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This Week in PNAS: Oct 23, 2012

A research team from New Zealand, South Africa, and the US has sequenced the mitochondrial genomes of four Polynesian individuals believed to be among the first people to settle in New Zealand an estimated 750 years ago. As they report in the early, online edition of the Proceedings of the National Academy of Sciences, the researchers used DNA from ancient remains found at a site called Wairau Bar on the northeastern coast of New Zealand's south island. The four mitochondrial genomes contained two of the three variants previously linked to Maori populations, the researchers report. But they also found diversity within the mtDNA, which fell into three different haplotypes. "These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers," University of Otago researcher Elizabeth Matisoo-Smith, the study's senior author, and her colleagues write, "and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia."

UK researchers used a combination of hybridization enrichment and high-throughput sequencing to genotype a historical strain of Mycobacterium tuberculosis in another early, online PNAS study. The team focused on a tuberculosis-infected skeletal sample excavated in 2009 from a 19th century burial site in Leeds called St. George's crypt. After nabbing particularly polymorphic bits of M. tuberculosis DNA by hybridization capture, the investigators sequenced these parts of the bug's genome with the SOLiD 5500. The approach yielded information at two M. tuberculosis repeat sequences, along with eight of the 11 small insertion/deletions and 218 of the 247 SNPs that they targeted. Using this data, the investigators determined that the ancient Yorkshire strain from the St. George's crypt site clustered genetically in an M. tuberculosis group that is currently quite rare, but which appears to have been present in North America just after the turn of the 20th century.

Finally, a University of Washington team describes the transcriptome analyses they used to explore the basis of anxious temperament in a non-human primate model. The group did behavioral and brain metabolite testing on two-dozen young rhesus macaque monkeys at multiple time points. Over time, they report, animals that were consistently prone to anxious temperament-like traits tended to have higher-than-usual metabolism in the central amygdala part of the brain. And when they did transcriptome profiling on post-mortem brain samples from that brain region using Affymetrix rhesus monkey microarrays, investigators detected gene expression patterns consistent with those metabolic shifts, including a dip in the expression of a gene called NTRK3 whose levels are inversely correlated with metabolism in the central amygdala. "Although there are likely many mediators of [anxious temperament], these gene expression data are consistent with a maladaptive neurodevelopment hypothesis as a basis for [anxious temperament]," the study's authors say.

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.