C.A.M.P.

C.A.M.P. is a journal club where we end our week with some libations and erudite discussion. Each Friday, the Hufford Lab and “camp”adres convene at Stomping Grounds @ 4:00pm for discussion of articles that attract our fancy. No tents or flashlights required.

Papers by date they are discussed:

July 24th, 2020
Abel et al. 2020
Mapping and characterization of structural variation in 17,795 human genomes

July 17th, 2020
Liu et al. 2020
Pan-Genome of Wild and Cultivated Soybeans

June 19th, 2020
Alonge et al. 2020
Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

June 12th, 2020
Burgess et al. 2020
Silencing of Mutator Elements in Maize Involves Distinct Populations of Small RNAs and Distinct Patterns of DNA Methylation

June 5th, 2020
Chen et al. 2020
The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication

May 29th, 2020
Lyu et al. 2020
Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice

May 15th, 2020
Josephs et al. 2020
The evolutionary forces shaping cis and trans regulation of gene expression within a population of outcrossing plants

May 8th, 2020
Skov et al. 2020
The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes

May 1st, 2020
Wang et al. 2020
Genome-wide selection and genetic improvement during modern maize breeding

April 24th, 2020
Moreno-Letelier et al. 2020
The relevance of gene flow with wild relatives in understanding the domestication process

April 17th, 2020
Xu et al. 2020
Adaptive evolution of DNA methylation reshaped gene regulation in maize

April 10th, 2020
Mérot et al. 2020
A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation

April 3rd, 2020
Wang et al. 2020
The genome evolution and domestication of tropical fruit mango

March 27th, 2020
Razifard et al. 2020
Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America

March 20th, 2020
Catherine Tubb & Tony Seba 2019
Rethinking Food and Agriculture 2020-2030, RethinkX Sector Disruption Report, September 2019

March 6th, 2020
Groen et al. 2020
The strength and pattern of natural selection on gene expression in rice

February 28th, 2020
Jia et al. 2020
A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield

February 21st, 2020
Zhou et al. 2019
Dynamic patterns of gene expression additivity and regulatory variation throughout maize development

January 17th, 2020
Hufford Lab Abstract Writing Fest

December 20th, 2019
Ho et al. 2019
Structural variation in the sequencing era

December 6th, 2019
Xie et al. 2019
The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype

November 22nd, 2019
Ricci et al. 2019
Widespread long-range cis-regulatory elements in the maize genome

November 8th, 2019
Bradbury et al. 2019
Spatial Population Genetics: It’s About Time

November 1st, 2019
Wisser et al. 2019
The Genomic Basis for Short-Term Evolution of Environmental Adaptation in Maize

October 18th, 2019
Chen et al. 2019
The bracteatus pineapple genome and domestication of clonally propagated crops

October 4th, 2019
Gaudinier et al. 2019
Evolutionary processes from the perspective of flowering time diversity

September 20th, 2019
Haberer et al. 2019
European maize genomes unveil pan-genomic dynamics of repeats and genes

September 13th, 2019
Roessler et al. 2019
The genome-wide dynamics of purging during selfing in maize

September 6th, 2019
Tian et al. 2019
Teosinte ligule allele narrows plant architecture and enhances high-density maize yields

August 30th, 2019
Tian et al. 2019
Chromosome-level assemblies of multiple Arabidopsis thaliana accessions reveal hotspots of genomic rearrangements

August 23rd, 2019
Lin et al. 2019
Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus)

June 14th, 2019
Yang et al. 2017
Contributions of Zea mays subspecies mexicana haplotypes to modern maize

June 7th, 2019
North Star Games – Evolution Board Game
Rules and Gameplay of Evolution

May 17th, 2019
Garrison et al. 2018
Variation graph toolkit improves read mapping by representing genetic variation in the reference

May 3rd, 2019
Wang et al. 2019
Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

April 19th, 2019
Murphy et al. 2017
Kin recognition, multilevel selection and altruism in crop sustainability

April 12th, 2019
Murphy et al. 2019
The genetic architecture of teosinte catalyzed and constrained maize domestication

April 5th, 2019
Stitzer et al. 2019
The Genomic Ecosystem of Transposable Elements in Maize

March 1st, 2019
Elgueta et al. 2019
Genetic and phenotypic diversity in 2000 years old maize (Zea mays L.) samples from the Tarapacá region, Atacama Desert, Chile

February 22nd, 2019
Gaut et al. 2018
Demography and its effects on genomic variation in crop domestication

February 1st, 2019
Kern et al. 2018
The Neutral Theory in Light of Natural Selection
Jensen et al. 2018
The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018

December 7th, 2018
Egan et al. 2018
Capturing genetic variation in crop wild relatives: An evolutionary approach

November 30th, 2018
Tan et al. 2017
Structure and Origin of the White Cap Locus and Its Role in Evolution of Grain Color in Maize

November 16th, 2018
Tanet al. 2017
DNA methylation footprints during soybean domestication and improvement

November 9th, 2018
Ellison et al. 2018
Carotenoid presence is associated with the Or gene in domesticated carrot

November 2nd, 2018
Enard and Petrov 2018
Evidence that RNA viruses drove adaptive introgression between Neanderthals and modern humans

October 26th, 2018
Bellon et al. 2018
Evolutionary and food supply implications of ongoing maize domestication by Mexican campesinos

October 12th, 2018
Slon et al. 2018
The genome of the offspring of a Neanderthal mother and a Denisovan father

October 5th, 2018
Lemmon et al. 2018
Rapid improvement of domestication traits in an orphan crop by genome editing

September 28th, 2018
Kuester et al. 2017
Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory

September 21st, 2018
Stitzer and Ross-Ibarra 2018
Maize domestication and gene interaction

September 14th, 2018
McKain et al. 2018
Ancestry of the two subgenomes of maize

August 31st, 2018
Joly-Lopez and Bureau 2018
Exaptation of transposable element coding sequences

August 24th, 2018
Van Deynzeet al. 2018
Nitrogen fixation in a landrace of maize is supported by mucilage-associated diazotrophic microbiota

May 4th, 2018
FRACTIONATION FRIDAY!!
Woodhouse et al. 2010
Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs
Renny-Byfieldet al. 2017
Gene Fractionation and Function in the Ancient Subgenomes of Maize
Wendel et al. 2018
The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation

April 27th, 2018
Mendoza et al. 2018
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

April 20th, 2018
Dawe et al. 2018
A kinesin-14 motor activates neocentromeres to promote meiotic drive in maize

April 13th, 2018
Kremling et al. 2018
Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

April 6th, 2018
Ghosh et al. 2016
Exposure to sound vibrations leads to transcriptomic, proteomic, and hormonal changes in Arabidopsis

March 30th, 2018
Geiger et al. 2018
A longitudinal study of phenotypic changes in early domestication of house mice
Additionally, please read this press release:
Self-domesticating mice show changes similar to intentionally domesticated animals

March 9, 2018
Corbi et al. 2017
Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions

March 2, 2018
Martín-Robleset al. 2017
Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species

February 23, 2018
Stein et al. 2018
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

February 16th, 2018
Niederhuth et al. 2016
Widespread natural variation of DNA methylation within angiosperms

February 9th, 2018
Petersen et al. 2013
Genetic diversity in the modern horse illustrated from genome-wide SNP data
Schubert et al. 2014
Prehistoric genomes reveal the genetic foundation and cost of horse domestication

February 2nd, 2018
Bay et al. 2018
Genomic signals of selection predict climate-driven population declines in a migratory bird

January 26th, 2018
Willi et al. 2018
Accumulation of mutational load at the edges of a species range

January 19th, 2018
Allard 1999
History of Plant Population Genetics

January 11th, 2018
Hardigan et al. 2017
Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato

December 15th, 2017
Szücs et al. 2017
Rapid adaptive evolution in novel environments acts as an architect of population range expansion

December 8th, 2017
Good et al. 2017
The dynamics of molecular evolution over 60,000 generations

December 1st, 2017
Murray et al. 2017
Natural selection shaped the rise and fall of passenger pigeon genomic diversity

November 18th, 2016
Hirsch et al. 2016
Draft assembly of the elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

November 11th, 2016
Studer et al. 2016
The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

November 4th, 2016
Racimo et al. 2016
Signatures or archaic adaptive introgression in present-day human populations

October 28th, 2016
Gould et al. 2016
Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation

October 21st, 2016
Pozhitkov et al. 2016
Thanatotranscriptome: genes actively expressed after organismal death

July 22nd, 2016
Schraiber and Akey 2015
Methods and models for unravelling human evolutionary history

July 15th, 2016
Bredeson et al. 2016
Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

July 8th, 2016
Funk et al. 2016
Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

July 1st, 2016
Uricchio et al. 2016
Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

June 24th, 2016
Sedghifar et al. 2016
Beyond clines: lineages and haplotype blocks in hybrid zones

June 17th, 2016
Zhang et al. 2016
Teff, an orphan cereal in the Chloridoideae, provides insights into the evolution of storage proteins in grasses

June 10th, 2016
Kono et al. 2016
The role of deleterious substitutions in crop genomes

June 3rd, 2016
Guo et al. 2016
Population genomic evidence for adaptive differentiation in the Baltic Sea herring

May 27th, 2016
Peterson et al. 2016
The scale of local adaptation in Mimulus guttatus: comparing life history races, ecotypes, and populations

May 20th, 2016
Koch et al. 2016
The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

May 13th, 2016
Cardoso-Moreira et al. 2016
Evidence for the fixation of gene duplications by positive selection in Drosophila

May 6th, 2016
Bankoff et al. 2016
Do aye-ayes echolocate? Studying convergent genomic evolution in a primate auditory specialist

April 29th, 2016
Fountain et al. 2016
Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

April 22nd, 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

April 15th, 2016
Bertioli et al. 2016
The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

April 8th, 2016
Llamas et al. 2016
Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

April 1st, 2016
Adhikariet al. 2016
A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

March 25th, 2016
Willing et al. 2015
Genomic expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

March 11th, 2016
Yao et al. 2014
Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments

March 4th, 2016
Besnard et al. 2013
The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant

February 26th, 2016
Schneider et al. 2016
Inbreeding drives maize centromere evolution

February 19th, 2016
Harris and Nielsen 2016
The genetic cost of Neanderthal introgression

February 12th, 2016
Olsen et al. 2016
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

February 5th, 2016
Dopico et al. 2015
Widespread seasonal gene expression reveals annual differences in human immunity and physiology

January 29th, 2016
Henn et al. 2016
Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

January 22nd, 2016
Marsden et al. 2016
Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

July 24th, 2015
Montano et al. 2015
Worldwide population structure, long-term demography, and local adaptation of Helicobacter pylori

July 17th, 2015
Wasser et al. 2015
Genetic assignment of large seizures of elephant ivory reveals Africa’s major poaching hotspots

July 10th, 2015
Zhang et al. 2014
Comparative genomics reveals insights into avian genome evolution and adaptation

June 12th, 2015
Brandvain et al. 2014
Speciation and introgression between Mimulus nasutus and Mimulus guttatus

June 5th, 2015
Kapheim et al. 2015
Genomic signatures of evolutionary transitions from solitary to group living

May 29th, 2015
Racimo et al. 2015
Evidence for archaic adaptive introgression in humans

May 22nd, 2015
Henn et al. 2015
Estimating the mutation load in human genomes

May 15th, 2015
Zhao et al. 2015
Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans</a>

May 8th, 2015
Palkopoulou et al. 2015
Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth

April 3rd, 2015
Bradburd et al. 2015
A spatial framework for understanding population structure and admixture

March 27th, 2015
Simons et al. 2014
The deleterious mutation load is insensitive to recent population history

February 27th, 2015
Neandertal Friday!!
Vernot and Akey 2015
Complex history of admixture between modern humans and Neandertals
Kim and Lohmueller 2015
Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations

February 20th, 2015
Lemmon et al. 2014
The role of cis regulatory evolution in maize domestication

February 13th, 2015
Genetic erosion in maize (a dialog from PNAS)
Dyer et al. 2014
Genetic erosion in maize’s center of origin
Brush et al. 2015
Assessing maize genetic erosion
Dyer et al. 2015
Reply to Brush et al.: Wake-up call for crop conservation science

February 6th, 2015
Zeng et al. 2014
The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

January 30th, 2015
Fontaine et al. 2015
Extensive introgression in a malaria vector species complex revealed by phylogenomics

January 16th, 2015
Berg and Coop 2014
A population genetic signal of polygenic adaptation

December 12th, 2014
Bergland et al. 2014
Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila

December 5th, 2014
Tiffin and Ross-Ibarra 2014
Advances and limits of using population genetics to understand local adaptation

November 3rd, 2014
Frantz et al. 2014
Analyses of Eurasian wild and domestic pig genomes reveals long-term gene-flow during domestication

October 27th, 2014
Pallares et al. 2014
Use of a natural hybrid zone for genome-wide association mapping of craniofacial traits in the house mouse

October 20th, 2014
Campbell et al. 2014
MAKER-P: A tool kit for the rapid creation, management, and quality control of plant genome annotations

October 13th, 2014
Romiguier et al. 2014
Comparative population genomics in animals uncovers the determinants of genetic diversity

October 6th, 2014
Ghaffari et al. 2013
Maize chromosomal knobs are located in gene-dense areas and suppress local recombination

September 29th, 2014
Hirsch et al. 2014
Insights into the effects of long-term artificial selection on seed size in maize

September 22nd, 2014
Brawand et al. 2014
The genomic substrate of adaptive radiation in African cichlid fish

September 15th, 2014
Huang et al. 2014
Genome-wide patterns of genetic variation within and among alternative selective regimes

September 8th, 2014
Carneiro et al. 2014
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

August 25th, 2014
Martin et al. 2014
Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture

August 18th, 2014
Yoder et al. 2013
Phylogenetic signal variation in the genomes of Medicago (Fabaceae)

August 4th, 2014
Hughes et al. 2014
The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

July 28th, 2014
Fang et al. 2014
Two genomic regions contribute disproportionately to geographic differentiation in wild barley

July 21st, 2014
Arnegard et al. 2014
Genetics of ecological divergence during speciation

July 14th, 2014
Schmutz et al. 2014
A reference genome for common bean and genome-wide analysis of dual domestications

July 7th, 2014
Poelstra et al. 2014
The genomic landscape underlying phenotypic plasticity in the face of gene flow in crows

June 30th, 2014
Schiffels & Durbin 2014
Inferring human population size and separation history from multiple genome sequences

June 23rd, 2014
Sekhon et al. 2014
Phenotypic and transcriptional analysis of divergently selected maize populations reveals the role of developmental timing in seed size determination

June 16th, 2014
Enard et al. 2014
Genome-wide signals of positive selection in human evolution

June 9th, 2014
Ellstrand 2014
Is gene flow the most important evolutionary force in plants?

June 2nd, 2014
Soria-Carrascoet al. 2014
Stick insect genomes reveal natural selection’s role in parallel speciation

May 19th, 2014
Do et al. 2014
No evidence that natural selection has been less effective at removing deleterious mutations in Europeans than in West Africans

May 12th, 2014
Sheehan et al. 2013
Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach

May 5th, 2014
Yoder et al. 2014
Genomic signature of adaptation to climate in Medicago truncatula

April 28th, 2014
Foll et al. 2014
Hierarchical Bayesian model of population structure reveals convergent adaptation to high altitude in human populations

April 21st, 2014
Decker et al. 2014
Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

April 14th, 2014
Wagner et al. 2014
Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

April 7th, 2014
Hirsch et al. 2014
Insights into the maize pan-genome and pan-transcriptome

March 31st, 2014
Gassmann et al. 2014
Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize

March 24th, 2014
Hellenthal et al. 2014
A genetic atlas of human admixture history

March 10th, 2014
Bhattacharya et al. 2013
Genome analysis of Elysia chlorotica egg DNA provides no evidence for horizontal gene transfer into the germ line of this kleptoplastic mollusk
For Background:
Rumpho et al. 2008
Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

March 3rd, 2014
Special Double Feature
Prüfer et al. 2014
The complete genome sequence of a Neanderthal from the Atlai Mountains
Sankararaman et al. 2014
The genomic landscape of Neanderthal ancestry in present-day humans

February 24th, 2014
Li and Durbin 2011
Inference of human population history through individual whole-genome sequences

February 17th, 2014
Freedman et al. 2014
Genome Sequencing Highlights the Dynamic Early History of Dogs

February 10th, 2014
Korneliussen et al. 2013
Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

January 27th, 2014
Tobler et al. 2014
Massive habitat-specific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments

January 20th, 2014
Murat et al. 2013
Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes

December 16th, 2013
Pickrell and Pritchard 2012
Inference of population splits and mixtures from genome-wide allele frequency data

December 9th, 2013
Qi et al. 2013
A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

December 2nd, 2013
Special Series on Macroevolution

November 18th, 2013
Special Series on Macroevolution

November 11th, 2013
Special Series on Macroevolution

November 4th, 2013
Bradic et al. 2013
The population genomics of repeated evolution in the blind cavefish Astyanax mexicanus

October 28th, 2013
Eckert et al. 2013
The evolutionary genetics of the genes underlying phenotypic associations for Loblolly Pine (Pinus taeda, Pinaceae)

October 21st, 2013
Wang et al. 2013
Function and evolution of DNA methylation in Nasonia vitripennis

October 14th, 2013
Parker et al. 2013
Genome-wide signatures of convergent evolution in echolocating mammals

October 7th, 2013
Long et al. 2014
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden