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This Week in Genome Research: Jan 6, 2016

Researchers from the UK, Netherlands, and Germany describe efforts to establish a database for doing prospective surveillance of methicillin-resistant Staphylococcus aureus (MRSA) in the UK and Ireland. The team did genome sequencing on 1,013 MRSA isolates, which had been collected in England, Ireland, Northern Ireland, Wales, and Scotland between 2001 and 2010 and submitted to the British Society for Antimicrobial Chemotherapy. Phylogenetic analyses based on SNPs in these genomes indicated that more than three-quarters of the isolates fell in a multilocus sequence typing clonal complex called CC22. The collection also offered clues to the origins of — and antibiotic resistance profiles for — isolates involved in past MRSA outbreaks in the UK.

The University of California, Los Angeles' Robert Wayne led an international team that looked at gray wolf genetic variation, admixture, and relationships to domestic dogs using cues from 34 canine genomes. As they report in Genome Research, the researchers brought together data for two dozen wolf genomes, the dog reference genome, six resequenced dog genomes, and genome data for three outgroup animals such as the Israeli golden jackal. From these data, they uncovered clusters of genetically similar canines from various parts of the world and put together a phylogenetic tree that pointed to Old World wolf origins for the domestic dog. Moreover, the study's authors note, the work indicated that "[d]ogs have influence the recent history of wolves through admixture and vice versa, potentially enhancing adaptation."

Investigators in the US and Qatar present genetic evidence pointing to an early split between the ancestors of indigenous Arab populations and the ancestors of other non-African populations. By sequencing and comparing the genomes of 56 indigenous Arab individuals and four dozen other individuals from the Arabian Peninsula, the team saw hints of divergence for indigenous Arab ancestors that occurred prior to the majority of mixing events between modern humans and Neanderthals in Eurasia. In addition, the authors' comparisons with 1000 Genomes Project data supported the notion that the group clusters near the base of the family tree for non-African populations, suggesting indigenous Arabs are "direct descendants of the first Eurasian populations established by the out of Africa migrations."

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.