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.1

There’s a conflict in the data on crop domestication, as the authors of a recent PNAS paper see it.2 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 paper3 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?

  1. LATER: Science Daily has now done a longish piece on the paper, with lots of quotes from the main author. []
  2. Allaby RG, Fuller DQ, Brown TA. 2008. The genetic expectations of a protracted model for the origins of domesticated crops. PNAS. []
  3. Beale, C. M., Lennon, J. J. & Gimona, A. 2008. PNAS. []

True That Chez Panisse Woman

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.1

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.2

  1. Long-time readers will realize that I am about to rail against The System. They can move smartly along. New readers, start here. []
  2. And hope that the traffic it drives by won’t wreck the high tone of our own comments. Obscurity has its benefits. Later … Blast! The Economist, rightly probably, allows no links in comments. Ah well, maybe readers will find us anyway. []

Arrant about (agricultural) biodiversity

There’s something happening out there; what it is ain’t exactly clear.

Over the past few days several people seem to have been talking in mystified terms about biodiversity; what it is, why it gets so little respect, what to do about that, whether it matters anyway. On Monday Luigi nibbled an IEED paper on biodiversity and the media. Mike Shanahan, a journalist for whom I have a lot of time, wondered why other journalists have “under-reported” the loss of biodiversity, and suggested that “researchers and policymakers have failed to communicate the issues”. A couple of days ago a blogger I hadn’t previously come across got into the issue repeatedly, most notably with What the Heck Is Biodiversity? And Why Should We Care?, which was prompted by Thomas Friedman’s new book — Hot, Flat and Crowded — and a new paper from Paul Ehrlich and Robert Pringle. Friedman’s book blurb doesn’t say so (which is ironic indeed) but the man himself thinks that the loss of biodiversity may be even more important than climate change. And Ehrlich and Pringle talk about “a grim future”. A little while ago Tyler Cowen, another person I respect enormously, asked to what extent is the ongoing loss of biodiversity a very serious problem?. Like Friedman, Cowen suspects that “in the long run this will prove a more important issue than global warming,” but he is “not sure”. Finally, and the reason to write this today, now, there’s a paper in tomorrow’s Science that calls for a Global Biodiversity Observing System, a snip at €200 million to €500 million.1

In each of these pieces, people who are convinced that the loss of biodiversity is A Bad Thing and (some of them) that Something Ought to Be Done, lament the fact that so few people agree and either that they don’t know what should be done, or that they do, but nobody worth squat is listening.

We kind of know why. It’s the hoary old boiled frog myth.2 The downside of biodiversity loss is so remote, in time and in space, and so diffuse, that most people really can’t rouse themselves even to think sensibly about it, let alone to act. We need a clear and present danger if we are to respond. Cary Fowler, the esteemed Executive Secretary of the Global Crop Diversity Trust, took this as his lesson in one of his recent reflections.

“[W]e will probably never have a “crop diversity crisis”, because of the lag time between cause and effect. Today’s oversights in caring for this resource provoke tomorrow’s emergencies, but at most we are hard-wired only to deal with the latter.”

Fowler, not surprisingly, is one of the few people I’ve cited who actually makes use of an argument based on agriculture and food. Success, he says, will come when “politicians … realize that positioning agricultural systems to provide food security in a climate changed world is the supreme benefit to be generated from crop diversity”.

As we lament so often, many of the people expressing concern about the loss of biodiversity don’t even recognize the value of diversity for and within agriculture. Among all the airy-fairy remote, distant and diffuse benefits of biodiversity, why do they ignore food?

We bang on about the need to preserve agricultural biodiversity in crops and wild relatives as insurance against disasters, but alas the disasters don’t seem to be happening, just yet. In vain I scan the headlines each day for news of a devastating outbreak of Asian soybean rust, or wheat rust UG99, or even good old potato blight, but they just refuse to happen. We know about past disasters, and we know how agricultural biodiversity helped to overcome them, but that’s ancient history. We’re much safer now.

A few of us cry wolf, and we are ignored, and we all know what happens to people who cry wolf too often. I sometimes wish I could summon some real demons to do some real damage to the food supply. Yes, a genuine crisis: but isn’t it the case that in chinese, the word for “crisis” is compounded from the words for “danger” and “opportunity”?3

Alas, a food crisis isn’t likely to help. At the risk of promoting yet another hoary old chinese myth, “well-fed people have many problems, hungry people have only one”. By the time politicians and policymakers are hungry (like that’s ever going to happen) protecting any kind of biodiversity will be the last thing on their minds.

In all seriousness, how do we get people — including conservationists — to understand that if they don’t conserve and make use of more agricultural biodiversity, they’re probably not going to be around to enjoy the benefits of conserving lots of wild biodiversity?

  1. Scholes, R.J., Mace, G.M., Turner, W., Geller, G.N., Jurgens, N., Larigauderie, A., Muchoney, D., Walther, B.A., Mooney, H.A. (2008). ECOLOGY: Toward a Global Biodiversity Observing System. Science, 321(5892), 1044-1045. DOI: 10.1126/science.1162055 []
  2. And yes, I know it’s a myth; the problem is nobody seems to care. []
  3. No, it isn’t. []

Ecologists breaking (unwritten) ecological laws

Andy Jarvis, our man with the global insights, sends this despatch:

This article just came out in Science about assisted colonization.1 That is the fancy term for moving a population from one place to another. Over the past few years this concept has been gaining ground, especially with the barrage of horror stories about the impacts of climate change on the geographic range of species. The authors propose a decision framework to identify candidate species for translocation (or assisted colonisation as it seems to now be called). The decision framework consists of criteria for threat, feasibility, and cost-benefit. Amazingly, the whole concept of ecological risk is not taken into account in the decision framework. The authors mention it in the text, and sidestep the issue somewhat by saying that these are short distance translocations, but this may not always be the case. With the best of intentions, we’ve had some really great “assisted colonisation” events in the past that have caused ecological disaster. See Australia, Lake Victoria, the Southern US, etc. etc. The list is endless.

Before I go too far, I must step back and state the positive side of this concept. After all, the objective is conservation. Done properly, with sound risk analysis of direct and indirect impacts on ecological communities (and anthropogenic systems, like … errrr… agriculture), assisted colonisation could save species from near certain doom. An innocent way of seeing it is that you are just lending a hand to species who can’t quite migrate as fast as others. If migration rates are lower than the speed of climate change, or a pesky river gets in their way, then ecologists come to the rescue and move you. It’s like helping an old lady across the road.

Avoiding long-distance assisted colonisation is a useful surrogate for “eco-safety” (a new term is born), but I think it is dangerous as many assumptions are being made with that one. Suggested next article: Risk analysis framework for assisted colonisation. Readers get going.

As a side note, and while I am in the mood for inventing new terms, we also need to come up with a name for this kind of conservation. We have in situ, we have ex situ. What would be good for this kind of conservation? Non-situ could well be the case if you don’t assist colonisation, but I can’t think of a good name for populations that are assisted. Anyone fancy a place in the history books by giving this a name?2

  1. O. Hoegh-Guldberg, L. Hughes, S. McIntyre, D. B. Lindenmayer, C. Parmesan, H. P. Possingham, C. D. Thomas (2008). ECOLOGY: Assisted Colonization and Rapid Climate Change Science, 321 (5887), 345-346 DOI: 10.1126/science.1157897 []
  2. I propose neo-situ. Ed. []

Diversity really does benefit farms and farmers

Anastasia and Jacob commented on the post about eating insects, to the effect that converting insects into chickens might, despite the inefficiencies involved, be a better way of using insects than converting them directly into people. I loved watching the film Jacob pointed to, not least because I used to work with chickens, love chickens, and love to hear the peeping of contented chicks. And I found Anastasia’s link to a company seeking to replace the fish protein in mass-produced chicken feed with mass-produced insect protein interesting and illuminating too, even though (especially because?) it comes at the problem from exactly the opposite end of the agro-industrial scale.

There is, of course, a middle-way, one that is applicable to more intensive operations in more developed countries. Let the chickens eat the insects growing on manure, without first collecting the manure! I know it sounds wacky, but it works, and has done for a few centuries, at least. After his week visiting Joel Salatin’s operation Michael Pollan waxed positively evangelical about how Salatin follows cows with chickens on his pasture, the miracle being that Salatin doesn’t let the chickens in immediately but waits four days, which is when the dung fly larvae are at their biggest, juiciest and most nutritious. Smart. I also remember visiting the Land Institute’s Sunshine Farm in Salinas, Kansas, back in the early 1990s, when it was under the care of the wonderful Marty Bender. (This is the closest I can get to his obit at The Land Institute’s site1, but here’s a taste.)

Marty showed me a huge pile of manure, way above my head, being worked on by a fine crowd of fit-looking hens. I can’t remember the details, but as I recall this was effectively the sweepings from the stock’s winter barn, just shovelled out the door with a bulldozer and left there. This is where I get hazy. I think that in due course the mound was reduced and spread out to the point where it could be used to grow veggies. And each spring a new mound would be created, moving around the winter barn. That’s it in principle anyway, a wonderful piece of integration on the farm.

Which leads me nicely to something else I read with pleasure recently. Gary Jones has a fine piece over at Muck and Mystery, explaining how farms, particularly in the Northern Plains of the US, integrated cows into their system through a technique called swath grazing. Farmers pile crop residue into rows called swathes and let the cattle graze them right through the winter. I won’t say more than that, because Gary has done a great job of explaining why that’s a good thing, why it stopped, and why it now might make good sense to start again.

d1177-1.jpg Gary’s post was prompted by a report from the USDA on recent research into Integrated Farming Systems. That’s the USDA’s picture of cows grazing on corn swathes in the winter snow in North Dakota. The money quote:

“Adding diversity brings sustainability to farms, both economically and environmentally.”

The Ghanaian chicken farmer, the Florida feed manufacturers, the farmers of the Great Plains and the corn belt; they’re all doing the same thing: making the best use of their resources. In farming, as in everything else: “the future is here. It’s just not evenly distributed yet.”

And one of the ways in which I think the future will change farming is that smaller will become more beautiful. This is something I’ve been thinking about a lot recently, brought into focus by the slight drubbing I’ve received from the same Gary Jones2 over my sloppy writing on pesticides. Until now, get big or get out was the way of industrial agriculture. But scale is going to have to change as it becomes more expensive to move things about the old way. The big guys have had the clout to make the system work only for them, effectively squeezing out the small fry. It happened with abattoirs in England and seed merchants throughout the European Union. And now its happening to small farmers hit by the same natural disasters as the big farmers but denied the same level of compensation by government. Maybe that will change too, but not without a fight.

  1. Come on people, you really need to do something about that. []
  2. See, no hard feelings. []