This really distills important aspects of human male behavior.
This really distills important aspects of human male behavior.
When every song sounded like this? We do.
The bar plot above shows the Kalash people in yellow as very distinctive group among a panoply of Eurasian populations. The figure is from a Rosenberg lab paper. There’s nothing aberrant about this result, you can generate this plot pretty easily by using any motley set of markers. The Kalash are distinctive. But it is important to keep the distinction in perspective. They’re not a relic population, remnants of an ancient race lost to time and memory. Rather, they happen to be a highly diverged northwest South Asian group. Their divergence is due to a small isolated breeding population which has been highly endogamous.
What this means is that the Kalash have a low long term effective population and have been more strongly impacted by drift in their allele frequency spectra. Small populations are subject to great allele frequency volatility generation to generation, and tend to lose a lot of their genetic diversity, and also fix many alleles. One consequence of this is genetic inbreeding and a higher recessive disease load. These populations with a lot of drift will have less efficacy of selection in removing deleterious alleles, and if a recessive expressing variant is fixed, then that’s that.
But another major consequence of strong drift on a population so that everyone is quasi-related for all practical purposes is that when you attempt some sort of clustering they naturally fall out as a very natural grouping. They’re low hanging fruit. When you plot populations on on a PCA you normally remove closely related individuals, because they will naturally form a tight cluster, and overwhelm the between population variation you’re looking for, hogging up all the highest dimensions making them distinct from non-relatives. Inbred groups like the Kalash do the same thing, if less boldly so. If you can keep this in mind it will allow for proper inferences about the natural history of a population. If you can’t, then you will be confused.
This is preface to a nice paper in PLOS GENETICS, Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference, which reports that an earlier publication, Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool, did not control for the effect of drift due to endogamy and so came to the wrong conclusion.* I won’t repeat the methods they used, as the paper is open access. But, they account for drift much better, and show that the divergence of a presumably genetically distinct caste had much more to do with increased drift due to endogamy than it did with the separation of the two lineages at some time in the distance past. Remember, drift builds up over any two pair of lineages which separate. But if the population size in one of the daughter lineages is very low, then drift will shift it away from the ancestral frequency spectra much faster, producing an artificially “long branch.”
The Kalash and the Ari are extreme cases of this. But they illustrate the general principle that we should be cautious about making inferences when we don’t control for the vicissitudes of demographic history, which may skew the power of our methods to see in a fair and balanced manner.
* There’s an overlap of authors across the two publications, showing that scientists do and can overturn their own conclusions if new data or analysis can persuade them.
When is a jackal a wolf? All the time apparently. At least according to a persuasive new paper, Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species.
First, let’s put this in context. Canids area big deal. They’re big social mammals whose distribution and speciose character have undergone big changes across the Pleistocene. Sound familiar? Is it any surprise that one of their kind is our “best friend.” And, according to the anthropologist Pat Shipman the symbiotic relationship between dog and man is responsible for the victory of our lineage of hominins in the evolutionary war of all against all. About six months ago that thesis would seem a stretch, as the origin of dogs does not date until almost the Holocene according most genetic scholarship (the paleontologists have found rather old suggestive skulls thought). So tens of thousands of years after modern humans replaced other lineages. But ancient DNA suggests problems with the calibration of earlier work, which may have dated their divergence from wolves too recently. That and the fact that the emergence of dogs as a distinct group of canids might be concurrent with the arrival of modern humans to Eurasia make Shipman’s thesis at least feasible, if not probable. And note that I stated divergence from wolves, not derivation. It turns out that dogs are a sister lineage to Palearctic wolves, not derived from them. As observed in this paper extant lineages of wolves are genetically rather homogeneous, and seem to have diversified relatively recently, within the last 20,000 years, on the order of 10 to 20 thousand years after the last common ancestor of extant wolves and dogs.
Where do jackals play into this? The golden jackal has a distribution which covers both Eurasia and Africa. The species’ was determined morphologically. In other words, they look similar across their range. But sometimes you can’t judge a book by its cover. As an obvious example, most people would think that a hyrax on superficial inspection was a rodent. But a close examination of anatomical details indicated a relationship to elephants to classical taxonomists, which has been validated by DNA. But, as the paper above states plainly in the title the DNA here contradicts inferences made from morphology. Wolves and dogs, and African golden jackals, form a monophyletic lineage, to which Eurasian golden jackals are an outgroup! This determination was achieved through mtDNA analyses, as well as phylogenetic reconstruction from specific genetic regions, and, genome-wide comparisons on millions of polymorphisms.
But wait there’s more! One major difference between the example above of the hyrax vs. elephant and jackal vs. wolf is that the phylogenetic distance in the latter case is far smaller across the tips of the branch. That probably explains why morphological characters were not sufficient to discern the shared ancestry and derived characteristics of the wolf and the African jackal, as opposed to the Eurasian jackal. And, a corollary to this is that hybridization between these lineages is possible. In other words, this isn’t a phylogenetic tree, it’s a phylogenetic graph! Using D-statistics the authors show that there has been a fair amount of gene flow between Eurasian wolves and Eurasian jackals. And, in particular a lot of admixture from the Eurasian jackal to the dingo and basenji breeds.
Is this starting to sound a bit familiar? As population genomics has increased coverage of human populations, modern and ancient, as well as increasing marker density and accuracy, first approximation coarse phylogenetic trees have given way to threads of gene flow edges tracing their away across the thick branches. The trees have given ways to myriad graphs which force us to make more subtle our understanding of the genetic background of our own lineage. I see no reason why the same will not be true for large mammals, or, frankly, an innumerable number of clades.
In the near feature sequencing will be ubiquitous in ecological and systematic studies. At the coarsest big picture scale we’ll still see a confirmation of the tree of life as it’s classically envisioned, exploding outward from node to node, in subdivisions of clean monophyletic lineages, pruned by extinction diversified by drift and selection. But as you focus in closely the bifurcations will turn in on themselves or thread together in tangle, as the branches begin to be stitched together by gene flow. Look even closer and you’ll see that even within a young species, like humans, our local geographic pedigrees also collapse in on themselves, and tangle and coalesce down to a set finite number of individuals, rather than the infinite space of genealogical possibilities.
Update: On Twitter it came to my attention that some think that this post is about growth Actually, my point is that the Communist period, and Mao’s period of domination, with the Great Leap Forward and the Cultural Revolution, probably are huge decrements to utility over the 20th century which the Chinese are now just compensating for. I think a KMT China, even if it unified less quickly and thoroughly than China, would probably have resulted in a far more prosperous China far earlier than in our “timeline.” Perhaps not as prosperous as South Korea, and definitely not Japan, but still quite prosperous over the past three generations in comparison to Communist China when state socialism was the dominant motor of the economy. Ergo, look not at the growth itself as opposed to the “area under the curve” from 1950 on.
Organized international Communism was responsible for on the order of tens of millions of deaths in a direct and concerted fashion, conservatively estimated. It also resulted in decades of repression for those who lived under it, but did not die under it. It fell with the Soviet Union, and today post-Communist (e.g., Russia) and quasi-Communist (e.g., China) nations are trying to move on beyond what was by and large a failed experiment in social engineering, with the failure resulting in massive levels of mortality and reduced life satisfaction on the part of those who lived under Communist regimes.
But can we move on? I have noted before that over the past generation in the aggregate Chinese economic development has resulted in the greatest reduction in poverty in the history of the world. With the economic crisis which is starting to afflict China, in all likelihood a deceleration from the very rapid growth phase induced by increased labor and capital inputs is upon us, and people are wondering about the long term trajectory of the nation. The problem is that China may grow old before it grows rich. The Chinese total labor force already peaked a few years ago. Over the next few decades its dependency ratio will shift in a direction similar to Japan’s. I am hopeful that the Chinese can meet their demographic challenges, and there are those who are optimistic. But we really don’t know.
And yet it has been brought to my attention that one could argue the Communist period in China is the cause of our current predicament. Compare the wealth trajectories of South Korea and Taiwan to the People’s Republic of China. It may be that for various reasons (e.g., Japanese investments in Korea and Taiwan, as well as differences between China’s Han population and the Fujianese preponderant in Taiwan) China under a non-communist regime would never have been as wealthy as South Korea or Taiwan are today. But does anyone doubt that China would be wealthier far earlier without the convulsions of the Great Leap Forward, Cultural Revolution, and grinding poverty of the 1970s? A billion people experienced deprivation due to the miscalculations of elite intellectuals in the mid-20th century, when Communism fused with nationalism was on the march. That’s behind us. But the late economic start for China is something we continue to live with today. We might have avoided this problem of China growing old before it grows rich, if it had a 30 year head start toward entrance into the modern economy. The world might have been a very different place…. (in fact, a best case scenario is that a dynamic China would have prodded India’s Permit Raj to liberalize earlier than the 1990s).
Update: I think Richard Stallman left a comment on my blog!!! OMG.
I remember very precisely that it was in the spring of 2008 that I finally transitioned toward being a total desktop Linux user. Basically I’d been in Linux for a few days…forgotten, and tried to watch something on Netflix streaming. I then realized I wasn’t in Windows! Now that Netflix works on Ubuntu I don’t really use Windows at all. I still have a dual-boot notebook, but I have two desktop computers than are Linux only machines.
Well, it looks like I’m somewhat of an outlier. I think the rise of Mac utilization among nerds over the past 10 years has really had an effect. Since you can go into the terminal on a Mac it removes a lot of the advantage of Ubuntu, which after all is still somewhat less “turn-key” that Windows or Mac OS.
Then of course there’s Android. So in a way Linux has won. Just not in the way people were imagining in the mid-2000s.
I get notifications for a lot of different things. Some of them are way off base (e.g., I think at some point a publicist sent me the contact information of a client who had written a book on homoepathy?). But some of them are spot on. I drink a lot of coffee. On the order of two to six large cups a day probably. So I was curious when I got a notification of a new KickStarter, Cultured Coffee: Reinventing Coffee. Of course for many people Folgers instant coffee will do, but that’s probably not most people who have the marginal income to engage in discretionary spending on coffee made from recently ground whole beans. Definitely curious where this will all go in the long run, though unlike the horrible “cupcake craze” it seems that coffee is here to stay.
The author of A New History of Western Philosophy admits a fondness for medieval thought, which he believes has been undervalued. There is something of a backlash to the Renaissance way of thinking about the “Middle Ages” recently, but it can get a little out of control. I have to be honest and admit that for whatever reason, many, though not all, medieval philosophers and their thoughts seem to be no more than hilarious language games. Much of this has to do with the fact that their metaphysics were different from what take for granted today. Or, perhaps more accurately they took metaphysics seriously, so their linguistic analyses of terms were a very serious affair for them.
But I’m taking a break to check out Michael Cook’s Ancient Religions, Modern Politics: The Islamic Case in Comparative Perspective. I got this on the recommendation of T Greer, and he is correct that I disagree with some of the premises. But, it’s pretty interesting and detailed on facts. I doubt I’ll finish it before getting back to A New History of Western Philosophy, but it will probably be a quick read once I have time.
This isn’t probably aimed at most readers, but I think it’s important to pass the word around, so, Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. An ungated version. From the abstract:
The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software clumpp. Next, clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in clumpp and simplifying the comparison of clustering results across different K values. clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. clumpak, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.
The website deploys the package as a web based application (kind of like Structure-harvester). I don’t do GUIs, but I thought I would mention it (the package is downloadable). I’ve shied away from posting admixture barplots not because I think they lack utility. Rather, over the years readers have had a hard time understanding their limitations, and tend to reify a little too much for my taste.
I was playing around with some data, and I saw a strange migration from Amerindians to Finns in one run. I looked through replicate runs the same pattern reoccurred. The weird thing is that I had a Siberian data set in there (Ngannassan, Koryak, and Chukchi). The Amerindians were a mix of Pima, Maya, and a few 1000 Genome Peruvians.
To explore this further I got ran TreeMix with progressively fewer populations. I got the Ancient North Eurasian genotype and also put it in there. Using various quality filters I got down to 112,000 SNPs. All of the plots are here, but representative ones are below.
As you can whatever I saw was an artifact. Probably due to merging the various Siberian populations together. Now there is a gene flow edge from at least near the Nganassans and Nenets toward the Finnic groups, or from the Finnic groups. The relationship of Mal’ta is complicated by the fact that it’s so old, and, the population structure of North-Central Eurasia seems to have changed several times over the past few tens of thousands of years.
About ten years ago David Reich and Nick Patterson were involved in a paper which posited “complex speciation” in the lineage that led to humans and chimpanzees. What that means is that there was some hybridization between the proto-chimp/bonobo lineage, and that leading to hominins. As the authors state: “These unexpected features [of the genome] would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.” The primary result happens to be a disjunction between the patterns you see in the broader genome, the autosome, and the X chromosome. The divergence from the X chromosome is far less than it should be if you would set your expectation from the autosome, suggesting that it harbors signatures of recent gene flow across the two lineages.
A new paper in PLOS GENETICS, Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence, offers up a different set of possibilities. One of the authors, Thomas Mailund, has a write-up of where they were going with this paper and how they got there. Definitely read what he has to say.
The crux of the issue seems to be that the diversity on the X chromosome varies in a peculiar manner. In particular, incomplete lineage sorting, basically the overlap of variation across two species due to common ancestral alleles, seems to exhibit a bimodal distribution on the X chromosome (the bottom panel above). Going beyond just a chromosome-wide summary or average, the authors found that there were huge deserts where variation was gone, in contrast with broad swaths of the X chromosome genome where the variation is totally in light with roughly neutral assumptions (i.e., the effective population of the X chromosome is ~3/4 of the autosome, so that increases the power of drift, etc.).
Why this pattern? One explanation could be background selection. This is basically the removal of deleterious alleles as they arise, often resulting in reduced variation across a genomic region because of linkage. The X chromosome has a peculiar dynamic because in males normally recessive alleles, whether favored or disfavored, are subject to the full force of selection (since most recessive mutations are deleterious, they’d be purged more effectively). But background selection is a relatively gentle and continuous process. The width of the flanking regions impacted by selection against a focal mutant should be modest. What they found was that there were huge genomic blocks without any segments of incomplete lineage sorting in humans and chimpanzees. That is, variation was removed in some portions of the genome and not others. One process that can cause this are positive selective sweeps. The authors posit there were many of these to explain how many regions of the X chromosome seem to have been affected.
What was driving these sweeps? At this point they’re really tentative. But they suggest meiotic drive. Meiotic drive is pretty famous from the deleterious t haplotype in mice, but there might be a major bias in when we see drive, because if it doesn’t have a deleterious drag it might result in such rapid sweeps to fixation that we won’t ever catch it in the act. It could be pervasive as a phenomenon, but we might have a skewed perspective of its basic nature.
Finally, they also report that these regions of reduced ILS correlate with regions of the X chromosome where there is very little Neanderthal admixture. So this might be part of a broader evolutionary dynamic among apes. Mailund promises more, and I’ll be waiting….