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This Week in Genome Research: May 13, 2009

In an early online article, scientists led by CSHL's Rob Martienssen have resequenced the fission yeast genome following mutagenesis to "readily identify a novel mutant involved in heterochromatic silencing." Candidate mutant genes were put back into a wild-type strain to reproduce the mutant phenotype, which allowed them to find an allele thatencodes an E2 ubiquitin ligase as being responsible for the swi*603 mutant phenotype.

Genome Research is commemorating Darwin's 200th birthday and 150 years since the initial publication of On the Origin of the Species in its May issue, with a slew of articles and papers on natural selection, population genomics, and genetic variation. In a perspective piece, University of Washington's Joshua Akey talks about constructing genomic maps of positive selection in humans. He looks at the recent history of human population genomics, assesses genome-wide scans for positive selection in humans, identifies gaps in knowledge, and discusses strategies for going from low-res maps to "a detailed molecular, mechanistic, phenotypic, and population genetics characterization of adaptive alleles," he writes.

Another perspective wonders about the genetic architecture of quantitative traits, comparing mice, flies, and humans. The authors show that the current model of large numbers of loci with small effects is true for all species they looked at, and that differences are mostly due to effects of experimental design.

Cornell's Carlos Bustamante led work that analyzed patterns of variation across 443,434 SNPs from 3,845 individuals from four continental regions, creating a "unique resource" for studying diversity in neglected populations at the genome-wide scale, including Latin Americans, South Asians, and Southern Europeans. "Key insights afforded by our analysis include quantifying the degree of admixture in a large collection of individuals from Guadalajara, Mexico; identifying language and geography as key determinants of population structure within India; and elucidating a north–south gradient in haplotype diversity within Europe."

In collaborative work with Andrew Clark, Bustamante and others have used sequence data from 13,400 protein-coding genes from 20 European-Americans and 19 African-Americans to create a model of human demography that incorporates divergence, migration, admixture, and changes in population size. The model is the first genome-wide analysis of allele frequency distributions in humans based on directly sequenced data and among other things, shows that miRNA-controlled genes evolved under high constraints and are more likely to experience negative selection than other genes.

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.