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Harlan II, day 3

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. ((Domestication in the not very strict sense of using more of relatively little exploited biological resources.)) 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.

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Top models reveal all

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. ((LATER: Science Daily has now done a longish piece on the paper, with lots of quotes from the main author.))

There’s a conflict in the data on crop domestication, as the authors of a recent PNAS paper see it. ((Allaby RG, Fuller DQ, Brown TA. 2008. The genetic expectations of a protracted model for the origins of domesticated crops. PNAS.)) 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 ((Beale, C. M., Lennon, J. J. & Gimona, A. 2008. PNAS.)) 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?

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Harlan II, day 2

Robert Hijmans weighs in with his second posting from the domestication front lines. Thanks, Robert. Previous post here.

Change. Obama wants it, McCain wants it, I want it, and perhaps you want it too. Farmers just do it. At least that seems to hold for many of the farmers living in the major agrobiodiverse areas. While they maintain diversity, it changes all the time. Whether deliberate or not, as time goes by farmers will never quite have the same set of varieties or genes. That was one of the main story lines of today’s presentations at the Harlan II symposium in Davis, California.

Jan Salick sampled the cassava varieties of a community in the Peruvian Amazon. In a period of 10 years most varieties were replaced, probably to get rid of virus infestation and other forms of degeneration. But people very actively exchange and spread new varieties. And while not all farmers select from spontaneous seedlings, some do. This practice seems very important in this otherwise vegetatively propagated crop; an observation also made yesterday by Doyle McKey. But how common? We seem to know little about that. There are also cases of relatively little change over 40 years, as documented by Karl Zimmerer for potatoes near Cusco, Peru.

Change in diversity is hard to measure. Yes, even current patterns are hard to measure without going the whole nine yards of molecular biology. Toby Hodgkin showed how variety names can be poor markers for genotypes. But farm level variety data from “in situ conservation” projects in several continents revealed some general patterns (see this paper) about the number and relative distribution of varieties. Whether these patterns will hold to be general I do not know, but they do provide a benchmark. That is useful. In situ conservation should be less about good intentions, and more about data and consequences.

Hodgkin and collaborators also described the importance of seed exchange networks. Millet farmers (mostly women) in Mali go to the market to exchange seed they will take home to try. If the seed are any good some genes will likely end up in their populations.

In many of these agrobiodiverse, and often marginal  — ecologically and/or economically — areas the Green Revolution has not made much of a difference. It seems to me that knowledge of these exchange processes that maintain crop diversity should not be only used to think about how to conserve  it in situ. It could be more important to think about how to make use of these networks to insert new diversity. Not as the perfect high yielding variety, but as diverse sets of reasonably adapted genotypes with interesting traits that could be incorporated into the farmer’s populations. Building on existing processes that allow for local resilience and adaptation seems to be a good strategy in the light of the rapid climate change and other changes we are witnessing and expecting to see more of in the future.

We really do not seem to know that much about what is going on. The global village is big place. But at least some are trying. Gary Nabhan is one of them. In a copious lecture he discussed some of the material in his recent book describing his efforts to follow the footsteps of Vavilov to asses change in the areas where the great man collected. ((Rumor has it that a certain Jeremy Cherfas is setting up a blog devoted to this
project.))

Nabhan found fewer apples near Alma Aty, the city of apples (and formerly of speed skating, I would add). Crops moving upslope in the Pamir mountains as its glaciers melt. In Ethiopia, wheat and barley are diminishing, giving way to a boom of the indigenous teff. The old crops of the southwestern USA are about to go extinct.

It is hard to generalize, but overall the news is not that good if you care about agrobiodiversity in the field. It does not seem to be going up in many places. Or is it?

Not too long ago, there were a million hectares of a single potato variety “mira” in southern China. Farmers had no idea that other varieties existed. I do not know what the situation is right now. But if is important to have agricultural biodiversity in the field, it will perhaps be more effective to increase it in crops and areas where diversity is low than trying to maintain it in areas where it is high.

Without understanding the context of the farming systems and the drivers and patterns of change, it is difficult to say something sensible about the fate of agrobiodiversity. I think the symposium organizers realized that. We had Bill Turner talk about  the collapse of Mayan agriculture — which was likely related to overexploitation. What used to be the home of one of the worlds most advanced cultures is today a rather empty land with few people and not much natural biodiversity either. Karl Zimmerer discussed more current land use patterns and change near Cochabamba, Bolivia. Male outmigration, leading to remittances and investments in irrigation. Fewer potatoes, more peaches…

We are moving forward in our understanding of the use of biodiversity on farms. But the world is changing much faster still. This is affecting agrobiodiversity in unprecedented ways. We need more data, we need more synthesis. We need it soon.

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Nibbles: Policy book, Seeds, Nicotiana, Kibera greens, Slow Food, Peas, Costa Rica