GIS – Page 20 – Agricultural Biodiversity Weblog

August 7, 2020August 6, 2020

Meta-Brainfood for the weekend

Time to clean up a few things, I think. For a while now, I’ve been hoarding links to edited volumes. My idea was to do a special dedicated Brainfood on each one, but I now fear that just ain’t gonna happen. Too much other stuff on. So here they are. Maybe one of you will help me out? You know what to do. A pithy one or two sentences summarizing each paper, based on the abstract only if you’re into the whole brevity thing. Interested? Let me know in the comments below, and we’ll set something up. Our first guest-curated Brainfood…

Here they are:

Do you remember the 2017 book Against The Grain: A Deep History of the Earliest States by James C. Scott? I think we may have blogged about it. Anyway, it suggested that it was grain (as opposed to tuber) cultivation that led to the development of hierarchical states. Grain is visible and portable, and so easy to tax, you see. There are interviews with the author galore if you like podcasts. Ok, well, the Cambridge Archaeological Journal had a whole Review Symposium deconstructing that particular revisionist narrative.
In 2018, something called the 1st International Conference on Genetic Resources and Biotechnology was held in Bogor, Indonesia. A bit of a misnomer, it was really mainly about “[i]nformation system and exchanges of genetic resources for effective crop improvement.” These are the proceedings, and all of the dozens of papers are open access. Maybe someone out there could do their Top 10.
This one is not as relevant as the others, but it’s interesting nonetheless: Remote Sensing of Plant Biodiversity. Surely some of the 20 contributions have something to say about agricultural biodiversity? Who’s willing to have a look?
Then there’s the Special Issue of Application in Plant Sciences on Machine Learning in Plant Biology: Advances Using Herbarium Specimen Images. Yummy. Automated identification of CWR specimens, anyone?
And finally, just out, a Topical Collection in Agriculture and Human Values on Agriculture, Food & Covid-19. Come on, who can resist a hot-take (well, a Rapid Response Opinion) entitled Maybe there is an alternative after all?

Looking forward to hearing from you.

And don’t worry, there’ll be a normal Brainfood on Monday as usual.

August 4, 2020August 4, 2020

Nibbles: UN training, Genebanks double, CG spatial data, Fruit IPR, Citrus greening, Sikkim diversity, Bulgarian lavender, Biogenetic Paradoxes, Heroin, Palestinian eggplant

Training courses on multilateral environmental agreements, including CBD and Plant Treaty.
CGIAR dashboard on the Genebank Platform. More data here.
Some of the above are included in this list of the world’s most high profile genebanks.
The latest spatial crop data from CGIAR. Useful for genebanks, among other things.
Protecting fruit intellectual property. Wait, that didn’t come out right.
I guess this fruit is next.
Sikkim’s agricultural diversity as colours on a palette.
Lavender is a nice colour, whether in France or Bulgaria.
Book on nation-building through agricultural biodiversity. Bulgarians unavailable for comment.
Poppy diversity being helped by solar panels to build something or other in Afghanistan.
Palestinian paean to the bitinjan. Jeremy goes to town on it in his latest newsletter.

July 17, 2020July 17, 2020

A Genesys use case for the weekend

I figured today I’d tweet about a cool new feature of Genesys, the online portal to genebank accessions. And I did, but then I thought I should really put it on here too. So here goes.

The use case I’ll consider today is:

I have an accession I like, and I know where it was collected. Show me all other accessions anywhere in the world that come from a roughly similar climate.

Here’s what you do. Hang on to your butts.

When you have selected the accession you like in Genesys, go to Map, and look for this on the far left.

Click on Show Climate…

Then click on your accession on the map. You’ll get a summary description of the climate at that point.

If you then click on List Accessions (bottom left hand corner), you’ll get a list of all accessions from places which are roughly comparable in climate to that of the accession which you clicked. I can explain how that’s calculated separately if people are interested.

Or, you can choose one of those bioclimatic variables listed, decide on some max and min values, go to Filter Accessions on the left of the map, and insert your chosen values in the appropriate place on the menu that should appear (scroll down).

Click on Apply Filters at the top of the menu, and there’s a list of accessions again, this time from places with climates within your chosen limits.

Let me know in comments if you have any questions, or indeed ideas for improvement.

Here’s a PDF of the Twitter thread.

July 6, 2020July 6, 2020

Brainfood: Biodiversity targets, Image software, Potato efficiency, Cassava cyanide, Popcorn, Payment for agrobiodiversity, Walnut conservation, Grapevine leaves, Pigeonpea haplotypes, Chakras, Diet & diversity, Seed activism, Seed longevity

Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved. Better than accession numbers? Well, yeah, but will it matter?
FIELDimageR: An R package to analyze orthomosaic images from agricultural field trials. Extract plot-level results from your drone shots, automagically.
Radiation Interception, Conversion and Partitioning Efficiency in Potato Landraces: How Far Are We from the Optimum? Quite far, but perhaps more interestingly you can predict tuber yield from time-series aerial imagery. Which means the above could come in useful.
Genetic architecture and gene mapping of cyanide in cassava (Manihot esculenta Crantz.). High cyanide alleles in 2 major genes mainly found along Amazonian rivers and in coastal areas of Brazil. Drones unavailable for comment.
Relationships among American popcorn and their links with landraces conserved in a microcenter of diversity. Did the diverse popcorns of southern Brazil derive from local diversification or independent local domestication? More work needed. Anyone going to mash this up with the cassava result above?
Payments for agrobiodiversity conservation services: An overview of Latin American experiences, lessons learned and upscaling challenges. 5 ha of each of 100 varieties will cost you US$70,000 p.a. at a 5% discount rate. Bargain.
Diversity Under Threat: Connecting Genetic Diversity and Threat Mapping to Set Conservation Priorities for Juglans regia L. Populations in Central Asia. Ex situ where threat level from climate change is severe, in situ where threat level due to climate change is minor, assisted natural regeneration where threat level from climate change is minor but severe from other things, like overgrazing. No word on payments for ecosystem services rendered.
Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves. Fancy maths used to composite leaf shapes along a shoot as a way of telling species apart.
Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). From 10 genes and about 300 genotypes to 17 accessions with 4 superior haplotypes.
Create Space for Indigenous Leadership to Preserve Agricultural Biodiversity. In the Ecuadorian Amazon, cacao production for cash is not driving down agrobiodiversity.
Conceptual Links between Landscape Diversity and Diet Diversity: A Roadmap for Transdisciplinary Research. There are 4 different pathways whereby diverse forested landscapes can lead to diet diversity.
‘Keeping seeds in our hands’: the rise of seed activism. While the formal sector is still arguing about farmers’ rights, activists have moved the paradigm to seed sovereignty.
Thirty-year monitoring and statistical analysis of 50 species’ germinability in genebank medium-term storage suggest specific characteristics in seed longevity. Huge dataset reveals some geographic variation in seed longevity within crops, among other things.

June 26, 2020June 25, 2020

Exploring Afghanistan’s wheat

There’s a new paper on the geographic distribution of wheat cultivation in Afghanistan. You can explore the data online. But here’s the bottom line, the paper’s Fig. 9.

I downloaded the cultivated wheat data from Genesys and imported everything into QGIS to play around with. That’s almost 5,000 genebank accessions, about half of which are geo-referenced. Here’s the result.

Circles are all cultivated wheats, red dots everything that is not bread wheat. Note the irrigated areas (dark blue) are more likely to have modern varieties, and that the area of rainfed cultivation (bright green) varies considerably from year to year with precipitation. Probably some more collecting to be done then, in particular in the rainfed northwestern region, based on this map. But I’m not going to bet on that until I see whereVIR’s 570-odd Afghan wheats were collected.