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Summarizing livestock domestication

You want a rapid gallop through what we have learned about livestock domestication from molecular markers? Here it is, courtesy of Groeneveld et al. Deep breath…

For all domestic species, mtDNA data have allowed the elucidation of the relationships with wild ancestor species, and for most species it is also informative at the intercontinental level… Sheep, goats, and taurine cattle (Bos taurus) are presumed to have been domesticated in Southwestern Asia. The Indus valley has been proposed to be the site of domestication of indicine cattle and the river type of water buffalo, while the swamp type of water buffalo is thought to have originated in the Yangtze valley. The domestication of pigs is considered to have happened across Eurasia and Eastern Asia in at least seven separate events involving both European and Asian subspecies of boar. The Yak is presumed to be the result of a single domestication event in China/Tibet with at least three maternal lineages contributing to the ancestral yak gene pool. Domestic chickens are thought to be the result of multiple domestication events, predominantly of Red jungle fowl (Gallus gallus) in Southeastern Asia and possibly also involving Gallus sonneratii and maybe Gallus lafayettii. Horses were domesticated in a broad area across the Eurasian steppe, and in this species the husbandry style has left considerable signatures. It is presumed that mares were domesticated numerous times, but that only a few stallions contributed to the genetic make-up of the domestic horse. The last finding illustrates the use of Y-chromosomal haplotypes as a marker for mammalian patrilines. This is still limited by the identification of haplotypes, but probably has the same potential as in human population genetics.

Quite a tour de force, I think you’ll agree. Read the paper itself for trenchant summaries of the results of literally dozens of molecular studies on these species, describing the relationships among breeds and geographic patterns in diversity. But if you’re just interested in the general principles, here they are:

  • There is evidence of multiple domestication events for most species.
  • These often involved more than one ancestor species or subspecies and
  • repeated introgression events of closely related ancestor species.
  • Genetic variability declines with increasing distance from centres of domestication.
  • All species show strong geographic structure in genetic diversity, except sheep.
  • Most of the genetic diversity is present within a breed and not between breeds.

The most interesting thing to me is the geographic structure, and the one thing the paper doesn’t do in any great detail is compare and contrast the patterns found in the different species. I mean, are horse breeds from Iberia more distinct from other European horse breeds than its cattle breeds are from other European cattle breeds, say? And if so, why? The paper describes the patterns found in each species, but doesn’t set them side-by-side, as it were. Once someone does that, we can go on to compare them with what we know about crops…

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Why the sorghum crop failed in Kongwa — it’s not what you think

ResearchBlogging.orgThe average agricultural research paper describes some kind of formal experiment, whether in the lab or the research station or even farmers’ fields, and that is as it should be. To know if something really works, you need to be able to keep everything else the same. But there are experiments going on all the time out there, in real life, if you but know how to look. There is surely room in the scientific literature for more of the kind of case study reported in a recent paper in Food Security entitled “The underlying cause of the 2009 sorghum failure in Kongwa district and its implications for Tanzania’s vulnerability to climate change.” 1

Through a series of in-depth household and farm surveys the authors seem to have been able to identify the reason why the sorghum crop failed in Kongwa in 2009, and use that information to make general recommendations about what should be done to prevent this happening again in the future, not just in that area but elsewhere in Tanzania.

So let’s set the scene. People in Kongwa are poor, most living on less than $1 a day. They are on the edge of subsistence. They used to grow mainly maize, increasing the area of sorghum when the early rains were poor. Since about 2003, however, sorghum has been the main crop. They grow a suite of local sorghum landraces called Lugugu: long-duration, good-tasting and hard-grained, which means they can be stored for a long time if need be. They also have access to three improved open-pollinated varieties from ICRISAT 2: shorter-duration, which means they can cope with drought, but softer and thus more susceptible to storage pests, and also prey to the parasitic herb Striga. But then there are two Striga-resistant varieties on the market, bred by World Food Prize winner Gebisa Ejeta and released in Tanzania in 2002. Often, the early varieties are grown as a cash crop, sold to buy maize, which is the preferred food still.

In 2009 the rains started badly, and farmers were encouraged by local politicians, in their inimitable way, to “plant drought-resistant crops.” Of course they did, as they would have done anyway, but crop production was nevertheless below requirement. Why?

In fact, it seems that overall the rains, although relatively poor, should have been more than enough for the short-duration varieties. Problem was, there was no seed of these varieties at the optimum time for planting them. And when it finally arrived, too late to take advantage of what early rain there was, it was infected with Covered Kernel Smut. There was no seed at all of the Striga-resistant varieties in the area.

This is not a new problem. Shortage of improved sorghum seed was identified as a constraint as far back as 1987. But none of the village-based seed production projects that have been carried out has had much of an impact, clearly. At least not after the donor funding ceased. And, unfortunately

…the Government of Tanzania has actively discouraged farmers from conserving local sorghum landraces and this has resulted in increasing dependence on so-called improved varieties and is a long term threat to household food security.

Actively discouraged from keeping their long-duration but storable varieties; actively encouraged to plant new varieties that are more drought-tolerant, sure, but can’t be stored, cost money that they don’t have and whose seed is not available anyhow, or at least not in time. Who’d be a Tanzanian farmer?

Now, it seems that “the short rainy season that characterised the 2008–09
cropping season may become the norm,” so some answers need to be found. Better water management is one. And improvement of local seed storage practices. Also,

…attention should be paid to conserving indigenous landraces and breeding improved short season varieties that can be stored for longer periods using traditional, on-farm practices, as this would reduce the need for expensive and unsustainable external seed multiplication systems.

And, I would add, perhaps look into the feasibility of push-pull control measures for Striga.

But mostly the study seems to me a damning indictment of the existing seed system, and of it’s seeming lack of integration with the breeding sector. What good is breeding those “improved short season varieties that can be stored for longer periods using traditional, on-farm practices” if they don’t get to the farmers in time? Indeed, why has storability not been a breeding objective? Well, perhaps it has, and weevil-resistant stuff is on the way. But will it ever get to the farmers?

Now, talk of an integrated germplasm pipeline — from genebank to breeder to farmer — is all the rage these days, and about time too. The case is only strengthened by studies such as this. You don’t always need a replicated trial to do useful science.

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Livestock biodiversity and conservation gets a global view

Animal Genetics has a Special Issue on “A Global View of Livestock Biodiversity and Conservation,” coordinated by Paolo Ajmone-Marsan and Licia Colli. It includes a review of genetic diversity in farm animals, and an assessment of what climate change means for the characterization, breeding and conservation of livestock. It’s all because of a 3-year EU project called GLOBALDIV.

It is formed by a core group of partners who participated in past EU or continental scale projects on Farm Animal Genetic Resources characterization and conservation. It also involves a much larger number of experts that are actively contributing to the success of the initiative. The project aims at improving the conservation, characterisation, collection and utilisation of genetic resources in agriculture in EU and beyond, complementing and promoting work undertaken in the Member States at the Community level and facilitating co-ordination of international undertakings on genetic resources in agriculture.

As one of the more info-savvy CG Centres, ILRI will no doubt have comments and analysis online very soon.

I got the news via Twitter.

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Tomatoes in Ghana

Cotton farmer suicides in India get all the press, but three years ago we noted briefly the apparent suicide of tomato growers in Ghana. Today sees a meeting in Accra “for a unique exchange of views on how to revive the strategic but ailing tomato sector.” Farmers, traders, processors, academics and donors will be thrashing out a more strategic approach to the tomato sector in Ghana under the watchful eye of the Ministry of Food and Agriculture and IFPRI (the International Food Policy Research Institute). IFPRI anticipates that:

Improvements across the board could reduce Ghana’s reliance on low-cost imported tomato paste, improve its foreign exchange reserves, and provide employment and development opportunities in poor rural areas.

How many wins is that?

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Vaccines, vitamins and er .. lemme see .. vital information!

Michael Specter is a staff writer for The New Yorker, has a book out called Denialism: How Irrational Thinking Hinders Scientific Progress, Harms the Planet, and Threatens Our Lives, and gave a recent TedTalk on The danger of science denial that has created quite a stir, most of it positive. And I’m mostly in accord.

People who refuse to vaccinate their children are indeed free-riding anti-social parasites, no matter what cockamamie reasons they give for their refusal, and those who aid and abet them by stoking fears about the dangers of vaccination are, if anything, worse, because their stupidity is a multiplier that endangers so many more of us.

And yes, people who spend (lots of) good money on vitamins and quack cures and other folderol that is not only not efficacious but sometimes downright harmful are indeed fools, easily parted from their money and probably suffering into the bargain, let alone the leeches who prey on them. 3

But — and here, at last, is where we approach the admittedly catholic tastes of this blog — when Specter turned to the denialism that, he says, condemns million of hungry people to miserable starvation and an early death, I got just the teeniest whiff of inconsistency. What were his chosen examples for the evidence-based decision-making that he wants us to embrace not only for vaccines and vitamins but also for the vital business of feeding people with GMOs? Golden rice and super-cassava.

I kid you not.

It’s true that modern rice varieties lack vitamin A precursors. It’s also true that golden rice 2.0 delivers more carotenoids than version 1.0. But so do many other foods that people can actually grow for themselves, that a diversified agriculture and diet can provide and that are almost certainly cheaper and more sustainable than golden rice. So where, precisely, is the evidence that golden rice is the best, or even a good, solution to the problem of vitamin A deficiency? Specter seems completely unaware that the alternatives even exist, let alone that they could be made available now, everywhere.

Likewise, Specter may not rate cassava all that highly, but the plant provides people with far, far more than the the “empty” calories that Specter assumes. For a start, cassava leaves are widely eaten, and supply many of the nutrients lacking in the tubers. I remember someone telling me that leaves infected with cassava mosaic virus may actually be more palatable and more nutritious than uninfected leaves (although I confess I cannot now find the details). Will one engineered super-cassava be suitable for all the places where it will be needed? How easy will it be to create the huge diversity of super-cassavas that Africa’s diverse growing conditions require?

Let me be absolutely clear. I am not against genetic engineering at all. How could I be, when it is only a tool? Indeed, I think that there are far more pressing problems than fortifying staples that deserve and are being denied a genetic engineering approach. I am not denying that one could deliver more vitamin A and other micronutrients by engineering rice and other staples. I am denying that this is the only way, or even a good way. We’ve been round and round these discussions here and elsewhere. What we really need, and what, I fear, Specter does not want, is a little more investment in the alternatives. It might even prove that I’m completely wrong. In which case I swear I’ll change my mind.

That’s how I use evidence.