The first phylogeny

The only diagram in the Origin is famously the hypothetical series of species forming a tree structure, but it isn’t an actual classification based on his…

New paper: GenomegaMap for dN/dS in over 10,000 genomes

Published this week in Molecular Biology and Evolution, is a new paper joint with the CRyPTIC Consortium "GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes".

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.
The paper includes detailed simulations that establish the validity of the approach, and it goes on to demonstrate how genomegaMap can detect advantageous mutations in 10,209 genomes of Mycobacterium tuberculosis, the bacterium that causes tuberculosis. The method reproduces known signals of advantageous mutations that make the bacteria resistant to antibiotics, and it discovers a new signal of advantageous mutations in a cold-shock protein called deaD or csdA.

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.

Virulence and vectors

Apropos of nothing, I am reminded of Paul Ewald’s book Evolution of infectious disease (1994). Ewald begins with the question of whether parasites and pathogens evolve…

New book contract

Well CRC Press haven’t learned their lesson yet, and have given me, Frank Zachos (Vienna) and Igor Pavlinov (Moscow) a contract for an edited book…

A not terribly good post on the species problem

As a biological phenomenon the species problem is worthy of serious study as an end in itself, and not as a mere corollary to work…

Evolution of the alphabet

Matt Baker provides this nifty diagram on how the alphabet changed over the centuries, evolving to what it is now. Grab the print.

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What is special about humans?

As soon as somebody asks the question “what is a ____?” we get into trouble. Not because we do not know about the thing in the blank, but because we tend to have the wrong idea about how to answer that question. Since the Greeks, the general feeling is that to answer a question about […]

Tree of Life

From Evogeneao:

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.

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The XV Collection: Perverse Outcomes of Novel Therapies

  The XV Collection: Perverse Outcomes of Novel Therapies Posted August 10, 2018 by post-info by Andrew Read Yale professor Steve Stearns once warned that the transition from Young Turk to Old Turkey happens quickly.

PLOS Biology in the media – July

  PLOS Biology in the media – July   post-info The year is flying past, and July has been another month with several of our papers making the news. This month we’re covering sleeping flies,