- Guidelines and best practices for the scientific use of global iNaturalist data. Citizen scientists have generated an enormous photographic record of biodiversity, but turning those observations into reliable scientific data requires some care. Here’s some practical guidance on accessing and using iNaturalist records and images, addressing taxonomic uncertainty, geoprivacy, observer bias, attribution and reproducibility.
- Mapping the spatial extent of agroforestry lands across Africa by characterizing tree spatial arrangements. Moving from individual biodiversity observations to the landscape, this study uses remote sensing to identify agroforestry across Africa by looking at the spatial arrangement of trees.
- AI tool for mapping smallholder crops proves itself in Senegal. Once we know where trees and agricultural landscapes are, the next question is what is actually being grown. Here researchers use Tessera, an open-source AI model trained on satellite imagery, to identify different crops in smallholder systems, achieving 84% accuracy while requiring considerably less computing power and labelled training data than other approaches.
- National Mapping of Monoculture and Intercropped Maize via Phenology-Assisted Sampling: Application in Kenya. Mapping crops is one thing; distinguishing how they are grown is another. This study distinguished intercropped from monocropped maize in smallholder farming systems, using satellite time series and phenological information to generate training samples for machine-learning classification.
- Smartphone-based proximal sensing as an accessible platform for improved physiological phenotyping. From mapping whole agricultural landscapes we move to the research station, and from satellites to smartphones. Using a smartphone to capture repeated images of plants in cowpea plots generated high-resolution time series, from which could be extracted information on vegetative growth, flowering and pod production.
- Determination of dry bean physiological maturity from UAS RGB time series using a stacking ensemble of color-derived spectral features. The cowpea study shows what can be extracted from repeated close-range images of individual plants. Here the emphasis shifts to using drone-mounted cameras to estimate a specific breeding trait: physiological maturity in dry beans. Combining colour-based indicators with time-series features and machine learning achieved a prediction error of only 2.68 days.
- Multi-scale spatial-temporal remote sensing fusion for phenology identification in rice germplasm resources. If maturity can be estimated from drone imagery in dry beans, can similar approaches monitor hundreds of different rice genotypes in a breeding collection? Apparently yes, by combining frequent medium-resolution images with less frequent high-resolution UAV imagery.
- Digitalization of the genotypic and phenotypic information retained within the FEM grapevine germplasm bank. We end where phenotyping meets conservation. The Fondazione Edmund Mach grapevine collection brings together more than 3,000 accessions, with genetic identity assessed using microsatellite markers and phenotypic characterisation covering vine development, ampelographic traits and responses to biotic stresses. The paper describes the digitisation of this information in FEMVitisDB, a FAIR-compliant database with links to international data infrastructures. And not a drone in sight. Yet
Brainfood: Ancient Madagascar cattle, American bison, Tibetan yaks, Korean silkworms, European cattle genomic selection, Slovenian cattle footprint, Nigerian ponds, African swine fever in Asia
- Past rapid spread of introduced livestock coincided with vegetation clearance on Madagascar. Ancient sheep, goat and cattle bones show livestock racing across the island about 1,200 years ago, in step with forest clearance and the loss of elephant birds and pygmy hippos. People had arrived long before, so hunting alone is an insufficient culprit. Also I can’t imagine pygmy hippos being all that nice to eat.
- Paleogenomic insight into the collapse, recovery, and management of American bison. 115 ancient and 45 modern genomes show that past bison populations were widely connected, which means that today’s herds, while more fragmented, retain more diversity than was feared. Also, many modern bison lack the cattle ancestry long assumed to be ubiquitous, but wood bison do carry plains bison ancestry from 1920s translocations. So, swings and roundabouts.
- Whole-genome resequencing reveals genetic diversity, population structure, and selection signatures in tibetan yak. Three recently recognised Xizang populations (Chawula, Jila and Niangya) prove genetically richer than many others and cluster with Yushu and wild yak. Selection signals turn up at coat colour genes such as MC1R and at candidates for meat production. Has anyone done selection signals in bison?
- Selection of a phenotypic and functional core set for South Korean silkworm genetic resources, Bombyx mori (Lepidoptera: Bombycidae). A core set is distilled from a larger collection on multiple morphological, physiological and quality criteria, a manageable shortlist so the genebank’s holdings can be more easily used rather than merely admired. What would a core collection for the bison look like, I wonder?
- Impact of genomic selection on genetic diversity in 5 local European cattle breeds. Genomic selection uses DNA information from across an animal’s genome to predict its breeding value, allowing breeders to select animals likely to pass desirable traits to their offspring earlier and more accurately than relying on observed characteristics or pedigree alone. But can it be bad for genetic diversity if applied to a small local breed? Well, it shortened sire generation intervals and evened out top-sire contributions, but inbreeding rose in two breeds and fell in three. Genetic management mattered more than genomic selection, so the lesson is to monitor, and adjust as needed. Possibly relevant to the bison?
- Adoption of support tools for biodiversity conservation: a mixed-methods analysis of ecosystem services awareness among Slovenian cattle farmers. Livestock farmers who are younger and with more positive attitudes to biodiversity and the European Green Deal are more likely to adopt biodiversity-supporting practices. Knowing this could have saved many pigmy hippos 1,200 years ago in Madagascar.
- A national fish pond dataset for Nigeria generated using automated detection and segmentation. A segmentation model run over imagery, with a Random Forest classifier filtering the candidates, yields an openly released map of aquaculture production that was previously hard to see, let alone manage.
- Pathways to recover Asian wild pigs from African swine fever. Since 2018 the virus has caused huge mortality in naive wild pig populations, and the authors set out eight priority actions, with early-warning surveillance, captive breeding and emergency financing the ones that can’t wait. Free-ranging domestic pigs and thin biosecurity at the wildlife-livestock interface keep kind of bring us back to where we began on Madagascar.
Nibbles: Standing variation, Indigenous dogs, Austrian apples, Jordanian olive oil, Island foods
- Ancient farmers didn’t have to wait for the genetic diversity that made domestication possible. They selected from variation already present in wild plants, including the ancestors of rice and maize. Domestication was as much about spotting (or happening upon) useful differences as creating new ones.
- English colonists in America called Indigenous dogs “wolves,” revealing as much about colonial perceptions as about the animals themselves. This history of Indigenous dogs shows how unfamiliar animals were classified through peculiarly European ideas about wildness.
- Austria is bringing forgotten apple varieties back to life. Saving old varieties in genebanks is one thing: getting people to grow, sell and eat them is another, but it can be done. Or at least tried.
- Jordan’s olive-oil heritage centres on traditional varieties such as Nabali and ancient Rumi trees, but most production is consumed locally, leaving exports limited and making provenance, cultivar and harvest date important indicators for buyers. Compare and contrast with Austrian apples.
- Small island developing states have distinctive food cultures and ingredients, but face particular challenges in building sustainable and resilient food systems. FAO’s A Taste of SIDS explores the connections between island food, biodiversity and culinary heritage. Nice to see diversity within crops considered, though a few local variety names would have been nice.
Brainfood: WorldCuP, Crop origins, Abrahamic plants, UK landraces double, Ex situ change, Santorini vineyards, Apulian olives
- WorldCuP: A database of checklists documenting the World’s Cultivated Plants and their distributions. Cool new database records 1,444,325 occurrences representing 91,358 accepted cultivated plant species across 2,718 regions in 156 countries. Geographic coverage is extensive but uneven, with notable gaps in parts of Africa, southwest and central Asia, and Oceania. Most of the taxa recorded are not in existing major crop and useful-plant databases.
- Integrating multiple disciplines to locate the origins of domestication of crops. Combining evidence from botany, biogeography, genetics, archaeology, linguistics, and history overturns the traditional Mesoamerican hypothesis for cacao origins, supporting domestication in western Amazonia, probably involving multiple events. Peach palm’s domestication is best placed in southwestern Amazonia. Cupuaçu remains unresolved. Now for the other 91,355 species.
- Plant Species Mentioned in Abrahamic Scriptures: Implications for Biodiversity and Traditional Agriculture and Horticulture. Olive, grapevine and fig, together with cereals such as wheat and barley, occur prominently across the three scriptural traditions examined, while date palm is particularly prominent in the Qur’an. Not clear whether scriptures qualify as checklists.
- Crop landrace conservation, status, challenges and motivations in Great Britain. A national inventory (checklist even) identifies 566 landrace populations maintained on farms by 197 growers, alongside 1,876 British-origin genebank accessions, representing a total of 1,201 distinct landraces. Cereal and vegetable landrace cultivation has gone up since 2004, but forage diversity is increasingly threatened. Climate change, labour shortages and lower yields are the main challenges reported by growers.
- An inventory, threat and conservation assessment of UK wheat landrace diversity. The UK currently has 27 wheat landrace varieties growing on more than 700 hectares, an increase in both variety numbers and cultivated area since 2009. Interviews with 50 farmers identify insufficient market demand and limited seed availability as key constraints. So, not climate change, labour shortages and lower yields.
- Strong differentiation between source and ex situ populations of rare plant species revealed by next-generation sequencing. Across four rare plant species, ex situ populations showed significant genetic differentiation from their wild sources despite only one generation in cultivation, while overall genetic diversity and inbreeding did not differ significantly. Unrepresentative seed collection, unconscious selection during propagation or genetic drift could explain the differences. Something to test on all those British landraces, labour permitting?
- Rethinking the vineyard of Santorini in a changing climate and preserving an historic wine region. Recommends a staged transition from vineyard recovery to ecological regeneration, prioritising soil organic matter, drought management and indigenous grapevine diversity. Sounds like lots of labour will be needed.
- Conservation dilemmas: Xylella fastidiosa and the future(s) of olive farming. In Puglia, disease management is pushing olive farming towards competing futures: intensive, mechanised production vs the preservation of ancient trees as cultural landscapes. The fate of traditional groves depends less on technical disease solutions than on whether markets, subsidies and labour arrangements make their continued care economically viable. Well that doesn’t sound promising. Maybe try prayer?
Weed all about it
I think I vaguely knew that USDA had a hemp collection, but I would definitely not have been able to tell you that it was located in Geneva, NY, that it may be the largest in the world, or that it only started in 2021. Fortunately, though, the researchers responsible for the collection organized a USDA Hemp Stakeholder Event at Cornell AgriTech on September 10, and the good people at the International Hemp Podcast are summarizing the proceedings in a series of four episodes. Episode 1 is out, and it includes those tidbits I began with, as well as lots of other interesting information, about hemp in particular but also more generally about how the US genebank system works. Well worth a listen.
But does USDA in fact have the largest hemp collection in the world? Well, the podcast says it has over 800 accessions, and GRIN does indeed return 871 (714 active, 92 available) hits. However, Genesys, which gets its USDA data from GRIN, says 569, which is at least closer to the “N > 600 accessions” on the webpage of the USDA Hemp Germplasm Laboratory. As it’s a fairly new collection, this all probably just means that its numbers go up fairly frequently and USDA just hasn’t updated either its website or its data on Genesys lately. Anyway, that would still give it more accessions than at VIR (491), though fewer than in Ukraine (610). That Ukraine number is split over two institutes, however. So it does look like USDA has managed to put together the world’s largest hemp collection in just 5 years. Pretty impressive. Too bad the podcast doesn’t go into how they did it.