In the early, online version of the Proceedings of the National Academy of Sciences, a team from Switzerland and the US present a genome-scale analysis of gene deletion effects on metabolic networks in 55 bacteria from nine species, including 46 Escherichia coli strains and two strains of Shigella. Based on their multi-gene deletion experiments, gene cluster mapping, synthetic lethal profiles, minimal metabolic genome analyses, horizontal gene transfer patterns, and more, the authors suggest "the ordering of metabolic genes in bacterial genomes provides phenotypic robustness against deleterious effects of large-scale gene deletions."
Researchers from the University of California, Merced, and the University of Rhode Island consider genetic responses to sea star wasting disease in Pisaster ochraceus, a sea star species that has experienced mass mortality since 2013. Using restriction site-associated DNA sequencing, the team profiled 374 representatives from 16 sea star populations off the north central California coast before and after a wasting disease outbreak. Over a few years, from 2012 to 2015, P. ochraceus populations had a median 81 percent mortality, the authors report, leading to dramatic allele frequency shifts at several sea star loci in remaining sea stars and new population recruits. "These results indicate a long-term species-wide change in allele frequencies will persist through future generations," they write, noting that such population genomic profiling "will be essential for documenting rapid genetic shifts in response to chronic and extreme events."
A team from the University of Massachusetts, University of Rhode Island, and Boston College explore genetic and developmental adaptations contributing to craniofacial diversity in cichlid fish, focusing on a Labeotropheus genus lineage with an exaggerated snout that are found in Lake Malawi. Along with immunohistochemistry, histology, and PCR-based expression experiments to understand the tissue and pathway tweaks that make this phenotype possible in the fish, the researchers used new and available quantitative trait locus mapping to highlight Tgf-beta pathway contributions to the facial features. "Given the functions of Tgf-beta signaling in tissue proliferation, migration, invasion, and organ fibrosis," they say, "this represents an example of the cooption of existing pathways in the evolution of novelty."