GIS – Page 43 – Agricultural Biodiversity Weblog

September 3, 2018September 4, 2018

R you interested in species distribution models?

If you always wanted to do species distribution modelling, it’s your lucky day. Let Robert Hijmans and Jane Elith take you by the hand.

This document provides an introduction to species distribution modeling with R. Species distribution modeling (SDM) is also known under other names including climate envelope-modeling, habitat modeling, and (environmental or ecological) niche-modeling. The aim of SDM is to estimate the similarity of the conditions at any site to the conditions at the locations of known occurrence (and perhaps of non-occurrence) of a phenomenon. A common application of this method is to predict species ranges with climate data as predictors.

August 25, 2018August 24, 2018

Nibbles: Apple diversity, Nutrition, Cali crops, Sourdough 101, Orphans, Nomenclature, Wheat genome, CWR Week, Replanting

The decline and fall of Golden Delicious.
Jess Fanzo on the nutritional triple threat.
Stunning map of California’s farms.
A sourdough library. Have you listened to Jeremy’s podcast on the subject?
Remembering forgotten crops.
How to name plants.
Tricky genome outwitted.
Crop Science Society of America is celebrating Crop Wild Relative Week September 22-29.
Chinese rural trees in cities.

August 6, 2018August 6, 2018

Brainfood: Ecology of domestication, Citizen soybeans, Silkworm domestication, Barley spread, Indigenous management, Maize domestication, Temperate maize, Nutrient yields, Amazon history double, Women & diets, Online classification, Charred breadcrumbs, Wheat drought

Crop domestication: anthropogenic effects on insect–plant interactions in agroecosystems. Domestication can upset trophic webs. Poor dears.
The soybean experiment ‘1000 Gardens’: a case study of citizen science for research, education, and beyond. 2492 gardens, in fact.
The evolutionary road from wild moth to domestic silkworm. Domestication in China, followed by multiple independent spreads and differentiation.
Barley heads east: Genetic analyses reveal routes of spread through diverse Eurasian landscapes. 3 taxa, 8 genepools, multiple routes for spread. A bit like silkworm but in the opposite direction.
A spatial overview of the global importance of Indigenous lands for conservation. 40% of all terrestrial protected areas.
Maize domestication and gene interaction. More than just the headline 5 genes.
Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize. Need to go back to tropical germplasm for adaptation to temperate conditions.
Moving beyond calories and protein: Micronutrient assessment of UK diets and land use. Roots, tubers and vegetables are the most land-efficient producers of 23 nutrients.
The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon. It is still with us.
Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre. And not just in the east.
Does women’s time in domestic work and agriculture affect women’s and children’s dietary diversity? Evidence from Bangladesh, Nepal, Cambodia, Ghana, and Mozambique. Yes, but varies with socioeconomic status.
Remap: An online remote sensing application for land cover classification and monitoring. Use your training set to detect habitat type(s) in Google Earth.
Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan. Before domestication.
Drought tolerance during reproductive development is important for increasing wheat yield potential under climate change in Europe. The good news is that germplasm close to the optimized ideotype for 2050 is already out there.

July 16, 2018July 11, 2018

Brainfood: Tunisian millet, Range expansion model, Ancient soils, Shocking maize, Ancient Chinese ag, Top questions, Maize subgenomes, Rapid breeding, Non-seed systems, Ag origins, Landscape services, Rice breeders, Using forests

Conservation priorities for endangered coastal North African Pennisetum glaucum L. landrace populations as inferred from phylogenetic considerations and population structure analysis. In other news, there’s pearl millet in costal Tunisia.
Is the sky the limit? On the expansion threshold of a species’ range. “…adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment.”
Soil analysis in discussions of agricultural feasibility for ancient civilizations: A critical review and reanalysis of the data and debate from Chaco Canyon, New Mexico. They grew crops there after all.
Future warming increases probability of globally synchronized maize production shocks. Summer is coming.
Early agriculture at the crossroads of China and Southeast Asia: Archaeobotanical evidence and radiocarbon dates from Baiyangcun, Yunnan. Rice, foxtail millet, broomcorn millet, soybeans and Vigna spp were cultivated 2600–2000 BCE.
Ten‐year assessment of the 100 priority questions for global biodiversity conservation. Mainly freshwater ecosystems, societal structures, and impacts.
Ancestry of the two subgenomes of maize. Out of Africa…
Global impact of accelerated plant breeding: Evidence from a meta-analysis on rice breeding. Fancy maths confirms faster is better.
Understanding root, tuber, and banana seed systems and coordination breakdown: a multi-stakeholder framework. Step one: admit they’re different from true seeds.
Hindcasting global population densities reveals forces enabling the origin of agriculture. Better conditions led to population increases led to agriculture.
The effects of landscape patterns on ecosystem services: meta-analyses of landscape services. Landscape complexity is positively associated with ecosystem services.
Global survey of rice breeders to investigate characteristics and willingness to adopt alternative breeding methods. Willingness to adopt new technology high, actual adoption low. Go figure.
Identification of rice landraces with promising yield and the associated genomic regions under low nitrogen. Will they adopt this “technology,” I wonder?
Aligning conservation efforts with resource use around protected areas. Being better off doesn’t necessarily decrease use of tiger reserves.

July 2, 2018July 13, 2018

Brainfood: Italian hotspots, Spanish apples, ICRISAT proso, Scattered trees, Underutilized Malaysian fruit, Saudi chickens, AnGR, Double dates, European threatened plants, Pepper origins, Intensification outcomes, Breeding & diversity, Cold storage, African rice

A methodological approach to identify agro-biodiversity hotspots for priority in situ conservation of plant genetic resources. Interestingly, the centre of Italy comes out on top.
Genetic diversity and core collection of Malus × domestica in northwestern Spain, Portugal and the Canary Islands by SSRs. There is material in common between Galicia and the Canary Islands.
Diversity and trait-specific sources for productivity and nutritional traits in the global proso millet (Panicum miliaceum L.) germplasm collection. Out of 200, 26 were high in at least 2 nutrients.
The importance of scattered trees for biodiversity conservation: A global meta‐analysis. It’s pretty high.
Origin and diversity of an underutilized fruit tree crop, cempedak (Artocarpus integer, Moraceae). The germplasm collections are not too bad, at least for the cultivated form.
Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers. The 6 breeds are diverse and show no inbreeding. Yet.
Conservation of breeds and maintenance of biodiversity: justification and methodology for the conservation of Animal Genetic Resources. Ah, so that’s why they did the above.
What are palm groves of Phoenix? Conservation of Phoenix palm groves in the European Union. Feral can still be useful.
Date Palm Agrobiodiversity (Phoenix dactylifera L.) in Siwa Oasis, Egypt: Combining Ethnography, Morphometry, and Genetics. Some locally recognized and named types are in fact collections of genetically distinct clones that somehow go together anyway: call them “ethnovarieties” if you wish. But not feral.
How to meet the 2020 GSPC target 8 in Europe: priority-setting for seed banking of native threatened plants. 62.7% of European threatened species are already in genebanks, but the others won’t collect themselves. No word on what to do about dates.
Evolutionary history of the chili pepper Capsicum baccatum L. (Solanaceae): domestication in South America and natural diversification in the Seasonally Dry Tropical Forests. Probably originated in Bolivian Amazonia and inter-Andean valleys.
Social-ecological outcomes of agricultural intensification. Win-wins are like hen’s teeth.
Plant breeding and diversity: A troubled relationship? There may be another bottleneck coming.
Rapid loss of seed viability in ex situ conserved wheat and barley at 4°C as compared to −20°C storage. 4°C is not cold enough for long-term conservation.
Genetic control of seed shattering during African rice domestication. Multiple genes lead to a range of non-shattering phenotypes.