It’s been a long while since I posted anything on this blog. That’s mainly because I’m now helping with fascinating work at Oxford’s Big Data Institute, which promises to re-write some of the foundations of evolutionary biology. Together with coding on the OneZoom tree of life project, it’s what has been taking up most of my research time.
The Big Data research involves two major ideas. The first is that an evolutionary approach can be used to compress genetic data by many orders of magnitude. The second is that inferring ancestors of pieces of DNA in the past can allow us to reconstruct evolutionary history across millions of genomes. These two ideas turn out to be intimately linked … Continue reading →
The visualisation of life at OneZoom.org shows all branch points as a split into two branches. Yet the Open Tree of Life, from whom much of the data is gathered, have many examples of large polytomies, where many branches emerge from a single point. These are almost entirely cases where a large number of species have been classified by taxonomists into a single group (say the ragworts), but where the OpenTree has not incorporated any extra studies that can resolve relationships between species within the group.
Looking out from Paviland cave, Palaeolithic burial site in foreground. (0)PUBLIC DOMAIN
Paviland Cave on the Gower peninsula of south Wales was the site for one of the oldest ceremonial burials in Western Europe, the misnamed Red Lady of Paviland. Tides make this cave rather difficult to access, and on a recent visit I couldn’t find many online details about accessing the cave by foot. I found two ways to reach the cave, one a short but rather dangerous scramble. Continue reading →
Here’s a new depiction of the ‘universal evolutionary tree of life’ which incorporates some recent advances in the field. In particular, some fast-evolving taxa that are known spuriously placed in previous ribosomal RNA trees have been omitted (e.g. microsporidia, which are known to fall within the fungi), and it also illustrates the increasingly popular idea that Eukaryotes nest within the Archaea. Unlike some other universal trees on the internet, this is shown as an unrooted tree, which is a more conservative approach than the (arguable) rooting of the tree of life between Eubacteria and Archaea. The tree has the distinct advantage that it (more or less) correctly reflects our understanding of the major groups of Eukaryotes (including plants, fungi & animals). In my opinion it is a more accurate depiction of our state of knowledge than other ‘universal trees of life’ commonly found on the internet. Continue reading →
I’ve been figuring out nice ways to use R to plot the entire geological timescale. This being R, there is a package (called “geoscale“) which does this already, but I want one where the age is converted linearly to greyscale, and which can fit entirely onto one page, with the short periods of the Holocene and Pleistocene crammed in somehow. I also want to be able to update it easily when new values are published. Continue reading →
As part of the second edition of the Ancestor’s Tale, I have been reassessing the dates on the backwards journey from today’s humans to the origin of animals. What is written below is rather technical, and mostly for my own benefit, and also for Richard Dawkins. Nevertheless, perhaps others may be interested in my reasoning, which I hope is seen as a pragmatic assessment of our current beliefs. Continue reading →
I’m very pleased have another query to answer from a listener to More or Less. And what a great question:
I am embarking on a Career as a James Bond baddie, and I want to make sure everything is very carefully planned. I am under no illusions that Commander Bond will thwart my first efforts to take over the world, however I am keen to become a recurring character, and that’s where you come in.
I intend to escape from Mr Bond at the last minute and I intend to populate an island or other planet, depending on budget. However I am not clear how many men and how many women I will need to take with me to ensure we do not have issues with inbreeding in the population creating genetic disorders and the like. How many people do you need to create a new race of people?
When I helped write the Ancestor’s Tale, one of the big tasks was to make a human-centred tree of life: to list of all the point at which, backwards in time, the human lineage joined with lineages of other extant lifeforms. In February last year I was forwarded an email from someone using these “rendezvous points” as the basis for a song and story for children. She had seen the O’Leary paper and wondered how much revision was needed to our original list.
A phylogenetically organised display of data for all placental mammal species. Red pixels are those without a picture on EoL.
Modern technology, coupled with molecular taxonomy, means we now have very large evolutionary trees: ones with tens or hundreds of thousands of species. In fact, the Open Tree of Life project aims to create a tree of all living things, which would have millions of species. The obvious question is how to display these enormous amounts of data.
Here’s one possibility I’ve come up with: use a single pixel for each tip of the tree (each species). Then, if we could use the whole of a one megapixel canvas, we could display information about a million or so species. Continue reading →