Genetic erosion

May 25, 2012May 26, 2012

Brothers in farms

Jeremy’s recent piece of detective work with the current edition of the Garden Seed Inventory, coming hot on the heels of my own piece on how diversity in French wheat has changed during the past hundred years, reminded me of a post of ours a couple of years back that could now bear revisiting. It was about a paper that had re-analyzed historical data from vegetable seed catalogues old and new to suggest that maybe the metanarrative of genetic erosion had been overdone:

If the meaning of diversity is linked to the survival of ancient varieties, then the lessons of the twentieth century are grim. If it refers instead to the multiplicity of present choices available to breeders, then the story is more hopeful. Perhaps the most accurate measure of diversity would be found in a comparative DNA analysis of equal random samples of old and new varieties, work that remains to be done.

The alleged grounds for hopefulness are that Drs Heald and Chapman, the authors, found 7100 varieties in 2004 catalogues, “only 2 percent fewer than one hundred years earlier. By this measure, consumers of seeds have seen almost no loss of overall varietal diversity”. Well of course that French wheat work is indeed as close as we’re likely to get to the “DNA analysis of equal random samples of old and new varieties.” And, alas, it shows what Jeremy said at the time was all too possible, and that is that genetic diversity can go down even when varietal diversity, meaning the number of cultivars of a crop, goes up. Grim after all.

Trawling seed catalogues is good fun, and can give you some clues as to what genetic erosion may be happening, but in the end it is diversity at the genetic level that really counts, let’s remember that. The geneticist JBS Haldane famously said that he would lay down his life for two of his brothers or eight of his cousins. That’s just a striking way of saying that you’re more closely related to your brother than to your cousin. The corollary of that is that there’s more genetic diversity in a group of cousins than in a group featuring the same, or indeed even a greater, number of brothers.

We still don’t know if those 7100 varieties in the 2004 catalogues are more brothers or cousins, but, if French wheat is anything to go by, the former is more likely. ((Though it need not be so.)) You may think you have a “multiplicity of present choices”, but if in fact you only have brothers to choose from, you could be forgiven for the temptation to trade a whole bunch of them for a cousin or two.

Assuming you can get hold of them, that is.

May 17, 2012May 17, 2012

D Landreth not so important to seed diversity

Thanks to the very good offices of our friends at Seed Savers Exchange, I now have a copy of the most recent (6th) edition of the Garden Seed Inventory. I wanted this in order to see whether the loss of The D. Landreth Seed Company, America’s oldest, as it happens, while tragic for the business and its customers, would also be a great loss for agricultural biodiversity. Long answer short: not so much.

The Garden Seed Inventory is a catalogue of catalogues, listing all the varieties available from all the catalogues SSE can get its hands on. That makes it a very useful snapshot of what is out there (in the US), how widely available it is, and the ebbs and flows in comercially-available diversity of crops and varieties. The Introduction to the book contains lots of analysis of this type, and I thought I remembered that it listed all the varieties that are available only from a single supplier and each supplier’s “unique” varieties. It doesn’t.

It does, however, list the 27 companies (10% of the total number covered by the inventory) that list the most unique varieties. D. Landreth is not among them. It also lists the companies that had introduced the most “new unique varieties”. Perhaps unexpectedly, there’s quite an overlap with the “most uniques”. and D Landreth isn’t in that list either. All of which suggests to me that while the passing of D Landreth would indeed be sad for its owners and customers, it would not be an immediate disaster for commercially-available agricultural biodiversity in the United States.

Does D Landreth have any varieties not available elsewhere? That one is difficult to answer using the Inventory. More than 450 pages of closely spaced entries is a lot to look through, searching for those with a single source coded La1. It ought to be a doddle from the database that stores the original records, but I’m sure SSE has much else on its mind at the moment. Mind you, if 45 owners of the Inventory were to scan 10 pages each …

May 14, 2012May 14, 2012

Brainfood: Bee diversity, Fodder innovation, African agrobiodiversity, Quinoa economy, Fragmentation and diversity, Rice in Madagascar, Rice in Thailand

Management increases genetic diversity of honey bees via admixture. No domestication bottleneck there!
Enhancing innovation in livestock value chains through networks: Lessons from fodder innovation case studies in developing countries. Fodder innovators of the world, organize. If you don’t, you will lose your value chains.
Introduction to special issue on agricultural biodiversity, ecosystems and environment linkages in Africa. Special issues? What special issue?
The construction of an alternative quinoa economy: balancing solidarity, household needs, and profit in San Agustín, Bolivia. Despite the allure of fancy denominations of origin and the like, old-fashioned cooperatives, and the much-maligned intermediary, manage to hang on in there.
Species–genetic diversity correlations in habitat fragmentation can be biased by small sample sizes. Can.
The original features of rice (Oryza sativa L.) genetic diversity and the importance of within-variety diversity in the highlands of Madagascar build a strong case for in situ conservation. Actually the way I read it, the stronger case is for ex situ. But see what you think.
Population structure of the primary gene pool of Oryza sativa in Thailand. In situ Strikes Back.

May 8, 2012May 8, 2012

The how and why of indicators of agricultural biodiversity

Let 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.))

April 18, 2012April 20, 2012

One silly thing is said about agricultural biodiversity every single day

You know, I think communicating about agrobiodiversity is really important. That’s why I contribute to this blog. Among various other things. But when I see the collective communication efforts of the agricultural biodiversity community culminate in the statement, made apparently in all seriousness, that “One crop seed becomes extinct every single day,” I do wonder whether the game is worth the candle. ((Admittedly, the rest of the article is not as bad as the title.))

LATER: Ok, maybe I was too sweeping in my vilification. Let me clarify. I don’t mind an editor crafting an attention-grabbing title for an article aimed at a popular audience. I can perhaps even live with a broad, “not even wrong” generalization about genetic erosion in such a title, if explained further in the text. No, what I really object to is the misuse of the word “seed” for “variety” in this particular context. Because it is unforgivably confusing, and simply not necessary. A seed, as the word is commonly understood, is just not something that goes extinct.