Thursday, October 8, 2009
Marsden Fund 2009: When Family Trees get convoluted
2009 has seen the 200th anniversary of Charles Darwin's birth and the 150th birthday of the book that changed everything. 172 isn't quite as round a number as the other two but as we celebrate Darwin's bicentenary the we should remember July 1837. Sometime in that month Darwin opened his brown notebook, wrote the words "I think" on the top of a page and drew his very first phylogenetic tree. Over the next 10 or so pages (you can read them here) Darwin scrawled out the implications of the big idea contained in that tree - that both the diversity seen in modern species and the continuity of form seen between them might be explained by ancient species splitting to from distinct lineages, changing and splitting again. Life as a branching tree.
It says something about Darwin that having for the first time sketched out his idea he didn't end with a hot blooded exclamation like Eureka! Instead he wrote cuidado - be careful. In fact, it took him 22 years of cautious letter writing and careful barnacle inspection (and one hell of a fright in a letter from Wallace) to publish The Origin. That book contained one illustration - a phylogenetic tree. In subsequent years the Tree of Life has become the central metaphor for Darwin's view of life and recovering the relationships between organisms has become a major part of how we do evolutionary biology. New Zealand mathematicians have been among the leaders in providing biologists with the tools to produce phylogenetic trees and an understanding of how they might be best applied. This year the Marsden Fund has given grants to three projects looking at how to recover trees from the murkiest evolutionary histories.
Well resolved phylogenies help us to test evolutionary hypotheses - are New Zealand's plants and animals relicts from Gondwana? Is Sphenodon guntheri really a distinct species of tuatara? Do kiwis descend from flying birds?* To put these sorts of questions to the test we need to estimate relationships between organisms, usually by reconstructing relationships between DNA sequences from them. In most cases these ''gene trees" are good proxies for the species trees we want to know about, but this biology so there are exceptions to the rule. Quite a few processes occur in populations and within genomes that drive gene trees away from species trees.
Charles Semple's project "unravelling the web of life" attempts to account for the fact the as well as being passed from parent by offspring genes can jump from one species to another. Although we've known that such Horizontal Gene Transfer (HGT) is possible since the 60s it's only more recently that it's become increasingly clear that att the very base of the tree of life the degree of HGT was so great the tree metaphor with it's simple one into two branching pattern breaks down, the tree becomes a tangled web. HGT is not limited to the base of the tree of life either, micro-organisms continue to swap genes with each other and your own genome contains quite a lot of virus DNA, inserted into your ancestor's genome to get the ancient viruses multiply and passed on to you. Semple's project aims to provide the same sort of mathematical basis we have for understanding tree like evolution for the much more complex pattern we see in evolutionary histories that include HGT.
James Degnan's project moves from the root of the tree of life to the tips. When the the process that forms new branches on trees, speciation kicks of each of the nascent species will inherit a suite of genes, each of which has its own history (the same lineages I've written about with respect to my mitochondria). If we try and infer species level relationships from just one gene's tree we fall into all sorts of problems, especially if we are dealing with recent or rapid speciation.(there are even genes that would place Gorillas as humans closest living relatives). Degnan has already worked on one of a bunch of programs avaliable to infer species trees from multiple gene trees and his "fast start" Marsden grant will allow him to keep working this field.
It's not just strange genetic quirks that strain Darwin's metaphor of tree like evolution. In plants, and at least some animals speciation sometimes occurs following hybridisation - two barnches into one. Even hybridisation isn't making new species it's a force that can provide conflicting phylogenetic signals to sequence data . Barbara Holland's grant for "Untangling complex evolution: when the Tree of Life is not a tree at all" will help to make better methods for revealing these kind of complex evolutionary histories and help biologists know when recovering the One True Tree for a groups isn't a sensible goal.
*The answers are "mostly not", "no" and "almost definitely"