Evolution of the scrollbar

Sébastien Matos used a straightforward view to show the evolution of the scrollbar, dating back to the Xerox 8010 Information System from 1981.

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Species-related publications

What’s a personal blog for, if not to blow my own horn? Well, it can only be to blow the horns of those who I…

The post Species-related publications appeared first on Evolving Thoughts.

Feet of clay problem

What to do with historical bastardry in our heroes? This is republished from my substack. Henceforth such posts – the equivalent of a magazine article…

✚ Getting Better at Making Charts

Welcome to issue #210 of The Process, where we look closer at how the charts get made. I’m Nathan Yau and I want to get better at making charts, because there’s always room for improvement — no matter how long you’ve been at it.

Become a member for access to this — plus tutorials, courses, and guides.

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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