Category Archives: Evolution
The dN/dS ratio is a popular statistic in evolutionary genetics that quantifies the relative rates of protein-altering and non-protein-altering mutations. The rate is adjusted so that under neutral evolution - i.e. when the survival and reproductive advantage of all variants is the same - it equals 1. Typically, dN/dS is observed to be less than 1 meaning that new mutations tend to be disfavoured, implying they are harmful to survival or reproduction. Occasionally, dN/dS is observed to be greater than 1 meaning that new mutations are favoured, implying they provide some survival or reproductive advantage. The aim of estimating dN/dS is usually to identify mutations that provide an advantage.
Theoreticians are often critical of dN/dS because it is more of a descriptive statistic than a process-driven model of evolution. This overlooks the problem that currently available models make simplifying assumptions such as minimal interference between adjacent mutations within genes. These assumptions are not obviously appropriate in many species, including infectious micro-organisms, that exchange genetic material infrequently.
There are many methods for measuring dN/dS. This new paper overcomes two common problems:
- It is fast no matter how many genomes are analysed together.
- It is robust whether there is frequent genetic exchange (which causes phylogenetic methods to report spurious signals of advantageous mutation) or infrequent genetic exchange.
Software that implements genomegaMap is available on Docker Hub and the source code and documentation are available on Git Hub.
With the steady rise of more and more genome sequences, the analysis of data becomes an increasing challenge even with modern computers, so it is hoped that this new method provides a useful way to exploit the opportunities in such large datasets to gain new insights into evolution.
This Tree of Life diagram is based primarily on the evolutionary relationships so wonderfully related in Dr. Richard Dawkins’ The Ancestor’s Tale, and timetree.org. The smallest branches are purely illustrative. They are intended to suggest the effect of mass extinctions on diversity, and changes in diversity through time. This diagram is NOT intended to be a scholarly reference tool! It is intended to be an easy-to-understand illustration of the core evolution principle; we are related not only to every living thing, but also to everything that has ever lived on Earth.
Design-wise, there are many things that could’ve made the graphic more readable, but something about it makes me like it just the way it is.