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This Week in Genome Research: Mar 2, 2016

A Louisiana State University-led team describes a new repeat family found in the genome of the common marmoset, Callithrix jacchus. Using a multiple alignment of sequences from common marmoset alongside human, chimp, orangutan, rhesus macaque, and squirrel monkey sequences, the researchers narrowed in on a common marmoset-specific chromosome 3 sequence with murky origins. After a series of follow-up analyses, they concluded that the sequence stemmed from a novel short interspersed element repeat family dubbed Platy-1, which includes more than 2,200 full-length elements in the common marmoset genome.

Using data generated for the Genome of the Netherlands project, an international team led by investigators at the Max Planck Institute for Evolutionary Anthropology tracked intra-individual variation in mitochondrial DNA, known as mtDNA heteroplasmy across hundreds of parent-child trios and within 18 quartets involving parents and their identical and non-identical twin children. In the process, the researchers tracked down 189 examples of mtDNA heteroplasmy in mothers from the trios, with more than half of those heteroplasmies being passed on to their children. Meanwhile, they estimated that some 70 percent of the 159 mitochondrial heteroplasmies found in children were inherited from their mothers. Even so, new heteroplasmies do not seem to appear willy-nilly, authors say. Instead, their results point to negative mtDNA heteroplasmy selection to deter deleterious transmission events.

Finally, researchers from the UK and elsewhere discuss findings from an effort to retrace the rise of the male-specific Y chromosome region in great apes. The researchers captured and sequenced 19 new great ape MSY regions, combining these data with existing sequences from dozens of chimps, bonobos, gorillas, or orangutans. After uncovering new MSY variants in the great apes, they put together phylogenies that put the most recent common ancestor of the western chimp MSY at fewer than 16,000 years and the central chimp MSY common ancestor at one million years ago or more. "Cross-species comparison within a single MSY phylogeny … reveals species-specific branch length variation that may reflect differences in long-term generation times," the authors say.