DNA – Page 52 – Agricultural Biodiversity Weblog

July 12, 2013July 12, 2013

Is this automated Musa phylogeny any good?

PhyloGenerator is “an open-source, stand-alone Python program, that makes use of pre-existing sequence data and taxonomic information to largely automate the estimation of phylogenies.” Sounds intriguing, no? I found out about it via this Twitter exchange with Rich Grenyer:

@rich_ @Phalaropus Sure, of course!

— AgroBioDiverse (@AgroBioDiverse) July 11, 2013

He very kindly shared his automatically generated Musa phylogeny, which is reproduced below. I’m afraid you’ll have to click on the image to read the species names.

So now I’m reaching out to all you banana taxonomists out there. Does this make any sense?

July 10, 2013July 9, 2013

Nibbles: Tree ID, Pyramid scheme, Looking ahead, Fun with mould, GM wheat, Sinai reclaimed

Stuff that’s been sitting around while I’ve been lying on a beach:

Speaking of apps for agriculture, here’s one that identifies North American trees.
R. Ford Denison spots the weakness in an afro-forestry get-rich-quick scheme.
Public Radio International has a big series on feeding the 9 billion — and wants photos of your lunch.
I’ve no idea why people are squeamish about smut. Huitlacoche is my personal favourite among Smithsonian MAG’s Four Fungi Fit For Your Plate.
No idea what’s happened lately to Monsanto’s GM wheat fiasco. Is the US National Center for Genetic Resources Preservation off the hook?
And something old yet new: reclaiming the Sinai for agriculture by reviving an ancient river.

July 9, 2013July 9, 2013

Nibbles: CePaCT aroids, Chinese pigs, Vanuatu banana processing, Yam meeting, AAB meeting, Araucaria, Aquaculture, Malting barley, CIRAD baobab videos, US wine, Ancient grains, Barcode centre

The Pacific pushes out its taros.
China holds on to its pigs.
Vanuatu preserves its bananas.
The world talks about yams in particular. And crop breeding in general.
How Britain got its monkey puzzles.
Bangladesh goes for mola culture. But not only.
Australia puts money into beer.
France gets into the whole baobab factsheet thing, but with a video twist.
Virginia makes wine. With infographic goodness.
UK tries to slow down its food.
Canada barcodes everything.

July 8, 2013July 3, 2013

Brainfood: Leafy greens, Korean rice, Molecular breeding, Poultry conservation, Tree genomes, Pathogen genetics, Grazers and CC, Sustainable rangelands, Available land, Ecosystem services

Analysis of urban consumers’ willingness to pay a premium for African Leafy Vegetables (ALVs) in Kenya: a case of Eldoret Town. An 80% premium! But in Eldoret. And Nairobi?
Analysis and comparison of the γ-oryzanol content based on phylogenetic groups in Korean landraces of rice (Oryza sativa L.). Some groups are browner than others.
What is the SMARTest way to breed plants and increase agrobiodiversity? Just another name for MAS. But some crops are SMARTer than others.
Conservation of local Turkish and Italian chicken breeds: a case study. Turks can learn from Italians. And probably vice versa, I bet, although that’s not explored as much here.
Open access to tree genomes: the path to a better forest. Hard to argue with. The open access bit more than the genomes bit.
Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens. Know your enemy. Easier to figure out how new species become different than how they stay that way.
Long-Term Climate Sensitivity of Grazer Performance: A Cross-Site Study. Hotter conditions means poorer forage quality means smaller bison. And maybe cattle. All other things being equal, like genetics, and range management. Which of course they never are.
Ecosystem function enhanced by combining four functional types of plant species in intensively managed grassland mixtures: a 3-year continental-scale field experiment. See what I mean? And more.
Estimating the world’s potentially available cropland using a bottom-up approach. Less than you’d think.
Spatial interactions among ecosystem services in an urbanizing agricultural watershed. Very very limited places provide multiple services, especially crop production and water quality, which means you need to protect huge areas. But they’ll be mosaics.

July 4, 2013July 3, 2013

Nibbles: Ug99, Heirloom & wild tomatoes, Opium, Healthy flavours, Quinoa descriptors, Wild yak community conservation, Phenotyping facility, Tree app, ABS & EU, C4, Barley in Ethiopia, Chinese coffee

Not totally wild genes protect wheat from Ug99.
Not really wild Texas Wild tomato brings Texan back to gardening. These in Peru are wild though.
Speaking of gardening, here’s Michael Pollan on his struggles with opium.
Wild, healthy fruit flavours becoming more popular on the soft drink market, but not clear to what extent they will come from actual plants, wild or otherwise. You know, plants with yield variation and other inconveniences. Plants that some people rely on for nutrition, by the way.
Descriptors for quinoa, including the wild species. And more, much more.
I wonder if there are descriptors for wild yaks.
New UK facility for phenotyping plants, including wild ones, I’m sure.
And if those wild UK plants are trees, you can use this app to identify them, before phenotyping them. Assuming you can dig them up and squeeze them into the new facility. Anyway, maybe one of them will be European Tree of the Year.
Of course, if you wanted access to the genetic resources of such trees, you’d have to deal with the Nagoya Protocol, which the EU is getting to grips with, don’t worry.
Not many C4 species among UK trees, I guess.
Teff is C4, but that isn’t stopping people trying to replace it with barley in injira.
Next thing you know the Chinese will be swapping tea for coffee. No, wait.