanseverino et al. 2015 Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.

July 2016

Friday July 29

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

Friday July 22

Sharp & Agrawal 2016 Low Genetic Quality Alters Key Dimensions of the Mutational Spectrum blog post

Friday July 15

Arnold et al. 2016 Borrowed alleles and convergence in serpentine adaptation

Friday July 8

Bailey et a 2015 The Effect of Selection Environment on the Probability of Parallel Evolution

Friday July 1

Zhena and Andolfatto 2012 Methods to Detect Selection on Noncoding DNA

June 2016

Friday June 24 2016

Quadrana et al The Arabidopsis thaliana mobilome and its impact at the species level

Friday June 17 2016

1001 Genomes Consortium 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Friday June 10 2016

Cardoso-Moreira et al. 2016 Evidence for the fixation of gene duplications by positive selection in Drosophila

Friday June 3 2016

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

May 2016

Friday May 27 2016

Paccard et al 2016 Quantitative Genetic Architecture at Latitudinal Range Boundaries: Reduced Variation but Higher Trait Independence

Friday May 20 2016

Keightley et al 2016 Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster

Friday May 13 2016

Exposito-Alonso et al preprint The rate and effect of de novo mutations in natural populations of Arabidopsis thaliana

Friday May 6 2016

Kelley et al 2016 The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana

Friday April 29 2016

Roles et al. 2016 Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana

April 2016

Friday April 22 2016

Sanjak et al. preprint The Genetic Architecture of a Complex Trait is more Sensitive to Genetic Model than Population Growth

Friday April 15 2016

Novikova et al. manuscript (see #papers channel on slack for pdf)

Friday April 8 2016

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

Friday April 1 2016

Lolle et al. 2005 Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis.

March 2016

Friday Mar 25

Marschall et al. preprint Computational Pan-Genomics: Status, Promises and Challenges

Friday Mar 18

No R.E.H.A.B. (Maize Meeting!)

Friday Mar 11

Lamichhaney et al. 2012 Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

Friday Mar 4

Keller and Fitzpatrick 2014 Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation

February 2016

Fri. Feb 26

Rausher and Delph 2015 When does understanding phenotypic evolution require identification of the underlying genes?

Fri. Feb 19 2016

Gao et al 2015 Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes

Fri. Feb 12 2016

Mäki-Tanila and Hill Influence of Gene Interaction on Complex Trait Variation with Multi-Locus Models

Fri. Feb 5 2016

Sheehan and Song preprint Deep learning for population genetic inference

January 2016

Fri. Jan 29 2016

Lamichhaney et al. 2016 Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).

Fri. Jan 22 2016

Stephan 2016 Signatures of positive selection: from selective sweeps atindividual loci to subtle allele frequency changes inpolygenic adaptation

Fri. Jan 15 2016

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

Fri. Jan 8 2016

Marsden et al. 2015 Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs


December 2015

Fri. Dec. 18 2015

Steige et al. preprint The impact of natural selection on the distribution of cis-regulatory variation across the genome of an outcrossing plant

Fri. Dec. 11 2015

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.

Fri. Dec. 4 2015

Remington 2015 Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

November 2015

Fri. Nov. 27 2015

No R.E.H.A.B. for the holidays. But you can get your fill of turkey popgen nonetheless.

Fri. Nov. 20 2015

Beissinger et al. 2015 Recent demography drives changes in linked selection across the maize genome

Fri. Nov. 13 2015

van Heerwaarden et al. 2015 Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits

Fri. Nov. 6 2015

Scheiner et al. 2015 The Genetics of Phenotypic Plasticity. XIV. Coevolution

October 2015

Fri. Oct. 30 2015

Chevin and Hospital 2008 (AGAIN!) Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

Fri. Oct. 23 2015

Chevin and Hospital 2008 Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

Fri. Oct. 16 2015

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

Fri. Oct. 9 2015

Heath and Nuismer 2014 Connecting functional and statistical definitions of genotype by genotype interactions in coevolutionary studies

Fri. Oct. 2 2015

Wang et al. 2015 Hybrid mimics and hybrid vigor in Arabidopsis blog post

September 2015

Fri. Sept. 25 2015

Lande and Arnold 1983 The measurement of selection on correlated characters

Fri. Sept. 18 2015

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

Fri. Sept. 11 2015

Renaut and Reiseberg 2015 The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops

Fri. Sept. 4 2015

Kuester et al. preprint A resurrection experiment finds evidence of both reduced genetic diversity and adaptive evolution in the agricultural weed Ipomoea purpurea

August 2015

Fri. Aug. 28 2015

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

Fri. Aug. 21 2015

Snir et al. 2015 The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming

Fri. Aug. 14 2015

Dubin et al. 2015 DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

Fri. Aug. 7 2015

Castellano et al. preprint Adaptive evolution is substantially impeded by Hill-Robertson interference in Drosophila

July 2015

Fri. July 31 2015

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

Fri. July 24 2015

Mazet et al. 2015 Demographic inference using genetic data from a single individual: separating population size variation from population structure

Fri. July 17 2015

Oakley et al 2015 Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana

Fri. July 10 2015

Monnahan et al. 2015 A genomic selection component analysis characterizes migration-selection balance

Fri. July 3 2015

Fierst et al. 2015 Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes

June 2015

Fri. June 26 2015

Asaf et al. 2015 Obstruction of adaptation in diploids by recessive, strongly deleterious alleles

Fri. June 19 2015

Mafessoni and Lachman preprint Selective strolls: fixation and extinction in diploids are slower for weakly selected mutations than for neutral ones

Fri. June 12 2015

Pease and Hahn 2015 Detection and Polarization of Introgression in a Five-taxon Phylogeny

Fri. June 5 2015

Wilkes 1977 Hybridization of Maize and Teosinte, in Mexico and Guatemala and the Improvement of Maize

May 2015

Fri. May 29, 2015

Van der Graf 2015 Rate, spectrum, and evolutionary dynamics of spontaneous epimutations.

Fri. May 22, 2015

Monnahan and Kelly 2015 Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus

Fri. May 15, 2015

Mathieson and McVean 2013 Estimating selection coefficients in spatially structured populations from time series data of allele frequencies

Fri. May 8, 2015

Sheng et al. preprint Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

Fri. May 1, 2015

Fishman and Kelly 2015 Centromere–associated meiotic drive and female fitness variation in Mimulus blog post

April 2015

Fri. April 24, 2015

Agren et al. 2014 No evidence that sex and transposable elements drive genome size variation in evening primroses

Fri. April 17, 2015

Douglas et al. 2015 Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

Fri. April 10, 2015

No R.E.H.A.B. Come to the UCDavis Plant Breeding Symposium instead.

Fri. April 3, 2015

Romero et al. SeeDs manuscript (email Jeff for the URL).

March 2015

Fri. March 27, 2015

Cesar Chavez Day; university closed. No R.E.H.A.B.

Fri. March 20, 2015

Jeffares et al 2015 The genomic and phenotypic diversity of Schizosaccharomyces pombe

Fri. March 13, 2015

NO R.E.H.A.B. – MGC baby!

Fri. March 6, 2015

Bergland et al 2014 Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

February 2015

Fri. Feb. 27, 2015

Brown and Levin 2011 Social dilemmas among supergenes: intragenomic sexual conflict and a selfing solution in Oenothera

Fri. Feb. 20, 2015

Huang et al 2014 Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes

Fri. Feb. 13, 2015

Li et al. Methylation manuscript. (printed version available from JRI).

Fri. Feb. 6, 2015

Rodgers-Melnick et al. Recombination manuscript. (printed version available from JRI).

January 2015

Fri. Jan 30, 2015

Brandvain et al. 2014 Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

Fri. Jan 23, 2015

Charlesworth 2015 Causes of natural variation in fitness: Evidence from studies of Drosophila populations

Fri. Jan 16, 2015

Antonovics 1976 The nature of limits to natural selection.

Fri. Jan 9, 2015

Wiser et al. 2013 Long-Term Dynamics of Adaptation in Asexual Populations

Fri. Jan 2, 2015

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.


December 2014

Fri. Dec. 26, 2014

No R.E.H.A.B., but feel free to get your plant genomics fix by reading up on the Christmas Tree genome

Fri. Dec. 19, 2014

R.E.H.A.B. unexpectedly cancelled due to lab partying (seriously).

Fri. Dec. 12, 2014

Poh et al. preprint On the prospect of identifying adaptive loci in recently bottlenecked populations

Fri. Dec. 5, 2014

Fu et al. 2014 Characteristics of Neutral and Deleterious Protein-Coding Variation among Individuals and Populations

November 2014

Fri. Nov. 28, 2014

No REHAB. But that doesn’t meant you can’t get a second helping of turkey genomics should you so desire.

Fri. Nov. 21, 2014

Takuno et al. in prep Independent molecular basis of convergent highland adaptation in maize

Fri. Nov. 14, 2014

Gravel preprint When is selection effective?

Fri. Nov. 7, 2014

Hough et al. 2014. Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus.

October 2014

Fri. Oct 31, 2014

Schiffels & Durbin. Inferring human population size and separation history from multiple genome sequences.

Fri. Oct 24, 2014

Caicedo et al. 2007. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice

Fri. Oct. 17, 2014

Crawford et al. preprint Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex

Fri. Oct. 10, 2014

Martin et al preprint. Evaluating the use of ABBA-BABA statistics to locate introgressed loci.

Fri. Oct. 3, 2014

Huber et al. 2014 Keeping it Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana.

September 2014

Fri. Sept. 26, 2014

Romiguier et al. 2014 Comparative population genomics in animals uncovers the determinants of genetic diversity

Fri. Sept. 19, 2014

Brawand et al. 2014 The genomic substrate for adaptive radiation in African cichlid fish

Fri. Sept 12, 2014

Spencer et al. 2006 The Influence of Recombination on Human Genetic Diversity

Fri. Sept 5, 2014

Carneiro et al. 2014 The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit.

August 2014

Fri. Aug 30, 2014

Kelley et al. 2014 Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.

Fri. Aug 23, 2014

Wilson et al. 2014. Soft Selective Sweeps in Complex Demographic Scenarios.

Fri. Aug 16, 2014

Comeron 2014. Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome

Fri. Aug 9, 2014

Enard et al. 2014. Genome-wide signals of positive selection in human evolution

Fri. Aug 1, 2014

Arnegard et al. 2014. Genetics of ecological divergence during speciation

July 2014

Fri. July 25, 2014

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

Fri. July 18, 2014

Macadangdang et al. 2014. Evolution of histone 2A for chromatin compaction in eukaryotes blog post

Fri. July 11, 2014

Guenther et al A molecular basis for classic blond hair color in Europeans

Fri. July 4, 2014

No R.E.H.A.B. Watch some fireworks instead!

June 2014

Fri. June 27, 2014

Ho and Zhang 2014. The Genotype–Phenotype Map of Yeast Complex Traits: Basic Parameters and the Role of Natural Selection

Fri. June 20, 2014

Yeaman 2013. Genomic rearrangements and the evolution of clusters of locally adaptive loci blog post

Fri. June 13, 2014

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 blog post

Fri. June 6, 2014

Balick et al. preprint. Response to a population bottleneck can be used to infer recessive selection

May 2014

Fri. May 30, 2014

Nadeau et al. 2014. Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato blog post

Fri. May 23, 2014

Soria-Carrasco et al. 2014. Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation blog post

Fri. May 16, 2014

Rogers et al. 2014. Tandem duplications and the limits of natural selection in Drosophila yakuba and Drosophila simulans blog post

Fri. May 9, 2014

Hawkins et al. 2014. Variation in allelic expression associated with a recombination hotspot in Zea mays blog post

Fri. May 2, 2014 (JRI)

Do et al. 2014. No evidence that natural selection has been less effective at removing deleterious mutations in Europeans than in West Africans

April 2014

Fri. April 25, 2014 (VB)

Li 2014. Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples.

\emph{Also see slides}

Fri. April 18, 2014 (JRI)

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

Fri. April 11, 2014 (JRI)

NO R.E.H.A.B. Check out the Plant Breeding Symposium instead!

Fri. April 4, 2014 (JRI)

Campos et al. 2014. The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster.

March 2014

Fri Mar. 28 2014 (JRI)

Hirsch et al. 2014. Insights into the maize pan-genome and pan-transcriptome.

Fri Mar. 21 2014 (SM)

Piepho and Möhring 2007. Computing Heritability and Selection Response From Unbalanced Plant Breeding Trials

Fri Mar. 14 2014 (DV)

Cortijo et al. Mapping the Epigenetic Basis of Complex Traits

Fri Mar. 7 2014 (SM)

Peiffer et al. 2014. The genetic architecture of maize height

February 2014

Fri Feb. 28 2014 (MS)

Cavrak et al. 2014. How a Retrotransposon Exploits the Plant’s Heat Stress Response for Its Activation

Fri Feb. 21 2014 (PB)

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

Fri Feb. 14 2014 (DV)

Han et al. 2013. Characterizing bias in population genetic inferences from low coverage sequencing data

Fri. Feb. 7 2014 (JRI)

Sankararaman et al. 2014. The genomic landscape of Neanderthal ancestry in present-day humans

January 2014

Fri. Jan 31 2014 (VB)

Nadachowska-Brzyska et al.. Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

Fri. Jan 24 2014 (VB)

Scally et al. 2012. Insights into hominid evolution from the gorilla genome sequence

Fri Jan. 17 2014 (JRI)

Chapman et al. 2013. Genomic Divergence during Speciation Driven by Adaptation to Altitude

Fri Jan. 3 2014 (AO)

<CANCELED> – There’s a first time for everything. (Translation: “CANCELLED” for our British and Canadian friends)

Fri Jan. 3 2014 (AO)

Karhunen et al. 2013. Bringing habitat information into statistical tests of local adaptation in quantitative traits: a case study of nine-spined sticklebacks.


December 2013

Fri Dec. 20 2013 (DV)

Rettelbach et al. 2013. Three modes of adaptive speciation in spatially structured populations

Fri Dec. 13 2013 (JRI)

Korneliussen et al. 2013. Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

Fri Dec 6 2013 (VB)

Teng et al. 2013. Genome-wide Consequences of Deleting Any Single Gene

November 2013

Fri Nov 29 2013

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

Fri Nov 22 2013 (VB,DV)

Thallmann et al. 2012. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs

Fri Nov 15 2013 (JRI)

Kijima and Innan 2013. Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

Fri Nov 08 2013 (JRI)

Review! Pick up hard copy in 262 Robbins.

Fri Nov 01 2013 (JRI)

Lohmueller 2013. The impact of population demography and selection on the genetic architecture of complex traits

October 2013

Fri Oct 25 2013 (OA)

Parker et al. 2013. Genome-wide signatures of convergent evolution in echolocating mammals

Fri Oct 18 2013 (AO,VB)

Peischl et al. arxiv. On the accumulation of deleterious mutations during range expansions

Fri Oct 11 2013 (PMG)

Ronen et al. 2013. Learning Natural Selection from the Site Frequency Spectrum

Fri Oct 04 2013 (JMB)

Szovenyi et al. 2013. Selection Is No More Efficient in Haploid than in Diploid Life Stages of an Angiosperm and a Moss

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