A new universal tree of life

A revised universal tree of life

A revised universal tree of life

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

A pragmatic redating of our 700 million year ancestry

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

Founding a new human population

I’m very pleased have another query to answer from a listener to More or Less. And what a great question:

BlofeldI 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?

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Ancestor’s Tale list of concestors, revised


Some surprises in store for Concestor 23

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.

For those who wish to skip to the chase, I’ve come up with a new list at the end of this post. Continue reading

Visualizing data on large phylogenies at the pixel-level


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

Schrëwdinger and her descendants

Mosaic of placental mammals

670 descendants of Concestor 13, appropriately arranged.

I’ve been meaning to write about this for a good while, ever since the release of a paper which hit the science headlines last year. For the first time to my knowledge, researchers have tried to do professionally what I, together with a graphic illustrator, did in an amateur fashion for The Ancestor’s Tale. I’m talking about attempting to reconstruct what our distant ancestors looked like, an intriguing task that also leads to some striking visual possibilities.

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Informative graphics: male and female lifespan

Plot from wikipedia of male and female life expectancy at birth from CIA factbook data. The apparent 3D volumes of the bubbles are linearly proportional to their population

Last month I recorded an update to my Radio 4 programme on why women live longer than men (which you can still listen to online). A cut down version was broadcast on the BBC World Service. For this we wanted to include statistics for different countries. I was busy investigating official UN sources for these data, when I noticed that morning’s papers were reporting a relevant set of studies published that day in the Lancet . A couple of thoughts followed. Firstly, these new data indicate that in 2010, men had a higher life expectancy than women in only 2 countries: Afghanistan and Jordan . That’s in contrast to the UN data, which finds this effect in a small number of African countries too – suggesting the UN data could be inaccurate in these cases. Secondly, the data are given with uncertainty intervals for the first time, which got me thinking about the best way to illustrate the data. In particular, I’ve been thinking about how to improve the plot above (taken from the wikipedia page listing the life expectancy of different countries).

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Reproducible plots of public data (Guardian Google spreadsheets, UNdata) using R

There’s a fair bit of of publicly available data that can be used to answer questions about global trends. Previously, I’ve used data from the UN and the UK (often the Office for National Statistics), but I’ve only just discovered the commendable data service being provided by the British paper “The Guardian“. They encourage public access to (and visualization of) the data on which their articles are based. This is done by tidying up data and putting it in publicly accessible Google spreadsheets.

Plot reproducible from free online data using R

With all this data available, it’s possible to carry out reproducible research and analysis, such as the plot opposite. For this you require an easy (and free) way to to carry out analysis using the datasets. Perhaps the most powerful way is to use something like R, which can be issued commands to carry out analysis, generate visualizations, etc. For maximum reproducibility, I’ve been trying to write R code that accesses these data sources directly, without having to download and tweak intermediate data files. This should make it easy to analyse datasets and produce attractive plots – for example, of estimated life expectancy and population size. Continue reading

Severe morning sickness and twins

Dizygotic (non-identical) twin sisters, image from Wikimedia Commons, ©2006 Dustin M. Ramsey

In the light of the recent hospital admission of the Duchess of Cambridge for an condition loosely associated with female babies and multiple births, I’ve been asked by the Radio 4 programme “More or Less” to calculate the probability that she is pregnant with more than one embryo. I’m somewhat reluctant to contribute to what is already a topic of rampant media speculation, and the attendant intrusive journalism that often plagues issues like this (which, after I had written this post, led to a sad and particularly tragic outcome). Nevertheless, few media articles seem to give links to solid data sources, and some even give rather misleading information, so I’ve overcome my reluctance in order to put some solid statistical facts into the public domain. Simply put, compared to the average, the probability of a mother having twins given that she has this condition is not quite doubled. However, it’s still likely to be a very low number: something like an increase from about 1.5% to a 2.4% chance. For the gory details, read on. Continue reading

The world’s rarest plant?

We’ll probably never see this plant again. Image from Wood (2012)

Many of the rarest and most endangered species we know of are plants. The sad story of Hibiscedelphus woodii, which I’ve only just read about, is not atypical. Of the 4 last known specimens, on a cliff in Hawaii,

three individuals of H. woodii were apparently crushed by a large fallen boulder and died between 1995 and 1998. on 17 August 2011, the last remaining H. woodii was observed dead. [zotpressInText  item=”X8HWMKBN”]

The unfortunate (but appropriate) choice of this as a endangered species at a recent event for the Society of Biology, prompted me to dig out the following, which I wrote in 2009 to answer the question “What is the world’s rarest plant”: Continue reading