R.E.H.A.B.

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 at de Vere’s Irish Pub at about 4:15 (on rare occasions when the pub is closed we improvise; email or call to find out the location). Sometimes we’re done at 5 and sometimes not until 6, depending on the paper and the crowd and interest and amount of beer being consumed.

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 EvolFri, C.A.M.P., E.H.R.A.B., (Re)views, detox, esfoyaza, Q.U.I.T., p.r.o.s.t. and frydomics.

And no, I won’t tell you what R.E.H.A.B. stands for, so don’t ask.

2017

Sept

Friday Sept 8

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

Friday Sept 1

Gage et al. 2017 The effect of artificial selection on phenotypic plasticity in maize (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. The Gene Regulatory Landscape of Local Adaptation

Friday June 16

Zeng et al. 2017 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. 2017 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 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 2017 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 2017 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 2016 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. 2016 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 2015 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 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 2016 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. 2016 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. 2016 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 2015 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. 2015 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. 2015 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. 2015 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 2015 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. 2015 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. 2014 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 2014 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. 2014 Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex

Fri. Oct. 10, 2014

Martin et al 2014. 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. 2014. 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.

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