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This Week in Nature: Dec 14, 2017

In this week's Nature Ecology & Evolution, a team led by scientists from the University of Melbourne report the sequenced genome of the Tasmanian tiger Thylacinus cynocephalus, an Australian marsupial predator that was found throughout the continent until about 3,000 years ago. Using DNA extracted from a 108-year-old, alcohol-preserved thylacine specimen, the researchers identified a steep decline in the animal's genetic diversity somewhere between 70,000 years and 120,000 years ago — before humans colonized Australia and overlapping with climate changes associated with the penultimate glacial cycle. The investigators also found significant phenotypic convergence between thylacines and canids, although comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. At the same time, genes and pathways targeted by positive selection differ markedly between the two species, all of which supports models of adaptive convergence driven primarily by cis-regulatory evolution, they write. GenomeWeb has more on this here.

And in Nature Biotechnology, investigators from Icahn School of Medicine at Mount Sinai, describe a new binning method for shotgun metagenomics analyses that overcomes the inability of existing computational binning methods to fully distinguish closely related species and strains. The method incorporates bacterial DNA methylation signatures detected using single-molecule real-time sequencing, and uses these signatures to resolve individual reads and assembled contigs into species- and strain-level bins. The researchers state that their approach can also be used to link plasmids and other mobile genetic elements to their host species in a real microbiome sample. "Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning," they write.