Tag: Domestication

What is going on with plant domestication?

By Razib Khan | October 3, 2012 12:44 am

PNAS has a paper on barley domestication out right now. It is nicely open access, so read it yourself, and come right back! I have to admit that I did not like the paper too much. It seemed to derive far too many conclusions from a few rudimentary (for today at least) phylogenetic methods. In particular I’m very skeptical of the idea that there are two barely lineages here which diverged ~3 million years B.P. But this isn’t particularly strange when it comes to the phylogenetic origins of cultivars. There have been long debates about whether there was one origin for rice, or several. Setting aside my major issues with this paper I wonder if perhaps our expectations and prejudices derived from the fact that animals are to a great extent the “null” organisms are muddying our interpretation of results from plants. The number of loci here seem sufficient to dismiss the possibility of introgression, but I’m not sure that the rate of evolution across these markers is quite so clock-like.

In any case, to understand domestication, and I suspect human evolution, these results from plants are going to have to be cleared up and systematized. Illumination would be helpful, but until then I suppose we keep on hoping that the papers keep flowing.

CATEGORIZED UNDER: Evolutionary Genetics
MORE ABOUT: Domestication

The last word on dog genesis is not nigh!

By Razib Khan | December 19, 2011 11:00 am

In my post below Rob commented:

Surely the genetic evidence is pointing towards a single domestication event (see http://news.sciencemag.org/sciencenow/2011/11/new-data-fuels-dogfight-over-the.html?ref=hp)

My general response is not to accept the latest press release about the genetic origin of dogs. I keep track of the literature and it’s rather fluid. For example, I woke up this morning, and this is what showed up in my RSS, Modern dogs are more Asian fusions than Euro pups, study finds:

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MORE ABOUT: Dogs, Domestication

Domestication as introgression and assimilation

By Razib Khan | June 13, 2011 3:31 am

ResearchBlogging.orgThe Pith: the spread of domestic rice may be a function not of the spread of rice per se, as much as a specific narrow set of genes which confer domestication to disparate rice lineages.

This has been a big month for rice. At least for me. Despite my background as a rice-eater I’ve generally moved away from it of late. It’s an American thing, as we’ve replaced a fear of fat with a fear of refined carbohydrates. My parents have even shifted from white rice to brown rice because of concerns with type 2 diabetes (this caused some consternation in 2004, as when we visited Bangladesh as honored guests my father was given to lecturing our hosts about the evils of the white rice on offer. Remember that in these societies brown rice is often considered the fair of the poor). But the reality is that much of the Old World of Asia still relies on rice, and will do so for the foreseeable future. So I still take an inordinate interest in the oriental staff-of-life. I already reviewed two papers on rice genetics recently, but now it’s time for a third.

Some things are similar, some things are different. Again the stars of the show are the two cultivars of O. ativa, indica and japonica, and wild rice, O. rufipogon, from which the domestic varieties are presumably derived. The question at issue are the possible differences in the genealogy of the total genome background of rice cultivars vs. particular regions of the genome relevant for domestication. In other words, did the genes responsible for domesticate traits spread and sweep across different rice lineages? Or are different rice lineages simply derived from a common ancestor which carried the original domestication traits from a singular selection event? The first paper I reviewed suggested that there was one single domestication event, and that later differentiation between indica and japonica may simply have been a function of isolation and possible hybridization with local wild strains in the case of indica. The second paper focused on genes responsible for domestication seemed to imply that indica and japonica may have been shaped by different selection events (more precisely, they couldn’t detect signatures of selection in indica at the same loci that they did for japonica). A new paper in PLoS Genetics seems to take a broader view, highlighting both the phylogeny of the total genome as a whole and the bouts of natural selection which might have reshaped specific genes in a particular manner. Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes:

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Why rice is so nice

By Razib Khan | June 7, 2011 5:49 am

The Pith: What makes rice nice in one varietal may not make it nice in another. Genetically that is….

Rice is edible and has high yields thanks to evolution. Specifically, the artificial selection processes which lead to domestication. The “genetically modified organisms” of yore! The details of this process have long been of interest to agricultural scientists because of possible implications for the production of the major crop which feeds the world. And just as much of Charles Darwin’s original insights derived from his detailed knowledge of breeding of domesticates in Victorian England, so evolutionary biologists can learn something about the general process through the repeated instantiations which occurred during domestication during the Neolithic era.

A new paper in PLoS ONE puts the spotlight on the domestication of rice, and specifically the connection between particular traits which are the hallmark of domestication and regions of the genome on chromosome 3. These are obviously two different domains, the study and analysis of the variety of traits across rice strains, and the patterns in the genome of an organism. But they are nicely spanned by classical genetic techniques such as linkage mapping which can adduce regions of the genome of possible interesting in controlling variations in the phenotype.

ResearchBlogging.orgIn this paper the authors used the guidelines of the older techniques to fix upon regions which might warrant further investigation, and then applied the new genomic techniques. Today we can now gain a more detailed sequence level picture of the genetic substrate which was only perceived at a remove in the past through abstractions such as the ‘genetic map.’ Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection:

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Of pigs, people and porcine polygenism

By Razib Khan | April 20, 2010 6:25 am

800px-Wild_Pig_KSC02pd0873Jared Diamond famously argued in Guns, Germs and Steel that only a small set of organisms have the characteristics which make them viable domesticates. Diamond’s thesis is that the distribution of these organisms congenial to a mutualistic relationship with man shaped the arc of our species’ history and the variation in wealth that we see (though his a human-centric tale, we may enslave them, eat and use them as beasts of burden, but these are also species which have spread across the world with our expansion). This thesis has been challenged, but the bigger point of putting a focus on how humans relate to their domesticated animals, and the complex co-evolutionary path between the two, is something that we need to consider. In a plain biological and physical sense animals have utility; we eat them, and for thousands of years they were critical to our transportation networks. Some have argued that the rise of Islam, Arab monotheism, was contingent on the domestication of the camel (which opened up interior trade networks previously unaccessible). In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the argument is made that the distribution of the Indo-European languages has to do with the facility of Central Eurasian plainsmen with their steeds. And of course there is the domestic dog, arguably the one creature which is able to read our emotions as if they were a con-specific.

I suspect that the evolution and ethology of domesticated animals will offer a window into our own evolution and ethology. Konrad Lorenz famously believed that humans were going through their own process of domestication all the while that they were selecting organisms suited to their own needs. More pliable, less intelligent, faster growing and maturing, and so forth. Know thy companions, and know thyself, so to speak.

What about an animal as intelligent as a dog, but famously tasty? (the combination of the two characters causing some ethical tension in the minds of many) I speak here of the pig. A few years ago research came out which showed that pig-culture was introduced to Europe from the Middle East. That is, Middle Eastern pigs came with Middle Eastern people in all likelihood. But modern European pigs do not derive from these lineages, rather, by comparing modern genetic variation with ancient DNA the authors showed that the Neolithic pigs had been replaced by local breeds. Just as pigs can go feral and fend for themselves rather easily, it seems that their basic morph can be derived from wild boar populations easily as well (by contrast, it will perhaps take some effort to derive a pekingese from wolf populations, offering a reason for why small dogs seem to have emerged once). A new paper explores the evolutionary history and phylogeography of the pigs of the swine-loving societies par excellence, those of East Asia. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA:
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CATEGORIZED UNDER: Culture, Genetics, Genomics, Science

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