Category: Wild relatives

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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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Nibbles: Yeast, Weeds, Bioprospecting, Iraq, Pine wilt, Vietnam, GM, GM, Insects, Bees, Sheep, Fowl

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Lost in genebank database hell

Navigating around germplasm databases can be a frustrating experience. A posting on the CropWildRelativesGroup alerted me to a Science Daily piece on tomato genomics which mentioned the wild relative Lycopersicon pennellii (or Solanum pennellii, but I’m not going there, at least not today). But how many accessions of this species are conserved ex situ? And where is it found in the wild?

Ok, so SINGER first, as that’s been much on my mind — and on this blog — of late. SINGER shows 61 accessions of L. pennellii, all from the AVRDC collection. Most of them are from Peru, although 7 accessions have USA, Mexico, Poland (?) or “unknown” as source country. None of these accessions seem to have geo-references, so no nice map from SINGER this time. Pity. But SINGER does give very neat summaries for your query results. ((Incidentally, AVRDC has its own Vegetable Genetic Resources Information System online, which has 65 records for L. pennellii.))

GRIN returns 51 accessions. I can’t find any easy way of working out the duplication between these and the AVRDC material, but I imagine it is significant. Again, most of the accessions are from Peru, but it’s kind of difficult to get summary information across all accessions in GRIN at the moment, though I know they are working on this. Now, tomato germplasm is conserved at the C.M. Rick Tomato Genetic Resources Center (GRIN tells you so), and they have a database of their own. Querying it results in 45 hits, but again there’s no easy way I can see of looking at summary information across all these. You have to look at each individual accession in turn to find out where they’re from, and if you do you get a little map too. The thing I don’t quite understand is why the accessions are geo-referenced in the Tomato Genetic Resources Center database, but not in GRIN. Maybe they’re upgrading the data gradually at the Centre and haven’t passed the latest version on to GRIN? That may also explain the discrepancy in accession numbers. It looks like they’re working on the geo-spatial part of the database, and it may well be possible to get a map of all the accessions of a particular species eventually.

You can of course do that in GBIF right now, but GBIF only has 8 geo-referenced L. pennellii records: from the Missouri Botanical Garden, the Dutch genebank and the European germplasm database, EURISCO. Too bad the Tomato Genetic Resources Center is not a GBIF data provider. And, indeed, that its geo-reference data is not included in GRIN, which is a GBIF provider.

So the answers to the questions I started with are: at least, and probably not much more than, 112, but that probably includes duplicates; and Peru. But I cannot produce a decent map of the distribution of L. pannellii online. I would have to mess around and download the data from the Tomato Genetic Resources Centre database, and then map it myself. Which I may well do, just to show it can be done. But this little exercise does show that there’s a lot of work to be done to improve the data in — and fully integrate — existing agrobiodiversity databases.

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Nibbles: Poppies, Gardening, Milk, Grapes, Genebanks, Meat, Biotech, IK, Plant health

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SINGER maps crop wild relatives

Putting the new SINGER interface through its paces, I find that it can do something interesting that GRIN cannot. Or at least I can’t see a way of doing it, let me know if you can. Below is a screenshot from SINGER showing a Google Map of the distribution of all wild Arachis accessions that the database knows about which have geographic coordinates. Very useful, I think. GRIN does map localities, but I could not manage to get it to do so for multiple species like this.