Category: Wild relatives

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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 1

From our man on the spot at Davis, Robert Hijmans.

It is only one day old, but the Harlan II symposium is the best I have been to for ages. That the subject is of some importance helps, of course. In his keynote speech, Jared Diamond called it nothing less than the most important event in the last million year of human history. Guess what, it has something to do with agrobiodiversity. It is plant and animal domestication, of course. Have a look at the program and you may understand that I am challenged to summarize the proceedings. But here are some impressions.

Domestication took a long time. Dorian Fuller summarized archaeological data to show that traits associated with domestication, such as non-shattering of grains, evolved slowly, over 1000s of years. Some speakers distinguished the initiation of cultivation from domestication. I had always thought of these two things as happening at the same time. But why not cultivate wild wheats, or rice? Benjamin Kilian showed data suggesting that wild einkorn was cultivated in Turkish parts of the Fertile Crescent. And Susan McCouch of Cornell University pointed out that, after 4000 years of cultivation, the common rice of West Africa, Oryza glaberrima is not domesticated yet: it still shatters. And I think there are many animal species that are not domesticated but that are nevertheless put to good use. Vicuña for example.

The question whether we domesticated plants or they domesticated us was not (yet) discussed, but there was reference to the self-domestication of dogs and cats. Robert Wayne showed that dogs were domesticated from Mediterranean grey wolves. But wolves are not very friendly to humans, how would you go about taming them? Wayne thinks that it was the wolves who approached our ancestors because they liked to eat the leftovers of their hunting parties. Over time, they may have lost some of their fear and aggression towards humans (obviously not realizing they would end up as chihuahuas). Likewise, cats may have approached ancient towns to catch some of the abundant mice in the granaries of the agricultural revolution.

Molecular biology rules. Remarkable progress is being made in analyzing the genetic make up of crops, the remains of ancient crops, and of crop wild relatives, to solve the puzzles of how our crops and domestic animals left their wild states. In some cases, this work leads to truly new insights in otherwise uncharted territory. In other cases, the molecular work confirms or refines insights that others had obtained from morphological, geographical, and archaeological data.

Even religion was invoked. John Burke explained that sunflower become a popular source of oil in Russia because it could be used during the Lent season, whereas all other sources of oil were on the black list of the Russian church. Gila Kahila Bar-Gal has put the insights from her ancient DNA work on archaeological remains of caprins (goat like creatures) to good use: she showed that the Dead Sea Scrolls were written on goat skin (not sheep). Unfortunately, there was also pieces of (wild) oryx skin — which is not kosher — but these were only used as wrapper; a relief.

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Feasting it up in the Neolithic

A Guardian article on the evidence for large-scale feasting at Stonehenge, and in particular on the long-range movement of cattle to the site, reminded me that I had wanted to link to a more general paper about the phenomenon of Neolithic feasting. I have only had access to the abstract so far, but the paper seems to argue that feasting and agriculture went hand in hand, and that in fact the practice may have led to the domestication of cattle. Bit of a chicken-and-egg problem there, at first sight, but I’ll wait for the full text before commenting on that at any greater length. In any case, it seems that barbecues go back much further than the Neolithic.

Actually, I may as well put another marker down. Dienekes’ Anthropology Blog, my source for the feasting paper, also recently had a post about crop domestication. Again, I don’t have the full text yet, and will discuss this more fully when I do. But it seems the paper argues that there is a tension in the data on crop domestication between archaeology, which shows that the process was slow, stop-start and dispersed geographically, and the genetics, “suggesting that domestication (sic) plants are monophyletic, the result of a single domestication event in a definite place.” Well, I don’t think the genetics is saying that at all for many crops, but, be that as it may, the paper apparently presents a simulation model which shows that “multiple-origin crops are actually more likely to result in monophyly than single-origin ones.”

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