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This Week in PLoS: Nov 11, 2008

A group of researchers assayed autosomal, mitochondrial, and Y-chromosome markers from 357 African and Asian lions and also assessed them for the lion version of the feline immunodeficiency virus. From their dataset, the authors determined the lion's recent evolutionary history. The Serengeti lions, they report, are three distinct populations with only recent admixture. Greg Laden breaks down the paper on his blog.

Also in PLoS Genetics, researchers report on a high-resolution copy number variation map they made of the human olfactory receptor gene superfamily. From their map, they found that a quarter of olfactory genes are affected by CNVs and that 15 olfactory receptor gene loci have human-specific deletions.

In PLoS One, Bruce Roe and his colleagues characterize microbiota of two 1,300-year-old human fecal samples from a cave in Mexico. After generating 45,000 shotgun DNA sequencing reads and analyzing them, the authors say the phylotyping and functional analysis shows that the ancient microbiota are consistent with what's in the modern human gut but also that the ancient samples are more similar to each other than with modern human microbiota.

Another paper reports the construction of a 50K SNP genotyping array for assaying cardiovascular, inflammatory, and metabolic candidate gene and pathway SNPs. The authors say the array uses cosmopolitan tagging to include the genetic diversity found in the HapMap and SeattleSNPs projects and that the array content is informed by genome-wide association studies and expression quantitative trait loci studies.

In PLoS Computational Biology, researchers led by Martin Reese report on a genome-wide analysis of human disease alleles. They identified disease-causing variants in the OMIM and the Human Genome Mutation Database and, using them, identified variants that would affect homologous positions in paralogous human proteins. "Knowledge of a sequence variant's paralogous relationships is useful for purposes of in-silico identification of novel disease-causing alleles," the authors write.


The Scan

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.

Could Cost Billions

NBC News reports that the new Alzheimer's disease drug from Biogen could cost Medicare in the US billions of dollars.

Not Quite Sent

The Biden Administration likely won't meet its goal of sending 80 million SARS-CoV-2 vaccine doses abroad by the end of the month, according to the Washington Post.