103 posts · 60,793 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
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- May 7, 2010
- 03:11 PM
- 3,792 views
The three layers of the Neandertal cake
by Razib Khan in Gene Expression
I assume by now that everyone has read A Draft Sequence of the Neandertal Genome. It’s free to all, so you should. At least look at the figures. Also, if you haven’t at least skimmed the supplement, you should do that as well. It’s nearly 200 pages, and basically feels more like a collection of [...]... Read more »
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.... (2010) A Draft Sequence of the Neandertal Genome. Science, 328(5979), 710-722. DOI: 10.1126/science.1188021
- February 23, 2011
- 05:44 PM
- 1,022 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 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
- August 23, 2010
- 07:40 AM
- 838 views
A thousand little adaptive platoons
by Razib Khan in Gene Expression
Last week I took an intellectual road trip back nearly a century and explored the historical context and scientific logic by which R. A. Fisher definitively fused Mendelian genetics with quantitative evolutionary biology. In the process he helped birth the field of population genetics. While the genetics which we today are more familiar with begins at [...]... Read more »
Sewall Wright. (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of The Sixth International Congress of Genetics. info:/
- July 8, 2011
- 07:13 PM
- 835 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 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
- February 22, 2011
- 04:45 AM
- 814 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 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
- September 7, 2010
- 06:15 AM
- 809 views
Genetic differences within European populations
by Razib Khan in Gene Expression
One of the more popular posts on this weblog (going by StumbleUpon and search engine referrers) focuses on genetic variation in Europe as a function of geography. In some ways the results are common sense; populations closer to each other are more genetically related. Why not? Historically people have married their neighbors and so gene [...]... Read more »
Moskvina V, Smith M, Ivanov D, Blackwood D, Stclair D, Hultman C, Toncheva D, Gill M, Corvin A, O'Dushlaine C.... (2010) Genetic Differences between Five European Populations. Human heredity, 70(2), 141-149. PMID: 20616560
- March 8, 2011
- 04:30 PM
- 772 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 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
- December 8, 2010
- 04:19 PM
- 771 views
The men of the north: the Sami
by Razib Khan in Gene Expression
Ole Magga, Norwegian politician
On this blog I regularly get questions about the Sami (Lapp*). That’s because I often talk about Finnish genetics, have readers such as Clark who are of part-Sami origin, and, the provenance and character of the Sami speak to broader questions about the emergence of the modern European gene pool. More precisely [...]... Read more »
Maki-Torkko, Elina, Aikio, Pekka, Sorri, Martti, Huentelman, Matthew J, & Camp, Guy Van. (2010) A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies. European Journal of Human Genetics. info:/10.1038/ejhg.2010.179
- April 19, 2010
- 11:12 AM
- 760 views
Cape Coloureds: an instance of a generality
by Razib Khan in Gene Expression
Several months ago I put up a post which reviewed the geographical connections within the total genome content of the Cape Coloureds of South Africa. These peoples (plural because distinctive ethnic groups such as the Griqua were subsumed into this category in the 20th century) are of diverse origin, though generally their African and European [...]... Read more »
Quintana-Murci, L., Harmant, C., Quach, H., Balanovsky, O., Zaporozhchenko, V., Bormans, C., van Helden, P., Hoal, E., & Behar, D. (2010) Strong Maternal Khoisan Contribution to the South African Coloured Population: A Case of Gender-Biased Admixture. The American Journal of Human Genetics, 86(4), 611-620. DOI: 10.1016/j.ajhg.2010.02.014
- May 12, 2010
- 08:28 AM
- 758 views
The post-Columbian panmictic “natural experiment”
by Razib Khan in Gene Expression
Economists in the last few years have been shifting toward testing their theoretical models, whether through the experiments of behavioral economics, or, “natural experiments.” The reason economists have had issues with testing their models is that experimentation on humans has some natural constraints. Macroeconomists have an even greater problem, as experimentation on whole societies not [...]... Read more »
Bryc K, Velez C, Karafet T, Moreno-Estrada A, Reynolds A, Auton A, Hammer M, Bustamante CD, & Ostrer H. (2010) In the Light of Evolution IV: The Human Condition Sackler Colloquium: Genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20445096
- April 23, 2010
- 04:58 AM
- 748 views
Nearly 100% Out-of-Africa in the past 100,000 years
by Razib Khan in Gene Expression
Since I’ve been talking about the possibility of admixture with “archaics” (I’m starting to think the term is a bit too H. sapiens sapiens-centric, is the Neandertal genome turning out to have more ancestral alleles?) I thought I’d point to a paper out in PLoS ONE which reiterates the basic fact that the overwhelming genetic [...]... Read more »
Laval G, Patin E, Barreiro LB, Quintana-Murci. (201) Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions. PLoS One. info:/10.1371/journal.pone.0010284
- January 14, 2011
- 04:58 PM
- 742 views
The inevitable rise of Amish machines
by Razib Khan in Gene Expression
About 20 years ago I lived for a year in a rural area where Amish were a common feature of country roads and farmers’ markets. My parents, being Muslims, would sometimes buy chickens from the local Amish and slaughter them according to halal. We had a relationship with a particular family. They were nice people, [...]... Read more »
Rowthorn R. (2011) Religion, fertility and genes: a dual inheritance model. Proceedings. Biological sciences / The Royal Society. PMID: 21227968
- May 5, 2010
- 01:43 PM
- 740 views
Genetic variation among African Americans
by Razib Khan in Gene Expression
There’s new paper in Genome Biology (tip: Dienekes) which doesn’t present too much in terms of new results, Characterizing the admixed African ancestry of African Americans, but has really, really, good visualization of the data:
Results
From cluster analysis, we found that all the African Americans are admixed in their African components of ancestry, with the majority [...]... Read more »
Zakharia F, Basu A, Absher D, Assimes TL, Go AS, Hlatky MA, Iribarren C, Knowles JW, Li J, Narasimhan B.... (2009) Characterizing the admixed African ancestry of African Americans. Genome biology, 10(12). PMID: 20025784
- April 19, 2011
- 05:48 PM
- 731 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 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
- May 14, 2010
- 07:29 AM
- 730 views
Breathing like Buddha: altitude & Tibet
by Razib Khan in Gene Expression
You probably are aware that different populations have different tolerances for high altitudes. Himalayan sherpas aren’t useful just because they have skills derived from their culture, they’re actually rather well adapted to high altitudes because of their biology. Additionally, different groups seem to have adapted to higher altitudes independently, exhibiting convergent evolution. But in [...]... Read more »
Tatum S. Simonson, Yingzhong Yang, Chad D. Huff, Haixia Yun, Ga Qin, David J. Witherspoon, Zhenzhong Bai, Felipe R. Lorenzo, Jinchuan Xing, Lynn B. Jorde.... (2010) Genetic Evidence for High-Altitude Adaptation in Tibet. Science. info:/10.1126/science.1189406
- April 27, 2010
- 09:41 AM
- 716 views
The ancestry of one Afrikaner
by Razib Khan in Gene Expression
A few weeks ago I reviewed a paper on the the genetics of the Cape Coloured population. Within it there was a refrence to another paper, Deconstructing Jaco: genetic heritage of an Afrikaner. The title refers to the author himself. It was an analysis of his own pedigree going back to the 17th century, along [...]... Read more »
Greeff, J. (2007) Deconstructing Jaco: Genetic Heritage of an Afrikaner. Annals of Human Genetics, 71(5), 674-688. DOI: 10.1111/j.1469-1809.2007.00363.x
- June 18, 2010
- 09:39 AM
- 716 views
The “how” of cystic fibrosis through the “why”
by Razib Khan in Gene Expression
It’s just a fact that contemporary human evolutionary genetics has relied upon its potential insights into disease to generate funding, support and interest. I don’t think that this is much of a silver lining when set next to the suffering caused by disease, but it’s a silver lining nevertheless. Therefore findings which would be of [...]... Read more »
Kosova G, Pickrell JK, Kelley JL, McArdle PF, Shuldiner AR, Abney M, & Ober C. (2010) The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate. PLoS genetics, 6(6). PMID: 20532200
- April 15, 2010
- 11:01 AM
- 715 views
When diversity is good for disease
by Razib Khan in Gene Expression
Yesterday I pointed to a new paper, Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. P. vivax is the least virulent of the malaria inducing pathogens, and it is presumably responsible for the fact that the Duffy antigen locus is one of the more ancestrally informative ones in the human genome. In [...]... Read more »
Ménard D, Barnadas C, Bouchier C, Henry-Halldin C, Gray LR, Ratsimbasoa A, Thonier V, Carod JF, Domarle O, Colin Y.... (2010) Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. Proceedings of the National Academy of Sciences of the United States of America, 107(13), 5967-71. PMID: 20231434
- January 5, 2011
- 04:54 AM
- 714 views
Profiling hair color by DNA
by Razib Khan in Gene Expression
Hair Color of Unknown Offenders Is No Longer a Secret: The research findings demonstrate that on the basis of DNA information it is possible to determine with an accuracy of more than 90 percent whether a person has red hair, with a similarly high accuracy whether a person has black hair, and with an accuracy [...]... Read more »
Branicki W, Liu F, van Duijn K, Draus-Barini J, Pośpiech E, Walsh S, Kupiec T, Wojas-Pelc A, & Kayser M. (2011) Model-based prediction of human hair color using DNA variants. Human genetics. PMID: 21197618
- February 25, 2011
- 04:30 AM
- 714 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 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
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