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This Week in Nature: Nov 7, 2013

In this week's Nature, researchers from Harvard University and Cornell University report on a method to study epistasis, the non-additive interactions between alleles that has been suggested to be involved in shaping population fitness. Noting that epistasis for fitness should also have a "genomic footprint," the researchers developed an approach to capture this signal based on detecting genotype ratio distortion as a sign of epistasis. They applied it to a large panel of Drosophila recombinant inbred lines and experimentally confirmed that instances of genotype ratio distortion represent loci with epistatic fitness effects. The findings indicate that the "raw material to drive reproductive isolation is segregating contemporaneously within species and does not necessarily require … the emergence of incompatible mutations independently derived and fixed in allopatry," the researchers write.

Meanwhile, in Nature Biotechnology, a team from the University of California, San Diego, and the Ludwig Institute for Cancer Research publish details on a new approach for whole-genome haplotype reconstruction called HaploSeq. Using proximity ligation and sequencing, the investigators showed that alleles on homologous chromosomes occupy distinct territories, and they were able to preferentially recover physically linked DNA variants on a homolog. Computational analysis of such datasets allows for accurate reconstruction of chromosome-spanning haplotypes for around 95 percent of alleles in hybrid mouse cells with 30x sequencing coverage, the researchers say. To resolve haplotypes for a human genome, they combined HaploSeq with local conditional phasing to obtain haplotypes for about 81 percent of alleles with approximately 98 percent accuracy from just 17x sequencing.