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Genetics, Genomics, Human Evolution and other topics
Razib Khan
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by Razib Khan in Gene Expression
The Pith: Afro-Indians are mostly African, with a substantial Indian minority ancestry. The latter is disproportionately female mediated. It also seems that that ancestry is more northwest Indian, and that natural selection has been operating upon them outside of the African environment.
Along the western coast of South Asia, from Makran in southwest Pakistan, down to the Konkan coast of southwest Iindia, there are isolated communities of Afro-Indians. They are called Siddis or Habshi. Their African origin is clear in their physical appearance, as well as aspects of their folk customs which tie them back to Sub-Saharan African. Nevertheless, they have assimilated to many Indian cultural traits. They generally speak the local language, and practice Islam, Hinduism, or Roman Catholic Christianity (in that order in proportion).
How and why did the Siddis arrive in India? The earliest date for their arrival almost certainly must be bounded by the period when Indo-Islamic polities rose to prominence in the early second millennium. The cosmopolitan melange of the armies of the Muslim warlords included diverse groups of Africans, some of whom took power, and established their own self-conscious Afro-Indian dynasties, set apart from the Turkish, Afghan, ...... Read more »
Anish M. Shah, Rakesh Tamang, Priya Moorjani, Deepa Selvi Rani, Periyasamy Govindaraj, Gururaj Kulkarni, Tanmoy Bhattacharya, Mohammed S. Mustak, L.V.K.S. Bhaskar, Alla G. Reddy.... (2011) Indian Siddis: African Descendants with Indian Admixture. American Journal of Human Genetics. info:/10.1016/j.ajhg.2011.05.030
Ankita Narang, Pankaj Jha, Vimal Rawat, Arijit Mukhopadhayay, Debasis Dash, Indian Genome Variation Consortium, Analabha Basu, & Mitali Mukerji. (2011) , Recent Admixture in an Indian Population of African Ancestry. American Journal of Human Genetics. info:/10.1016/j.ajhg.2011.06.004
by Razib Khan in Gene Expression
The Pith: The primary reason for the pervasiveness of sex among complex organisms is to maintain genomic integrity, not to increase genetic variation..
I just read a very strange article in the journal Evolution, Sex reduces genetic variation. In it the authors argue that contrary to conventional wisdom and evolutionary orthodoxy the rationale for the prevalence of sex amongst eukaryotic organisms is not maintenance of genetic variation, but rather a constraint upon genetic variation! This is a very peculiar view, and as someone not immersed in the literature on sex totally surprising to me.
The standard model is simple: sex allows organisms to swap genetic material and generate new combinations. This is at a particular premium for large, complex, and slow-breeding lineages, as is the norm amongst eukaryotes. In contrast, bacteria and their ilk have huge population sizes to draw from, and are quite literally protean in their ability to shift strategies to climb whatever adaptive landscape nature throws at them. Carl has a nice review of a paper in Science which reported just this finding in keeping with expectation. Increase the pathogen pressure, and eukaryotes which exchange genes marginalize those which do not because ...... Read more »
Gorelick R, & Heng HH. (2011) Sex reduces genetic variation: a multidisciplinary review. Evolution; international journal of organic evolution, 65(4), 1088-98. PMID: 21091466
by Razib Khan in Gene Expression
The Pith: When it comes to the final outcome of a largely biologically specified trait like human height it looks as if it isn’t just the genes your parents give you that matters. Rather, the relationship of their genes also counts. The more dissimilar they are genetically, the taller you are likely to be (all things equal).
Dienekes points me to an interesting new paper in the American Journal of Physical Anthropology, Isolation by distance between spouses and its effect on children’s growth in height. The results are rather straightforward: the greater the distance between the origin of one’s parents, the taller one is likely to be, especially in the case of males. These findings were robust even after controlling for confounds such as socioeconomic status. Their explanation? Heterosis, whether through heterozygote advantage or the masking of recessive deleterious alleles.
The paper is short and sweet, but first one has to keep in mind the long history of this sort of research in the murky domain of human quantitative genetics. This is not a straight-forward molecular genetic paper where there’s a laser-like focus on one locus, and the mechanistic issues are ...... Read more »
Sławomir Kozieł, Dariusz P. Danel, & Monika Zaręba. (2011) Isolation by distance between spouses and its effect on children's growth in height. American journal of physical anthropology. info:/10.1002/ajpa.21482
by Razib Khan in Gene Expression
The Pith: The rarer the genetic variant, the more likely that variant is to be specific to a distinct population. Including information about the distribution of these genetic variants missed in current techniques can increase greatly the precision of statistical inferences.
A few days ago I mentioned in passing an article in The New York Times which reported on results from a paper which illustrated how starkly differentiated populations might be on rare alleles. By this, I mean that some genetic variants are present at very low frequencies. It turns out that many of these are low frequency variants private to particular populations, in contrast to higher frequency variants which span varied human populations. The explanation presented by one of the authors of the referenced paper was that higher frequency variants presumably date back to a time before human populations had become geographically diversified across the world. Shared variants at higher frequencies then are shadows of shared past history. In contrast, rare variants are a reflection of more recent events, narrowing the circle of those effected.
I have now read the paper in question, Demographic history and rare allele sharing among human populations. ...... Read more »
Simon Gravel, Brenna M. Henn, Ryan N. Gutenkunst, Amit R. Indap, Gabor T. Marth, Andrew G. Clark, Fuli Yu, Richard A. Gibbs, The 1000 Genomes Project, & and Carlos D. Bustamante. (2011) Demographic history and rare allele sharing among human populations. PNAS. info:/10.1073/pnas.1019276108
by Razib Khan in Gene Expression
In reading The cultural niche: Why social learning is essential for human adaptation in PNAS I couldn’t help but think back to a conversation I had with a few old friends in Evanston in 2003. They were graduate students in mathematics at Northwestern, and at one point one of them expressed some serious frustration at the fact that so many of the science and business students in his introductory calculus courses simply wanted to “learn” a disparate set of techniques, rather than understand calculus. The reality of course is that the vast majority of people who ever encounter calculus aim to learn it for reasons of utility, not so that they can grok the fundamental theorem of calculus. With the proliferation of tools such as Mathematica and powerful portable calculators fewer and fewer people are getting their hands dirty with calculus in an analytic sense, and more often see it as simply a “requirement” which they have to pass.
Calculus, and mathematics generally, is a clean and crisp human invention. In the late 17th century Isaac Newton and Gottfried Leibniz originated calculus as we understand it. Later thinkers extended their work. But for the vast ...... Read more »
Robert Boyd, Peter J. Richerson, & Joseph Henrich. (2011) The cultural niche: Why social learning is essential for human adaptation. PNAS. info:/10.1073/pnas.1100290108
by Razib Khan in Gene Expression
In reading The cultural niche: Why social learning is essential for human adaptation in PNAS I couldn’t help but think back to a conversation I had with a few old friends in Evanston in 2003. They were graduate students in mathematics at Northwestern, and at one point one of them expressed some serious frustration at the fact that so many of the science and business students in his introductory calculus courses simply wanted to “learn” a disparate set of techniques, rather than understand calculus. The reality of course is that the vast majority of people who ever encounter calculus aim to learn it for reasons of utility, not so that they can grok the fundamental theorem of calculus. With the proliferation of tools such as Mathematica and powerful portable calculators fewer and fewer people are getting their hands dirty with calculus in an analytic sense, and more often see it as simply a “requirement” which they have to pass.
Calculus, and mathematics generally, is a clean and crisp human invention. In the late 17th century Isaac Newton and Gottfried Leibniz originated calculus as we understand it. Later thinkers extended their work. But for the vast ...... Read more »
Robert Boyd, Peter J. Richerson, & Joseph Henrich. (2011) The cultural niche: Why social learning is essential for human adaptation. PNAS. info:/10.1073/pnas.1100290108
by Razib Khan in Gene Expression
In the image to the left you see three human males. You can generate three pairings of these individuals. When comparing these pairs which would you presume are more closely related than the other pairs? Now let me give you some more information. The rightmost image is of the president of Tanzania. The middle image is of the president of Taiwan (Republic of China). And finally, the leftmost image is of the prime minister of Papua New Guinea. With this information you should now know with certainty that the prime minister of Papua New Guinea and the president of Taiwan are much more closely related than either are to the president of Tanzania. But some of you may not have guessed that initially. Why? I suspect that physical inspection may have misled you. One of the most salient visible human characteristics is of the complexion of our largest organ, the skin. Its prominence naturally leads many to mistakenly infer relationships where they do not exist.
This was certainly an issue when European explorers encountered the peoples of Melanesia. An older ...... Read more »
Tennessen JA, & Akey JM. (2011) Parallel Adaptive Divergence among Geographically Diverse Human Populations. PLoS Genetics. info:/
by Razib Khan in Gene Expression
In the image to the left you see three human males. You can generate three pairings of these individuals. When comparing these pairs which would you presume are more closely related than the other pairs? Now let me give you some more information. The rightmost image is of the president of Tanzania. The middle image is of the president of Taiwan (Republic of China). And finally, the leftmost image is of the prime minister of Papua New Guinea. With this information you should now know with certainty that the prime minister of Papua New Guinea and the president of Taiwan are much more closely related than either are to the president of Tanzania. But some of you may not have guessed that initially. Why? I suspect that physical inspection may have misled you. One of the most salient visible human characteristics is of the complexion of our largest organ, the skin. Its prominence naturally leads many to mistakenly infer relationships where they do not exist.
This was certainly an issue when European explorers encountered the peoples of Melanesia. An older ...... Read more »
Tennessen JA, & Akey JM. (2011) Parallel Adaptive Divergence among Geographically Diverse Human Populations. PLoS Genetics. info:/
by Razib Khan in Gene Expression
In the image to the left you see three human males. You can generate three pairings of these individuals. When comparing these pairs which would you presume are more closely related than the other pairs? Now let me give you some more information. The rightmost image is of the president of Tanzania. The middle image is of the president of Taiwan (Republic of China). And finally, the leftmost image is of the prime minister of Papua New Guinea. With this information you should now know with certainty that the prime minister of Papua New Guinea and the president of Taiwan are much more closely related than either are to the president of Tanzania. But some of you may not have guessed that initially. Why? I suspect that physical inspection may have misled you. One of the most salient visible human characteristics is of the complexion of our largest organ, the skin. Its prominence naturally leads many to mistakenly infer relationships where they do not exist.
This was certainly an issue when European explorers encountered the peoples of Melanesia. An older ...... Read more »
Tennessen JA, & Akey JM. (2011) Parallel Adaptive Divergence among Geographically Diverse Human Populations. PLoS Genetics. info:/
by Razib Khan in Gene Expression
Foraminifera, Wikimedia Commons
The Pith: The tree if life is nourished by agon, but pruned by the gods. More literally, both interactions between living organisms and the changes in the environment impact the pulsing of speciation and extinction.
No one can be a true “Renaissance Man” today. One has to pick & choose the set of focuses to which one must turn one’s labor to. Life is finite and subject to trade offs. My interest in evolutionary science as a child was triggered by a fascination with paleontology. In particular the megafauna of the Mesozoic and the Cenozoic, dinosaurs and other assorted reptilian lineages as well as the hosts of extinct and exotic mammals which are no more. Obviously I don’t put much time into those older interests at this point, and I’m as much of a civilian when I read Laelaps as you are. More generally when it comes to evolution I focus on the scale of microevolution rather than macroevolution. Evolutionary genetics and the like, rather than paleontology. This is in part because I lean toward a scale independence in evolutionary process, so that the ...... Read more »
Ezard TH, Aze T, Pearson PN, & Purvis A. (2011) Interplay between changing climate and species' ecology drives macroevolutionary dynamics. Science (New York, N.Y.), 332(6027), 349-51. PMID: 21493859
by Razib Khan in Gene Expression
The Pith: Over the past 10,000 years a small coterie of farming populations expanded rapidly and replaced hunter-gatherer groups which were once dominant across the landscape. So, the vast majority of the ancestry of modern Europeans can be traced back to farming cultures of the eastern Mediterranean which swept over the west of Eurasia between 10 and 5 thousand years before the before.
Dienekes Pontikos points me to a new paper in PNAS which uses a coalescent model of 400+ mitochondrial DNA lineages to infer the pattern of expansions of populations over the past ~40,000 years. Remember that mtDNA is passed just through the maternal lineage. That means it is not subject to the confounding dynamic of recombination, allowing for easier modeling as a phylogenetic tree. Unlike the autosomal genome there’s no reticulation. Additionally, mtDNA tends to be highly mutable, and many regions have been presumed to be selectively neutral. So they are the perfect molecular clock. There straightforward drawback is that the history of one’s foremothers may not be a good representative of the history of one’s ...... Read more »
Gignoux CR, Henn BM, & Mountain JL. (2011) Rapid, global demographic expansions after the origins of agriculture. Proceedings of the National Academy of Sciences of the United States of America, 108(15), 6044-9. PMID: 21444824
by Razib Khan in Gene Expression
Ornithomimosaurian dinosaur and ostrich, image credit Nobu Tamura & James G. Howes
Imagine if you will a portal to another universe which you have access to. By fiat let’s give you a “pod” which allows you to move freely throughout this universe, and also let’s assume that you can travel fast enough to go from planet to planet. What if you see that on all the planets there’s a sludgy living “goo” of some sort? To complexify the issue imagine that upon further inspection the goo is divided between a predominant photosynthetic element, and “parasitic” heterotrophs. But aside from these two niches there’s little diversity to be seen in this cosmos. The “climax ecology” of all the planets resemble each other, in case after case convergent evolution toward the one-morphology-to-out-fit-them-all. We could from these observations construct a general theory of evolution which deemphasizes the role of contingency. In other words, there are broad general dynamics which shape and prune the tree of life in this hypothetical universe so that there is always a final terminal steady-state of the most fit morphology.
... Read more »
Salverda ML, Dellus E, Gorter FA, Debets AJ, van der Oost J, Hoekstra RF, Tawfik DS, & de Visser JA. (2011) Initial mutations direct alternative pathways of protein evolution. PLoS genetics, 7(3). PMID: 21408208
by Razib Khan in Gene Expression
Image credit
The Pith: In this post I review a paper which covers the evolutionary dimension of human childbirth. Specifically, the traits and tendencies peculiar to our species, the genes which may underpin those traits and tendencies, and how that may relate to broader public health considerations.
Human babies are special. Unlike the offspring of organisms such as lizards or snakes human babies are exceedingly helpless, and exhibit an incredible amount of neoteny in relation to adults. This is true to some extent for all mammals, but obviously there’s still a difference between a newborn foal and a newborn human. One presumes that the closest analogs to human babies are those of our closest relatives, the “Great Apes.” And certainly the young of chimpanzees exhibit the same element of “cuteness” which is appealing to human adults. Still there is a difference of degree here. As a childophobic friend observed human infants resemble “larvae.” The ultimate and proximate reason for this relative underdevelopment of human newborns is usually attributed to our huge brains, which run up against the limiting factor of the pelvic opening of women. If a ...... Read more »
Plunkett J, Doniger S, Orabona G, Morgan T, Haataja R, & et al. (2011) An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing. PLoS Genetics. info:/10.1371/journal.pgen.1001365
by Razib Khan in Gene Expression
The Pith: In evolution if you want to win in the long run you don’t want all your eggs in one basket, even if that’s the choicest basket. Sh*t happens, and you better have some back up strategies.
Diversity is a major question in evolutionary biology. In particular, why is there so much diversity, so that the tree of life manifests a multitude of morphs? Might there not be some supreme replicator which emerges from the maelstrom to conquer all before it? This is actually the scenario which unfolds in much of science fiction, with monomorphic grey goo eating everything in its path (a more aesthetically differentiated variant of the super-species emerges in Brian W. Aldiss’ Helliconia Winter). As it is, liin thisfe on earth does not seem to be converging upon an optimum phenotype for all individuals. In contrast, it seems to be going in the opposite direction broadly speaking (thinking on billion year scales), with the shift from the monotony of communal cyanobacteria to the riotous diversity of tropical forest biomes and coral reefs.
There are many ways you might be able to explain this diversity. Temporal and spatial ...... Read more »
Beardmore RE, Gudelj I, Lipson DA, & Hurst LD. (2011) Metabolic trade-offs and the maintenance of the fittest and the flattest. Nature. PMID: 21441905
by Razib Khan in Gene Expression
The Pith: I review a recent paper which argues for a southern African origin of modern humanity. I argue that the statistical inference shouldn’t be trusted as the final word. This paper reinforces previously known facts, but does not add much that both novel and robust.
I have now read the paper which I expressed a touch of skepticism toward yesterday. Do note, I did not dispute the validity of their results. They seem eminently plausible. I was simply skeptical that we could, with any level of robustness, claim that anatomically modern humans arose in southern vs. eastern, or western, Africa. If I had to bet, my rank order would be southern ~ eastern > western. But my confidence in my assessment is very low.
First things first. You should read the whole paper, since someone paid for it to be open access. Second, much props to whoever decided to put their original SNP data online. I’ve already pulled it down, and sent off emails to Zack, David, and Dienekes. There are some northern African populations which allow us to expand beyond the Mozabites, though unfortunately there are only 55,000 ...... Read more »
Brenna M. Henn, Christopher R. Gignoux, Matthew Jobin, Julie M. Granka, J. M. Macpherson, Jeffrey M. Kidd, Laura Rodríguez-Botigué, Sohini Ramachandran, Lawrence Hon, Abra Brisbin.... (2011) Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. PNAS. info:/10.1073/pnas.1017511108
by Razib Khan in Gene Expression
Credit: Dragon Horse
The Pith: Brazil is often portrayed as the second largest black nation in the world, after Nigeria. But it turns out that the majority of the ancestors for non-white Brazilians is European.
One of the more popular sources of search engine traffic to this website has to do with the population genomics of Latin America. For example, my post showing that Argentina is not quite as European a country as it likes to consider itself is regularly cited in online arguments (people of various “persuasions” are invested in the racial status of the Argentine people). But last week in PLoS ONE a paper looking at the patterns of ancestry in the Brazilian population came to a somewhat inverse conclusion as to the self-conception or perception of the preponderant racial identity of that nation. Let me quote from the conclusion of the paper:
Among the actions of the State in the sphere of race relations are initiatives aimed at strengthening racial identity, especially “Black identity” encompassing the sum of those self-categorized as Brown or Black in the censuses and government surveys. The argument that ...... Read more »
Pena SDJ, Di Pietro G, Fuchshube-Moraes M, Genro JP, & Hutz MH. (2011) The Genomic Ancestry of Individuals from Different Geographical Regions of Brazil Is More Uniform Than Expected. PLoS ONE . info:/10.1371/journal.pone.0017063
by Razib Khan in Gene Expression
Credit: Karl Magnacca
A few days ago I titled a post “The evolution of man is no cartoon”. The reason I titled it such is that as the methods become more refined and our data sets more robust it seems that previously held models of how humans evolved, and evolution’s impact on our genomes, are being refined. Evolutionary genetics at its most elegantly spare can be reduced down to several general parameters. Drift, selection, migration, etc. Exogenous phenomena such as the flux in census size, or environmental variation, has a straightforward relationship to these parameters. But, to some extent the broadest truths are nearly trivial. Down to the brass tacks what are these general assertions telling us? We don’t know yet. We’re in a time of transitions, though not troubles.
Going back to cartoons, starting around 1970 there were a series of debates which hinged around the role of deterministic adaptive forces and random neutral ones in the domain of evolutionary process. You have probably heard terms like “adaptationist,” “ultra-Darwinian,” and “evolution by jerks” thrown around. All great fun, and certainly ripe “hooks” to ...... Read more »
Sattath S, Elyashiv E, Kolodny O, Rinott Y, & Sella G. (2011) Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans. PLoS Genetics. info:/10.1371/journal.pgen.100130
by Razib Khan in Gene Expression
I was semi-offline for much of last week, so I only randomly heard from someone about the “Science paper” on which Molly Przeworski is an author. Finally having a chance to read it front to back it seems rather a complement to other papers, addressed to both man and beast. The major “value add” seems to be the extra juice they squeezed out of the data because they looked at the full genomes, instead of just genotypes. As I occasionally note the chips are marvels of technology, but the markers which they are geared to detect are tuned to the polymorphisms of Europeans.
Classic Selective Sweeps Were Rare in Recent Human Evolution:
Efforts to identify the genetic basis of human adaptations from polymorphism data have sought footprints of “classic selective sweeps” (in which a beneficial mutation arises and rapidly fixes in the population). Yet it remains unknown whether this form of natural selection was common in our evolution. We examined the evidence for classic sweeps in resequencing data from 179 human genomes. As expected under a recurrent-sweep model, we found that diversity levels decrease near exons and conserved noncoding regions. In contrast ...... Read more »
Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, 1000 Genomes Project, Sella G, & Przeworski M. (2011) Classic selective sweeps were rare in recent human evolution. Science (New York, N.Y.), 331(6019), 920-4. PMID: 21330547
by Razib Khan in Gene Expression
Credit: David Shankbone
The more and more I see fine-scale genomic analyses of population structure across the world the more and more I believe that the “stylized” models which were in vogue in the early 2000s which explained how the world was re-populated after the last Ice Age (and before) were wrong in deep ways. I’m talking about the grand narratives outlined in works such as Bryan Sykes’ The Seven Daughters of Eve, the subtitle of which was “The Science That Reveals Our Genetic Ancestry.” If I had less faith in science to always ultimately right its course I’d probably become a post-modernist type who asserts that all these stories are fictions. Sykes’ model in particular seems to be very likely incorrect because of the utilization of ancient DNA to elucidate population movements past in Europe. From what we can gather it looks like coarse attempts to infer past distributions from current distributions (of specific lineages and their diversity) resulted in a great deal of false clarity. We’re not talking differences on the margins, but fundamental confusions. For example, Basques were always assumed to be a viable ...... Read more »
Salmela E, Lappalainen T, Liu J, Sistonen P, & Andersen PM. (2011) Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data. PLoS ONE . info:/10.1371/journal.pone.0016747
by Razib Khan in Gene Expression
If you are an engaged patient who has been prescribed medication I assume you’ve done your due diligence and double-checked your doctor’s recommendations (no, unfortunately an M.D. does not mean that an individual is omniscient). Several times when I’ve been prescribed a medication I have seen a note about different recommended dosages by race when I did further research. Because of my own personal background I am curious when it says “Asian.” The problem with this term in medical literature is that “Asian” in the American context is derived from a Census category constructed in 1980 for bureaucratic and political purposes. It amalgamates populations which are genetically relatively close, East and Southeast Asians, with more distant ones, South Asians (when my siblings were born I remember that my parents listed their race as “Asian” when they filled out paper work for the hospital).
But at least the issues with an “Asian” category are clear. Consider the “Hispanic/Latino” category. In the the USA this term also became popular through government fiat around 1970, as a catchall for people whose ancestry derives from the Spanish speaking Americas, with Spaniards, Portuguese, and Brazilians, ...... Read more »
Yang JJ, Cheng C, Devidas M, Cao X, Fan Y, Campana D, Yang W, Neale G, Cox NJ, Scheet P.... (2011) Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia. Nature genetics. PMID: 21297632
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