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This Week in PNAS: Aug 13, 2013

A three-part model that's been proposed for Native American migration into North America does not appear to account for the mitochondrial diversity present in existing populations, according to a study in the early, online edition of the Proceedings of the National Academy of Sciences. Using new and available mitochondrial data, an international team led by investigators at the University of Pavia in Italy considered patterns present in two Native American mitochondrial haplogroups already known for their puzzling geographic distributions. Based on the sub-clades they identified and their phylogenetic analysis, the study's authors argue that "the first American founders left the greatest genetic mark but the original maternal makeup of North American Natives was subsequently re-shaped by additional streams of gene flow and local population dynamics, making a three-wave view too simplistic."

Researchers from the Chinese Academy of Agricultural Sciences, BGI-Shenzhen, and other centers in China report on findings from a re-sequencing study of recombinant inbred rice lines developed from a so-called "superhybrid" rice variety from China called Liang-You-Pei-Jiu. Using sequence data for 132 such lines, as well as sequence data for the parental strains originally used to create the superhybrid, the investigators managed to improve the existing parental genome assemblies. They also put together a linkage map that helped them track down dozens of quantitative trait loci with apparent ties to rice production and yield, including two QTLs that were characterized in detail.

Finally, a University College London team tries to understand the role of age-associated DNA methylation shifts using a systems biology-based approach. By considering this epigenetic drift at various genes with an eye to protein interaction networks, the researchers found that genes coding for proteins at the edges of such networks are more prone to age-related changes to their DNA methylation status than those coding for components at protein network centers. "[O]ur results demonstrate that [genes with age-associated methylation changes in their promoters] occupy preferentially peripheral network positions," the study's authors note, "yet form extensive sub-networks when combined with other age-related gene classes."