Agricultural Biodiversity Weblog

January 15, 2014January 16, 2014

Filling the gaps in Lacunas

A paper in Biodiversity and Conservation caught my eye: “Lacunas: a web interface to identify plant knowledge gaps to support informed decision-making.” ¹ I knew that Brazilian biodiversity researchers had been working hard on bringing their data together, and this sounded like the information was now ready to be put to some use:

SpeciesLink’s thematic network, INCT-Virtual Herbarium of Plants and Fungi and the List of Species of the Brazilian Flora, are used as primary data sources to develop Lacunas, an information system with a public web interface that generates detailed reports of the status of plant species occurrence data. Lacunas also integrates information about endemism, conservation status, and collecting efforts over time.

I couldn’t resist doing a quick roadtest of Lacunas, of course. It’s available in both Portuguese and English, and it has a simple, intuitive interface, so it wasn’t a chore. Naturally I selected a crop wild relative: Oryza grandiglumis (Döll) Prod.

You get a nice map. And a bunch of tables summarizing various statistics (both for the exact species name and for phonetically similar species names, which is a nice touch):

Number of records per year collected

Total number of records available in different herbaria in the speciesLink network

Total number of records available in the speciesLink network by georeferencing status

Total number of records available in the speciesLink network with distinct geographic coordinates

I grabbed a screenshot of one of the tables, because that was the only way I could see to save the results, and I thought I might blog about Lacunas one day. It was a pity about that saving thing, though, because the statistics the portal provides are genuinely useful in giving an idea of the quality and quantity of the data we have on different species in Brazil. For example, for our wild rice there are 31 records in all, but only 4 have original georeferences. Fortunately, for 15 of those that don’t have original latitude and longitude coordinates, it was possible to infer georeferences from other associated data. But that still leaves a significant number of herbarium specimens which cannot be used in mapping the distribution of the species. Anyway, I left a comment to that effect on the website. Then I moved on to other stuff, and the blogging got pushed down the to-do list, what with one thing and another.

Imagine my surprise then when I got notification of a fix within a couple of days. A fix which allows me to link to a results page, rather than include that clunky screengrab here. And imagine my further surprise when the guy who provided the fix turned out to be an old friend. Small world. Anyway, thanks to Sidnei for the help, and the chat.

Now, it would be great to compare the Lacunas data with those in the Crop Wild Relatives Global Atlas. But first I need to convince the developers of that incredible resource to make sharing results a little easier.

January 13, 2014January 13, 2014

Brainfood: Diversity in restoration, Niche model validation, Dutch diets, Markets in conservation, Genomics for stress, Protected agroecosystems, Cocksfoot diversity, Tree breeding, Organic in India, Coconut origins, Dope diversity

Application of genetic diversity–ecosystem function research to ecological restoration. Cultivars vs local populations vs genetic diversity approaches in restoration reviewed. More research needed, natch, but genetic diversity should not be dismissed out of hand in a bid for rapid establishment or long-term persistence, as it may well be best for ecosystem functioning.
Application of consensus theory to formalize expert evaluations of plant species distribution models. Given arm-twisting, experts like models.
Exploring dietary guidelines based on ecological and nutritional values: A comparison of six dietary patterns. The Dutch should eat less meat. No word on beer.
Market-based mechanisms for biodiversity conservation: a review of existing schemes and an outline for a global mechanism. You can’t monetize what you can’t measure.
Genomic resources for breeding crops with enhanced abiotic stress tolerance. You still need the phenotyping.
Perceptual distinctiveness in Native American maize (Zea mays L.) landraces has practical implications. Kernel colour diversity is a marker for other, more interesting, kinds of diversity.
Can agro-ecosystems efficiently complement protected area networks? Yes, but only in combination with expansion of protected natural habitats. For birds in Israel, that is.
Indicators for genetic and phenotypic diversity of Dactylis glomerata in Swiss permanent grassland. Management alters both genotype and phenotype.
A ‘Reality Check’ in the Management of Tree Breeding Programmes. Have come far, but still a ways to go, in particular with regard to the balance between DNA-based vs conventional breeding and genetic gain vs genetic preservation.
Yield and Economic Performance of Organic and Conventional Cotton-Based Farming Systems — Results from a Field Trial in India. Organic soybean may be a viable long-term option. Cotton and wheat, jury still out. But early days yet, these rotation trials take a long time to get going.
Long-distance dispersal of the coconut palm by migration within the coral atoll ecosystem. Hugh Harries, one of the authors, in a recent email to us: “Recent reviews have blown dust from old reports of pre-Colombian coconuts in Panama and demonstrated how the rate of germination distinguishes the naturally selected wild coconut from the domestically selected sort. This review formulates a hypothesis which could identify a previously unconsidered route along which the primordial coconut might travel between the South American and Indian tectonic plates without being indigenous on either.” That is, atoll-hopping.
Differentiation between fiber and drug types of hemp (Cannabis sativa L.) from a collection of wild and domesticated accessions. Must have been fun doing the evaluation.

January 11, 2014January 12, 2014

Dope diversity denied?

There’s one thing I want to know about what’s going to happen now that marijuana has been legalized in a couple of states in the US. And it’s not on CNN’s list. ² No, not where a visitor can actually smoke the stuff legally, as opposed to just buying it. Or how I can get a job in the industry. What I want to know is what will happen to diversity. There are some indications that legalization may lead to an increase in intellectual property protection over particular strains. I hope someone out there is gathering the baseline data, and saving the seeds, just in case. Not to mention learning lessons that could then be applied to, I dunno, opium in Afghanistan?

January 10, 2014January 10, 2014

Dorian Fuller on domestication, and not only of donkeys

Speaking of Dorian Fuller, in addition to his always fascinating The Archaeobotanist blog, he also curates five — count them — topics on Scoop.it, reflecting the wide range of his interests. Unlike many others on Sccop.it, including me, Dr Fuller always provides trenchant commentary on the material he posts. Browsing through his stuff, I ran across a post on a paper on donkey domestication which I had missed last year. I hope he won’t mind if I reproduce his insights here, to give a flavour of what you can expect if you follow him.

Donkey’s are undoubtedly one of the most important domesticates from Africa, but less well-documented then cattle or many crops, as they have rarely been food sources. This article provides updated review of the archaeology and genetics of donkey, including some ancient DNA evidence such as Uan Muhhgiag donkeys from prehistoric Libya. Of interest is the argument that reports of “wild” donkeys in the Levant or Arabia, such as the quantities from Ash-Shumah in Yemen, are early domesticates and not endemic wild populations. If this is the case then it would put donkey herding back to the early Holocene before 6000 BC, putting them in competition of Bos africanus for the earliest African domesticates [excluding Pleistocene bottlegourds]. Alternatively, as mapped in Boivin & Fuller (2009 in J. of World Prehistory) we extend the map of wild donkeys through the Sinai and down the west coast of Arabia to make the Ash-Shumah remains those of hunted wild animals. The latter would open the possibility of southern Levant donkey domestication. The current review by Kimura, Marshall and colleagues makes an interesting but inconclusive case against this. (Historical linguistic evidence does tend to point to African domestication among Afroasiatic/Cushitic sub-groups). As this paper concludes there is a need for more targetted research on donkeys!

Which also allows me to post one of the pix from my recent holiday on Lamu island off the coast of Kenya, where donkeys are of course the only form of transportation.

January 10, 2014

Prof. David Harris RIP

Prof. David Harris, one of the giants of the study of the origins of agriculture, died during the holiday period. He was Professor Emeritus of Human Environment at the Institute of Archaeology (UCL) and a former director of the institute (1989-1996). Dorian Fuller, a friend and colleague at the institute, has an informative and touching piece about Prof. Harris on his blog. The comments there, and on my re-posting of Dr Fuller’s piece (see below), are ample evidence of Prof. Harris’ impact and legacy.