Conference today

I am visiting a conference this week, Understanding Biodiversity Dynamics Using Diverse Data Sources. But as it takes place in the city where I work I don't have to go far - the talks are just down the hill from my office. Some of the talks today were inspiring and utterly fascinating.

Two in particular I want to mention very quickly, although for very different reasons. The first was, from my perspective, perhaps the highlight of the day, but more importantly it was highly relevant to my recent discussion of the merits of phylogenetic diversity. Among other things, Professor Marc Cadotte talked about the claim, already advanced by Charles Darwin, that, all else being equal, a biome containing more phylogenetic diversity (PD) is more productive than a biome with less.

And he presented an ingeniously simple field experiment to test this claim quantitatively: They planted numerous experimental plots with one, two or four species of varying evolutionary relatedness, taking care to replicate close relatedness in various groups (two grasses, two Lamiaceae, and so on). The result was a beautiful and clear positive correlation of grassland productivity with PD.

As I wrote above, this is highly relevant to the question of whether PD is correlated with feature diversity, only in this case there is another mental step involved. The underlying idea is that a community of four distantly related species would be more productive than one of four closely related ones because it would have higher feature diversity in the sense that the species are more divergent and can thus utilise more different resources than the same number of supposedly more similar, closely related species.

The positive result of the experiment can thus be read as another vindication of PD, and surely the unseen characters that allow these plants to complement each other in the utilisation of local resources are "conservation relevant", to use the words of the PD critics I discussed a few days ago.

The other talk that I briefly want to mention was sadly somewhat less sparkly. The thing is, there are many snobbish molecular and evolutionary biologists who consider natural history collections and the research they do as mere "stamp collecting" and a tedious description of patters instead of something that increases our understanding of relevant processes.

I will admit there are some colleagues who fit that description, who would go and bore the socks off an audience by showing them half an hour worth of insect mouthparts or leaf shapes without betraying any underlying research question.

But bizarrely, at the moment I have examples showing the exact opposite. In my backpack is a paper I am peer reviewing where the authors examined a highly topical but supposedly hard to test evolutionary question through the simple expedient of measuring a few macroscopic characters on dusty old herbarium specimens and doing some simple statistics. Conversely, today at the conference I had to sit through a 30 minute talk by a scientist working with cutting-edge genomics and bioinformatics techniques who filled virtually the entire time with one "and this transcription factor has this effect on the insect wing" after the other. It was purely descriptive, and I never understood why anybody should care to know this stuff.

That just goes to show that it is not what tools you have but what you do with them.

Is phylogenetic diversity flawed?

As indicated in my previous post on phylogenetic diversity (PD), what I really want to discuss is a recent paper, Kelly et al. (2014), that casts doubt on the utility of PD for conservation decisions. Again, understanding what this is about will require some excurses and explanations, but as we will see the main point is ultimately surprisingly banal.

As illustrated with the example of many species of grasses versus fewer species of oaks, lilies, grasses and ferns, the background is that PD is supposed to provide a metric for a form of diversity that we want to conserve. Now many of us would say that this form of diversity is evolutionary distinctness and be happy; we intuitively consider isolated lineages to be worthy of special protection. However, PD is often advertised as a proxy of what Kelly et al. call "feature diversity" (subsequently FD). That is, what we want to conserve in an area is not phylogenetic diversity per se but instead maximum diversity of some (morphological? ecological? genetic?) features. However, it is assumed that the more distant two species are in their evolutionary relationships, the more different they are likely to be in any given feature, and that is why we assume that high PD means high diversity of conservation relevant features.

Kelly et al. set out to test this assumption. Maybe one of their thoughts was that it may not actually be true because of convergence. One could argue that it doesn't make a lot of difference whether we protect a grass in the Poaceae family as long as there is a very similar looking grass-like Cyperaceae around. They have converged on the same ecological niche, so same thing really, right? But that is already the interpretation, perhaps it behoves me to stay with the methodology for the moment.

Phylogenetic diversity

Yesterday we discussed in our local journal club a recent paper arguing that the concept of phylogenetic diversity is flawed, or at a minimum not useful as a proxy for what the authors call "feature diversity".

Obviously to make sense of what I just wrote, a bit of background is needed. I will therefore use this post to explain what phylogenetic diversity is, and then discuss the actual problem (if there is one) the next time.