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This Week in Genome Research: Nov 11, 2015

A team from the US and Brazil put together a feline phylogenetic tree pointing to historical hybridizations between different cat species. The researchers did array-based genotyping profiles and mitochondrial genome sequencing on representatives from across the cat family. Through a phylogenetic analysis focused on the maternal and paternal histories within eight main cat lineages, the study's authors saw signs of mixing between species that had seemingly split from one another. "Our observations of historical admixture between many pairs of cat species are consistent with evidence for contemporary inter-specific hybridization and captivity spanning large phylogenetic distances," they write. "Ongoing whole genome sequencing efforts … should provide much greater resolution and insight into the genomic landscape of admixture."

While comparing the nature and frequency of mutations in two genotypes of the water flea, Daphnia pulex, researchers from the US, Germany, and the UK uncovered an uptick in large copy number changes in the organism. As they report in Genome Research, the team saw base substitution rates on par with those found in other multicellular eukaryotes when it did deep sequencing on D. pulex genotypes known for either obligate asexuality or cyclical parthogenesis. On the other hand, the mutation accumulation experiments revealed frequent de novo duplications and deletions. These large copy number variants appeared to be less common in natural D. pulex populations, authors say, apparently due to purifying selection effects.

Finally, Chinese researchers introduce an allele frequency-based computational approach for assessing differences in natural selection between human populations — an approach that's expected to help in finding variants involved in adaptation. When the team tested this probabilistic modeling approach using data from Han Chinese and Tibetan populations, for example, it saw distinct selection effects on the altitude-related genes EPAS1 and EGLN1, along with apparent selection differences affecting genes behind melanin pigmentation.