Yesterday I pointed to a paper which was interesting enough, but didn’t pass the smell test in relation to other evidence we have (at least in my opinion!). A primary concern was the fact that uniparental (male and female lineages) show a peculiar distribution of variation in comparison to autosomal genetic variation (i.e., the vast majority of the genome) in the case of Europe (genome-wide analysis suggest more of Europe’s variation is partitioned north-south, but Y and mtDNA results often imply an east-west split). But a secondary concern I had was that I felt the models were a bit too stylized. In particular following Cavalli-Sforza and Ammerman the authors concluded that demic diffusion better fits their results of genetic variation in Europe (as opposed to continuity of Paleolithic hunter-gatherers). This is likely correct, but these are not the only two models.
A paper out in Nature Communications, using analysis of the phylogenetics of whole ancient mitchondrial genomes, outlines my primary concern when it comes to the models being tested, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans:
Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
Since John Hawks already hit it I don’t have much to add about the dog-starch-adaptation-paper in Nature, The genomic signature of dog domestication reveals adaptation to a starch-rich diet. I’m impressed at the yield from the sample sizes that they had, but as John alludes to this area of study has huge possibilities. The authors suggest that agriculture catalyzed domestication. That’s fair enough, and carefully stated I’d say, because the Amerindians seem to have brought domestic dogs to the New World long before agriculture. In other words, the “domestication” event was probably a multi-layered affair. Looking through the supporting information it’s obvious that the domestics were almost all Western breeds. As the search for adaptive variants expands to other lineages we might be in for surprises in terms of the signatures of selection as they vary across the dogs.
The above image, and the one to the left, are screenshots from my father’s 23andMe profile. Interestingly, his mtDNA haplogroup is not particularly common among ethnic Bengalis, who are more than ~80% on a branch of M. This reality is clear in the map above which illustrates the Central Asian distribution my father’s mtDNA lineage. In contrast, his whole genome is predominantly South Asianform, as is evident in the estimate that 23andMe provided via their ancestry composition feature, which utilizes the broader genome. The key takeaway here is that the mtDNA is informative, but it should not be considered to be representative, or anything like the last word on one’s ancestry in this day and age.
I mentioned this in passing on my post on ASHG 2012, but it seems useful to make explicit. For the past few years there has been word of research pointing to connections between the Khoisan and the Cushitic people of Ethiopia. To a great extent in the paper which is forthcoming there is the likely answer to the question of who lived in East Africa before the Bantu, and before the most recent back-migration of West Eurasians. On one level I’m confused as to why this has to be something of a mystery, because the most recent genetic evidence suggests a admixture on the order of 2-3,000 years before the past.* If the admixture was so recent we should find many of the “first people,” no? As it is, we don’t. I think these groups, and perhaps the Sandawe, are the closest we’ll get.
Publication is imminent at this point (of this, I was assured), so I’m going to just state the likely candidate population (or at least one of them): the Sanye, who speak a Cushitic language with possible Khoisan influences. There really isn’t that much information on these people, which is why when I first heard about the preliminary results a few years back and looked around for Khoisan-like populations in Kenya I wasn’t sure I’d hit upon the right group. But at ASHG I saw some STRUCTURE plots with the correct populations, and the Sanye were one of them. I would have liked to see something like TreeMix, but the STRUCTURE results were of a quality that I could accept that these populations were not being well modeled by the variation which dominated their data set. Though Cushitic in language the Sanye had far less of the West Eurasian element present among other Cushitic speaking populations of the Horn of Africa. Neither were their African ancestral components quite like that of the Nilotic or Bantu populations. The clustering algorithm was having a “hard time” making sense of them (it seemed to wanted to model them as linear combinations of more familiar groups, but was doing a bad job of it).
Here is an interesting article on these groups: Little known tribe that census forgot. Like the Sandawe this is a population which seems to have been hunter-gatherers very recently, and to some extent still engage in this lifestyle. In this way I think they are fundamentally different from Indian tribal populations, who are often held up to be the “first people” of the subcontinent. More and more it seems that the tribes of India are less the descendants of the original inhabitants of the subcontinent, at least when compared to the typical Indian peasant, and more simply those segments of the Indian population which were marginalized and pushed into less productive territory. Over time they naturally diverged culturally because of their isolation, but the difference was not primal. In contrast, groups like the Sanye and Sandawe may have mixed to a great extent with their neighbors (and lost their language like the Pygmies), but evidence of full featured hunting & gathering lifestyles implies a sort of direct cultural continuity with the landscape of eastern Africa before the arrival of farmers and pastoralists from the west and north.
* I understand some readers refuse to accept the likelihood of these results because of other lines of information. I am just relaying the results of the geneticists. I am not interested in re-litigating prior discussions on this. We’ll probably have a resolution soon enough.
A few weeks ago I alluded to the controversy around proposition 37. This was the GMO labeling law proposal. Many life scientists in California opposed this law. One aspect of this issue is that it is an area where the Left may be stated to be “anti-science.” This is why this was highlighted in Science Left Behind. But there’s a problem with this narrative: the survey data for it is weak. There are broad suggestive patterns…but the reality is that the strongest predictor of skepticism of genetically modified organisms is lower socioeconomic status. The GSS has a variable, EATGM. Here are the results by ideology:
|Don’t care whether or not food has been genetically modified||15||16||17|
|Willing to eat but would prefer unmodified foods||55||53||52|
|Will not eat genetically modified food||30||30||31|
I would caution that the sample size is small. But, if you dig deeper into the survey data you can find evidence that conservatives are more unalloyed in their support of biotech.
And yet with all this said, today I noticed that the California proposition 37 results are rather stark in their geographic distribution. The measure failed statewide, but 2/3 of the people in San Francisco and Santa Cruz counties supported it, as did 60% of the people in Marin (interestingly, only a little over 50% supported it in San Mateo and Santa Clara). I couldn’t find a tabular list with the results by county, but there are interactive maps. If someone was industrious (and had more time than I do) they would go and collect the data from the maps, and do a loess of “support proposition 37” vs. “support Obama.”
I cropped the image above from the paper Inference of Population Structure using Dense Haplotype Data. The main reason was emphasize the distinctiveness of the Sardinian cluster, on the bottom right. As you can see this population exhibits a lot of coancestry across individuals. This isn’t too surprising, Sardinia is an island, and islands are often genetically distinctive. Random genetic drift prevents populations from diverging through gene flow, but water is a major impediment to gradual isolation by distance dynamics. The original Sardinians are naturally going to diverge from mainlanders over time, and begin to share the same set of common ancestors in the recent past, because their space of reasonable mating possibilities is constrained. The other population which is similar in the heat map above are the residents of the Orkneys, off the north coast of Scotland (the Orkneys has a much smaller population than Sardinia, but, it is also much closer to the mainland).
This is on my mind because Dienekes has a long post where he explores the D-statistic results of various European populations, using Sardinians as one of the references. You don’t need to know the details, just that Northern European populations seem to exhibit an affinity to East Asians. Our favorite human genomicsts at Broad highlighted this tendency, and Dienekes went looking (if David Reich et al. were inclined toward mischief they should just posit some crazy scenario, and see if Dienekes assembles the requisite data set!). Which is all fine, and we’ll see more of this in the near future. It isn’t as if others aren’t using Sardinians.
There’s a new ancient DNA paper out which examines the maternal lineage and the autosomal background of two individuals extracted from a Spanish site dated to 7,000 years before the present. That is, during the European Mesolithic. In other words, these are the last wave of Iberian hunter-gatherers before agriculture. I have placed the PCA, with some informative labels, to illustrate the peculiarity of these samples. Here’s the abstract:
The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic…is poorly understood, both due to the scarcity of human remains from that period…The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.
Here’s another PCA showing one individual on a more fine-grained representation of European populations:
Halford Mackinder’s conceptualization of the world
With the recent publication of the paper on the archaeogenetics of Neolithic Sweden I feel like we’re nearing a precipice. That precipice overlooks lands of great richness, filled with hope. It’s nothing to fear. It is in short a total re-ordering of our conception of the recent human past, at minimum. The “pots not people” paradigm arose in archaeology over the past few generations due to both scholarly and ideological factors. The scholarly ones being that intellectuals of the 19th and early 20th century made assumptions of extremely tight correspondence between material and cultural characteristics, and demographic dynamics, which seem to have been false. Therefore, the rise of an Anglo-Saxon England and the marginalization of Celtic Britain to the western fringes was not just a cultural reality, but also a fundamentally racial one, as Germans replaced Celts in totality. The ideological problem is that this particular framework was take as a given by the Nazis during World War II, lending a bad odor to the
A new paper in Science has just been published which in its broad outlines has been described in conference presentations. When examining the autosomal genetic variation of three individuals of the hunter-gatherer Pitted Ware Culture (PWC), and one of the agriculturalist Funnel Beaker Culture (TRB), the authors found that the two groups were sharply differentiated. The number of SNPs was on the order of 10,000 or so if I read the methods correctly. This is rather thin for studying contemporary within European population differences (~100,000 or more seems to be safe), in particular using hypothesis based clustering algorithms (it seems more manageable for PCA). But the findings are strong enough that I think we shouldn’t discount them. The most fascinating aspect of the results is that while the PWC seem to exhibit affinities with Northern and Northeastern Europeans, the TRB individual seems more similar to extant Southern Europeans!
Others have already commented extensively on the results. Keeping in mind the small sample sizes, limitation of comparisons, and the relatively thin marker set, I think the primary result we can take away from these findings is that old models of pure cultural and demographic diffusion are false. By this, I mean that prior debates which culminated in the early aughts on the “Paleolithic vs. Neolithic” contribution to the ancestry of modern Europeans were fundamentally premised on a demographic diffusion dynamic, whereby genes and ideas exhibited a continuous flow across a flat and featureless landscape. On the contrary, the basic outlines we are seeing here is that the human past exhibited spatial and temporal discontinuity. And why should this surprise us? There is no dialect continuum between Spanish and Chinese across Eurasia. Rather, broad language families are sharply differentiated from each other at zones of contact. Though there are theoretical reasons why the variation in genes should be more clinal, the reality remains that cultural parameters are going to shape the outlines of genetic variation, and those parameters are discontinuous.
There’s a new paper in AJHG which caught my eye, The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times (ungated). The first thing you need to know about this paper is that it focuses on only the direct maternal lineage of Basques via the mtDNA. In some ways this is weak tea, since it doesn’t give us a total genome estimate. But there are major upsides to mtDNA and Y. First, because of the lack of recombination it is relatively easy to generate a nice phylogenetic tree using a coalescent model. And second, for mtDNA the molecular clock is considered relatively reliable.
In this specific paper they also expanded the scope of their analysis to the whole mtDNA sequence, instead of just the hypervariable region. Not only did they look at whole sequences, but they also had an enormous sample size. They sequenced over 400 mtDNA genomes from the Basque country and neighboring regions. Haplogroup H peaks in frequency among Basques, and drops off among their neighbors (Gascons, Spaniards, etc.). Because the Basque speak a non-Indo-European language they are usually presumed to be indigenous in relation to their neighbors (or at least more indigenous). Until recently there was a strong presupposition that the Basque were ideal representatives of the pre-Neolithic populations of Western Europe. One common method of analysis would be to use the Basque as a pre-Neolithic “reference,” and simply estimate the impact of a Neolithic demographic wave of advance by using a eastern Mediterranean population as a second “reference” within an admixture framework. But more recent work has muddled the idea that the Basque are the descendants of Paleolithic Europeans. Finally, I suspect we’ll also have to acknowledge complexity in demographic histories. To say that the Basque exhibit continuity with Mesolithic Iberians may not contradict a substantial Neolithic contribution. South Asians for example are one numerous modern group which exhibits sharply divergent affinities if you use Y chromosomes (West Eurasian) or mtDNA (not West Eurasian). Why? The details are prehistorical.
For some scholars of human history in Amazonia, the geoglyphs in the Brazilian state of Acre and other archaeological sites suggest that the forests of the western Amazon, previously considered uninhabitable for sophisticated societies partly because of the quality of their soils, may not have been as “Edenic” as some environmentalists contend.
Instead of being pristine forests, barely inhabited by people, parts of the Amazon may have been home for centuries to large populations numbering well into the thousands and living in dozens of towns connected by road networks, explains the American writer Charles C. Mann. In fact, according to Mr. Mann, the British explorer Percy Fawcett vanished on his 1925 quest to find the lost “City of Z” in the Xingu, one area with such urban settlements.
In addition to parts of the Amazon being “much more thickly populated than previously thought,” Mr. Mann, the author of “1491,” a groundbreaking book about the Americas before the arrival of Columbus, said, “these people purposefully modified their environment in long-lasting ways.”
“If one wants to recreate pre-Columbian Amazonia, most of the forest needs to be removed, with many people and a managed, highly productive landscape replacing it,” said William Woods, a geographer at the University of Kansas who is part of a team studying the Acre geoglyphs.
“I know that this will not sit well with ardent environmentalists,” Mr. Woods said, “but what else can one say?”
Over at Scientific American Eric Michael Johnson has a very long post up, The Case of the Missing Polygamists. It is a re-post of something he already published at Psychology Today a few years ago. Though provisionally a review of Sex at Dawn, Johnson covers a lot of ground, and also has extensive quotations from Sarah Blaffer Hrdy.
I’m reflecting upon the post for a second time because it is very rich in ideas, and lays out may different general concepts and specific propositions. The bottom line from what I can gather is that Johnson agrees with those thinkers who believe that agriculture and the Neolithic revolution to a great extent reshaped social relations, and give us a skewed perception of “normal” human societies. I’m not going to rehash all of the points in the piece, but will focus on just a few which I think I can extend upon fruitfully.
Dienekes has an important post up, The womb of nations: how West Eurasians came to be. He outlines a scenario where a rapid expansion of a farming population has overlain much of Western Eurasia, atop aboriginal substrata. A few years ago you’d have laughed at such a model, mostly due to the authority of archaeologists and phylogeographers relying on mtDNA lineage distributions. No longer. This is not necessarily an orthodoxy, and the details of the model vary, but here is my verbal rendering of the simplest scenario:
1) ~50 thousand years hybridization between Eurasian hominins and “Out of Africa”
2) ~40-10 thousand years before the present, crystallization of the Paleolithic order of human population structure, derived from groups seeded in the original migration
3) ~10 thousand to a few thousand years before the present, the Paleolithic order is replaced and assimilated by farmers expanding from a few hearths
Below the fold is a stylized tree representation of what I have in mind.
The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.
If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be “off-cline” by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.
This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians. In other words, pulling out the distinct elements in Europeans is likely a more difficult task because the constituents of the mixture resemble each other quite a bit when compared to “Ancestral North Indians” vs. “Ancestral South Indians.”
In light of the recent results in human evolutionary history some readers have appealed to me to create some sort of clearer infographic. There’s a lot to juggle in your head when it comes to the new models and the errors and uncertainties in estimates derived from statistical inference. Words are not always optimal, and there’s often something left out.
So I spent a few hours creating a series of maps which distill my own best guess as to what occurred over the past 100,000 years. I want to emphasize that this purely my own interpretation, based on what I know. This is naturally going to be biased (I don’t know as much about uniparental lineages as some of my readers, and have a weak grasp of a lot of morphological changes, etc.). But it is a place to start. I’ve put the maps into a slideshow. Please observe that in brackets I’ve put qualifies such as “high”, “medium” and “low” in regards to my assertions. That shows you how confident I am about a given assertion. I’m 100% sure that I’m wrong in a lot of the details here, but this is my best guess as to the shape of things over the past 100,000 years. Feel free to ask more in the comments. Also, take the dates with a little fudge room. If I used exact precise dates for everything there would be too many slides.
Note: You can’t see the slideshow in the RSS browser.
As many of you know when you have two adjacent demes, breeding populations, they often rapidly equilibrate in gene frequencies if they were originally distinct. There are plenty of good concrete examples of this. The Hui of China are Muslims who speak local Chinese dialects. The most probable root of this community goes back to the enormous population of Central Asia Muslims brought by the Mongol Yuan dynasty that ruled ruled China for over a century from the late 1200s to 1300s. Genetic studies of this group that I’ve seen indicate that a high bound estimate for West Eurasian ancestry is ~10%. The other ~90% is interchangeable with the Han Chinese. So let’s assume that the Hui are ~10% West Asian. If you assume that in the year 1400 the Hui were “pure,” you have 24 generations (25 years per generation). The original population of “Central Asian Muslims” were heterogeneous, including Iranians and Turks. But let’s take it granted that they were 50% East Eurasian and 50% West Eurasian in ancestry at the time of their arrival. What would the intermarriage rate per generation have to be so that the Hui are ~10% West Eurasian at t = 24 (24 generations after the beginning of intermarriage assuming 50/50 West vs. East Eurasian splits)? Turns out all you need is a constant 7% intermarriage rate per generation (the Han Chinese population is so large in relation to the Hui that you can model it as infinite in size).
The situation gets even simpler when you have one population which divides into two. For example, imagine that the Serbs and Croats fissioned from a set of unstructured South Slavic tribes which filtered into ancient Illyria ~600 A.D. Soon enough there was a cultural division between the two in terms of religion (Western vs. Eastern Christian) which threw up a population genetic barrier. If you assume that genetically the two groups were totally similar at t = 0, and you separated them perfectly, over time they would diverge due to drift in their allele frequencies. But the reality is that barriers between geographically close groups do not prevent all intermarriage. Even extremely insular groups in a cultural sense such as the Roma of Eastern Europe are clearly heavily admixed with their surrounding populations, as they seem to be no more than ~50% South Asian in total genome content. Going back to the South Slavs, who start out very similar in our putative scenario, how much intermarriage will be necessary for them to not diverge? The issue is not the rate of intermarriage, rather, one migrant per generation across the two demes will be sufficient to equilibrate allele frequencies. On the face of it this seems implausible, but recall that divergence is driven mostly by drifting of genes as well as new variation (whether through other exogenous migratory sources or mutation). Very small populations are subject to a lot of drift, and so diverge rapidly, but only very few migrants are needed to bring it back into alignment, because they are proportionally significant. In contrast, the frequencies of large populations are less buffeted by generation-to-generation sample variance (e.g., 10 tosses of a coin will deviate more from 50/50 proportionally than 100 tosses), requiring less gene flow proportionally to maintain parity.
Back when this sort of thing was cutting edge mtDNA haplogroup J was a pretty big deal. This was the haplogroup often associated with the demic diffusion of Middle Eastern farmers into Europe. This was the “Jasmine” clade in Seven Daughters of Eve. A new paper in PLoS ONE makes an audacious claim: that J is not a lineage which underwent recent demographic expansion, but rather one which has been subject to a specific set of evolutionary dynamics which have skewed the interpretations due to a false “molecular clock” assumption. By this assumption, I mean that mtDNA, which is passed down in an unbroken chain from mother to daughter, is by and large neutral to forces like natural selection and subject to a constant mutational rate which can serve as a calibration clock to the last common ancestor between two different lineages. Additionally, mtDNA has a high mutational rate, so it accumulates lots of variation to sample, and, it is copious, so easy to extract. What’s not to like?
I just finished reading a review of the literature since 1984 on the bioarchaeology of the transition to agriculture. Stature and robusticity during the agricultural transition: Evidence from the bioarchaeological record:
The population explosion that followed the Neolithic revolution was initially explained by improved health experiences for agriculturalists. However, empirical studies of societies shifting subsistence from foraging to primary food production have found evidence for deteriorating health from an increase in infectious and dental disease and a rise in nutritional deficiencies. In Paleopathology at the Origins of Agriculture (Cohen and Armelagos, 1984), this trend towards declining health was observed for 19 of 21 societies undergoing the agricultural transformation. The counterintuitive increase in nutritional diseases resulted from seasonal hunger, reliance on single crops deficient in essential nutrients, crop blights, social inequalities, and trade. In this study, we examined the evidence of stature reduction in studies since 1984 to evaluate if the trend towards decreased health after agricultural transitions remains. The trend towards a decrease in adult height and a general reduction of overall health during times of subsistence change remains valid, with the majority of studies finding stature to decline as the reliance on agriculture increased. The impact of agriculture, accompanied by increasing population density and a rise in infectious disease, was observed to decrease stature in populations from across the entire globe and regardless of the temporal period during which agriculture was adopted, including Europe, Africa, the Middle East, Asia, South America, and North America.
The abstract makes the conclusion more cut & dried than it is. It’s the result of aggregating their literature review and arriving at a net conclusion. Yes, on the balance agriculture did result in the deterioration of health. The old truism that farmers are a small and ill lot in comparison to hunter-gatherers seem to be correct in the generality. But the literature review also makes it clear that when it comes to something like stature there are often periodic reversals of the trend toward decrease in size. There may be spottiness of the record, and sampling error, but I began to wonder if we might not be seeing evidence of evolution & innovation in action!
Consider the checkered history of the potato in Ireland. In the 18th century the Irish shifted toward the potato faster than most other European peoples, and so entered into a phase of massive population expansion. On a per unit basis the potato was nutritional gold. Unfortunately we all know that the blight of the 19th century triggered a series of social and demographic catastrophes.
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: