Some new developments in stories that have appeared in these pages:

Labels: bellbird, evolution, human genome, Korimako, population genetics, sci-blogs, science

My sciblogs scibling Fabiana dedicates one post a week to celebrating important new findings, furthering the cause of Open Access science and other such important stuff. Me? I like weird invertebrates. So, starting today you can tune in here on Sunday morning and see some photos from the other 95% of the animal kingdom.

I found the subject of the first edition of Sunday Spinelessness in our living room, hanging out on a bunch of flowers I'd brought inside. It's a brown lacewing, probably the introduced species Micromus tasmaniae. Lacewings are part of one of the slightly less familiar insect Orders - the Neuroptera which are named after their net-like wings. I could have used these photos to illustrate my piece on Danial Williamson's crazy ideas because the Neuroptera are one of the groups that undergoes complete metamorphosis. As a larva our lacewing probably dined out on the the aphids that seem to love the our tulip flowers (if I ever take a decent photo of the aphids you'll see it here). Unusually, the adult lacewing above is probably making its living in much the same way - the prevention of intergenerational competition is often cited as one of the advantages of complex lifecycles but a lot of lacewings species are carnivorous as larvae and adults.

Other Neuropterans include the freaky looking mantidflies the fearful antlions (which, along with New Zealand's glow worms are among the very few animals with a common name that refers to the larval form) and more than a few beautiful species like this one photographed by Isidro Martiniez:

Labels: insects, might interest someone, neuroptera, photos, sci-blogs, sunday spinelessness

When I started out as a genetics student the big goal everyone was talking about was understanding "The Genome" - that monolithic set of DNA bases that make us human. Of course, there is no such thing. Pick two human genomes at random and you'll likely find 2 million single-base differences and plenty of structural differences on top of that. As with just about everything in life understanding the range of variation and the diversity in human genomes is much more interesting than focusing on the average of that diversity.

The publication of a draft sequence from the Human Genome Project in 2001 really was the begining of a new epoch in genetics (and a revelation in itself- it takes 20 000 genes to make a nematode and 25 000 to make us?) but the real value of that project has been the generation of a scaffold that subsequent projects like the super-optimistic 1000 genomes project, hapmap and the genographic project (which New Zealand researchers contribute to) have been able to inherit in their attempts to understand genomic diversity. This week Nature has a special issue focussing how data built on information from the Human Genome Project is contributing to the way we understand disease and even allowing personalised testing for genetic risk.

Unfortunately they've stuck one of the most interesting articles behind a pay wall (Nature, the people that bring you a special on science and society but don't let society read it...) Bruce Lahn and Lanny Ebenstein have an opinion piece on genetics and race.

The current moral position is a sort of 'biological egalitarianism'. ... the view that no or almost no meaningful genetically based biological differences exist among human groups, with the exception of a few superficial traits such as skin colour. Proponents of this view seem to hope that, by promoting biological sameness, discrimination against groups or individuals will become groundless.

Of course, as Ebenstein and Lahn point out, there is a problem with this view - race almost certainly does have a genetic basis beyond a few superficial traits. To take the local slant Polynesians and in particular Māori represent the furthest extent of the series of migrations that followed our ancestors moving out from Africa. Settling the Pacific must have involved a series of population bottlenecks - events in which small groups form a new population representing only a fraction of the genetic diversity in the parental population. Such bottlenecks will have inevitably left a mark on the gene pool of Māori and Pacific Island populations that more recent interbreeding won't yet have erased. There will be some genes that are unique to Polynesian populations and others that are orders of magnitude more or less common than they are in other populations. If we embrace that genetic diversity we might be able to understand why Māori face a much greater risk to, for instance, diabetes, gout and liver disease than Pakeha. To, as people have really suggested, ignore that genetic diversity because racists might use it to further their stupid cause is, in the words of Lahn and Ebenstein "llogical, even dangerous"

Oh, and by the way, whatever we find out about the genetic basis of race I think it's safe to say that genes won't care too much for national borders - but that's not going to stop the UK from genetically screening assylum seekers...

Labels: genetics, genomics, human genome, sci-blogs, science and society

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"

Labels: evolution, Marsden Fund 2009, phylogenetics, sci-blogs

Voting is already under way in 2009's most brutal high stakes political battle - the Forest and Bird Society's Bird of the Year poll. A scroll down the current standings reveals plenty of birds that have sunk to employing murky political ties and celebrity endorsements (1, 2, 3) to sell their case. There is one bird in this race that can speak for itself. There is an expression used in Māori to describe the most gifted orators: “Ka rite ki te kopara e ko nei I te ata”, like the bellbird singing in the morning. Listen to Radio New Zealand's recording of of the bellbird's song and you'll see why it's such an honour to be compared to kopara (also known as korimako and mokamako)

I'm sure I heard bellbirds growing up in the Wairarapa but there are parts of the world that young men are just insensible to. The first time I really noticed the bellbird's song was, of all the places in the world, on Castle St in Dunedin. That street may be famed for its annual riot but it's also adjacent to the Botanical Gardens and part of Dunedin's very large greenbelt. In Dunedin bellbrids make their way into the city at the start of winter and on this day a chorus of perhaps ten birds was calling as they flew up and down the stand of trees that run alongside the Leith at the southern end of the gardens. I can't describe the song, or the feeling of being struck by it, without drifting into awful prose-poetry (I'm just not skilled enough as a writer to be trusted with words like ecstasy or mellifluous) so I'll let Joseph Banks describe the experience:

They seemed to strain their throats with emulation, and made, perhaps, the most melodious wild music I have ever heard, almost imitating small bells, but with the most tunable silver imaginable

The other bellbird encounter that has really stuck in my mind happened in the Kahurangi National Park. I was a fair way from the beaten path on the trail of log dwelling invertebrates when I heard a single note ring out perhaps 20 metres away from me. A few seconds later a reply, again a single note this one a tone or two higher than the first, came from 50 metres to the other side. For the next few minutes I was in the middle of this pair's duet of rolling, liquid peels. It was an amazing privilege to get to hear that song and to be part of that pair's territory for the next couple of hours as they flew, wings whirring, from trunk to trunk.

It's hard to delight in the bellbird's song without thinking about how much of the chorus that Banks was so enthusiastic about is now lost to us. We'll never hear a piopio or a huia sing and few of us will ever get a chance to listen to a pair of kōkako. At the turn of the 20th century it was generally thought the bellbird would go the same way but it has since recovered to the point that is not uncommon in gardens in Dunedin and parts of Christchurch and is even staging a comeback in Wellington thanks to the Karori Sanctuary. New Zealander's should embrace the bellbird, not just for its beautiful song but because it is a reminder of a much more diverse chorus that once filled our forests, for that reason I urge everyone to Vote Bellbird in '09

Labels: bellbird, environment and ecology, Korimako, sci-blogs