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This Week in PNAS: Aug 14, 2018

In the early, online edition of the Proceedings of the National Academy of Sciences, a Pennsylvania State University-led team takes a look at the history and genetic diversity of the scarlet macaw, Ara macao cyanoptera, with samples from the southern US and northern Mexico that stretched back 800 years to more than 1,100 years. The researchers sequenced complete or nearly complete mitochondrial genome sequences from 14 of these ancient scarlet macaw samples collected at five sites in New Mexico. By analyzing the haplogroup genetic diversity in the samples and considering their phylogenetic relationships with macaws sampled more recently, the authors found evidence for a managed breeding colony in the area. "Our results suggest that people at an undiscovered Pre-Hispanic settlement dating between 900 and 1200 CE managed a macaw breeding colony outside their endemic range and distributed these symbolically important birds through the [southwestern US]," they write.

Researchers from the Fred Hutchinson Cancer Research Center, the University of Washington, and the Scripps Research Institute explore a mutational scanning-based approach for predicting human flu virus evolution. Using a high-throughput, deep sequencing experimental approach, the team looked at the relationship between mutant viral libraries and cell growth, systematically measuring the growth consequences of individual amino acid changes in hemagglutinin protein from a human H3N2 influenza strain. The results indicate that growth-enriching mutations do coincide with those boosting flu fitness, the authors report. Based on these and other experiments, they write, "experimental measurements of mutational effects can be leveraged to help understand the evolutionary fates of viral lineages in nature — but only when the measurements are made on a viral strain similar to the ones being studied in nature."

A University of California, Los Angeles, and UC-Davis team profiles hypomethylated regions in the genomes of developing Arabidopsis and soybean seeds using bisulfite sequencing and other approaches. After following bulk methylation across seed development in these plants, the researchers brought in chromatin immunoprecipitation sequencing-based histone modification and other data to investigate the "DNA methylation valleys" they detected. From the patterns they uncovered, the authors suggest that hypomethylated sites in the plant seeds "are enriched in transcription factor genes and are decorated with histone marks that fluctuate developmentally, resembling their animal counterparts in significant ways."