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This Week in Nature: Dec 29, 2016

In this week's Nature, a team of British scientists publishes a genomic analysis of European ash trees (Fraxinus excelsior), providing clues as to why the British variant of these trees may be less susceptible to a fungal disease — called ash dieback — currently affecting much of the species. The team sequenced the genomes of one British ash tree and 37 others from throughout Europe, then compared the findings to the DNA sequences of 10 other plant species. They found that about a quarter of the ash's roughly 39,000 protein-coding genes are unique to the species, and among many of these genes were variants associated with disease resistance. Notably, a review of the different variants suggests that British ash trees may generally be more resistant than trees from other locations. GenomeWeb has more on this here.

And in Nature Genetics, a University of California, Berkeley-led group reports on a new statistical tool for inferring population history from unphased genomes. Called SMC++, the tool can analyze orders of magnitude more samples than existing inference methods, inferring population size histories and split times in diverged populations. It also features a novel spline regularization scheme that greatly reduces estimation error. To demonstrate SMC++, the researchers used it to analyze sequence data from more a thousand human genomes from people in Africa and Eurasia, hundreds of genomes from a Drosophila melanogaster population in Africa, and tens of genomes from zebra finch and long-tailed finch populations in Australia.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.