Agrobiodiversity is crops, livestock, foodways, microbes, pollinators, wild relatives …
Not content with bringing you Our Man Hijmans’ dynamite written dispatches from Harlan II, today, The Spoken Word. David Williams, coordinator of the CGIAR’s System-wide Genetic Resources Programme, appeared on Insight, a daily in-depth interview programme hosted by radio station KXJZ in Sacramento, California. David talked about domestication, genetic modification, the history of collecting, the importance of crop wild relatives and much else besides.
Listen to it here. (About 12 minutes.)
Robert Hijmans’ third dispatch from Davis. Previous one here. Keep ’em coming, Robert!
Day 3 of the Harlan II symposium had another cornucopia of fine presentations. Farmed fish, genetic chips, fruits for the poor, improving desert crops, ecosystems services research, transgenic goats, selling diversity to the rich to name a few topics. One subject shared by several talks was on-going and future domestication. 1 From conservation to innovation.
Dennis Hedgecock described the big wave of domestication in our time: aquaculture. Within a decade or so, there will be more fish produced on farms than caught in the oceans. The ocean catch won’t increase much any more (or worse); we have reached the limits. And how wild is caught fish anyway? Fish stocks in the ocean are increasingly being replenished with small fish from hatcheries. The majority of Japanese fish descends from hatchery fish. Whether this is good or bad for the genetic diversity of the fish depends how it is done. Guess how it is done.
Overfishing of oceans and the subsequent shift to farming is strikingly similar to the domestication pathways of some land animals that were also hunted before they were domesticated (discussed yesterday by Melinda Zeder). So what is all this fish farming about? Shrimp, salmon, tilapia? No. Number 1 is the Pacific Oyster and 60% of fish farming is carp production in China.
The breeders are at it too. They have developed a tetraploid Pacific Oyster. Crossing it with the normal diploids creates infertile, but larger, triploid offspring. They are not being commercially produced yet, but here aquaculture mimicks plant domestication.
Roger Leakey described a project of further or re-domestication of tree crops. Going into villages in West Africa, Leakey and colleagues asked farmers what trees they valued and would like to have more of. They then looked at the variation in the species, selected some with good fruits, and helped find a place for them in the farming system, e.g. as shade crop in cacao. Seems like fairly simple work, if labour intensive.
In some places the result was stunning, with very poor farmers earning an extra US$700 per year from a few trees in their field. Diversity can improve livelihoods of poor farmers. We will need to revise the agronomy curricula to make it happen on a large scale.
Meanwhile, in India, good old pigeonpea is being renewed. Landraces are perennial bushy plants. But Laxmipathi Gowda and collaborators at ICRISAT have produced many other types: short duration; determinate; daylength insensitive; and even hybrids. And in California there might be renewed attempts to use jojoba, now for bio-energy. Stephen Kaffka talked about some of the difficulties of domesticating a highly heterozygous, variable, and slow growing shrub. So far there is no evidence that we can use our new molecular biology prowess to reduce the domestication process from 1000(0) years to 10.
Food trends start in California, said Karen Caplan. Perhaps she is right. Perhaps most societies will go through an agrobiodiversity bottleneck when they urbanize; but then bounce back when they get rich enough. In a respectable farmers’ market here in Northern California there will — in the right season — always be a stand with only tomatoes, and a least twenty varieties of them. The weirder the shape the better, as long as they taste good. Guess what I had for dinner in my Best Western hotel. T-bone steak? No, a heirloom tomato salad.
Caplan discussed some of the inner workings of getting more agricultural biodiversity through the modern food-chain. Flavor is king. Ignore obstacles. Use influencers such as TV cooks and movie stars to rave about your new potato or brassica. Get it mentioned on a blog.
Ok, the title is a shameless attempt to boost our visit count, but I did in fact want to talk about two modeling studies today — though of very different kinds. I already mentioned the first in a recent post. I have now got hold of the paper on the genetic modeling of domestication and can talk about it in a bit more detail. 2
There’s a conflict in the data on crop domestication, as the authors of a recent PNAS paper see it. 3 The conventional scenario divides the transition to agriculture in the Levant during the period of climate change around the Pleistocene-Holocene boundary into three steps: wild gathering, predomestication cultivation, and fixation of the domestication syndrome. Based on archaeology, field experiments and climatic considerations, each of these steps was thought to be fairly short: the transition was very rapid. The main genetic consequence of such a scenario should be monophyletic crops. And if you look at the number of mutant alleles connected with each bit of the domestication syndrome (the brittle rachis, for example), or the extent of narrowing of genetic diversity from wild relative to cultivated crop, or phylogenetic relationships based on molecular markers of different kinds, you do in fact get evidence that domestication happened only once in many crops, in a fairly restricted area (barley being an exception).
The problem is that archaeologists have now put a spanner in the works. They’ve changed their mind on the timescale, and in a pretty spectacular way. Rather than maybe 2,000 years, they are now saying the whole domestication process took closer to 12,000 years in the Levant, elongating each of its component stages quite considerably. This extended timeline means that the likelihood of independent, multiple, geographically dispersed domestications of a given crop — and indeed of the different crops making up the Neolithic Package — is much greater. That, however, would be expected to lead to polyphyletic crops.
So how do you reconcile a protracted domestication process with crops which genome-wide surveys suggest are monophyletic? Well, according to the authors, there is in fact nothing to reconcile.
They build an in silico model consisting of virtual plants with chromosomes carrying lots of biallelic markers, put them through one or more domestication bottlenecks and a subsequent expansion, with varying possibilities for population amalgamation in the multiple domestication case, left the populations to cycle through a range of different numbers of generations, and then looked at the phylogenies for each chromosome.
The result was surprising, even counterintuitive. For multilocus systems, “multiple-origin crops are actually more likely to result in monophyly than single-origin ones.” All the simulations eventually led to monophyletic crops, the speed with which they did so depending on population size: by 2N generations, a crop was monophyletic whether it had been domesticated only once or multiple times.
What does it mean if the transition to agriculture was indeed as protracted as the archaeological evidence suggests — and as the genetic evidence can also be interpreted to suggest, at least based on this modeling study? Well, I suppose one thing that could be said is that the balance between artificial and natural selection may not have shifted as completely and suddenly as was thought. Which would perhaps strengthen the hand of those looking for ways of facilitating the use of large collections through provenance data.
The other kind of model I want to discuss is “climate envelopes.” We have also blogged about this before. The idea behind these things is simple. You dot-map the present distribution of a species. You then extract the climatic data for the places where the species has been observed. That’s your envelope for the species. You then say, ok, what’s going to happen in these places under climate change? Some places will change so much they will move out of the envelope. Other places which are nearby geographically but currently outside the envelope will move into it. The assumption is that, given no change in adaptation, the species will either migrate from the old to the new places, or go extinct. Apocalyptic estimates of possible extinctions due to climate change have been reached using these methods.
But it seems there may be some problems with such an approach, according to another PNAS paper 4 We’ve always known that they omit things that are important in determining species distributions: soils, competitive effects, human interference. But there may be an even more fundamental flaw. The authors built climate envelopes for 100 European bird species both based on real data about species occurrence and also based on random collections of points “designed to mimic the spatial structure of the birds’ real distribution.”
The result?
For 68 of the 100 species, the five distributions that fitted their climate envelopes best were null distributions. So climate envelopes generated from real distribution data did not describe that data as well as some of the climate envelopes fitted to distribution data made up without any thought of climate.
Climate is no better than chance as a way of describing the distribution of many species. At least of European birds. Time to test if it is the same for crop wild relatives, say?
Luigi homed right in on the money quote when he nibbled an Economist article about changed foodways in one small part of America:
35 years ago, I was bringing seeds from France to California. Now I’m bringing seeds back to my friends in France.
Alice Waters, founder of the fabled Chez Panisse restaurant in Berkeley and the soffrito of the US food movement, with a pithy sound bite. But what does it mean? The Economist quotes other luminaries to suggest that the Europeans are defending a food culture while the Americans are building one, whatever that means, but doesn’t actually unpack why the trade in seeds should have reversed direction. 5
I can think of two reasons.
First, plant breeders in the US have been busy at work creating new varieties that are particularly suited for the loving local care now being lavished on food. That certainly is true. I know of a few examples, some of whose wares are being grown in Europe.
Secondly, and more likely, varieties that French gardeners and growers developed and nurtured are no longer freely available in France. They successfully made a new life in the New World, and now, like lots of older first generation immigrants, they’re coming home on an assisted passage in Ms Waters’ luggage.
European regulations guarantee that seed you buy will be distinct, uniform and stable and will actually be what it says it is. America and all other countries often have a similar system for those who want it, but they’re also willing to let growers take their chances on an unregistered variety. In Europe, it’s registered seed or nothing. Even the latest regulations, to permit the marketing of so-called conservation varieties, do nothing to encourage further development. They simply preserve in aspic seeds that can be grown by besmocked jolly peasant farmers, equally pickled.
I’m a little surprised that the staunchly free-market Economist has not itself had a go at the monolithic European regulations, and I would have said so there. Alas, comments at high-traffic web sites are almost uniformly unreadable, a perfect example of Sturgeon’s Law in action. Perhaps I’ll just pop in to link to this. 6