Quercus tree rings

<p>photos from</p> <p> </p> <p>May, M.R., M. Provance, A. Sanders, N. Ellstrand, and J. Ross-Ibarra. 2009. A Pleistocene clone of Palmer's Oak persisting in Southern California. PLoS ONE 4: e8346</p

Review Template

<p>review template</p> <p> </p

Popgen Stats from Hufford et al. 2012 Nat. Gen.

<p>Summary statistics for 10kb windows genome-wide and for genes in the maize v2 filtered gene set.  Data are from Hufford et al. 2012:</p> <p>http://www.nature.com/ng/journal/v44/n7/full/ng.2309.html</p> <p>See details in the paper for criteria for calling SNPs, data used for statistics, etc.</p> <p> </p> <p>Columns are: </p> <p>locus: GRM name of gene in the filtered gene set</p> <p>S: number of Segregating sites</p> <p>ThetaW: Watterson's estimate of theta (per locus)</p> <p>ThetaPi: nucleotide diversity (per locus)</p> <p>ThetaH: Fay and Wu (2000) estimator (per locus)</p> <p>TajD: Tajima's D</p> <p>seqbp: # of bp sequenced. this should be used as the denominator to calculate per bp. values of the above statistics.</p

RNAseq_dolores

<p>RNAseq analysis of teosinte in late Holocene conditions</p

GTF and GFF for maize

<p>GFF and GTF files for maize versions 2 and 3</p

Recombination rho in maize

<p>Files are estimates of rho using Hudson's maxhap for teosinte, landraces, and maize from Hufford et al. Nat. Gen. 2012 (though these data were not published with the paper). The files are a bit redundant, but each line looks like:</p> <p>1 100 141 100 14 0.000098</p> <p>Which is chromosome, window, and number of SNPs repeated twice, followed by the MLE of rho. So the line above would be the 100th 10kb window on chromosome 1 (on reference genome AGPv1), with a rho=0.000098. I would be hesitant to trust the values with low S (definitely <10 and probably <20 <30), as those probably reflect noise more than anything else.</p

Data from van Heerwaarden et al. 2012

<p>SNP data from</p> <p> </p> <p>van Heerwaarden, J., M.B. Hufford, J. Ross-Ibarra. 2012. Historical genomics of North American maize. PNAS 109: 12420-12425</p

Genotype data from highland and lowland maize

GBS and 55K SNP data from 94 maize lines from highland and lowland Mexico. Included are passport data for the samples as well

Gerke et al. Iowa RRS

<p>Data from Gerke et al. http://arxiv.org/abs/1307.7313</p

"Domestication, demography, and deleterious alleles in maize." Talk at 2016 SMBE domestication symposium.

<div> <div> <div> <p>Diversity across plant and animal genomes is patterned by the combined effects of drift and natural selection. To better understand the role of these processes in domesticated organisms, we investigated diversity across the genomes of domesticated maize and its wild relative teosinte. We first show that there is little evidence of selection on beneficial amino acid substitutions, and that the domestication bottleneck led to a decline in the efficiency of purifying selection in maize. We then show that rapid expansion post-domestication dramatically changed this relationship, with stronger purifying selection in maize, reflecting the much larger effective size of present day populations. Finally, we resequenced a number of genomes of landrace maize to show the impacts of colonization and demography on the distribution of deleterious alleles in the maize genome. </p> </div> </div> </div