phylogeny comparison applet

A nifty little web-based applet for comparing the topology of two phylogenies and identifying where the differences lie. Could be useful in the future. Works for me on a G5 with Firefox. The paper referring to it is:

Nye, T. M. W., Lio, P. & Gilks, W. R. (2006) A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics, 22: 117-119.

alumni events

The University of Auckland is having an alumni event in London next month. I’m vaguely interested in the proposal (for a Centre for NZ Studies in the University of London system), but more importantly, I’m wondering about networking opportunities. I’ve not made an effort with alumni events so far (granted, they’re limited on the other side of the world), but in under a year I shall be Seeking Employment, and wonder if I should get on that ship and start sailing.

expectant dads get fat + parable of hats

New Scientist reports on research in Biology Letters, demonstrating that, in marmosets and tamarind monkeys at least, dads-to-be put on weight during pregnancy as well as the mothers. The hypothesis is that the extra weight gain (about 10%) provides an energetic reserve for when the infants are born and dad has to cart them about on his back.

Pharygula has the most marvellously satiric parable: Planet of the Hats.

Darwin Correspondence

The Rev. Charles Kingsley (he wrote The Water Babies) received a copy of Origin from CD and wrote the following letter:


Eversley Rectory, Winchfield,
November 18th, 1859.

Dear Sir,

I have to thank you for the unexpected honour of your book. That the Naturalist whom, of all naturalists living, I most wish to know and to learn from, should have sent a scientist like me his book, encourages me at least to observe more carefully, and perhaps more slowly.

I am so poorly (in brain), that I fear I cannot read your book just now as I ought. All I have seen of it awes me; both with the heap of facts and the prestige of your name, and also with the clear intuition, that if you be right, I must give up much that I have believed and written.

In that I care little. Let God be true, and every man a liar! Let us know what is, and, as old Socrates has it, epesthai to logo-follow up the villainous shifty fox of an argument, into whatsoever unexpected bogs and brakes he may lead us, if we do but run into him at last.

From two common superstitions, at least, I shall be free while judging of your books:—

(1.) I have long since, from watching the crossing of domesticated animals and plants, learnt to disbelieve the dogma of the permanence of species.

(2.) I have gradually learnt to see that it is just as noble a conception of Deity, to believe that he created primal forms capable of self development into all forms needful pro tempore and pro loco, as to believe that He required a fresh act of intervention to supply the lacunas which He Himself had made. I question whether the former be not the loftier thought.

Be it as it may, I shall prize your book, both for itself, and as a proof that you are aware of the existence of such a person as

Your faithful servant,

I doubt many clerics nowadays would be willing to go so far in their acceptance of radical new ideas. It says much about the Victorian delight in the exchange of ideas.

Language: hip-hop

Hip-hop and linguistics: you ain’t heard no research like it. Calgary linguist Daryn Howe investigates Black vernacular in hip-hop lyrics. Jeff Long, the GWUM[1], was the hip-hop fan here. The message: Black speech has lots of ain’t.

I was sitting on the bus this week idly eavesdropping on conversations and just could not understand the boys behind me, who were conversing in their particular northeast London urban Black/chav patois that I assume is an “in-group” dialect and meant to be unintelligible to me. It succeeded. It succeeded so well that I thought one of them was replying in French to his mate. I could make out a few words, but my ear honestly thought the pronounciation was Gallic. When I listened harder it became apparent it was the aforementioned dialect, but really? Couldn’t understand for the life of me.

[1] Grunt-Work Undergraduate Minion. We’ve all been there.

Edited to add:  I wondered about the possible offensiveness of my phrase “northeast London urban Black/chav patois”, but I can’t really think of a better way to put it. It’s not exclusively Black. It’s not exclusively a class thing, either, and chav is the nearest I can come up with.

Darwin Correspondence

The Writings of Charles Darwin on the Web is an amazing resource which allows you to search the texts–including, at an offshoot site, some of his correspondence! When I was writing my honours dissertation I had to stop myself reading the letters obsessively, seeing if I could glean some overlooked insight about language buried in amongst the natural history anecdotes and Darwin’s bleating about his poor health.

This letter (reference only) to his sister Caroline was a great find. In it, Charles used the hypothetical age of the Indo-European languages, and their differences from Chinese to agree with Herschel that yes, the earth must indeed be older than 6000 years as argued by the Bible.
I also love this one (below) that CD wrote to Thomas Henry Huxley. I confess to being a bit of a Huxley fan myself, but their mutual admiration society makes me smile…

Continue reading →

Paper: Application of Phylogenetic Networks in Evolutionary Studies

Application of Phylogenetic Networks in Evolutionary Studies
Daniel H. Huson and David Bryant

Molecular Biology and Evolution 2006 23(2):254-267 [link]

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.


Found today while adding sites to the Link List at the side:

PhyloTaxis, a nifty visualisation thing, that gathers science news headlines and turns them into this geometric flash array.

Surname Profiler. A UCL GIS project which produces a spatial map of the frequency of your surname in the UK. The wonders of GIS! My surname increased in frequency quite dramatically in the last century, and according to this, is pretty much confined to English and (in a minor way) Irish persons – which makes sense, given that Ireland is where my dad’s father’s family are from.

The different categories at visualcomplexity have fascinating topics. I like this one: London Connections, which is a spatial representation of a social network of one person in London.

Am well impressed with the bloggers at ScienceBlogs. Am assuming that joining the hosting service requires some sort of proof of science blogging, which I should get further underway with before knocking on the door.