Agricultural Biodiversity Weblog

January 9, 2023January 10, 2023

Mo’ better agrobiodiversity graphics

Wouldn’t want you to miss out on this nice find from Jeremy’s last Eat This Newsletter of 2022, just because we’re in a new year now. But why not subscribe, eh? Incidentally, since we’re talking about the movement of crops around the world, and fancy graphics, you might as well also check out Bloomberg’s cool re-visualizations of the data in the 2014 paper “Increasing homogeneity in global food supplies and the implications for food security.”

In the decades after 1492 “a massive multidirectional transfer of biota, diseases, technology and humans occurred between Afro-Eurasia and the Americas”. But if you look at the standard maps of these movements, collectively known as the Columbian Exchange, you miss almost all the complexity and context of what moved, where, why, and what else was going on.

That’s the conclusion of a new paper: (Re)Mapping the Columbian Exchange. Suggestions for an Updated Cartography. The paper itself is behind a paywall, although one of the authors is a friend of the podcast so I may well invite him on to discuss the story in more detail. Thankfully, the maps themselves are available to download, and even a superficial glance shows that the story is much more interesting than the standard maps imply.

You can’t see the wealth of detail in this map, but you can download the full-sized version.

Each of them overcomes the “overly constrained geographic scope, chronological compression, non-depiction of the contemporaneous movement of important cultural, technological and biological elements of each product, ethnocentrism and the obscuring of human consequences” of the standard map, and I look forward to reading the new plant biographies just as soon as I get hold of the paper.

December 19, 2022December 14, 2022

Brainfood: Neolithic microbiomes, Transeurasian languages, Rice history, Chinese Neolithic, Indo-European origins, Chalcolithic stews, Indus Valley hydrology, Bronze Age opium, Cassava storage

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture. The adoption of agriculture was gradual.
Triangulation supports agricultural spread of the Transeurasian languages. The ancestors of the speakers of 98 related languages — including Japanese, Korean, Tungusic, Mongolic and Turkic — were the first millet farmers gradually spreading across Northeast Asia.
Modelling the chronology and dynamics of the spread of Asian rice from ca. 8000 BCE to 1000 CE. Deep breath. Rice domestication originated in eastern China (7430 BCE) and northeastern South Asia (6460 BCE). Then gradually spread in 2 waves: (1) in the 4th-3rd millennia BCE to the rest of China and SE Asia, associated with millet cultivation (Transeurasian speakers?), and (2) in 1st BCE-1st CE to Liao River region, Central Asia, and Africa.
Plant foods consumed at the Neolithic site of Qujialing (ca. 5800-4200 BP) in Jianghan Plain of the middle catchment of Yangtze River, China. Not just rice and millets but also job’s tears, lotus roots, yam, acorns and beans.
Indo-European cereal terminology suggests a Northwest Pontic homeland for the core Indo-European languages. The speakers of Proto-Indo-European, on the other hand, gradually making their way from the steppes, were not farmers.
Revealing invisible stews: new results of organic residue analyses of Beveled Rim Bowls from the Late Chalcolithic site of Shakhi Kora, Kurdistan Region of Iraq. Not by bread alone… Iconic, hastily-made, throw-away pottery bowls from 3500 BCE were not bread moulds but rather held tasty stews. No job’s tears and lotus roots, alas, though.
Phytoliths as indicators of plant water availability: The case of millets cultivation in the Indus Valley civilization. Sorghum and millets were growing under water stress at several Mature Harappan (2500–1900 BCE) sites. But they could take it.
Opium trade and use during the Late Bronze Age: Organic residue analysis of ceramic vessels from the burials of Tel Yehud, Israel. People were getting high in the 14th century BCE. And who can blame them, after millennia of domesticating plants and gradually spreading around the world.
Adaptations of Pre-Columbian Manioc Storage Techniques as Strategies to Adapt to Extreme Climatic Events in Amazonian Floodplains. Some current agricultural practices can be seen in the archaeological record. And not just getting high on opium.
See you in the new year, everyone!

December 14, 2022December 14, 2022

A chat with ChatGPT about genebanks

Along with everyone else, or so it seems, I’ve been playing with AI-based text generators. In particular, OpenAI’s conversational model ChatGPT. I started with the question: What is a genebank?

A genebank is a type of repository that stores genetic material, typically in the form of seeds or other plant material, for the purpose of conservation and preservation. Genebanks play an important role in protecting the diversity of plant species and maintaining the genetic resources that are essential for agricultural production and the development of new plant varieties. In addition to storing seeds, genebanks may also provide facilities for research and education, and may offer services such as seed testing and variety identification.

Allrighty then. Followed that up with a question about the disadvantages of genebanks.

There are a few potential disadvantages to genebanks. One is that the long-term preservation of genetic material can be challenging, and there is always a risk of samples being lost or degraded over time. Additionally, the use of genebanks can raise ethical concerns, particularly when it comes to the storage and use of genetic material from endangered or protected species. There can also be practical challenges associated with the distribution and access to genetic material in genebanks, as well as issues related to intellectual property and benefit sharing. Overall, while genebanks provide a valuable resource, it is important to carefully consider and address these potential disadvantages.

Damn. So is in situ conservation better?

In situ conservation refers to the preservation of plants and animals in their natural habitats, rather than in artificial environments like genebanks. In many cases, in situ conservation can be a more effective approach to preserving biodiversity, as it allows species to continue to thrive in their natural environments. This can also help to preserve the relationships between species and their ecosystems, which is important for the long-term health of the ecosystem. However, in situ conservation is not always possible, and genebanks can play an important role in preserving genetic material for future use. Both in situ conservation and genebanks can be important tools for conservation efforts, and the best approach will depend on the specific circumstances and goals of the conservation effort.

But which approach does ChatGPT prefer?

As a language model trained by OpenAI, I do not have personal preferences or opinions. My purpose is to provide accurate and reliable information to the best of my ability. In the case of conservation efforts, the most effective approach will depend on the specific goals and circumstances of the situation. Both in situ conservation and genebanks can be valuable tools, and the best approach may involve using a combination of both methods. Ultimately, the goal of conservation is to protect and preserve the diversity of life on Earth, and the most effective approach will depend on the unique needs of each species and ecosystem.

Ok, fair enough, let’s get a little more specific then: What’s the best way to conserve apple diversity?

There are several ways to conserve apple diversity, and the best approach will depend on the specific goals and resources available. Some potential strategies include:

In situ conservation: This involves preserving apple trees and their associated ecosystems in their natural habitats. This can help to protect the full range of genetic diversity within a species, as well as the relationships between apples and other species in the ecosystem.

Ex situ conservation: This involves collecting and storing samples of apple genetic material in a genebank for future use. This can help to preserve genetic diversity that may be lost in the wild, and can provide a valuable resource for research and breeding efforts.

Collaborative conservation efforts: This involves working with farmers, researchers, and other stakeholders to conserve apple diversity and promote sustainable apple production. This can include initiatives such as breeding programs, farm management practices, and education and outreach efforts.

Supporting conservation organizations: One of the best ways to support apple conservation is to donate to organizations that are working on apple conservation efforts. This can help to fund research and conservation efforts, and can make a real difference in protecting apple diversity.

Uff. Time to retire, methinks.

November 28, 2022January 10, 2023

Brainfood: Silkworm, Donkey, Cat, Chicken, Neolithic, Shamans, Locusts

High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation. The silkworm was domesticated 5000 years ago in the middle Yellow River (along with millets?), but was improved independently and in different directions in China and Japan.
The genomic history and global expansion of domestic donkeys. The donkey was domesticated in the Horn of Africa 7000 years ago and then developed in different directions in Africa and Eurasia.
Your horse is a donkey! Identifying domesticated equids from Western Iberia using collagen fingerprinting. Turns out you can tell horses and donkeys apart easily and cheaply from ancient collagen in archaeological remains.
Genetics of randomly bred cats support the cradle of cat domestication being in the Near East. Humans were domesticated by cats in the eastern Mediterranean basin about 12,000 years ago.
The history of the domestic cat in Central Europe. Wait, the Near Eastern wildcat, from which all domestic cats are derived, could have been in central Europe before the Neolithic.
Missing puzzle piece for the origins of domestic chickens. Recent dating of chicken domestication from archaeological remains in Thailand at 1650–1250 BC underestimates the timescale. By a lot.
Was the Fishing Village of Lepenski Vir Built by Europe’s First Farmers? And did they have cats?
Shamanism at the transition from foraging to farming in Southwest Asia: sacra, ritual, and performance at Neolithic WF16 (southern Jordan). You need shamans to help you cope with all that animal domestication.
Contributions of black locust (Robinia pseudoacacia L.) to livelihoods of peri-urban dwellers in the Free State Province of South Africa. Wait, black locusts are not animals? Hmm, they do seem to have some things in common with cats though.

November 26, 2022

Interested in genetic diversity in the post-2020 Global Biodiversity Framework?

Well, who isn’t right? Anyway, point is, the Coalition for Conservation Genetics has you covered with a dedicated website of resources in support of the CBD’s COP15. Extremely useful.