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wuwei_horseThe present is often only a faint echo of the past. That is why ancient DNA has totally revolutionized our understanding of the evolutionary past of many branches of the trees of life. The tips of the tree that we see around us today are all that remains of diverse and chaotic brambles which have been thoroughly pruned by chance and necessity. Utilizing present genetic variation researchers have been able to make some very interesting inferences, but you can’t infer that which you lack all evidence for. When it comes to the “megafauna” (i.e., anything bigger than a rat) the past two million years have been very trying, with cold alternating with short warm spells. This has no doubt resulted in thinning every so often as populations go extinct across vast swaths of Eurasia in the face of advancing glaciers. In time the range expands, as populations are re-founded by surviving lineages. But these oscillations drive down long term genetic diversity. In addition, the rise of modern humans has resulted in a great wipe out of whole lineages due to our predatory and avaricious behavior.

Domestic animals are arguably the most extreme case of this dynamic. A recent paper on the genomics of the domestic dog highlighted just how wrongheaded previous assumptions were. The standard thinking was that modern dogs are a derived form of wolf. In other words, dogs are simply a specialized subset of wolves. A domestic wolf as it were. Using whole genome sequencing it turns out that wolves that we see around us today are a sister lineage to dogs. Using wolves as the ancestral form of the dog may not therefore be quite as obvious as we’d thought. Of course it seems likely that the ancestors of the dogs were a wolf lineage of some sort, but we can’t assume that they resemble modern Holarctic wolves.

A similar, more complicated, dynamic is being illustrated by ancient DNA for our own lineage. And now a new paper in PNAS highlights similar dynamics to dogs in horses, Prehistoric genomes reveal the genetic foundation and cost of horse domestication. The authors sequenced two horses from the Taymyr regio
in Siberia with medium and high coverage. The horses were from 15 and 40 thousand years ago. That means they well predate domestication, which probably occurred in the 5 to 10 thousand year interval.

These results confirm that the wild Przewalski horses are not ancestral to the domestic lineages, and that rather they are simply the single wild lineage which persisted down to the modern period. The horses from Taymyr are more distantly related to modern horses than the Przewalski are, but intriguingly tests of admixture indicate that there was gene flow from lineages more closely related to the Taymyr individuals to the modern lineages. This gene flow has to be very close to the root of the origination of modern domestic horses since all breeds are equally represented in the signal of admixture. In short, the modern lineages of horse, wild and domestic, are but a fraction of the variation of the ancient populations.

They confirm this in a population genomic sense by looking at the enrichment for deleterious mutations. A major confound is that many lineages of horse are inbred, so they corrected for that. It turns out that all modern horses exhibit signs of being subject to a load due to accumulation of deleterious variants because of small population size (specifically, bottlenecks), as selection is less efficient at removing these mutations in small population because it is overwhelmed by random drift.

Finally, there is a lot in the paper on signals of selection around various causal alleles. It’s the typical laundry list. Many of the genes are associated with various pathologies and abnormalities, which shows you the cost of reshaping organisms and their behaviors which can occur due to domestication. Strong selection on major effect alleles often result in a cost due to antagonistic pleiotropy. If the selection benefit is high, then negative consequences be damned! Now, horses are notoriously dumb compared to donkeys, so I’d be curious if the cognitive/behavioral signals are found in humans and other mammals, and how they may have changed over time.

• Category: Science • Tags: Domestication 
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It’s about domestication, with a focus on the results from the recent PNAS paper. Our Cats, Ourselves:

It’s commonplace to call our cats “pets.” But anyone sharing a cat’s household can tell you that, much as we might like to choose when they eat in the morning, or when they come inside for the night, cats are only partly domesticated.

The likely ancestors of the domestic dog date from more than 30,000 years ago. But domestic cats’ forebears join us in the skeletal record only about 9,500 years ago. This difference fits our intuition about their comparative degrees of domestication: Dogs want to be “man’s best friend”; cats, not so much.

• Category: Science • Tags: Domestication 
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Citation: Freedman, Adam H., et al. "Genome sequencing highlights the dynamic early history of dogs." PLoS Genetics 10.1 (2014): e1004016.

Citation: Freedman, Adam H., et al. “Genome sequencing highlights the dynamic early history of dogs.” PLoS Genetics 10.1 (2014): e1004016.

The more we scratch beneath the surface with powerful genomic techniques, the more we see that natural history which we had presumed to have a crisp understanding of is quite a bit more muddled. Once the muddle clears what we’ll gain is the gift of accurate complexity, but in many areas right now there is little such clarity. It is a truth that a new discovery or inference does not mean that there are enough points in space to construct a new explanatory constellation when the old does not suffice. Due to the biomedical focus of modern genomics there has been a disproportionate focus on humans, but over time it is clear that this will expand out across the tree of life, and the light shall give way to a temporary fog. First up are organisms of particular human interest and/or model organisms (the latter are species which are useful for elucidating general biological phenomena, and the subjects of study of a large community of researchers). Domestic dogs have the virtue of falling into both categories.


Red Basenji

There are many theories about the origins of our “best friend.” One school of thought (though not necessarily dominant) is that dogs are relatively recent obligate companions of humanity, part of the toolkit of the Neolithic revolution. To be fair this view was rejected by many researchers on the common sense grounds that dogs arrived with the Amerindians 10,000-15,000 years ago. These were clearly hunter-gatherer populations which predated the Neolithic. But there were some genomic research which did imply that even if there were early domestication events, the preponderance of modern domestic dog ancestry dated to the Middle East ~10,000 years before the present. The newest work in genomics seems to falsify that hypothesis rather robustly. These researchers have shown how looking closely and thoroughly at whole genomes (billions of base pairs) organisms, as opposed to a subset of polymorphisms (on the order of tens or hundreds of thousands of base pairs), can yield deeper historical insight.

A new paper out in PLOS GENETICS, Genome Sequencing Highlights the Dynamic Early History of Dogs, has been out as a preprint for a while now, but it seems useful to review what it highlights we now know, and don’t know. As illustrated by the figure above a key element of the revised natural history of the domestic dog must include a minimal level of complexity in the phylogenetic origins of the species. A caricature of the simplest story about the origin of the dog is that it is a tamed wolf. Highly derived from the ancestral state (many characteristics have shifted from the last common ancestor with wolves), but a wolf nonetheless. This idea needs updating because the work in the paper above highlights that extant wolves are not perfect representatives of Pleistocene wolf populations, from which dogs derive. This was already clear with some ancient DNA, but looking at whole genomes of three wolves from disparate regions of Eurasia, a West African Basenji, and an Australian Dingo (along with the Boxer as a reference domestic dog genome and a Golden Jack as an outgroup), a major finding seems to be that modern dogs derive from a population of wolves which are not represented in the populations sampled above. This is important because many inferences about dogs are made simply by assuming that modern wolves are appropriate proxies for the last common ancestor of both lineages.

This substitution seems to be rather shakier than we’d have thought, and this comes to play most obviously in the genetic diversity and bottleneck results we’d take for granted. If modern wolves are the standard for the ancestral population from which dogs derive then the bottleneck is a relatively mild one of a few fold drop in size (wolves are more diverse, but not that much more diverse). But what the authors above found by looking at patterns of genetic diversity across the whole genomes of these wolves is that all three, sampled from Croatia, Israel, and China, also exhibit evidence of a population bottleneck. This makes more sense of the result that it looks as if modern dog lineages underwent a population bottleneck on the order of one magnitude (16 fold). The timing using different methods also definitely predates the Neolithic revolution ~10,000 years ago, and so aligns with the archaeological evidence. Wolves were the companions of hunter-gatherers first before they were associated with farmers. Any possible adaptation of dogs to a starchy diet occurred after the initial bottleneck and separation of the ancestors of this lineage from the ancestors of modern wolves (who seem to have enough variation to have had this trait as part of the ancestral range of the trait in any case). Additionally, there are dog lineages, such as the Dingo, which don’t exhibit any adaptation to starch diets, which makes historical sense as they did not coexist with agricultural populations until recently.

I do want to caution that genomics does not change everything. Many of the broad outlines of what was known before with classical genetic techniques, comparative anatomy, and paleontology, do hold up. For example the domestic dogs do seem to form a monophyletic lineage. By this one simply means that domestic dogs the world over seem to share a small set of common ancestors, rather than being instances of convergent morphological evolution from disparate wolf lineages. What is more surprising though is that these results imply reciprocal monophyly with wolves. This means that domestic dogs are not a specialized branch of a particular population of modern wolves, but a sister lineage to contemporary wolves. Though it is common to say that a dog is just a tamed wolf, one might as easily state that a wolf is a wild dog (yes, I will grant that the dog is likely more derived, but I don’t think we can just substitute modern wolves for ancient ones and call it good). Both are subsets of a wider range of canid ancestors which flourished in the Pleistocene. The tests of admixture of particular lineages suggest that the origins of dogs seem to suggest gene flow with local wolf lineages. This would confound attempts to ascertain a particular zone of domestication or adaptation, as prior genetic affinities or clines in diversity may be due to gene flow rather than patterns of descent (earlier attempts to assert that domestic dogs derive from the Middle East or China may be premised on false assumptions, as well as limitations of less dense marker sets than whole genomes).

The main drawback of this study is obviously the limited sample size. It is freely acknowledged in the paper, but that is why the authors also attempted to select individuals from populations which were highly informative, both geographically and culturally (e.g., Dingoes are outside the range of the wolf, and, not coexistent with ancient agricultural populations). I am more skeptical about assuming that the wolf samples are representative than I am about their selection of three dog lineages (Basenji, Dingo, and the Boxer reference). We know a lot more about the genetics and history of dogs than we do about wolves, and it seems more likely that there are going to be more surprising loose ends in the case of the latter than the former. But if I had to bet I’d say the authors are right, and their inferences are going to hold up (reciprocal monophyly, the bottleneck in wolves, etc.). Yet there’s no doubt going to be a lot of detail added to this model as the sample sizes increase, and ancient DNA is is included in the analysis. Though recent studies seem to establish rather clearly that domestication was a function of the later Pleistocene (and not the Holocene) in the case of dogs, the exact details of where, when, an who, are still quite woolly.

But the ultimate big picture is emphasized by the title above: the Pleistocene is going to seem like a strange country after all is said and done. Many of the organisms which are going to be sequenced in great depth (high coverage) and large sample sizes first are mammals of Palearctic origin which were shaped by the Pleistocene. The importance of this geological period for humans has long been a subject of scholarly attention, but genomics and the light it sheds upon quirks of natural history, might emphasize the ecology-wide reshaping role that Ice Ages had upon the natural history of so many familiar and charismatic species. This is where genomics will open the door to evolutionary ecology of grand scope.

Citation: Freedman, Adam H., et al. “Genome sequencing highlights the dynamic early history of dogs.” PLoS Genetics 10.1 (2014): e1004016.

Related: Please see a post from one of the authors at Haldane’s Sieve.

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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.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Domestication, Evolutionary Genetics 
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In my post below Rob commented:

Surely the genetic evidence is pointing towards a single domestication event (see

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:

Results from the study, which examined the DNA of 642 dogs, suggest that European and American canine breeds were much more influenced by dogs from Southeast Asia than by ancient Western dogs or by dogs from the Middle East, as was previously thought.

Findings from the study by collaborators in California, Iran, Taiwan and Israel appear online in the journal Public Library of Science (PLoS) One.

“The two most hotly debated theories propose that dogs originated in Southeast Asia or the Middle East,” said study co-author Ben Sacks, director of the Canid Diversity and Conservation Group in the Veterinary Genetics Laboratory in the UC Davis School of Veterinary Medicine. The laboratory is an international leader in animal genetics research and provides DNA testing and forensic analysis for numerous wildlife, companion animal and livestock species.

“In contrast to those theories, our findings suggest that modern European and American dogs are overwhelmingly derived from dogs that were imported from Asia since the silk trade, rather than having descended directly from ancient dogs native to Europe,” Sacks said. “Therefore, previous arguments against Europe as a potential site of dog origins, based on modern European dog DNA, must be reconsidered, and our high-resolution Y-chromosome data from indigenous dogs of the Middle East and Southeast Asia now provide the means to test this hypothesis using ancient European dog DNA.”

I assume that as man’s best friend dog genetics is going to be where human genetics is in a few years. I’m not well aware of how good the dog reference genome is, though I hear the cat genome isn’t very good. After whole genome analysis gets going with humans I assume people will start looking at domesticates, companion animals as well as those with more direct economic productivity implications.

(Republished from Discover/GNXP by permission of author or representative)
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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:

The origin of two cultivated rice Oryza sativa indica and O. sativa japonica has been an interesting topic in evolutionary biology. Through whole-genome sequencing, we show that the rice genome embodies two different evolutionary trajectories. Overall genome-wide pattern supports a history of independent origin of two cultivars from their wild population. However, genomic segments bearing important agronomic traits originated only once in one population and spread across all cultivars through introgression and human selection. Population genetic analysis allows us to pinpoint 13 additional candidate domestication genes.

From what I can gather the paper which argued for a common origin of indica and japonica in the same domestication event covered a much smaller fraction of the genome than this paper. All things equal then I’d lean toward the assessment of the relationship between the two in this paper, though they aren’t particular unequivocal either as to the relationship between indica and japonica. As in the second paper on domestication genes and selection they found a lot more diversity on indica than japonica. In fact indica was only marginally less diverse than rufipogon. The big headline results are in figure 5. The top two panels, A and C, are just showing you θ across the respective chromosomes for each lineage. θ is just a measure of nucelotide diversity. The higher the θ, the more diverse the genomic region. R, J, and I are the three rice lineages, rufipogon, japonica, and indica. The second two panels show the genetic distance between two pairwise lineages using Fst measures. Fst just reports the amount of genetic diversity which is partitioned in group level differences (e.g., Fst across continental human races is ~0.15). As Fst approaches 0, that means all the genetic diversity can be reduced to variance within the groups. As Fst approaches 1, that means that all the diversity can be accounted for by noting the differences between groups.

It’s pretty clear from these panels that japonica is the outlier when it comes to genetic diversity. It doesn’t have nearly as much as the other two lineages. This is in line with what the paper I blogged last week reported. In fact, there’s not much of a difference between indicia and rufipogon using this statistic. But when you move to between population differences an interesting pattern emerges. Across much of these two chromosomes (rice as 12 chromosomes by the way) the three lineages exhibit about equal genetic distance from each other, but there are segments of sharply decreased genetic distance between the two domestic cultivars! These are extended regions of reduced genetic diversity overall. And very interestingly some genes implicated in domestication are found just here. Of course it may be that the alleles which can drive domestication were part of the standing genetic variation of the wild lineages. This means that there’s a normal range of variation in a population, and independent selection events swept up in frequency the same alleles derived from the ancestral wild types. But this is not what it looks like when you examine the genomic regions around these alleles. They share the same exact variants, which implies a common selective sweep event in which an ancestral allele and its neighbors were the target of a powerful adaptive force.

The authors suggest that this peculiar constellations of disjunctions in the evolutionary histories of different regions of the genome can not be explained by simple demographic processes such as selfing, bottlenecks, etc. Rather, it is the outcome of a complex process whereby hybridization events allowed from the introgression of ancestral domestication genes from one lineage to another, and the sweeping to fixation of these domestication genes across two lineages with very different ancestries. In other words, common traits don’t always emerge from common ancestors, but rather, often from common experiences.

We know this for humans. The figure to the right is from Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. A of this figure shows the total genetic distances between West Africans (WA), Europeans (EU), South Asians (SA), Island Melanesians (EA), and Native Americans (NA). Each successive panel shows genetic distances on specific loci implicated in variation in pigmentation. Notice how incongruent they are with the tree in A in many cases. Look at E, where Europeans are a clear outgroup on the locus, and all other populations cluster. This is a variant on SLC45A2 which is highly diagnostic of Europeans, and is correlated with light complexion (the minority of Europeans who carry the variant found in the rest of the world are much more likely to have dark eyes, black hair, and olive skin, than not). We don’t need to go into the possible evolutionary reasons why dark skin and light skin are distributed as they are here. Rather, we can see in the case of this trait that the histories of the specific genes may not reflect the history as told in the total genome content, because of the importance of local adaptations and selection pressures. The case of rice may be an inversion, insofar as instead of a location adaptation differentiating relatively closer groups (e.g., look at South Asians vs. Europeans in C, D, and E), it may be a case where very different groups exhibit similarities because of convergent evolution. That convergent pressure being the impulse toward domestication.

Speaking of which, that impulse may be related to the arrival of the Munda populations from Southeast Asia into India. If the model above is correct than indica was a local cultivar, perhaps at some stage of domestication, which was improved by hybridization with japonica. Eventually admixture swamped out most of the japonica genetic background, but recurrent selection favored japonica alleles at a large set of loci implicated in domestication. In this paper they lacked the power to ascertain whether the haplotypes jumped from indica to japonica or vice versa. But I’d be willing to bet $250 dollars that it is going to turn out to have come from japonica because of other aspects of archeobotany, combined with japonica‘s extreme homogeneity, which may be a hallmark of a process of a very powerful set of selection events which gave rise to domestic rice.

Citation: Ziwen He, Weiwei Zhai, Haijun Wen, Tian Tang1, Yu Wang, Xuemei Lu, Anthony J. Greenberg, Richard R. Hudson, Chung-I Wu, & Suhua Shi (2011). Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes PLoS Genetics : 10.1371/journal.pgen.1002100

(Republished from Discover/GNXP by permission of author or representative)
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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. In 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:

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativaindica and tropical japonica—as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

Here’s what seems relevant for the two domestic varieties from Wikipedia:

Oryza sativa contains two major subspecies: the sticky, short grained japonica or sinica variety, and the non-sticky, long-grained indica variety. Japonica are usually cultivated in dry fields, in temperate East Asia, upland areas of Southeast Asia and high elevations in South Asia, while indica are mainly lowland rices, grown mostly submerged, throughout tropical Asia….

There’s long been debate about the exact phylogenetic relationship between these two strains of domestic rice. More on that later. In regards to domestication there are three categories we need to focus on in terms of adaptation: 1) traits which are common to all domestic cereals and tend to crop up almost immediately, 2) traits which are extensions and improvements upon the initial domestic prototype, 3) traits which are regional diversifications, often adaptations to climate. Consider an analogy to horses. The original domestic horse was rather small, and was only fit for drawing chariots. Eventually the breeds became larger, and suitable for cavalry. Finally, there was a diversification by task (e.g., workhorses vs. race horses) and to some extent climate.

As noted above previous classical genetic techniques had narrowed down the genetic regions responsible for various domesticate traits when comparing japonica to the wild rufipogon. Since domestication usually entails a process of selection the authors naturally presumed that they might be able to detect signatures of selection within the genome. What are the genomic tells of selection?

There are many, just as there are different types of selection. In this case what we know suggests that due to #1 there’s going to be an initial bout of adaptation and rapid shift from wild diversity to fixed traits suitable for a crop which is going to be controlled by humans. Just as the riotous diversity of the wild varieties become constrained to monocultures, so the diversity of the wild type often gets swept away by a few genetic variants which are responsible for the favored traits. So what they might see in the domestic varieties is a sharp reduction of variation around the quantitative trait loci (QTLs) reported earlier, because those QTLs have presumably been the target of selection. In other words, a selective sweep.

That’s what they found. At least in one lineage.

Left to right you have indica, japonica, and rufipogon. Front to back in each chart you see the three QTLs, and the distribution of nucleotide diversities by genetic fragments within these QTLs. The extremely skewed distribution of the domestic varieties in relation to the wild type rufipogon is rather obvious. Additionally, you see a stronger skew in japonica in relation to indica. The skew in the domestic strains is toward a greater proportion of the fragments having very low nucleotide diversity.

What could cause this? You need a further piece of information here. The domestic varieties have long regions of the genome characterized by linkage disequilibrium (actually, japonica is so homogeneous that you barely have enough variation to calculate LD!). So particular genetic variants are associated with each other, resulting in long runs of similar sequences, haplotypes. It’s as if a chunk of some ancient chromosome just “blew up” and took over that segment of the genome in japonica.

Natural selection could do this. Imagine that an ancestral rufipogon has a genetic variant which confers a domestic trait. It would be selected. Even if crossed with other strains with other domestic characteristics its particular QTL would be transmitted down to the descendants in general. But not only would the specific genetic variant which conferred the favored trait be passed on, but many of the flanking genomic regions carrying other variants would also be transmitted! This explains the extremely low genetic diversity in japonica, if there’s a sweep up in frequency of a particular ancestral haplotype then what were polymorphisms in the wild type become monomorphic in the domesticate.

Another explanation though could be that demographic history produced these results. Random genetic drift due to small populations, whether via bottleneck or systematic inbreeding/selfing, can also drive up the frequency of alleles favored by lady-luck and render extinct all others. To check for this the authors constructed a model where japonica and indica went through bottlenecks enforced by the domestication (note that strong selection can drive down population size as well). Even with this model the diversity in japonica in these QTLs remained far too low (though indica’s skew did not reach statistical significance).

Since both of the domestic strains exhibit traits of domestication the lack of a selective event in indica at these QTLs does not allow us to infer that there are no genes which were selected for these traits in the past in indica. On the contrary, there certainly were and are such genes. But where are they? The authors moot the possibility that selection exists at the loci under consideration, but was simply missed because the selection was by a different dynamic which might not be picked up by their test. For various reasons they are skeptical of this on its own merits, but I think the bigger issue is that the original linkage mapping was performed with japonica vs. wild type strains, so naturally if the two domestic subspecies differed in their genetic architectures then the QTLs of interest of indica would not be discovered simultaneously.

Something which I’m rather perplexed by is how this comports or aligns with the finding by many of the same researchers that the two domestic varietals derive from the same ancestral population which was domesticated from East Asian wild rice. It could be that the history of domestication is more serial than we know, and that the common QTLs to both japonica and indica have been rendered irrelevant by new adaptations subsequent to their separation. Or, one or the other may have experienced introgression at that locus and so diverged after domestication. Interestingly in figure 7 of the paper they show that phylogenetic trees which illustrates the relationship of alleles associated with each strain. It indicates that indica is not monophyletic on these regions, while japonica is. This means that the japonica variants share a common ancestor, from which all are descended. In contrast, indica variants do not. Such a pattern is consistent with the story of strong positive selection upon a single variant at some time in the past for japonica. From what I can tell they may actually have sent the PLoS ONE paper to the reviewers before the PNAS paper which I reviewed earlier. Because these two papers were published so close to each other they don’t cite each other, though in some ways the first paper in PNAS would have fleshed out the natural history of domestic rice somewhat. As it is, they kind of leave of us hanging in relation to indica.

Why does all of this matter? Yes, agricultural genetics is important for agriculture. But let’s get back to people. There is a hypothesis that man is a ‘self-domesticated’ organism. Whatever quibbles I have with artificial terms like domestication I do think that there may be broad analogies to be drawn between our own species and the organisms associated with us.

Citation: Xianfa Xie1, Jeanmaire Molina, Ryan Hernandez, Andy Reynolds, Adam R. Boyko, Carlos D. Bustamante, & Michael D. Purugganan (2011). Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection PLoS ONE : 10.1371/journal.pone.0020670

Image Credit: IRRI Images

(Republished from Discover/GNXP by permission of author or representative)
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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:

The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as “cryptic domestication,” given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.

They used conventional phylogeographic techniques to catalog the variation in modern populations, as well as supplementing their data set with ancient samples. Here the genetic variance they’re looking at is the mtDNA, the maternal lineage. Easy to get at, and easy to analyze (lots of it, and non-recombinant). In general they seem to have found that there is a common genetic heritage of East Asian domestic pigs, who are embedded geographically among varieties of wild pig who exhibit localized genetic variants. Additionally, there are other varieties of domestic pig in Southeast and South Asia who seem to have arisen from their own boar populations (though there is a Pacific pig variant which seems to have been from mainland Southeast Asia, but that original source population has now been replaced by East Asian pigs). Finallythey find a strong continuity between ancient domestic East Asian pigs and the modern populations. This is a contrast with the findings in European which exhibited disjunction between past and present. Perhaps this has to do with the fact that East Asian pigs are more genuinely indigenous, derived from local wild lineages with regional adaptations, while the Middle Eastern pigs brought to Europe were short-term kludges easily superseded by domesticates derived from European boar populations.

pigfig2This figure shows the nature of haplotype sharing between wild and ancient & contemporary domestic pigs. The larger the pie, the more frequent the haplotype. The slices of the pie by color show wild (black), ancient (red) and modern domestic (white) shares of that haplotype. The line across the networks show the putative separation between the genetic variants relatively private to the wild populations, and those which lean toward a mix of wild & domesticates. The wild populations seem more diverse. 45 haplotypes out of 167 samples are found only in wild specimens, 92 haplotypes out of 339 samples are found only in domestic specimens, and 21 haplotypes are found in both 87 wild and 582 domestic pigs. One assumes that the domesticates are derived from a small subset of wild pigs, and that population underwent demographic expansion within the last 10,000 years. That’s not too different from our species, we’re descended from a small subset of H. sapiens, and we’ve undergone major demographic expansion. Our “wild” cousins among the great apes tend to have a lot more genetic variation even within their small populations because their demographic history has presumably been a bit more staid. As man was, so shall he turn his domesticates. And yet a major difference between the domestic pig and man seems to be that some variant of multiregionalism, the evolution of modern pigs from local lineages, and their subsequent hybridization to produce a genetically unified species, has been operative. One major caution with these studies is that they’re looking at mtDNA. The dog genomics work has been modified and overturned when they shifted from the mtDNA that most phylogeographers focus on to the total genome. One does not know the evolutionary history of an organism by one locus alone.

The pig is a peculiar beast, retaining its feral nature as evident by the periodic reemergence of morphs from released domestic populations which have no difficulty in going “wild.” There are 4 million feral hogs in the United States, and they can get quite large indeed. What would the pekingese do in a world without man? Probably be some other creature’s meal. But generalists like the pigs would no doubt flourish. The story of the pig is a story of piggybacking, so to speak, on the success of the upright ape and spreading across the world on the backs of the other white meat.

Let me finish from the author’s conclusion:

The evidence presented here suggests the following evolutionary history of pigs in East Asia. Having originally evolved in ISEA [Island Southeast Asia], wild Sus scrofa migrated (without human assistance) across the Kra Isthmus on the MalayPeninsula into Mainland Asia. From here, they spread across the landscape and, after traveling over land bridges, onto the islands of Japan, the Ryukyu chain, Taiwan, and Lanyu where they evolved unique mitochondrial signatures. After millennia of hunting and gathering, a major biocultural transition occurred early in the Holocene during which human populations in East Asia domesticated a variety of plants and animals, including pigs. This process took place at least once in the Yellow River drainage basin wheremilletmay have been first domesticated as early as 10,000 B.P…and may have also taken place independently in the downstream Yangtze River region where rice may have been domesticated…Two things are clear from the ancient DNA evidence presented here. First, unlike Europe, modern Chinese domestic pigs are the direct descendants of the first domestic pigs in this region. Second, despite the occurrence of a genetically distinct population of wild boar throughout modern China, this population has neither been incorporated into domestic stocks nor exterminated.

Citation: Larson, G., Liu, R., Zhao, X., Yuan, J., Fuller, D., Barton, L., Dobney, K., Fan, Q., Gu, Z., Liu, X., Luo, Y., Lv, P., Andersson, L., & Li, N. (2010). Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0912264107

Image credit: NASA

(Republished from Discover/GNXP by permission of author or representative)
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"