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Not too early for an early warning system for PGRFA

It turns out that if you keep a blog going long enough, you start to notice that you’re not so much writing new posts as filing updates to old ones. Looking back over two decades of the blog, a few obsessions definitely surface again and again, some healthy, others not so much. One of my main ones has been: Why do we still not have a proper early warning system for genetic erosion? You tell me if it’s healthy or not.

I first raised the question in 2009, in a post cheekily titled “Reporting threats to agrobiodiversity: A modest proposal”. I was inspired by ProMED, the disease-outbreak reporting system, and by a participatory mapping tool called pestMapper. Oh, and by Jonathan Swift.

The analogy seemed obvious. If a new pathogen appears somewhere, people can report it, someone can assess the information, and the reports can be aggregated to give us a picture of where the threat is spreading, or indeed where there are multiple threats. So why not do something similar for genetic erosion? What if losing a crop or variety in a particular place triggered the same kind of alarm as the outbreak of a new pathogen?

I even sketched out what a putative…wait, what shall we call it? The Global Agrobiodiversity Surveillance Programme — GASP for short? Yes, let’s go with that. What might GASP look like? Well, for a start: a way for people to report diversity that was disappearing, being replaced or becoming difficult to find; a system capable of dealing, somehow, with the inconvenient fact that the same variety might have several names, and similar issues; and maps and other visuals that could reveal trouble before it became irreversible.

And perhaps, I suggested, we could bundle in something contributors to the system might actually directly benefit from — like a way to get seeds, for example — so that it didn’t become another worthy database that nobody visited.

Worthy indeed. Seventeen years on, nobody has built the thing. Yet.

It has, however, been mildly gratifying, in a slightly irritating told-you-so sort of way, to see the idea keep resurfacing in other people’s work, dressed up in new technology each time.

For example, at one point I got excited about a Slow Food appeal for information on Italian vineyards under threat of destruction. Could crowdsourced alarm-raising like that be the closest thing yet to the system I had been going on about?

I don’t think I blogged about it, but there was also a project in Puglia that used Open Data Kit and Google Fusion Tables to collect information, including GPS readings and photographs, on vegetable crops at risk, then map and share it. Well, that sounds a bit familiar.

But there was kind of a fundamental problem. Before you can warn about genetic erosion, you need to know what genetic erosion looks like. And that’s not always easy.

This is where the notorious “75% of crop diversity has been lost” statistic comes in. I spent a lot of time on the blog — maybe too much time? — taking that claim apart, because we didn’t seem to know what the 75% was 75% of, or how either the starting point or the loss had been measured. We can’t build an early warning system out of made-up numbers. As I put it at the time, we should admit that we don’t know how much crop diversity has been lost overall, and go out and get better numbers. Fifteen years later, we do have some better numbers, indeed we have a review of all the numbers, I’m still “100% sure that 75% is incorrect”. But I still don’t know what headline number for the crop diversity we have lost to give to a journalist.

Yes, genetic erosion is annoyingly slippery. A farmer can stop growing a variety without losing the seed. A variety can survive in one village after disappearing from ten others. Two varieties can acquire the same name. One variety can acquire several names. A new variety can replace an old one without reducing the total number of varieties. The number of varieties can stay constant while their genetic complement and composition changes.

An example of this comes from two studies of sorghum in Ethiopia I blogged about in 2008. One found that farmers had stopped growing some varieties, but that the number of distinct variety names in the area had actually increased. Another found important varieties disappearing or becoming marginalised, while overall phenotypic diversity did not show a decline. The picture was one of “tremendous dynamism”: local losses, but also gains and turnover.

A snapshot tells you what exists. You need a time series to tell you what is changing.

And because farmers’ diversity doesn’t exist in isolation, monitoring those changes would need to connect with the processes that actually make diversity move. In other words, we shouldn’t just monitor the plants. We should monitor the systems that determine which plants get grown.

More recently, the technology for doing that has become rather tantalising. Satellite data on global human modification of ecosystems had me daydreaming yet again about a real-time version focused specifically on farming landscapes — “a perennial favourite here,” as I put it at the time, by which point I wasn’t even pretending to have an original idea anymore.

Then a Brainfood roundup mentioned remote monitoring of drought stress. If satellites can give us early warnings of drought, why shouldn’t we eventually be able to detect environmental and other changes that put crop diversity at risk? At this point, any spatial dataset that smells vaguely of early warning gets roped into the running list.

And it isn’t only satellites. Just a few weeks ago I pointed to FAO’s work on tools for capturing wild foods in dietary surveys: local inventories, market surveys, harvest calendars and identification aids. Why not adapt those methods to crop diversity? If they get widely adopted, you just need to mine the resulting information and aggregate it.

In “Listening for genetic erosion”, I wrote about a longitudinal study in which researchers returned to the same Australian livestock producers and landscapes after about fifteen years, using repeat photographs and interviews to understand what had changed. I was particularly taken by their use of “I-Poems”: first-person statements assembled from interviews to capture how people themselves experienced change. Why not do something similar with crop diversity? And feed the poems into the system.

A variety doesn’t usually go from “important” to “extinct” in a single bound. There is a story in between, and those stories may provide some of our best early warnings.

Put all this together and, after twenty years, I think I have a better idea of what GASP might actually look like. Not one giant database, and not a map with little red flashing lights, but a collection of imperfect sensors: threat reports, repeated field surveys, seed-system information, farmer interviews, spatial data, genebank records, remote sensing, all monitored in real time — presumably by Skynet — helping to identify places where the probability of important diversity being lost is increasing.

We keep half-finding the tool. Someone builds a citizen science app. Someone else maps a global index of something or other. Someone develops a new way of surveying crops from space. Someone puts a clever machine-learning model on top of a mountain of data. Someone creates a fancy dashboard.

And I write a post going: “Ooh. Is this it?”

It never quite is, and I go back to waiting for the next piece of the puzzle.

It’s like Twain said. Making predictions is always difficult, particularly about the future. Spotting genetic erosion is genuinely hard, especially before it happens. But I’m pretty sure we’ll eventually crack it. The technology will get better, the datasets will start talking to each other and someone will finally build something that truly deserves to be called GASP.

And then, of course, we’ll have a new problem.

Because knowing that crop diversity is in danger of disappearing is not the same as doing something about it. An early warning system can tell us that a landrace is becoming rare, that a landscape is changing, or that some other signal deserves attention. It can tell us where to look and perhaps even how urgent the situation is. But then someone has to decide what happens next.

Is the diversity already safely conserved somewhere? Should it be collected? Should farmers be supported to keep growing it? Does the seed system need strengthening? Is there someone who needs to be told about it? Or is this actually a perfectly normal bit of turnover that doesn’t require a conservation response at all?

In other words, once we finally solve the problem of seeing genetic erosion coming, we’ll have to get good at responding to it.

Which is probably the chief lesson of twenty years of discussing this on the blog. The problem keeps moving one step further downstream. First we needed to know what had been lost. Then we needed to know what was in danger of being lost. Now we need to work out how to turn a warning into a solution.

I’m quite looking forward to that problem, though. It seems like a healthier one to have.

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The apples of our eye

Apples have been another recurring obsession on the blog, maybe because they make the conservation problem unusually tangible, and immediate. Pretty much everyone thinks they know what an apple is, but the diversity hidden behind that word is enormous, and not much visible in supermarkets. A lot of it may have disappeared, but you can pretty much guarantee a slew of heritage apple stories in the press come autumn (and so it begins), so I guess people care. Here’s a selection of posts about apples spanning 15 years. There’s a lot more out there in the archive for you to explore.

Let’s start at the beginning, or as close to it as the genetics can get us. In 2016’s The Adam and Eve of apples?, I discussed the wild apple forests of southeastern Kazakhstan, where all of the world’s apple varieties can be traced back to an ancestral population of Malus sieversii — spread, if you believe the more colourful tellings, by bears eating the sweetest fruit and pooping the seeds around the forest. As usual, though, the genetics turned out to be more interesting than the headline. The cultivated apple isn’t a simple straight line from one mother tree; it’s the product of a long history of movement, hybridization and exchange between wild and domesticated populations all along the old trade routes out of Central Asia.

But those forests are in danger. Back in 2009, in Wild fruit relatives threatened in Central Asia, I looked at how the wild relatives of apples and other crops were vanishing along with their habitat. Among them was Malus niedzwetzkyana, the remarkable red-fleshed apple of Kyrgyzstan. These aren’t just obscure wild trees: they represented genetic diversity that has already made its way into cultivated apples, and might still have something to offer breeders. That red-fleshed apple came back a year later in Not the world’s first red apple. A new red-fleshed variety was being breathlessly presented in the press as a novelty — not GM, just 15 years of patient crossing and 20,000 rejected seedlings — but nature had got there first. M. niedzwetzkyana has been doing red flesh for millennia.

The cultivated stock has its own story of loss. In 2009’s Saving an apple a day, I looked at the loss of American apple varieties, and at the people trying to rescue what remained. Thousands of named varieties had once been grown in the United States; only a fraction survived in orchards, collections and the memories of the people who knew what they tasted like. It was a nice illustration of a familiar conservation paradox: you can lose a lot of diversity without even noticing, because the supermarket keeps selling you apples.

However, that same year, a study added a wrinkle to the “thousands lost” narrative. In Lost apples found, Jeremy pushed back a little on the standard version of the story — the one where 6,800 of 7,100 named 19th-century American apple varieties are simply gone. A team from the University of Arizona and USDA had gone looking for ghosts among old apple trees on historic farmsteads in Arizona, Utah and New Mexico. Only 34 of the resulting genotypes matched a known variety. The other 110, spread across 160 trees, matched nothing on record. Some of those are probably unnamed seedlings that never had a name to lose in the first place. But some, surely, are the supposedly lost varieties everyone had given up on. Not extinct, just lurking.

Seven years on, the USDA apple folks came back with another version of the answer. In As American as apples, Gayle Volk summarized her and Adam Henk’s trawl through historic nursery catalogues, which turned up 891 named apple cultivars grown in the US before 1908. They went looking for the 150 that seemed to matter most. The payoff: 90% are still findable today, safely tucked away in genebanks, private collections or specialist nurseries. Only 51 high-priority cultivars remained unaccounted for in any collection. For now.

The lesson isn’t that genetic erosion doesn’t happen. It plainly does, and 30 fruit nurseries vanishing a year is not nothing. No, the lesson is that “extinct” is much harder to prove than “endangered,” and pomologists with their equivalent of a swab kit keep turning out to be more patient, and luckier, than we have any right to hope.

Conserving what’s left, of course, depends on people as much as on collections and gene sequencers. In 2014, I offered up Irish eyes smiling about apple conservation. The post was prompted by Michael Hennerty’s beautiful book on the Irish apple, but the real story was the people who had nurtured the 68 varieties documented in the book over the years. Conservation often depends on a motley collection of people keeping things alive long enough for some fancy institution to discover that they matter. A few years later, Jeremy went into much more detail on Irish apples on his podcast.

Institutions, though, can be just as precarious as the work of any orchard-keeper or amateur gardener. Across the Irish Sea, the story of the UK’s apple collection showed just how fragile even a major national genebank can be. The National Fruit Collection at Brogdale in Kent, with its hundreds of apple varieties, came under threat when its funding was thrown into doubt, prompting a succession of stories about sales, new management and relocations. Oh, and royalty. Anyway, the collection is fine, but the saga was a reminder that conservation is not just about keeping things alive. You have to keep them alive with enough institutional resilience that they can survive the next crisis.

Taken together, these posts highlight a sometimes overlooked aspect of safeguarding agrobiodiversity. Conservation is not just putting varieties safely into collections, nor, on the other hand, is it just protecting wild populations from destruction. Apples show that the two are connected — or should be. These are, in the jargon, complementary conservation strategies. The diversity in a genebank has a history outside it, and the diversity out in the wild and in farms may only have a future in a genebank. We really do need both, it’s not just mom and apple pie rhetoric.

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Mapping out the problem of crop mapping

Time to celebrate the fact that I’ve spent a surprisingly large part of the life of this blog trying to answer what sounds like a simple question: Where are crops actually grown?

In Where do bananas grow anyway?, for example, I compared several supposedly authoritative maps of banana distribution and found that they disagreed in all sorts of interesting ways. That was followed by Yes, we have more banana distribution data, which summarized the discussion that followed that post and tried to tie up some loose ends. I dread to think how many of those datasets are still available.

Why bother, you may ask? Well, because knowing where a crop can be found is necessary if genebanks want to plan gap-filling collecting: map where the crop is grown, subtract what the genebanks already have, and explore the gaps. Alas, the reality was rather less tidy, hence Gap-filling may be harder than we thought. Tell me about it.

I kept returning to the problem, though. In The geography of black rice, I wrestled with the practical business of joining passport and characterization data just to get diversity onto a map. In Ground-truthing SPAM, a global crop-distribution model confidently put crops on my mother-in-law’s farm that she and her neighbours didn’t actually grow. Bambara groundnut produced another set of contradictory maps.

Years later, the tools were a bit better: I explored Afghan wheat in QGIS, and overlaid Kenyan bean accessions on a new crop atlas.

And by earlier this year Colin Khoury was able to summarize the whole historical trajectory of gap analysis in a guest post. A trick he then repeated elsewhere.

Looking back over all these endeavours, what strikes me is how often the answer seemed to be just one step away. A better crop map, better coordinates, a more complete genebank database, a cleverer GIS analysis. And each time the new thing helped, but also exposed another problem: the crop map was wrong here, the accession wasn’t georeferenced there, or the apparent gap didn’t mean what we thought it meant. I guess that’s science.

A lot has changed since I started writing about this problem, but the basic challenge remains. We want to know where diversity is, where it might be missing, and where it is worth looking for more. Getting all the relevant data into the same map is only the beginning, but it needs to be done. There’s more data now, and making maps is easier to do. But, unless you’re a GIS expert, it’s still way too hard.

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Good news from Beltsville?

After the recent worrying announcement about the USDA closing the Beltsville Agricultural Research Center, there may now be some good news. US Secretary of Agriculture Brooke Rollins has just announced a $180 million Seed Sovereignty Initiative to genotype collections of “major crops” in the National Plant Germplasm System, which holds more than 600,000 accessions of over 16,000 species. The two-year programme aims to reveal useful traits, identify gaps in the collections, and accelerate the development of new varieties. That’s a substantial investment in resources that are all too often taken for granted.

But the language is worth a closer look. This is framed as a matter of seed sovereignty and national security: the United States must not depend on “foreign adversaries” for its agricultural production, while foreign competitors are busy sequencing genetic resources. The emphasis is on turning America’s crop diversity collections, which are in the Multilateral System of the Plant Treaty, into a strategic national asset, and giving American farmers a competitive advantage.

None of that makes the investment unwelcome. Better genetic characterization could benefit researchers and breeders well beyond the United States, provided the resulting information is accessible. And understanding what genebanks hold, and what remains missing, is precisely the sort of work that should have been a priority all along.

Still, there is a difference between recognizing the strategic importance of crop diversity and treating it as a weapon in geopolitical competition. Will this initiative strengthen the shared knowledge base on which global crop improvement depends, or will national advantage determine what gets studied, shared and used? The $180 million investment is good news. The rhetoric, and the priorities it may signal, deserve rather more scrutiny.

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The chocolate formerly known as lost

The Quest to Save the World’s Most Coveted Chocolate is an engaging story in Smithsonian Magazine about Ecuador’s ancient, iconic Nacional cacao. It was published three years ago, but I only just came across it. It rang a bell, so I went back through the archive. And there was lots more there than I suspected. Again in celebration of our twentieth anniversary, let’s go through it.

It all started in 2009, when Jeremy first described how witches’ broom had devastated Nacional cultivation in the early 1900s, how breeders responded, and how farmers eventually widely adopted the more productive and resistant, but much less tasty, new variety known as CCN51. Nacional basically disappeared.

But not totally. In 2011, we Nibbled the rediscovery of Nacional populations in northern Peru by a USDA team, as reported in the N.Y. Times. A glimmer of hope, perhaps?

In 2015, Jeremy returned to the story. We learned that more than half of Ecuador’s cacao trees were then CCN51, which of course made the industry again vulnerable to the next disease. And, even worse, that the chocolate they produced tasted like “rusty nails.”

But now — thankfully — comes a much happier chapter, nicely described in the Smithsonian piece.

Encouraged by the discovery of Nacional in Peru, a motley crew of conservationists, chocolate makers and agricultural scientists went looking for it in Ecuador. In 2013, they found a grove of century-old trees in a coastal valley called Piedra de Plata. DNA showed that nine of 47 trees they sampled were genetically pure Nacional. They established them in a field genebank in 2018, and started producing planting material for interested local farmers.

More than 30 families are now working … to reforest their lands using seedlings from the nearly extinct tree. The rebirth of this once-lost treasure isn’t just a miracle for the chocolate-loving world — it’s also a milestone in reviving the rich heritage of Ecuador’s coastal forests and farming. And it may even offer hope for saving other endangered trees worldwide.

The plan was that within three years the nursery would be producing 5,000 Nacional seedlings annually. That would be about now. Alas, I was not able to find an update, but I do hope they’re on track.

The moral? Conservation pays — especially when what you’re conserving makes chocolate that doesn’t taste like rusty nails.