UA-111121320-1 C.A.M.P. | The Hufford Lab @ ISU

C.A.M.P. is a journal club in which 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 journal articles that attract our fancy. No tents or flashlights required.

Papers by date they are discussed:

***Please be aware of dates as papers will periodically be posted several weeks in advance!!***

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

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 sub genomes of maize

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

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

May 4th, 2018:
Woodhouse et al. 2010
Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs


Renny-Byfield et al. 2017
Gene fractionation and function in the ancient subgenomes of maize

AND (to place these papers in context):

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**

March 16th & 23rd, 2018:
Spring Break and the Maize Meeting! 🌽🇫🇷

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-Robles et 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:
🐎🐎🐎 Horses, Horses, Horses 🐴🐴🐴
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 22nd & 29th, 2017:

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 24th, 2017:

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:
Adhikari et 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

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)
***Special Triple Feature***
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 23rd, 2015: NO CAMP! Mexico Phenotyping Trip

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

December 19th and 26th, 2014: NO CAMP! Christmas Break

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

September 1st, 2014:

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 11th, 2014:
Pollination Hiatus!!

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-Carrasco et al. 2014
Stick insect genomes reveal natural selection’s role in parallel speciation

May 26th, 2014: No C.A.M.P. Have a great Memorial Day!!

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*

*this is a preprint posted on the arXiv repository

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*

*this is a preprint posted on the arXiv repository

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 17th, 2014: NO C.A.M.P., Matt in China

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
and for background:
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**
et al. 2014
The complete genome sequence of a Neanderthal from the Atlai Mountains
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

February 3rd, 2014: NO C.A.M.P., Matt at University of Minnesota

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…contact Matt for papers!

November 25th, 2013:
No C.A.M.P. this week…Happy Thanksgiving!

November 18th, 2013:
Special Series on Macroevolution…contact Matt for papers!

November 11th, 2013:
Special Series on Macroevolution…contact Matt for papers!

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:

et al. 2013
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden