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.
2019
August
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
July
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
June
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
May
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
April
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
March
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
February
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
February
Friday Feb 1
Lee et al. preprint Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2/3 islands located in euchromatic genome
January
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)
2018
December
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
November
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.
October
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
September
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
August
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
July
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
June
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
May
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
April
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
March
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
February
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
January
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
2017
December
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.
November
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
October
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.
September
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)
August
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.
July
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
June
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
May
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
April
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
March
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
2016
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
2015
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.
2014
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.
2013
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