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This Week in Nature: Jan 18, 2018

In this week's Nature Ecology & Evolution, a team of US and European researchers reports the recovery of Salmonella enterica genomes from individuals who died in 16th century Mexico during a devastating epidemic of disputed origin. The findings represent the earliest known occurrence of salmonella infection in the Americas. Using a new metagenomic analysis tool called Megan Alignment Tool — or MALT — the scientists were able to identify Salmonella DNA in the teeth of the 10 individuals buried in an epidemic cemetery in Southern Mexico around the time Europeans first made contact. The findings suggest the epidemic was caused by typhoid, which is caused by S. enterica and likely introduced by Europeans, and highlights the utility of MALT in identifying pathogenic agents involved in ancient and modern disease. GenomeWeb has more on this, here.

And in Nature Genetics, Decode Genetics investigators report the genomic reconstruction of Hans Jonatan, who was born in the Caribbean in 1784 to an enslaved African mother and European father, and who later migrated to Iceland. The team genotyped 182 of his 788 descendants using SNP chips and sequenced the whole genomes of 20 of them. Using the resulting data to reconstruct 38 percent of Jonatan's maternal genome, the scientists were able to determine that his mother was from a region spanning Benin, Nigeria, and Cameroon. GenomeWeb also covers this study, here.

Also in Nature Genetics, a group of Chinese researchers publishes a genomic analysis of rice, offering insights into the extent of genomic variation between cultivated and wild versions of the plant. The scientists constructed a pan-genome dataset of Oryza sativa and Oryza rufipogon species using deep sequencing and de novo assembly of 66 divergent accessions, and identified 23 million sequence variants in the rice genome. "This catalog of sequence variations includes many known quantitative trait nucleotides and will be helpful in pinpointing new causal variants that underlie complex traits," the study authors write. The resource is also expected to help future evolutionary and functional studies in rice.

The Scan

Science Confidence Boost

The New York Times reports that a new poll finds trust in science and scientists has increased with the COVID-19 pandemic.

Appeal and Funds

Some grant applications denied funding due to an Australian Research Council rule change have now been funded following an appeal, the Guardian reports.

Surveillance for Variants

Vox writes that the detection of the Omicron SARS-CoV-2 variant highlights the need for improved viral genomic surveillance.

Nature Papers Examine Taxonomic Gaps in Plant Sequencing, SARS-CoV-2-Human Interactome

In Nature this week: plant genome sequencing dominated by affluent countries, and more.