Author: Luigi Guarino

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Harlan II – Field trip

Robert Hijmans puts his money where his mouth is.

I took the train to Berkeley, less than two hours from Davis towards San Francisco. I checked in at the French hotel and dined in the restaurant across the street. We are talking about Alice Waters’ place, Chez Panisse a restaurant well known to the readers of this blog and in-flight magazines.

There is the formal restaurant downstairs (fully booked) and the café upstairs (a late table was available). I had wine made of Zinfandel grapes. ((Quintessential Napa, only recently discovered to be the Croatian variety “Crljenak Kasteljanski” — or so I learned at Harlan II.))

I took the US$29 fixed menu. It had a garden lettuce salad, spaghetti alla Norma with eggplant, tomato, basil, and ricotta salata, and a Concord grape sherbet with roasted Thompson seedless grapes and langues de chat. ((Sic. Why the mix of English, Italian and French?))

These were the variety names on today’s menu: Concord grape, Thompson seedless grapes, and Little Gems lettuce.

And these were the farm names on the menu: Cannard Farm ((As in: “Cannard Farm rocket with shaved zucchini, pine nuts, and pecorino, $9.00”)), Andante Dairy, Soul Food Farm, Marin Sun Farm, Lagier Ranches, and Frog Hollow Farm.

Terroir trumps agrobiodiversity at Alice’s place.

It is a good restaurant. It is very French. The waiter spoke of terroir as if his name were Claude Duchateu. It is very cheap for a famous restaurant. It has a local twist to it. The food is good. But is mainstream now. The menu in the Davis Best Western Palm Court was not that different.

I suppose it is fair what everybody says, that Alice created some sort of revolution. From the wasteland of the American diner to Good Food. Just like her neighbor Alfred Peet transformed mainstream American coffee from diluted sewage to the best coffee anywhere save (perhaps) Italy. But that is ancient history.

But, just for your information, Chez Panisse is passé now. Go look somewhere else. I have heard of an underground restaurant movement in New York.

Chez Panisse is sold out every night, I think. Alice can experiment. But she does not. She chooses the middle of the road. Their produce comes from “farms, ranches, and fisheries guided by principles of sustainability” but the majority of entrees (main dishes) are a fish or meat dish.

Chuck out the meat. Serve different varieties of other veggies than tomatoes (even the Andronico’s supermarket across the street sells heirlooms).  Use something locally evolved rather than merely locally grown. The native Californians used hundreds of edible plants. ((Full disclosure: After being captured and given the opportunity, Ishi, the last ‘wild’ Californian Indian, quickly switched to a doughnut diet.)) But no miner’s lettuce or acorns on the menu of the Queen of Slow Food.  Come on, Alice, surprise me!

P.S. That pasta was really good though. I will go back tomorrow to further investigate the case.

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Harlan II, day 4

From a very tired and emotional Robert Hijmans. Previously….

No domestication without relaxation. Today was excursion day at the Harlan II symposium.  All to the Napa wineries you’d think, but no, there were not enough registrants for that. ((Editor’s note: Excuse me?)) But there was a  tour of  the Charles Rick Tomato Genebank and a “Native Biodiversity and Plant/Pollinator Interactions”  tour, visiting field sites used by Claire Kremen’s group. But I had my own program. Before I get to that, which I will do in a separate post, allow me to make to parting comment on the Harlan II symposium.

On day 1, I mentioned that molecular biology rules. The increased understanding of the relatedness of populations of different crop taxa and their wild relatives is having a tremendous effect on our understanding of domestication and dispersal of agrobiodiversity. The flurry of recent papers on this subject has probably not escaped the attention of readers of this blog.

Be that as may, I should also have mentioned the explosion of archaeological data and analysis. Compared to 10 years ago, there are now many more late Pleistocene to early Holocene settlements that have been analyzed. This is providing a much more refined insight into early agriculture and domestication than was previously possible.

I do not know why there has been such an increase, all of a sudden. More people and money thrown at it, no doubt, but why now? At the same time, and perhaps not unrelated, there appears to have been an important increase in the sophistication of the methods used to study agricultural origins. Extracting charred starch particles from pot fragments or mortars. Determining minor differences in grain sizes to classify them as one type or the other. Tallies of bone sizes to determine whether the animals were hunted or farmed. And then there is the analysis of ancient DNA. And so forth. Not much Indiana Jones in it, but it is quite safe and more intellectually rewarding.

Most insights about agricultural origins still come from the Levant. While other areas are much less explored, they are also moving along. For many places and periods, we now have a good idea about what plants and animals were eaten. That is why we now know that there was a long transition from cultivation to domestication. This is why Dorian Fuller was able to show us graphs with changes in crop characteristics over time for multiple crops (wheat, barley, rice).

The origins of agriculture and the domestication process that took place about 10,000 yrs ago are fascinating and fundamental to the understanding of the history of humans. But domestication has never stopped, and will not stop, despite EU regulations. There are many other stories, from other regions, from other (not cereal) crops that have been much less explored.

Jared Diamond is convinced that no more crops or animals of major importance will be domesticated. He says that crop and animal domestication happened where there were species predisposed to be domesticated. We found them millennia ago. That is why agriculture originated where it did, and this is one of the reasons why some places are richer than others.

I wonder whether we can be more imaginative about what domestication could do to some wild plant or animal. We now know what it takes and can engage it what Melinda Zeder calls “directed domestication”. Perhaps something for an X-Prize.  A hundred million dollars for anyone who can develop a crop that is now insignificant (say less than 10,000 ha) to an area of at least 10 million ha. I agree that it is hard to image that  this will happen with staple food crops, but it is bound to happen with an energy crop.

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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?