Domestication – Page 50 – Agricultural Biodiversity Weblog

February 7, 2019February 7, 2019

8000 years of agricultural history in two papers

A paper just out in Quaternary Science Reviews provides an overview of the first 3000 years of the spread of cultivated cereals around Eurasia, based on archaeobotanical evidence. The paper has some nice maps, but the press release has a really cool animated gif, which I had no hesitation in stealing.

Here’s a quick summary:

Before 5000 BCE: farming communities used foothill, alluvial and catchment locations in different parts of Eurasia.
Between 5000-2500 BCE: crops move around, but remain ecologically constrained, with the Tibetan Plateau and the Asian monsoons separating east from west, and north from south.
Between 2500-1500 BCE: crops are taken to new thermal and hydrologic contexts, bringing previously isolated agricultural systems together.

And where are we now? Well, for that you need another new paper, this one in PLOS ONE: Regional and global shifts in crop diversity through the Anthropocene. As luck would have it, three phases here too, covering the past 50 years:

little change in crop diversity from 1961 through to the late 1970s
a 10-year period of sharp diversification through the early 1980s
“levelling-off” of crop diversification beginning in the early 1990s

No gif, alas, but there’s a little video accompanying the press release in which the author summarizes the results.

The title of that press release says it all really: “A small number of crops are dominating globally. And that’s bad news for sustainable agriculture.” Compare and contrast with the findings of Colin Khoury and friends from a couple of years back on the increasing homogeneity of global diets. Basically looking at the same data in a somewhat different way: pretty much the same result.

February 4, 2019February 5, 2019

Brainfood: Sinotato, Photophenomics, Bangladesh lentils, Vernalization gene, Droning on, Pathogen identification, Human domestication, Citrus cryo, Purple rain, Teff diversity, Mining biodiversity lit, Wild dates, Buckwheat improvement, Panicum genome

Potato and Food Security in China. Huge expansion, mainly due to product diversification, but still room for growth. But how will it end? Like bananas?
Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency. Chlorophyll fluorescence technologies are revolutionizing phenotyping. Now everyone will want another gadget.
Is DNA fingerprinting the gold standard for estimation of adoption and impacts of improved lentil varieties? It’s not about yield.
A florigen paralog is required for short-day vernalization in a pooid grass. Nope, I can’t say it better than the press release: Ancient gene duplication gave grasses multiple ways to wait out winter.
Drones for Conservation in Protected Areas: Present and Future. Sure, why not. On-farm too?
Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. Sort of barcoding for bugs.
Self-domestication in Homo sapiens: Insights from comparative genomics. There’s a domestication syndrome for humans too.
Cryopreservation of Citrus limon (L.) Burm. F Shoot Tips Using a Droplet-vitrification Method. Well, at least two varieties work.
Farmers Drive Genetic Diversity of Thai Purple Rice (Oryza sativa L.) Landraces. Well, who else?
Genetic Diversity of Ethiopian Tef [(Eragrostis tef (Zucc.) Trotter] Released and Selected Farmers’ Varieties along with Two Wild Relatives as Revealed by Microsatellite Markers. The landraces are distinct from the released varieties, and more diverse.
Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Nice enough, but you need to upload a PDF corpus. Why not let it loose on the internet?
Cross-species hybridization and the origin of North African date palms. I always knew that P. theophrasti would come in useful.
Revisiting the versatile buckwheat: reinvigorating genetic gains through integrated breeding and genomics approach. Start with a database, core collection, and wild relatives. Gratifyingly old-fashioned.
The genome of broomcorn millet. That would be Panicum miliaceum.

January 21, 2019January 13, 2019

Brainfood: Tibetan barley, Eastern Sahel domestication, CC & coffee, Good bugs, Garden Organic, Amazonian domestication, Maize domestication, Maize & CC, Acidless citrus, Seed commons book, Crispy blueberry, African hunter-gatherers, Indian forages, Brazilian PGR, Cloudberry picking, Wheat & CC

Origin and evolution of qingke barley in Tibet. Tibetan barley was introduced from the southwest.
On the Origins and Dissemination of Domesticated Sorghum and Pearl Millet across Africa and into India: a View from the Butana Group of the Far Eastern Sahel. Sorghum and pearl millet got to India from Sudan. No word on whether they ever got to Tibet.
Was there ever a Neolithic in the Neotropics? Plant familiarisation and biodiversity in the Amazon. Depends on how you define it.
The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding. The earliest proto-maize was inbred.
Evaluating Future Impacts of Climate Change on Traditional Mexican Maize Suitability and Indigenous Communities in Mexico. Landraces are going to lose half their area of suitability.
Why could the coffee crop endure climate change and global warming to a greater extent than previously estimated? Because of carbon dioxide?
Understanding and exploiting plant beneficial microbes. We’re going to need microbial consortia.
Genetic analysis of a heritage variety collection. The Heritage Seed Library, in fact.
Noemi Controls Production of Flavonoid Pigments and Fruit Acidity and Illustrates the Domestication Routes of Modern Citrus Varieties. In citron, limetta, sweet lime, lemon, and sweet orange, acidless phenotypes are associated with large deletions or insertions of retrotransposons in a single gene. Some of them go back a long way, and are associated with ritual use in Jewish culture.
Introduction: Commoning the seeds: the future of agrobiodiversity and food security. Is there a way out of the current impasse? Maybe.
Molecular and Genetic Bases of Fruit Firmness Variation in Blueberry—A Review. It’s still unclear whether firmness is a quantitative trait or monogenic.
Hunter-gatherer genomes reveal diverse demographic trajectories following the rise of farming in East Africa. Hunter-gatherers were more inventive in Africa than in Europe in the face of agricultural expansion.
Tropical Forage Legumes in India: Status and Scope for Sustaining Livestock Production. >3200 accessions conserved, >50 cultivars released.
Conservation of crop genetic resources in Brazil in the context of the target 9 of the Global Strategy for Plant Conservation. A lot done, a lot still to do. CWR remain a gap.
The Impacts of Climate and Social Changes on Cloudberry (Bakeapple) Picking: a Case Study from Southeastern Labrador. Social changes have been more significant, but for how long?
Global wheat production with 1.5 and 2.0°C above pre‐industrial warming. Frequency of extreme low yields and variability will increase in hot places like India. Assuming no new varieties.

January 14, 2019January 12, 2019

Brainfood: Coca phylogeny, Potato taste & nutrition & resistance, CC & nutrition, Light & nutrition, Remote poverty, Spicy toms, Input subsidies, Broilerocene, European livestock then & now, Bean domestication, Peach domestication, Machine conservation, Habitat fragmentation, Conservation planning, Taxidermy, Wheat diversity, Livestock GS

Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species). Morphology is not enough.
Improving Flavor to Increase Consumption. Yield is not enough.
The Nutritional Contribution of Potato Varietal Diversity in Andean Food Systems: a Case Study. Yield is not enough.
Stacking three late blight resistance genes from wild species directly into African highland potato varieties confers complete field resistance to local blight races. One resistance gene is not enough.
Income growth and climate change effects on global nutrition security to mid-century. Calories will not be enough.
Urbanization and Child Nutritional Outcomes. Urbanization is enough.
Socioecologically informed use of remote sensing data to predict rural household poverty. Night light is not enough.
Capsaicinoids: Pungency beyond Capsicum. Peppers and tomatoes are not enough.
The impact of agricultural input subsidies on food and nutrition security: a systematic review. The data are not enough.
The broiler chicken as a signal of a human reconfigured biosphere. The broiler is enough.
Pre-Roman improvements to agricultural production: Evidence from livestock husbandry in late prehistoric Italy. The Romans were not enough.
Optimizing ex situ genetic resource collections for European livestock conservation. One genebank is not enough.
Does the Genomic Landscape of Species Divergence in Phaseolus Beans Coerce Parallel Signatures of Adaptation and Domestication? One genome is enough.
Genome re-sequencing reveals the evolutionary history of peach fruit edibility. Human selection was not enough.
Predicting plant conservation priorities on a global scale. This black box is enough.
Is habitat fragmentation bad for biodiversity? Small patches may be enough.
Synergies between the key biodiversity area and systematic conservation planning approaches. One conservation approach is not enough.
Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland. Stuffed goats are enough.
Decline in climate resilience of European wheat. The current varieties are not enough.
Harnessing genomic information for livestock improvement. Genomic selection was going to be enough.

January 7, 2019December 14, 2018

Brainfood: Distribution modelling, New mycorrhiza, Bean diversity, Collecting, Intensification, Wildish rice, Wild tomato genome, Conservation prioritization, Horizon scanning, Maize domestication, Livestock sustainability, Asexual rice

Incorporating knowledge uncertainty into species distribution modelling. Not sure about this.
A mycorrhizal revolution. “Fine root endophytes are arbuscule-forming fungi unexpectedly placed in Mucoromycotina.” Wow. I think.
Genetic Diversity within Snap Beans and Their Relation to Dry Beans. Snap beans came from dry beans, but maybe more than once and from both Andean and Mesoamerican genepools, and now they make up 8 genepools.
Two decades of evolutionary changes in Brassica rapa in response to fluctuations in precipitation and severe drought. It matters when you collect germplasm.
Agricultural intensification, dietary diversity, and markets in the global food security narrative. What if it’s intensification through diversification, though? Didn’t think of that, did you?
Seed characteristic variations and genetic structure of wild Zizania latifolia along a latitudinal gradient in China: implications for neo-domestication as a grain crop. Crop wild relative that is also a crop might be a good candidate to become another crop.
The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance. It’s all in the inositol pathway.
Not all data are equal: Influence of data type and amount in spatial conservation prioritisation. Follow the money. Ok, to unpack that, read this.
A Horizon Scan of Emerging Issues for Global Conservation in 2019. Biotechnological advances in crop breeding may impact insects and land use.
Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Linguistics, archaeology and genetics say maize left Mexico semi-domesticated, was finished off and diversified in Amazonia.
Assessing the Role of Cattle in Sustainable Food Systems. They still have one.
A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Clonal propagation of hybrids. What could possibly go wrong?