A ‘Chimp’ Off The Old Block

Ultra-deep whole genome sequencing has helped scientists to estimate the inter-generational mutation rate for chimpanzees.

AsianScientist (Nov. 15, 2017) – In a study published in Scientific Reports, scientists in Japan have used deep sequencing to estimate the mutation rate from one generation to the next in chimpanzees.

Mutations generate genetic variation and are a major driving force of evolution. Therefore, examining mutation rates and modes are essential to better understand the genetic basis for physiology and evolution.

One traditional method to estimate this rate is a ‘phylogenetic’ approach that examines the sequence divergence between two species and the time between divergence events. However, this method entails many uncertainties, such as the extent of ancestral polymorphisms, effective population size and generation time.

In this study, a team of researchers, including Professor Tetsuro Matsuzawa of the Kyoto University Institute for Advanced Study (KUIAS) and Associate Professor Yasuhiro Go of Japan’s National Institutes of Natural Sciences (NINS), conducted a study utilizing high-quality whole genome sequencing of a chimpanzee parent-offspring trio to determine the precise mutation rates and modes by which mutations transmit from parents to offspring.

In this study, 574, 463, and 468 gigabases of DNA were analyzed from three chimpanzees—Akira, Ai, and Ayumu (father, mother, son)—that have participated in a wide variety of comparative cognitive research. The scientists were able to decipher precise mutation trajectories occurring within one generation.

When analyzed, the rate of germline, newly-formed mutations was calculated to be 1.48 new mutations for every 100 million bases, higher than that for humans, which has been reported as 0.96 to 1.2 new mutations.

A strong, male-biased mutation spectrum was also measured, wherein three-quarters of mutations occurred in sperm during spermatogenesis. Structural alterations, such as changes in gene conversion and copy number, were also observed in male sperm DNA. This is particularly important as the precise rates and modes of new structural alterations are still poorly understood, even in humans.

The team anticipates that the experimental and methodological framework developed in this study will be useful for further inquiry into the complex nature of genomic changes.

The article can be found at: Tatsumoto et al. (2017) Direct Estimation of de novo Mutation Rates in a Chimpanzee Parent-offspring Trio by Ultra-deep Whole Genome Sequencing.


Source: Kyoto University; Photo: Pexels.
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