Agricultural Biodiversity Weblog

April 24, 2012April 24, 2012

Featured: Models

Marleen Cobben gives more details on her fascinating model:

The results from our model suggest that the spatial process of range shifting under climate change can have a big impact on the genetic composition of new populations. This is because the individuals arriving first in a new climatically suitable natural area, have a competitive advantage (in numbers) over individuals arriving later. So even if these latter individuals are better adapted to the local conditions, adaptation of the population takes a while because there’s initially so little to select for. No news thus far I’d say. The problem is, that this ‘while’ is fairly long compared to the predicted rate of temperature increase.

And there’s a lot more, all of it interesting. Have a look.

April 24, 2012April 24, 2012

Tricky stuff, extinction rates

There’s a BBC radio programme called More or Less that I like a lot, mostly because it takes the trouble to think about things. A new series has just started, and I was thrilled to see that the programme was going to tackle extinction rates. Not anything as simple as extinction rates for crop seeds, or agricultural biodiversity in general (which is always 75%), but the biggie, the global extinction rate for (wild) species. All power to them, they really did try, at the same time having some fun with some of the more inane pronouncements on the topic. But I must say, even knowing a bit about the topic, I found it really hard to follow.

Not sure how widely available the programme will be, or for how long, so if it isn’t at the BBC, you can also find the relevant bits here.

And to repeat what the programme said, just because we don’t accurately know what the rates of extinction are, doesn’t mean that the loss is unimportant. Except that, really, it would be nice to know the birth rate of new bacterial biodiversity.

April 23, 2012April 23, 2012

An open letter to open up EU seed laws

There’s an open letter floating around that is addressed to Members of the European Parliament and to a variety of EU Commissioners for this that and the other. The intent is to advocate for opening up the EU legislation on the Marketing of Seed and Plant Propagating Material, in order to:

[M]ake it more respectful towards the environment, consumers’ expectations and the needs of small actors in the seed chain.

No argument from us on that score. Indeed, we’ve always found the one-size-fits-all approach of the EU suitable only for the largest. Why varieties must be certified, when simple consumer-protection laws are enough to protect against sharp practice, remains a mystery. The letter appeals to everything, from freedom of choice via reduced use of pesticides to an improved environment, better conservation, and more rural jobs.

It’s a good effort, and most welcome, even if it is probably doomed to failure. The sad part is that the list of signatories is completely dominated by the usual suspects. It’s almost as if the heavy hitters who are so keen on agricultural biodiversity for developing countries (and we all know who they are) see no common cause with what’s happening in their own back garden.

Organizations and individuals have until 2 May to sign up.

April 23, 2012April 16, 2012

Brainfood: Lupin restoration, Balkan wheat drought tolerance, Metabarcoding, Wild sheep genetics, Organic vegetables, Diversity protects, Sorghum geneflow, Wild sunflower genetics

A Molecular and Fitness Evaluation of Commercially Available versus Locally Collected Blue Lupine Lupinus perennis L. Seeds for Use in Ecosystem Restoration Efforts. Commercial seed sources can be dodgy, and that’s a problem.
Comparison of responses to drought stress of 100 wheat accessions and landraces to identify opportunities for improving wheat drought resistance. 20 Balkan landraces seemed to be more drought tolerant than 80 accessions sourced globally.
Towards next-generation biodiversity assessment using DNA metabarcoding. You gotta be kidding me, metabarcoding? Will they be applying it to soils? Yep.
Selection and microevolution of coat pattern are cryptic in a wild population of sheep. You need to look at the genes.
Will they buy it? The potential for marketing organic vegetables in the food vending sector to strengthen vegetable safety: A choice experiment study in three West African cities. Not enough.
Plant diversity improves protection against soil-borne pathogens by fostering antagonistic bacterial communities. Chalk another one up to diversity. Did they say soil?
Local scale patterns of gene flow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural field conditions in Kenya. Mostly crop-to-wild, which could be a problem if transgenics are ever grown. If.
Adaptation with gene flow across the landscape in a dune sunflower… is leading to “ecological” speciation.

April 22, 2012April 22, 2012

Pitfalls in modeling the effects of climate change on genetic diversity

Don’t you just hate it when a striking message from an elegant model is complicated by, well, facts? I may have Nibbled a press release on a recent modeling study from Wageningen University. The crux of the results was that as species migrate north due to climate change, they shed diversity from the central, most diverse part of their distribution, which is bad for their ability to adapt.

Plant and animal species can lose their ability to adapt as a result of climate change. This is shown by research performed by Marleen Cobben with which she hopes to obtain her doctorate at Wageningen University (part of Wageningen UR) on 17 April 2012. Cobben used computer calculations to illustrate how the genetic base of plants and animals is seriously deteriorating due to climate change. The smaller genetic base makes species more vulnerable to problems such as diseases. Moreover, the fragmentation of landscapes and the loss of wildlife areas is accelerating this decline.

This was interesting to me because we routinely, and perhaps somewhat blindingly, these days say that climate change will lead to shifts in the distributions of species. Crop wild relatives, say. Shift that will absolutely require germplasm collecting and ex situ conservation. Nothing else will do. Forget about in situ, ex situ it must be. That’s because, when added up, these shifts in the distributions of individual species will result in profound alterations in the geographic patterns of species diversity. Some hotspots will disappear, some diversity-poor areas will be enriched. Difficult to plan in situ conservation under these conditions. Ergo, need to collect. Also, the distributional shifts required for a species to track the climate will in most cases surely be faster than the rate of migration of the species, leading inexorably to its extinction. Need to collect, and quick. I mean, what can a poor species do under climate change besides move or perish? Need to collect, I tell you.

Well, adapt, of course, that’s what it can do. And collecting is not going to help with that. Need to do in situ, maybe assisted migration, you clod.

So a study which suggests that climate change is likely to also result in a decrease in genetic diversity within species would seem to push the pendulum further towards ex situ. Without being able to delve into the particularities of the model, the results seemed plausible to me, assuming that the highest diversity was indeed found in the central part of the distribution. Genetic erosion ensues. Won’t be able to adapt. Need to collect!

I can’t remember if I did nibble it, but I certainly sent the link to the Crop Wild Relatives mailing list. And it elicited an interesting, skeptical reply from Prof. Jonathan Gressel of the Weizmann Institute of Science in Israel. The professor pointed to a possible mechanism by which climate change could conceivably increase genetic diversity.

Unfortunately it is common for modelers to to say that their research “shows” (in this case), demonstrates or even proves something. As a sometime modeler (first model on herbicide resistance published in the Journal of Theoretical Biology in 1978), the best models can do is suggest priorities for experimentation to validate them. Ignoring (or not knowing) one important parameter can skew the model. My mathematician colleague always kept mumbling at me: “Garbage in, Garbage Out”. I would hazard a guess that one parameter was left out of the simulations: the fact that sub-lethal stresses increase mutation rates. Thus, climate change stress will increase mutational diversity in pre-existing genes. For a discussion of this, see: Pest Management Science 67:253-257, 2011.

Oh no, you mean we have to do both ex situ and in situ? Well that won’t do at all. While I naturally hope Marleen Cobb successfully defended her PhD last week, I hope that when she comes round she’ll tweak her model and help us decide once and for all.