Genetic diversity

April 12, 2017February 16, 2018

Mapping wheat diversity in Turkey

No sooner did I blog about a paper which mapped diversity in a crop in Mexico across time, that I came across one mapping diversity in another crop in Turkey. ((Morgounov, A., Keser, M., Kan, M., Küçükçongar, M., Özdemir, F., Gummadov, N., Muminjanov, H., Zuev, E., & Qualset, C. (2016). Wheat Landraces Currently Grown in Turkey: Distribution, Diversity, and Use Crop Science, 56 (6) DOI: 10.2135/cropsci2016.03.0192))

The authors — a truly international bunch from the Bahri Dagdas International Agricultural Research Institute, the Vavilov Institute, CIMMYT, ICARDA, FAO, and UC Davis — describe a huge effort to collect and describe wheat from all over the country during 2009-2014. They then compare the resulting socioeconomic and geographic patterns of diversity with a previous survey done by the Vavilov Institute in the 1920s, the results of which were published in 1935-9 by Mirza Gökgöl, a Turkish scientist who accompanied that expedition. ((Gökgöl, M. 1935. Turkish wheats, Vol. I. Ministry of Agriculture, Yesilkoy Seed Breeding Institute Publications No. 7, Devlet Press, Istanbul, Turkey (In Turkish).
Gökgöl, M. 1939. Turkish wheats, Vol. II. Ministry of Agriculture, Yesilkoy Seed Breeding Institute Publications No. 14, Tan Press, Istanbul, Turkey (In Turkish).))

As in the Mexican maize study, diversity in the crop was measured in terms of distinct morphological types, and was unevenly distributed around the country, but unlike in that work, diversity was calculated for each administrative province, rather than in each square in a grid. As provinces vary widely in size, and in the extent to which wheat is grown in them, this approach is not ideal.

Nevertheless, it was possible to make direct comparisons between the two study periods for about 17 provinces. Discounting some very rare and very minor morphological variants, it seems fairly safe to say that for these provinces, the number of distinct wheat types went down about 59% overall, though with large differences among provinces. There is no map showing this in the paper, but, thanks to my colleague Nora Castañeda, I can help you with that. Red is down, green is up.

Data from Morgounov et al. (2016) Table 4. Wheat landrace diversity for selected provinces in Turkey found in the 1920s compared with the current results (2000s).

What explains wheat landraces still thriving in some places, and not in others?

Socioeconomic data indicated that landrace farmers are found mostly in remote mountainous subsistence communities with very little grain trade, small areas planted to wheat, and relatively simple production technologies. The key reasons famers continue to grow landraces are their grain qualities and adaptation to abiotic stresses.

April 10, 2017April 10, 2017

Brainfood: Slow Food, Runner bean diversity, Bamboo diversity, Istrian grapes, Smelly cheeses, Wild pseudocereals, Diversity & phenology, VAM diversity, Oases apocalypse, Wild wheat physiology, PepperHub, Bactrian camel diversity, Swiss livestock, CWR conservation, Tree database

Developing radically-new meanings through the collaboration with radical circles: Slow Food as a platform for envisioning innovative meanings. Companies should collaborate with radicals. Presumably in order to turn them. #resist
Unraveling agronomic and genetic aspects of runner bean (Phaseolus coccineus L.). At least we know what we don’t know.
Total leaf crude protein, amino acid composition and elemental content in the USDA-ARS bamboo germplasm collections. If you want to use bamboo as feed, you need to choose among the 100-odd species very carefully.
The Gene Collection of Autochthonous Wine Grape Varieties at the Institute as a Contribution to the Sustainable Development of Wine Growing and Viticulture in Istria. 3591 seems a hell of a lot, but wow.
Phage Biodiversity in Artisanal Cheese Wheys Reflects the Complexity of the Fermentation Process. Modern methods kill a lot of phages.
Setting conservation priorities for Argentina’s pseudocereal crop wild relatives. Go north, young CWR researcher!
Flowering phenology shifts in response to biodiversity loss. Experimentally decreasing diversity in a California grassland advanced phenology.
Activity, diversity and function of arbuscular mycorrhizae vary with changes in agricultural management intensity. No-till helps VAM, helps soils.
Oases in Southern Tunisia: The End or the Renewal of a Clever Human Invention? I’m not hopeful.
Physiological responses to drought stress in wild relatives of wheat: implications for wheat improvement. 4 species show promise.
PepperHub, a Pepper Informatics Hub for the chilli pepper research community. Hot off the presses.
Molecular diversity and phylogenetic analysis of domestic and wild Bactrian camel populations based on the mitochondrial ATP8 and ATP6 genes. The wild species is not the ancestor, and the domesticated species is a geographic mess.
GenMon-CH: a Web-GIS application for the monitoring of Farm Animal Genetic Resources (FAnGR) in Switzerland. Upload data on your herd or flock, end up with a map of where the breed is most endangered.
Stealing into the wild: conservation science, plant breeding and the makings of new seed enclosures. Ouch!
GlobalTreeSearch – the first complete global database of tree species and country distributions. 60,065, about 10% crop wild relatives.

April 7, 2017April 7, 2017

Nibbles: Viking dope, Garden survey, Ancient olive press, Proposal writing, Nice figures, Old garden books, Chestnuts, Cannibalism, Saving coffee, Vanilla history, Seed book, Spanish brassica

Vikings got high.
“How can you and your garden help us find out more about the global biodiversity associated with the plants in gardens?” Here’s how.
The oldest olive press in Anatolia.
“The Mistake: Writing a proposal that showcased knowledge rather than addressing the audience’s needs.” Indeed.
The Solution: cool downloads from Gapminder.
The only surviving illustrated Old English herbal. And, from several centuries later, a medieval book on how gardens will save you.
AramcoWorld on my favourite nut.
Cannibalism is a choice.
One kick-ass botanist.
Saving Ethiopia’s coffee forests. Nah, let’s just map the genome.
Vanilla has dark side.
The Profit of the Earth: cool new book on seeds, dark side and all.
Remember my little trip to the Spanish genebank? What they’re doing on brassica.

April 6, 2017April 10, 2017

Mapping the hell out of maize diversity in Mexico

Thanks to a Facebook post, I’ve just come across the “mapoteca digital” of CONABIO, the Comisión Nacional para el Conocimiento y Uso de la Biodiversidad of Mexico. ((Which, incidentally, has one of the coolest street addresses ever.)) It has point maps of the distribution of both wild and cultivated beans and calabazas, and of wild maize; but most interesting to me were the maps of the distribution of the richness of cultivated maize races, based on collections made at different times in the past. The data were put together by the “Proyecto Global de Maíces” (2006-2010), and the maps are also available in a PDF.

Here’s the map for 1940-1965, based on about 3,000 collections.

And here’s the map for 1991-2000, based on 12,000 collections.

The legend used in both maps is at the left here. Looking at the maps, lots of questions came to mind. Why are we getting higher numbers of races in the 1990’s? Is it that the collecting was more thorough then? Or are races moving around more now? There is lots of information on the individual races on the project website, including actual and potential distribution maps. And you can download the raw data. So another thing that came to mind was that surely someone must have gone through all this stuff in detail. And sure enough, yes someone had indeed gone through all this stuff in detail, Peralta & Golicher in 2014. ((Perales, H., & Golicher, D. (2014). Mapping the Diversity of Maize Races in Mexico PLoS ONE, 9 (12) DOI: 10.1371/journal.pone.0114657))

The high rank correlation between the three collection efforts indicate that relative abundance of races has not changed considerably since 1950. Races that were common in 1950 were also common in 2005, and the same can be said for rare races, none of these were apparently more common in 1950. Correspondingly, the comparison of distribution and richness models for the three sampling efforts does not suggest a general decline in richness nor in distribution for 43 of the 47 races studied, and in the other four cases the declines are relatively minor and require verification. The recent increase in distribution for two races (Tuxpeño and Celaya) may be explained by the outstanding importance these have had as components in commercial cultivars, it is not uncommon to find recycled and creolized landraces that had their origin as commercial seeds. Also, no extinctions were reported for the 47 races studied since all were sampled in the last collection effort between 1997 and 2010. Therefore, in a broad sense, at the race level of classification we do not find signs of substantial genetic erosion between 1943 and 2010. That is not to say no losses of local populations have occurred.

I can’t for the life of me understand why I haven’t blogged about this paper before (or indeed the project that generated the data), bringing together as it does two of my very favourite things, agrobiodiversity and mapping ((Quite apart from undermining the genetic erosion narrative.)), but I’m more than happy to rectify that oversight here and now. I can’t help thinking there’s more to be mined from this dataset yet.

April 3, 2017April 10, 2017

Brainfood: Banana identification, Donkey domestication, Mouse domestication, African cattle, Pig domestication, Biofuels, Biofortification, Genomics for breeding, Species movement, Crop diversity double, N fixation, Ag commercialization models, Wild beans, Brassica domestication, Teaching biodiversity

Molecular and cytological characterization of the global Musa germplasm collection provides insights into the treasure of banana diversity. 16% of 1500 accessions need taxonomic verification. Could have been much worse.
Why the Donkey Did Not Go South: Disease as a Constraint on the Spread of Equus asinus into Southern Africa. Gap in distribution between Kenya and southern Africa until colonial times probably down to trypanosomiasis.
Origins of house mice in ecological niches created by settled hunter-gatherers in the Levant 15,000 y ago. Hunter gatherers inadvertently domesticated the mouse.
The genome landscape of indigenous African cattle. Now we know where the genes for heat tolerance and tick resistance can be found, and it’s where you’d think.
Insights into early pig domestication provided by ancient DNA analysis. In northern Europe, around 4000 BC, people started crossing pigs from the south with local wild boars. What were they thinking?
Recent grassland losses are concentrated around U.S. ethanol refineries. The revenge of geography.
Provitamin A biofortification of crop plants: a gold rush with many miners. “One crucial aspect that needs further experimentation is whether β-carotene-fortified crops can improve vitamin A status in the main targets of the biofortification efforts, that is, malnourished adults and children.” Just going to leave that out there.
Genomic innovation for crop improvement. Longer reads needed. Is there no satisfying these gene-jockeys?
Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being. Species movements affect ecosystem functioning and service provision: “The indirect effects of climate change on food webs are also expected to compound the direct effects on crops.”
Feeding the Household, Growing the Business, or Just Showing Off? Farmers’ Motivations for Crop Diversity Choices in Papua New Guinea. Some people grow lots of crops because it’s cool. But why wasn’t this done at the intraspecific level?
To Specialize or Diversify: Agricultural Diversity and Poverty Dynamics in Ethiopia. Forget coolness, crop diversity makes you less poor.
Biogeography of nodulated legumes and their nitrogen-fixing symbionts. Australia is weird.
Plantations, outgrowers and commercial farming in Africa: agricultural commercialisation and implications for agrarian change. They all have their place.
Genomic history of the origin and domestication of common bean unveils its closest sister species. Wild populations from northern Peru and Ecuador are not derived from wild Phaseolus vulgaris which migrated there from Mesoamerica but are actually a different species which predates the evolution of wild common bean.
Genomic inferences of domestication events are corroborated by written records in Brassica rapa. Five genetic groups, with rapini at the base.
Walking and talking the tree of life: Why and how to teach about biodiversity. Forget ranks, try clades.