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This Week in Genome Research: Aug 16, 2017

A team from Italy, the UK, the US, and Switzerland consider sex-biased gene expression evolution in Anopheles mosquito species capable of transmitting malaria-causing parasites. The researchers did RNA sequencing on several tissues from four Anopheles species, focusing on features for genes with enhanced expression in female mosquitos, which feed on blood and may transmit parasites in the process. Based on gene expression and sequence data for An. gambiae, An. arabiensis, An. minimus, and An. albimanus mosquitos assessed by DESeq2, the authors saw a dearth of male-biased genes on mosquito X chromosomes and note that "in contrast to what has been found in many other organisms, female-biased genes are more rapidly evolving in sequence, expression, and genic turnover than male-biased genes."

Max Planck Institute for Evolutionary Anthropology investigators describe a computational method known as Extended Lineage Sorting (ELS) that's designed to pick up on the presence of ancient selective sweeps in the human genome relative to Neanderthals and Denisovans. After applying the approach to simulated data, the team used ELS to search for signs of ancient positive selection with 1000 Genomes Project data for 185 African individuals, who are less likely to carry confounding Neanderthal sequences than individuals from populations outside of Africa. The search led to 81 candidate regions, including apparent selection sweeps affecting regulatory sequences.

Researchers from Aarhus University provide a look at 100 Danish major histocompatibility complex haplotypes using data for 25 of the parent-child trios from the Danish Pan-Genome project. Using a pipeline that started with de novo sequencing and assembly, the team carved out four parental MHC haplotypes per trio, uncovering structural variants and more than 700,000 bases of new sequence. For their subsequent analyses, the authors used the most fully phased MHC haplotypes to explore population genetics, linked selection, recombination, and other features in the immune response-related region.