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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

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.