Ancient agricultural DNA everywhere

Heady days for ancient DNA researchers. There have been two major papers in the past month looking at the DNA of Neolithic farmers. Back in June, a huge research consortium published “The genetic structure of the world’s first farmers” as a preprint in bioRxiv, with subsequent write-up in Nature. And now a different huge consortium comes out with “Early Neolithic genomes from the eastern Fertile Crescent,” in Science. That also got widely picked up.

Don’t ask me why two separate research groups need to be working on basically the same problem, in basically the same way. I suppose they’re using somewhat different methods on different material. I really couldn’t tell you whether it would have been better to pool the material, or standardize the methods, or indeed both. Maybe someone out there will tell us. In any case, it’s reassuring, I suppose, that the two studies came to broadly similar conclusions, namely that there were genetic differences among early farmers, and that genetically distinct people from different parts of the Fertile Crescent migrated north into Europe and eastwards further into Asia. Which in turn suggests to some that the origins of agriculture may be described as “federal”:

Different and genetically distinct populations were all engaged in this same general project, albeit exchanging ideas with each or other or sometimes coming up with the same idea independently.

Meanwhile, sequencing of DNA from a 6000-year-old barley from the Dead Sea shows close similarity with varieties still grown in the southern Levant and Egypt. Intriguing to speculate whether a similar study of material from the Zagros Mountains would show a parallel pattern to the human DNA. But will it need a different group of researchers to do it.

Brainfood: Ghana cassava, Paspalum hybrids, Wild safflower, Genotyping for phenotyping

One for the birds

There’s a great set of photographs on the Facebook page of Leo Sebastian, Regional Program Leader, Southeast Asia at CGIAR Research Program on Climate Change, Agriculture and Food Security, based in Los Baños, Philippines. It’s entitled Birds in Rice Selection, and the idea behind it is pretty simple:

How about using birds to select for new rice varieties? Observing the birds in the field, they prefer certain varieties to feed on. Such observation can give us a clue of certain grain quality characteristics.

Here’s an example.

rice

Milyang 23 is apparently a popular Korean rice variety. I wonder how they record the results in the database.

Brainfood: African land use, Sorghum double, NUS trifecta, Grape hybrids, Sunflower genome, Fungi, Tree dispersal

The biodiversity of beer

We are extremely grateful to Ove Fosså, President of the Slow Food Ark of Taste commission in Norway, for this contribution, inspired by a recent Facebook post of his. We hope it is the first of many.

Beer is a fermented beverage usually made from just water, barley, hops and yeasts. That simple recipe can, however, produce a large variety of beers, and can harbour an immense range of biodiversity.

Bøgedal Bryghus is a small Danish brewery located at the idyllic 1840s Bøgedal farm. The brewery was established in 2004 and makes around 30,000 bottles per year. Each batch of around 800 bottles is different, and the batches are numbered, not named. Some of Bøgedal’s beers are made from heritage barley, sourced from the Nordic Genetic Resources Center. This barley is grown on a neighbouring farm, and malted in Denmark. They take great pride in using heritage varieties. The beer labels list both the variety names and the genebank accession numbers.

Bøgedal no. 450 made from two heritage varieties of barley, Nordic Genebank #13416 and #6273.1. Photo Ove Fosså.
Bøgedal no. 450 made from two heritage varieties of barley, Nordic Genebank #13416 and #6273.1. Photo Ove Fosså.

‘Chevallier’ barley provided some of the best malts and was one of the most popular varieties up until the 1930s, when other more productive varieties took over. It has been revived recently by the John Innes Institute, and used to produce a limited edition beer, the Govinda ‘Chevallier Edition’ IPA by the Cheshire Brewhouse. According to the brewer, it…

…is NOT a beer that’s about in your face HOPS! Quite the opposite, it is a beer that has been brewed to try and replicate an authentic 1830’s Burton upon Trent Pale Ale, and I have tried to manufacture it to an as authentic a process as I can, so as to try and replicate an authentic Victorian beer!

There are other beers using heritage ingredients, but they are few, and hard to find. The Svalbard Global Seed Vault has 69,000 accessions of barley as of today. Relatively few of these will be suited for malting, but still, the potensial for variation is huge.

Few beers advertise the variety of barley used. More often, you will find the name of the hop varieties on the bottle. Hops have not changed much over time, and many old clones are still in use. ‘East Kent Goldings’ has been around since 1838 and is the only hop to have a Protected Designation of Origin (PDO). Hops cannot be reproduced reliably by seed, and are kept in clone collections. The Svalbard Seed Vault has only 18 seed accessions of hops. The USDA/ARS National Clonal Germplasm Repository (NCGR) has a field collection of 587 accessions of hops and some further accessions in a greenhouse collection and a tissue culture collection.

An often neglected aspect of biodiversity is the diversity of microorganisms. In beer production, this is mainly brewer’s yeast. Many, probably most, breweries today use commercial yeast cultures, and are more concerned with standardisation than with local character.

Norwegian breweries have mostly copied foreign beers and thus also started out with imported yeast cultures. These eventually evolved into specific strains which are now guarded by their owners, and master cultures are stored at the Alfred Jørgensen Collection in Copenhagen, now owned by Cara Technology Ltd. They have a collection of 850 strains of brewing yeasts. The National Collection of Yeast Cultures (NCYC) in the UK holds over 4,000 strains of yeast cultures, including 800 brewing yeasts. The American Type Culture Collection (ATCC) holds more than 18,000 strains of bacteria, 3,000 types of animal viruses, 1,000 plant viruses and over 7,500 yeasts and fungi.

Wild, or spontaneous, fermentation is quite trendy in winemaking today, producing ‘natural’ wines with local bacteria. In one area of Belgium, spontaneous fermentation never went out of fashion. From the Pajottenland west of Brussels comes lambic and gueuze, ‘sour’ beers, in some ways more similar to wine than to other beers. Wild fermentation can never be reproduced faithfully by commercial strains of microbes because of the diversity.

In Norway, a project to collect information on local raw materials for beer production was started in 2012. The focus is on barley varieties and hop clones, but wild herbs are evaluated, too. So far, no beers seem to have come out of this. The project does not take yeast cultures into account. Luckily, some home brewers work with local starter cultures, called kveik (literally kindling). Commercial breweries are following. The Nøgne Ø brewery has just released Norsk Høst (Norwegian Autumn), a beer based on Norwegian ingredients only, including kveik, spruce shoots, and bog myrtle. But, alas, the malt seems to be from modern barley.