The how and why of indicators of agricultural biodiversity

ResearchBlogging.orgLet us assume, for the sake of argument, that one crop variety does disappear every single day. The question still remains: does it matter? After all, the variety that was just lost yesterday might be very similar to one that’s still out there today. That’s part of the reason why a group of French researchers has just come up with “A new integrative indicator to assess crop genetic diversity,” which is the title of their paper in Ecological Indicators. ((Bonneuil, C., Goffaux, R., Bonnin, I., Montalent, P., Hamon, C., Balfourier, F., & Goldringer, I. (2012). A new integrative indicator to assess crop genetic diversity Ecological Indicators, 23, 280-289 DOI: 10.1016/j.ecolind.2012.04.002))

Christophe Bonneuil and his co-workers thought that, given the data, they could come up with something more powerful and more widely applicable than richness (i.e. the number of different varieties) or the standard diversity indicators (i.e. various combinations of richness and evenness). So they started with number of varieties, but then they factored in the relative extent to which each was grown in their study area, the departement of Eure-et-Loire in France (which is the evenness bit), how genetically distinct each was (which is the bit which addresses the pesky question of how different the variety that disapeared today is from all the other ones left behind), and how much genetic diversity there was inside each.

They got the data on genetic differences among varieties by comparing genebank samples of all the wheat types grown in Eure-et-Loire from 1878 and 2006 at 35 microsatellite loci, and data on acreage of each variety at different points in time from various archival sources. Internal genetic diversity was set at one of three values derived from the literature, depending on whether the variety was a landrace, an old commercial line or a modern pure line.

They put all that together into this monster indicator of allelic diversity in the landscape,

and then calculated it for different times periods, and got this:

That shows a decrease in diversity as landraces are replaced with modern varieties, but, interestingly, something of a resurgence after the mid-1960s, as more diverse germplasm is introduced into breeding programmes. The indicator has been on a downward trend just lately, as the genetic relatedness of the most frequent varieties has increased. ((A result that you might like to compare with the one we discussed not so long ago for the diversity in modern breeding programmes.)) Overall, it’s maybe a 50% drop since 1878. Not entirely dissimilar to the iconic 75% figure, and at least this wasn’t plucked out of thin air.

Interesting enough, but check out the trend in number of varieties over the same period:

Totally different. Pretty much an upward trend, albeit with some stuttering. Certainly no evidence from these data of massive erosion of diversity. Maybe the findings of Jarvis et al. (2008) that simple richness can be a useful indicator of diversity should be applied with caution if you’re not just dealing with landraces.

But how significant is it really that the value of this particular indicator of diversity, for all its fanciness, has decreased? Has anyone actually suffered as a result? I don’t know, but a second paper I came across this week suggests how one could find out. Roseline Remans and others associated with the Millennium Villages Project have a study out in PLoS ONE which adds yet another — different — nuance to diversity. ((Remans, R., Flynn, D., DeClerck, F., Diru, W., Fanzo, J., Gaynor, K., Lambrecht, I., Mudiope, J., Mutuo, P., Nkhoma, P., Siriri, D., Sullivan, C., & Palm, C. (2011). Assessing Nutritional Diversity of Cropping Systems in African Villages PLoS ONE, 6 (6) DOI: 10.1371/journal.pone.0021235)) Their index considers not just how many different crops are grown on a farm, but also how different they are in their nutritional composition. Think of it as the nutritional analogue of the inter-varietal genetic diversity term in the French indicator. The more different in nutritional composition two crops are, the more complementary they are to local diets, the more important it is that both are there, the higher the resulting “functional” diversity index. And in fact the authors did find a positive relationship between their diversity indicator and nutritional status, at least at the village level.

Easy to imagine (though perhaps less easy to actually implement) a further refinement of Bonneuil et al.’s indicator which additionally integrates nutritional data, to yield an indicator of crop genetic and functional diversity. And, of course, once you have such a super-indicator, it might actually be possible to reward people on the basis of their success in maintaining it at high levels. Which, as it happens, is the subject of yet another paper I happened across last week. ((Hasund, K. (2013). Indicator-based agri-environmental payments: A payment-by-result model for public goods with a Swedish application Land Use Policy, 30 (1), 223-233 DOI: 10.1016/j.landusepol.2012.03.011)) But maybe that’s a paper too far for now. ((And yes, you do remember these papers from Brainfood. It’s just that it sometimes takes a day or two for us to tease out the connections.))

Brainfood: Species prioritization, In situ costs, Mycorrhiza, Crop diversity indicator, Diet diversity indicator, Ag & Nutrition, Chestnut blight, Oyster translocation, Maize introgression, Italian asses, New hosts for pests

Going, going, not gone?

My circles on GooglePlus alerted me to a report from NPR in the US, that the country’s oldest extant seed company is facing bankruptcy. The D. Landreth Seed Company has been going since 1784, and is credited with introducing the zinnia to the US and with popularising the tomato when it offered seed for the first time in 1820. Now the company is in trouble with its creditors.

That’s a great shame, the more so because it is happening in a country that, unlike some, ((And today is the deadline for signing up to a hopeless attempt to open up EU seed laws.)) does not enjoy legislation preventing the sale of specific varieties. So what about market demand? Don’t people want the seeds that D. Landreth has to offer? Could it be that the company’s website is, as one commenter suggests, not entirely up to date?

At G+ Anastasia Bodnar said “it’d be sort of sad if the company went under, but as it says in the article, it’s not like the germplasm would disappear, it’d be auctioned off”.

Well, maybe, but what guarantee is there that whoever buys it would maintain it? And if Landreth can’t make a living selling that germplasm, maybe the reason is that lots of other people have the self-same varieties and are selling them successfully.

My question is this: “how many varieties offered by Landreth are not offered by another seed company in the US or elsewhere?”

In the old days, I might have checked by looking in Seed Savers Exchange’s wonderful publication the Fruit, Nut & Berry Inventory, but I see there hasn’t been a new edition since 2001, and I can’t see the database on which it was based anywhere. Having produced a UK version myself, I know how hard it is to do this kind of information wrangling, but it is really worthwhile.

<dream>Maybe I should attempt to Kickstart that effort again. </dream>

Brainfood: Alfalfa, Date palm, Apricot, Collecting, Reintroduction, Ribes, Payments

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.