103 posts · 140,046 views
Razib Khan has an academic background in the biological sciences and has worked in software. He is an Unz Foundation Junior Fellow and lives in the western United States.
Gene Expression
103 posts
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- July 8, 2011
- 08:13 PM
- 2,173 views
On the genetic structure of Afro-Indians
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 Afr........ 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
- July 8, 2011
- 04:19 AM
- 1,475 views
Everything I didn’t know about sex
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 ........ 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
- July 7, 2011
- 04:34 AM
- 2,007 views
Marry far and breed tall strong sons
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’........ 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
- July 6, 2011
- 06:07 AM
- 1,540 views
Tightening the interval of the expected
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 genet........ 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
- June 21, 2011
- 07:23 AM
- 1,195 views
We stand on the shoulders of cultural giants
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........ 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
- June 21, 2011
- 07:23 AM
- 1,062 views
We stand on the shoulders of cultural giants
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........ 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
- June 20, 2011
- 08:04 AM
- 1,160 views
Convergent evolution happens!
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 certain........ Read more »
Tennessen JA, & Akey JM. (2011) Parallel Adaptive Divergence among Geographically Diverse Human Populations. PLoS Genetics. info:/
- June 20, 2011
- 08:04 AM
- 1,142 views
Convergent evolution happens!
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 certain........ Read more »
Tennessen JA, & Akey JM. (2011) Parallel Adaptive Divergence among Geographically Diverse Human Populations. PLoS Genetics. info:/
- June 20, 2011
- 08:04 AM
- 988 views
Convergent evolution happens!
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 certain........ Read more »
Tennessen JA, & Akey JM. (2011) Parallel Adaptive Divergence among Geographically Diverse Human Populations. PLoS Genetics. info:/
- April 20, 2011
- 05:16 AM
- 1,682 views
Evolutionary pressures, within and without
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 trigge........ 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
- April 19, 2011
- 06:48 PM
- 2,043 views
Europeans as Middle Eastern farmers
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 l........ 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
- April 18, 2011
- 04:22 AM
- 1,469 views
Evolution in higher dimensions
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 ........ 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
- April 16, 2011
- 09:36 PM
- 1,752 views
Evolution may explain why baby comes early
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........ 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
- March 29, 2011
- 06:10 AM
- 1,492 views
The flat and the fit
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 scenari........ 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
- March 8, 2011
- 05:30 PM
- 2,423 views
Where in the world did anatomically modern humans come from?
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 le........ 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
- February 25, 2011
- 05:30 AM
- 2,094 views
Brazilians, more European than not?
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........ 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
- February 23, 2011
- 06:44 PM
- 1,992 views
Sweeping through a fly’s genome
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........ 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
- February 22, 2011
- 05:45 AM
- 1,888 views
The evolution of man is no cartoon
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 techn........ 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
- February 10, 2011
- 05:37 PM
- 2,092 views
Swedes not so homogeneous?
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 ........ 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
- February 8, 2011
- 05:07 AM
- 1,616 views
Health care costs and ancestry
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........ 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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