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A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
Gene Expression Blog

Merry Christmas! No one in my family is Christian (inclusive of first degree in-laws) so there’s no explicit religious content in the celebration of the holiday, but it’s still a big deal. I think that a mid-winter holiday is a pretty straightforward aspect of “evoked culture” in the temperate climes. That is, it was bound to arise, and it is no surprise that modern Christmas was unable to slough off the many strands of European pagan custom and belief which threaded these mid-winter festivals together.

I’m going to queue the open thread for Sunday now as I’ll be sporadic checking in on this website for a bit.

• Category: Miscellaneous • Tags: Christmas 

700px-BIG_LEAF_MAPLES_HOHIn an article titled Restored Forests Breathe Life Into Efforts Against Climate Change, there’s an interesting portion which talks about how farming techniques relate to reforestation:

Around the world, trees are often cut down to make room for farming, and so the single biggest threat to forests remains the need to feed growing populations, particularly an expanding global middle class with the means to eat better. Saving forests, if it can be done, will require producing food much more intensively, on less land.

Life is about trade-offs, even if you don’t want to admit it. Organic farming uses more land to produce the same amount of food. Basically, it’s a luxury good if you can afford it (and highly profitable for agribusiness!). The poorest farmers in the world are organic producers because they have to. There are many downsides with industrial agriculture, but one of its upsides is that it produces the maximum amount of calories using the minimum amount of land. New England reforested in part because much of the farmland was abandoned due to low productivity (and the availability of much better land in the Old Northwest territories amenable to farms which could take advantage of economies of scale). One major tool of modern farming, genetically modified organisms (GMO), has been resisted and stymied for several decades by public suspicion and adherence to the precautionary principle (e.g., many types of plants which could be easily GMOed are not even in the United States). Most of the time environmentalists are quite skeptical of GMO because of the precautionary principle, but the fact is that “natural” local organic farming can have a much larger carbon footprint than something artificial. To some extent all of human life is touched by artificiality today.

27-shanghai-artist-impressionAnother developing trend which opens up the potential for rewilding spaces now given to human habitation, would be a transition toward greater density and urbanization. As someone who grew up in the Pacific Northwest it is striking that here you have a land of contrasts, as small rural towns dependent on logging decline, and the greater Portland and Seattle metropolitan areas have ballooned. Urban dwellers venture to the outdoors quite often, but they do not live in the wild. A shift toward density and vertical habitation would likely result in greater economic efficiency and reduced carbon footprints.

The irony is that the lowest impact future in relation to the environment may be the most ‘high tech.’ A world of mechanized farms growing bioengineered crops, meat cultures grown in vast industrial vats, and the predominant form of habitation being within organically developing arcologies which replace the megacities of today is positively out of science fiction. But, it would also be a much greener world than the ‘natural’ alternatives. With the exception of a scenario that includes mass die off of most of the human race.

• Category: Science • Tags: Future 

Rashida Jones

Geneticists are people of their time. I’m rather sure that if Charles Davenport had written a book with the title Race Crossing in Jamaica today it would end with a far different moral, because the dominant Zeitgeist in regards to racial admixture in the United States is far different nearly 100 years on. In my post below where I review interesting aspects of the new study from researchers in David Reich’s lab and 23andMe, The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States, I didn’t cover the variation in admixture in black and white Americans too much in detail. Partly that’s because this study only improved the bigger picture on the margins, and with finer geographic grain (though these were interesting obviously). We knew that the vast majority of white Americans who are not Hispanic do not have detectable non-European ancestry. It has also long been reported and verified that a substantial minority of the total ancestry of black Americans is of European origin, with a small Native American fraction as well. Additionally, this non-African ancestry in black Americans varies by geography as well as individual to individual a great deal.

euro So I have to take issue when The New York Times posts articles with headlines such as White? Black? A Murky Distinction Grows Still Murkier. What genetics is showing is that in fact white Americans are shockingly European to an incredibly high degree for a population with roots on this continent for 400 years. If we removed all the history that we take for granted we’d be amazed that the indigenous peoples had so little demographic impact, and, that the larger numbers of people of partial African ancestry did not move into the general “white” population. This is in fact the case across much of Latin America, where many self-identified whites, blanco, have African and indigenous ancestry. But we do know the reasons for why North America was unique, a combination of a smaller indigenous population which underwent a mass die off, and folk migrations on a huge scale previously unimaginable in human history. Whole villages in Poland and Norway, not just working age males, decamped for the New World. The original Anglo settler stock on the North American seaboard underwent a period of incredible demography expansion driven by high birthrates, in particular in New England, which in the 17th century had some of the highest total fertility rates recorded in human history.

The peculiar nature of white Americans is evident in the figure to the left. You see that black Americans span the gamut from being mostly African to mostly European (I believe that individuals who are 100% European but state they are black are probably due to error in self-identification on the survey). Though it isn’t quite clear on these sorts of plots (yes, I know why there’s moderate opacity), the black American distribution of African/European ancestry is not symmetrical, but is skewed, so that a small minority of black Americans are more than 50% European in ancestry, while the majority are less than 25% European. With the Latino populations you see admixture with both Africans and Native Americans. Though typical Mexican people are presumed to be mixed between European and Native, most Mexicans seem to have low, but detectable, levels of African ancestry. This is almost certainly due to the attested slave population across the Spanish colonies. And, this is contrast to the situation in the United States, where even “Old Stock” Anglo-Americans whose ancestors have been coexistent with people of African origin for at least 250 years by and large.

51TZ-cnJTrL._SS500_ My own hunch is that the contrast between Anglo-America and Latin America when it comes to admixture has a lot to do with the fact that a far larger proportion of the European settlers were female. This allowed for a total replication of European populations, norms, and mores, rather than enforcing a sort of synthesis, as was necessary in Latin America. In the Spanish colonies European males were initially very polygynous, establishing liaisons with many women, both indigenous and black. A modest stream of men from European could quickly “whiten” what had initially been a mixed first generation, resulting in a elite creole caste which was predominantly European, but whose Europeanization had been male mediated atop a foundational base which featured non-European women. This can explain with the mtDNA lineages are so much more indigenous than total genome content might lead one to suspect. In Latin America individuals with obvious non-European ancestry, such as Vincente Guerrero, could rise to positions of prominence, and forward the project of a European-dominated society. In contrast someone with mixed blood in the United States would have been socially marginalized, and had minimal prospects outside of a few exceptional cases (e.g., among the mixed race Creoles of Louisiana).

41AFhg61TZL._SY344_BO1,204,203,200_ Of course even with balanced sex ratios relations across racial lines occurred. This brings us to the next step of a peculiarity in the ideology of white American racial supremacy: hypodescent. This is the rule by which mixed offspring inherit the racial identity and social status of the parent whose is of the inferior race. In the United States this operationally meant that children born to slave mothers of free white fathers were considered black, and condemned to slavery (this is in contrast to the official rule in Islam, where children of the master who were recognized were free). In some ways this practice seems similar to lack of rights which non-legitimate offspring experience in many societies. But in the American context it was highly racialized. The norm of hypodescent also resulted in scientific theories which buttressed it, such as Madison Grant’s contention that mixing between superior and inferior races always resulted in a population which resembled the inferior race (the law of “reversion toward the lower type”). Charles Davenport even went so far as to argue that admixture produced offspring inferior to both parental types, a form of hybrid breakdown.

It is entirely reasonable to argue that racial categories in the United States are blurred if one holds to a Platonic and essentialist view which resembles that which underpinned white racial supremacy and the law of hypdoescent. But as it is these views have no necessary scientific basis, and a percent or two of African ancestry in someone who is ~98 percent of European ancestry does not make them non-white in any rational sense. The 12 year old paper, Categorization of humans in biomedical research: genes, race and disease, has aged well in my opinion. A conclusion that 10 percent of whites in South Carolina are actually black because they have detectable African ancestry strikes me as crazy. But then, hypodescent also strikes me as somewhat crazy, though the rationale which drove it is also eminently understandable (i.e., the exclusion of illegitimate children and maintenance of a racial order). I hold that the racial lines are “blurred” only if you hold to the criteria which arose in the 17th and 18th centuries in the culture of the American South.

There is one aspect of paper and The New York Times article which I think is worth commenting on:

Most Americans with less than 28 percent African-American ancestry say they are white, the researchers found. Above that threshold, people tended to describe themselves as African-American.

Katarzyna Bryc, a 23andMe researcher and co-author of the new study, didn’t want to speculate about why people’s sense of ethnic identity pivots at that point.

I will speculate. The 28 percent proportion is about where African ancestry becomes salient, or not. In a de facto sense today the law of hypodescent applies only those who have visible African ancestry. In the United States these individuals are classified as black, no matter the preponderance of their lineage. A good example here is Rashida Jones, the daughter of Quincy Jones and Peggy Lipton. Quincy Jones has had some genetic analysis done, and he is about 2/3 African and 1/3 European. The expected value then for Rashida Jones is that she is 1/3 African in ancestry, though that may vary up or down a bit (her mother is an Ashkenazi Jew). Rashida Jones regularly plays white characters in film and television, and she does so because African features are not very evident in her. In contrast, her sister Kidada is just a bit more African in her features, and profiles of them growing up have indicated that while Rashida identified with her Jewish side (and still does), Kidada felt more black. In contrast, people who are 1/4th Asian, such as Keanu Reeves, are not subject to hypodescent in the United States, because Asian features are not as salient to white and black Americans, and white supremacy in the American South was generally aimed at blacks (my friend David Boxenhorn, who is Ashkenazi Jewish, finds it amusing that both my children have lighter eyes than any of his children).

Geetali Norah Jones Shankar

Geetali Norah Jones Shankar

But, with the rise in intermarriage and a clearly mixed-race Latino population the lines between the races will become blurred genetically more and more. A substantial number of American children today are multiracial, and that fraction looks to increase. If 23andMe did a survey of American genetics 25 years from now I’d be much more amenable to the interpretation that the media is putting on this survey. In one generation the world of the Baby Boomers, American, black and white, will be gone. With all that being said, I think it is highly likely that many people with known non-white ancestry (e.g., 1/4th Japanese, as a blonde haired and blue eyed friend of mine is) are going to identify as white. That means that to be “white” in the United States will be much more in keeping with the norm in Latin America, where a generally European appearance and preponderant ancestry are sufficient. And, it also means that race and racism will continue to be features of American life, just as they are in Latin America. Just differently.

Related: Steve says many of the same things.

• Category: Race/Ethnicity, Science • Tags: Hypodescent 

abany2One of the weird things that annoys me about American politics is the idea that support for abortion rights is particular in some way to women. This is very common on the Left side of the political spectrum, but strangely for the self-described “reality based community” it has basically no correspondence with reality at the first pass.* All you need to do is look at the General Social Survey, which as a variable “ABANY” which asks respondents if it should be legal for a woman to have an abortion for any reason. The question has been asked every few years since 1977. I limited the data to whites only, and what you can see above is that year to year there is actually a correlation between men and women when it came to a “Yes” response. I was actually surprised by that. The jumps are not total noise, but reflect changes in the Zeitgeist (the rule of thumb is that the populace becomes more pro-choice during Republican presidencies and more pro-life during Democratic ones).

The second plot illustrates that for most of the years since 1977 men have supported abortion on demand at a higher clip than women. It doesn’t prove anything, except that reality is a little more “problematic” than some people who regularly call in to NPR might think (that’s what triggered this post).

* If you look close, there is evidence that a smaller well educated segment of liberal women are particularly intense about abortion rights.

• Category: Ideology • Tags: Abortion 
Cite: Bryc, Katarzyna, et al. "The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States." The American Journal of Human Genetics (2014).

Cite: Bryc, Katarzyna, et al. “The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States.” The American Journal of Human Genetics (2014).

The recent paper, The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States, brings together a lot of results which 23andMe has been letting slip in bits and pieces over the years. Most of the press coverage has focused on racial dynamics at the level we’re used to talking about today in the United States. White, black, and Latino (of whatever race). But as I told the first author at BAPG a few weeks ago the dynamics among white Americans is probably where their massive data set can shine. You see it in the figure above, which confirms what many have suspected: the states of the inland South have retained a predominant Anglo-American settler population down to the present. This is clear in their very high fraction of people of “British-Irish descent” in 23andMe Ancestry Composition nomenclature. Including the black American population the overwhelming majority of the population likely descends from people were already resident in the future continental United States in 1776 in this region. Additionally, you can tell that these results are not crazy because in the north Indiana has higher fractions than either Ohio or Illinois, which is exactly what you’d expect if you knew something about the demographic histories of these states. Indiana experienced less migration from European populations who were not of settler stock than Illinois (Chicago) and Ohio (Cleveland and Cincinnati). Similarly, Maine’s elevated fraction makes sense since rural Yankees are demographic more dominant in northern New England than they are in the southern states. Finally, the states of the old Yankee Empire of the northern Old Northwest have been totally demographically transformed by the massive waves of migration from Germany and Scandinavia.

The distinction between settler and immigrant Europeans is clear in relation to detectable non-European ancestry:

We find very low levels of African and Native American ancestry in Europeans with four grandparents born in Europe. We estimate that only 0.98% of Europeans carry African ancestry and 0.26% of Europeans carry Native American ancestry. These levels are substantially lower than the 3.5% and 2.7% of European Americans who carry African and Native American ancestry, respectively…Excluding countries that had major and minor ports in the Atlantic with strong connections to the slave trade (namely Portugal, Spain, France, and United Kingdom) and Malta, which has been the site of migrations from Africa and the Middle East, we obtain a data set of 9,701 Europeans, where we find African and Native American ancestry is virtually absent, with only 0.04% of individuals carrying 1% or more African ancestry and 0.01% carrying 1% or more Native American ancestry, within the margins of survey error estimates.

32081 The African admixture in places like the American South is almost all a function of admixture in the first 150 years or so of settlement (the exception might be Louisiana, where Spanish Creoles may have contributed some African ancestry). The historical and genetic data seem to align there. Though the racial caste system in the American South had an early origin, it became progressively more calcified and stationary as the decades progressed. But by the late 19th century when Jim Crow laws were enacted the African admixture in many Southerners was a very distant memory and thoroughly diluted. To gauge the social and demographic import, recall that detection of genetic fragments does not reflect the total genealogy. Many people with ancestors who were black American slaves do not carry any segments from those individuals, while the ones being detected in this study exhibit a relative enrichment.

In the future I would be very curious about exploring the patterns of relationship of the Anglo-American folkways, as outlined in works such as Albion’s Seed and the The Cousins’ Wars. A major problem though is that these are genetically very close to begin with. The first author of the above work suggested to me that they would need the People of the British Isles data set to get good reference populations. Perhaps in the near future that will be feasible.

• Category: Science • Tags: History 

Noahs_ArkMost biological concepts exhibit striking clarity and intuitive accessibility at the highest levels, but engender confusion when you drill down to the details. You can see this in an understanding of evolution. Most people can grasp the idea of common descent with modification relatively easily. But when it comes to getting an good intuitive grasp of evolutionary process, and what that might entail, people are often left grasping at straws. Consider the reality that many people believe that evolution works by benefiting the species, even though the mainstream position within the discipline is that operates through variation in individual fitness. What is likely happening is that our cognitive intuitions are slipping into our understanding of science. We imagine evolutionary process as changing an entire species, rather than the mass action of individuals within the species.
519gldjJoALThis is clear when you look at the research on “folk taxonomy.” Humans have an idea of what a species is, and it often corresponds relatively closely to the biological species concept. Though higher and lower taxonomic scales such as genus and subspecies reflect genuine information about the structure of reality, species is considered special by many in that it is a clear and distinct level of organization where groups are of organisms are neatly encapsulated from other groups of organisms. It’s “real.” Here intuition and folk taxonomy align with our understanding of biology. The problem is that species is neither so general, nor so neat and airtight even in cases where one might think it applies. First, the biological species concept obviously makes sense only in the context of sexual organisms. Asexual organisms are living things too., and important ones at that. There are after all an order of magnitude more bacterial cells in our body than somatic cells. Second, even many sexual organisms (e.g., plants) engage in hybridization quite regularly. Species are useful semantic sugar, but they have no atomic Platonic reality. They are not one of the fundamental units of organization of the universe around us, but rather a term which maps upon a dynamic which is of great interest to humans (i.e., the fission of complex eukaryotic sexual organisms into distinct populations over time).

51D2RoDDkXL._SY344_BO1,204,203,200_ The reality that for most biologists species are viewed in instrumental terms is not always clear to the broader public. The constant war of words with Creationists which revolves around speciation and macroevolution is actually somewhat beside the point, because the very idea of species is not coherent or consistent, despite its genuine utility. And isn’t just Creationists who have drafted our cognitive Platonism toward their ends. Disputes over the Endangered Species Act get bogged down in minutiae as to what a species is, and what sort of diversity is worth preserving (or not). That’s what happens when you take a scientific concept which is not airtight on the margins and introduce activists, lawyers, and various assorted interests with no compunction about using casuistical arguments in the service of their preferred ends.

The same general confusion seems to crop up when you move below the level of species. In my post below, Fear of Race Mixing in Biodiversity, I make a pass at the fallacy of the blending theory of inheritance, which was overturned by a little known field which goes by the name of Mendelian genetics. Nevertheless in the comments the blending theory of inheritance pops right back up, even though I dismissed it in the post itself:

What about the modern Auroch? It has been reconstructed through selective breeding though no geneticist would consider it the same as an ancient Auroch. It may look similiar but it is no more Auroch from a genetic standpoint than a spanish fighting bull. Once a breeding population is lost in its isolation and genetic uniqueness. It can not be reassembled any more than two cans of paint can be unmixed. Even if the original genes still exist in the mixed population. Your viewpoint also assumes that all phenotypes have the same reproductive and behavioral tendencies. Which does not seem to be the case for nothern euros in comparison with more tropicaly evolved peoples. So unless blondeness or ruffocity convey some selective advantage over other phenotypes they will dissapear in time, especially the platinum or ash blonde varieties.

download (1) First, let me say that I really don’t understand about half of this comment, and told my interlocutor exactly that. But the portion relating to the analogy of mixing with paint is obviously leveraging the intuition about the blending theory of inheritance, and it turns out to just be false (also, a rule of thumb might be to not engage in analogies with a geneticist about genetics; just get to the point in plain language). In the early 20th century Mendelian genetics, which traces patterns of inheritance of traits across generations and sieves it through a particular model, turned out be exactly what was needed to allow for the persistence of the variation which is the raw material of evolution. The necessity and maintenance of this variation was a paradox which confronted Charles Darwin in the 19th century, and he never quite resolved it. Basically, if offspring are the blended mix of their parents, then each generation should be progressively more blended and uniform. That uniformity removes the variation which is necessary for adaptation through natural selection. Attempts to maintain variation through processes such as high mutational rates were simply not plausible. The genius of Mendelian genetics was that inheritance was transformed into a process mediated by discrete particulate units. Genes. In sexual organisms the patterns of inheritance are governed by the law of segregation and the law of independent assortment.

download (2) When I teach undergraduates basic genetics and these laws I always tell them to conceptualize them physically, because we know now that genes are actually embodied in strings of base pairs. Mendelian genetics, and the abstract understanding of the genome in its essence, long predate the discovery of DNA. But through a grasp of both the abstraction of genetic inheritance, as well as its concrete manifestation in the sequence of DNA, one can infer the dynamic of microevolutionary process. Because of segregation there is variation in the ancestry inherited from the grandparents. Because of recombination the law of independent assortment holds beyond a certain genetic distance even on the same chromosome. Evolution can be thought of now not as simply phenotypic change, but rather as fluctuations in allele frequencies over generations, unto extinction and fixation. Finally, the nature of quantitative traits due to polygenetic architectures becomes much more transparent if one simply imagines the combined effect of numerous genes producing a final outcome.

The above explains why racial admixture of modern populations will not lead to uniformity and homogeneity. Consider the case of skin color, where variation in ~10 genes accounts for ~90 percent of the inter-continental variation in complexion. Populations where many of these genes are segregating, such as in Brazil or India, are not of uniform coloration, but manifest the full range of ancestral complexions. On average the complexion lies at the midpoint, but the underlying allelic variation remains. In fact, because admixed populations exhibit combinations of multi-locus genotypes not found in the ancestral populations they’re likely to be more diverse overall than the total variation in the summed ancestral groups (e.g., which group has more phenotypic diversity, Spaniards and Amerindians separately, or mestizos?). From the standpoint of anti-racists who may hope for a post-racial world where amalgamation leads to the abolition of race, that will not happen. First, the data from Latin America is clear that phenotypic race remains even after genetic admixture because individuals vary a great deal in appearance. Second, most modern races themselves are almost certainly the product of admixture events over the past ~10,000 years. Racial categorization can be useful, and reflects real history, but it is not a fundamental unit of special genetic structure. Races are neither primal nor Platonic. But given rather conventional conditions they seem to emerge out of folk taxonomies. They’re an evoked part of human culture.

product_thumbnail Following the comments of my interlocutor I don’t really believe the issue at heart was scientific. It’s patently false that once genotypes are scrambled they can’t be unscrambled. The law of segregation and the law of independent assortment offer up exactly the manner in which you can reassemble ancestral types from admixed populations. The root concern derives not from biology at all, but psychology, and an intersection between folk taxonomy and ideas of Platonic essences and contagion. Once the category of the Northern European phenotype is sullied in some way, it is lost forever. Rather than conceiving of Northern Europeans as a biophysical expression of discrete alleles, which are a very recent event in history due to admixture from diverse lineages and in situ evolution, the implicit cognitive assumption is that they have a particular unitary racial spirit, and that their racial category is fundamental and primordial. These might seem to be antiquated early 20th century concerns, but though the sentiment is sublimated I’m pretty sure it’s still very common, because that’s the only reason I can think that phenomena such as the “disappearing blonde gene hoax” often go viral so quickly.

When conceptualizing genetic and evolutionary processes one can frame it as a spectrum, from gradual change on polygenic characters to the emergence of single gene traits. The human default frame seems to veer erratically between the two. On the one hand blending inheritance theory implicitly underpins many intuitions about the nature of how characters change over time. Yet there is also a craving for a specific and singular concrete gene for a given condition. The latter likely emerges from the reality that DNA and modern methods, starting with linkage analysis, zero in on very specific positions in the genome and are localized to a particular gene for many Mendelian diseases. What gets lost is the Mendelian framework, which is a conceptual model which can integrate both the quantitative genetic characters and the monocausal traits and diseases conditioned upon a very specific change in one region of DNA.

• Category: Science • Tags: Genetics 

This week Planet Money had an episode about the economic angle of how gyms make money off you not using your services (transcript). The basics are easy enough to understand. If you buy a memership to a gym, and actually showed up every day, then you’d wear out the equipment. If you are a member and pay dues and don’t utilize the services then the costs are kept down. In fact it is obvious that gyms have many more members than they have capacity to service at any given time. The radio piece quotes one manager as saying that her Planet Fitness has 6,000 members, but a capacity of only 300 (and often it is rather empty). In fact the whole idea of gyms like Planet Fitness is to mix a portfolio of projecting the ideal of fitness while enabling your more slothful tendencies. People join for the cardio machines, but they stay for the pizza nights and socials.

In contrast another gym they profiled, Precision Athlete, serves an opposite clientele. While Planet Fitness charges $10 a month, Precision Athlete charges $500. Some of this has to be the fixed costs of a small operation with high level trainers, but it is also clear that their equipment gets used, a lot. This puts in stark relief the peculiarities of the normal gym, where there’s a power law distribution of utilization. About 10% of the members probably use 90% of the “gym time.”

Addendum: In some ways Planet Fitness perfectly encapsulates are our contemporary ethos among a certain set of middle class Americans. Since actually working out is “triggering,” they ban or discourage it.

• Category: Economics • Tags: Athletics 

165280 Currently reading Mathematical Models of Social Evolution: A Guide for the Perplexed. Though there is a focus on the social aspect, this is really a book on evolutionary modeling more generally. And, it’s less daunting than many other works that I’ve run into. The authors also make a nice case for why analytical modeling is still important in an age of simulations.

Been very busy with stuff, trying to get as much work done as possible before Christmas. You know how it is.

• Category: Miscellaneous • Tags: Open Thread 

Abolishing diversity, one child at a time!

One of the often overlooked historical oddities in the development of the environmental movement in the United States is its past close relationship to what we would today term white supremacy. Though many praise Teddy Roosevelt for his embrace of conservationism and evolutionary theory, he also adhered to the normative racial beliefs of the day, which presumed the superiority of Anglo-Saxon people, and couched that superiority in Darwinian terms. Even less well known is the activism of race theorist Madison Grant, who was as much a conservationist as the intellectual doyen of white supremacy that he is remembered as today (see Defending the Master Race: Conservation, Eugenics, and the Legacy of Madison Grant). In some ways the connection is reasonable and not surprising, in that both are fundamentally conservative preservationist instincts. To preserve the environment and the racial order of the day. The association was clear well into the 20th century, Charles Lindbergh was a prominent eugenicist, but later became an environmentalist, while Garrett Hardin, who originated the term “tragedy of the commons,” opposed high immigration levels and was skeptical of racial diversity.

cover_passing Because of environmentalism’s place within the cultural Left in the United States these corollaries no longer apply. In fact, the Sierra Club and other such organizations tend to be careful to not oppose immigration on environmental grounds any longer because of its racial implications. But, I’ve noticed that many people with an environmental orientation still use what strikes me as quite racialist language in the context of animals. I don’t think it is a problem. Different moral and ethical standards apply to animals. We eat them. We don’t eat humans. But I also think it is funny, as well as somewhat wrong-headed. This came to my attention again because of an article in Nautilus, A Strange New Gene Pool of Animals Is Brewing in the Arctic. There’s a lot of talk about issues like hybrid zones, and pre- and postzygotic isolation (at least implicitly). But this section is just totally confused:

In September, in an inlet some 1,800 miles north of Fargo, North Dakota, where the North American landmass dissolves into the Arctic Ocean, the whales met in the middle. They spent two weeks together, and although not much happened before they turned around, the meeting was historic. The fossil record indicates the last time Pacific and Atlantic bowhead whales came into contact was at least 10,000 years ago.

While it’s tempting to imagine a strange new Arctic teeming with “grolar bears” and “narlugas,” hybridization comes at a cost. Arctic biodiversity will be reduced through gradual consolidation, taking with it a blend of genes that have evolved by natural selection over millennia. “There’s going to be a whole bunch of organisms containing genes that we’re going to lose,” Kelly says. Which genes, exactly, is unclear….

The problem here is that the terms are being mixed up. “Biodiversity” is often applied at the level of species or races, with a diversity index calculated from discrete numbers of population types. If you calculate a diversity index based on Swedish, Nigerians, and Chinese, you start out with three populations and look at their proportions (the more skewed the proportions, the lower the diversity). If you take them all and mix them so they are one random mating population obviously the ecological diversity index is going to go down. But the genetic diversity is not going to down, because genes don’t “mix”. Mixing implies a blending theory of inheritance, what Mendelian genetics overthrew with its understanding of discrete and particulate units of inheritance. The same confusion crops up with the ideas of “disappearing blondes” and “disappearing redheads.” The phenotypes may change in frequency, but the understanding alleles, the genetic variants, remain. From a genetic perspective if you wanted to you could probably pull back out the original populations through selective breeding. Not only does the allelic diversity of the pooled populations not change, but the genotypic diversity increases, because of elevated heterozygosity. Finally, new potential combination genotypes arise from the mixing, so the phenotypic diversity in totality also probably increases (e.g., Brazilians exhibit a wider range of skin color variation than Africans or Europeans).

Of course this is predicated on racial/subspecies level variation and divergence. If the populations are separated long enough then there will be barriers to easy gene flow. This is evident in the modern human-Neandertal event, where the X chromosome seems to have been purified of Neandertal alleles (this is a common tendency with hybridization events). But please note above that the people in the piece are concerned about populations of whales separated for 10,000 years. There are plenty of human populations separated for 10,000, and even 100,000 years. So this isn’t really a terrifying number of generations.

• Category: Science • Tags: Hybridization 

wuwei_horseThe present is often only a faint echo of the past. That is why ancient DNA has totally revolutionized our understanding of the evolutionary past of many branches of the trees of life. The tips of the tree that we see around us today are all that remains of diverse and chaotic brambles which have been thoroughly pruned by chance and necessity. Utilizing present genetic variation researchers have been able to make some very interesting inferences, but you can’t infer that which you lack all evidence for. When it comes to the “megafauna” (i.e., anything bigger than a rat) the past two million years have been very trying, with cold alternating with short warm spells. This has no doubt resulted in thinning every so often as populations go extinct across vast swaths of Eurasia in the face of advancing glaciers. In time the range expands, as populations are re-founded by surviving lineages. But these oscillations drive down long term genetic diversity. In addition, the rise of modern humans has resulted in a great wipe out of whole lineages due to our predatory and avaricious behavior.

Domestic animals are arguably the most extreme case of this dynamic. A recent paper on the genomics of the domestic dog highlighted just how wrongheaded previous assumptions were. The standard thinking was that modern dogs are a derived form of wolf. In other words, dogs are simply a specialized subset of wolves. A domestic wolf as it were. Using whole genome sequencing it turns out that wolves that we see around us today are a sister lineage to dogs. Using wolves as the ancestral form of the dog may not therefore be quite as obvious as we’d thought. Of course it seems likely that the ancestors of the dogs were a wolf lineage of some sort, but we can’t assume that they resemble modern Holarctic wolves.

A similar, more complicated, dynamic is being illustrated by ancient DNA for our own lineage. And now a new paper in PNAS highlights similar dynamics to dogs in horses, Prehistoric genomes reveal the genetic foundation and cost of horse domestication. The authors sequenced two horses from the Taymyr regio
in Siberia with medium and high coverage. The horses were from 15 and 40 thousand years ago. That means they well predate domestication, which probably occurred in the 5 to 10 thousand year interval.

These results confirm that the wild Przewalski horses are not ancestral to the domestic lineages, and that rather they are simply the single wild lineage which persisted down to the modern period. The horses from Taymyr are more distantly related to modern horses than the Przewalski are, but intriguingly tests of admixture indicate that there was gene flow from lineages more closely related to the Taymyr individuals to the modern lineages. This gene flow has to be very close to the root of the origination of modern domestic horses since all breeds are equally represented in the signal of admixture. In short, the modern lineages of horse, wild and domestic, are but a fraction of the variation of the ancient populations.

They confirm this in a population genomic sense by looking at the enrichment for deleterious mutations. A major confound is that many lineages of horse are inbred, so they corrected for that. It turns out that all modern horses exhibit signs of being subject to a load due to accumulation of deleterious variants because of small population size (specifically, bottlenecks), as selection is less efficient at removing these mutations in small population because it is overwhelmed by random drift.

Finally, there is a lot in the paper on signals of selection around various causal alleles. It’s the typical laundry list. Many of the genes are associated with various pathologies and abnormalities, which shows you the cost of reshaping organisms and their behaviors which can occur due to domestication. Strong selection on major effect alleles often result in a cost due to antagonistic pleiotropy. If the selection benefit is high, then negative consequences be damned! Now, horses are notoriously dumb compared to donkeys, so I’d be curious if the cognitive/behavioral signals are found in humans and other mammals, and how they may have changed over time.

• Category: Science • Tags: Domestication 

I guess this is taking “world music” to the next level, going back to the ancient Mesopotamians. The artist is Stef Conner, and you can read about how this reconstruction was done over at Newsweek, where there is a Soundcloud preview of her full album, The Flood. I’d actually purchase it if I could find a full digital copy, but I don’t see any out there right now (the article says it will be on iTunes next month). You can buy a physical copy at her website, but the last time I purchased a C.D. was probably in the early 2000s, so that’s not happening. Anyway, do listen the preview on Soundcloud. The drinking song above is probably not representative.

• Category: Miscellaneous • Tags: Culture 

513367 In my books list below I tried to not focus too much on evolutionary genetics and genomics. But I still feel that I was a bit narrow. Over the years my interest in science has become rather narrow because of professional focus, but when I was younger I used to read quite a bit of popular physics, such as John Gribbin’s In Search of Schrodinger’s Cat. This sort of narrowing of focus is probably inevitable, but still pretty worrying for me. Probably the last popular physics book which I read front to back was Lee Smolin’s The Trouble With Physics, nearly 8 years ago.

In other news, I’m going to try and take a break from the internet for a few days around the New Year. More precisely, I’m going to try and take a vacation with my growing family somewhere sunny and hopefully warm. We’ll see how that works out. But please don’t be concerned if I don’t post on Twitter or have a blog update for a few days +/- January 1st of 2015.

• Category: Miscellaneous 

Founder of the Royal Society

Founder of the Royal Society

A few years ago Joe Pickrell wrote a very influential post, The first steps towards a modern system of scientific publication. Influential because it seems have to been a reason for the development of SciReader.The developers behind PubChase also took some lessons from it. Of course we know the role that “open access” and PLOS have played in shifting the ecosystem of the consumption and production of scientific knowledge (if you don’t know what I’m talking about, an Eisen will enlighten). And Haldane’s Sieve has been instrumental in bringing preprints to biology (in particular, evolutionary biology and genomics). Finally, events like the Bay Area Population Genomics meetings fill the gap between inter-personal relationships which are critical to scientific production, and massive conferences which have an enormous overhead in implementation for the organizers and non-trivial cost of attendance for the conference-goers.

a190So is there more to say? I think so. That’s why something I wrote with Laurie Goodman and David Mittleman just dropped in Genome Biology, Dragging scientific publishing into the 21st century. It’s open access, you can read it all, and I encourage you to do so. The question that framed my thought was a simple one: how can scientific publishing become more than simply a PDF delivery platform? Using the internet to deliver PDFs is like using a gasoline engine to draw a conventional carriage designed with horses in mind. And it’s feasible because scientific publishing is a profitable field dominated by a comfortable oligopoly which captures rents from the institutional structure of modern science. Remember, high impact journals are not high impact because they provide a better experience for scientists, who are the producers and consumers of the product. They’re high impact because they are high impact, and as long as they are high impact people will need to publish in them to gain scientific credibility and prestige. Many researchers would label this a vicious circle. There’s a reason that they call Science, Nature, and Cell “glamor mags.” It’s about being seen. Ultimately, a matter of fashion, not substance.

What can not continue, will not continue. There isn’t a need to talk about creative destruction today as if it’s a novel concept, we’ve seen “smartphones” swallow the functionality of whole industries (e.g., watches and cameras), and it seems inevitable that ride-sharing will radically transform the nature of the taxi industry in the United States. I hold that the dominance and profitability of scientific publishing firms today is in large part a function of norms within modern science which enable and perpetuate a coordination problem. Once the norm starts shifting, it will change very fast, because many of the people who are publishing in the glamour magazines only do so begrudgingly because they feel they have to.

So is there a future for organizations such as the Nature Publishing Group? I think there is. The key is to take more to heart the idea that scientists are their customers. I don’t think the sector will be as awash in money in the future, so it needs to be leaner and more efficient. Publishers need to really start innovating so that scientists don’t just focus on something like “impact factor,” but also questions such as “is this journal going to package and present my results in a way that communicate well with my colleagues?” In other words, one needs to focus on the substance of what scientific publishing is supposed to be about, beyond obtaining a tenure track position, the furtherance of mutual understanding! Second, the journals can also invest in sharpening their style so that they always maintain some value-add over spare operations such as preprint servers. The ecosystem of scientific communication will remain vast, but it will evolve. Scientific publishers need to reposition themselves into a smaller but more specialized niche soon, because the market is likely to shift underneath their feet before they know it.

• Category: Science • Tags: Publishing 

41PHSZN6AEL My friend Randall Parker sent me an email where he suggested I should put up a post relating to books for the holidays. This makes sense, since I’m a book nerd. Over the years I’ve started to realize time is precious, and have offloaded a lot of the hard work of figuring out things to others who have domain specific specialties (e.g., I have friends who are into nutrition or exercise, and rely on them to give me appropriate pointers and direction). As implied by the title I’ll probably try and do this every year now. Also, I’ll avoid textbooks in the following list, and will attempt to be more diverse in my disciplinary focus than usual….

The Genetical Theory of Natural Selection. The variorum edition from 1958 with J. H. Bennett is what you want. R. A. Fisher is dense, but this isn’t a textbook. If you understand 10%, that’s a lot of understanding.

The Isles. Norman Davies’ magisterial narrative history of the British Isles.

In Gods We Trust. You won’t look at religion the same way after.

kwonhardcoverKnowledge and the Wealth of Nations. All about endogenous growth theory and its origins. More interesting than it sounds. As important as it sounds.

From Plato to NATO. This book has had many lesser copycats.

The Truth About Everything. A history of western philosophy. It has illustrations.

Prehistory of the Mind. Underrated hybrid of evolutionary psychology and paleoanthropology.

The Fall of Rome. A materialist take on the decline and fall of the Roman Empire. I’ve read this book three times.

The Number Sense. Like The Language Instinct for numeracy.

What_Hath_God_Wrought_-_The_Transformation_of_AmericaWhat Hath God Wrought. An anti-Jacksonian history of early America.

When Genius Failed. The template for “too big to fail.”

The Imitation Factor. Great short read on behavioral ecology.

Mutants. Armand Leroi can write beautifully even about the grotesque.

Descartes’ Baby. The child is the father of the man.

downloadCalculus Made Easy. This is an old and chatty book. It’s not a text.

A Beautiful Math. Game theory and John Nash’s science.

Grand New Party. Not the Tea Party.

Genome. Compulsively readable.

The Human Web. One of William H. McNeill’s later books.

From Dawn to Decadence. Jacques Barzun’s magnum opus.

Readers are invited to offer their list of 20 in the comments. Randall has been challenged to put one up at his blog. Though I hope people will try and make the books at least somewhat accessible and relevant to a general intelligent audience (e.g., no books on Design Patterns or The Art of Computer Programming).

• Category: Miscellaneous • Tags: Books 


Sometimes results precede an appropriate interpretative framework. I am beginning to think that that was the case with the explosion in analysis of Y and mtDNA phylogenies around the year 2000. This was a research program which took the direct male (Y) and female (mtDNA) lineages of humans, inferred a phylogenetic tree, and drew historical and demographic inferences. Part of the reason that this research program flourished is that these lineages are easy to model as a tree, because there isn’t recombination and sex on these lineages. The genealogy of these markers is actually a straightforward tree. And, in the case of mtDNA it is copious, so extraction was and is relatively easy.

The_Journey_of_Man_-_A_Genetic_Odyssey This period not only resulted in an explosion of research, but also several seminal popularizations, in particular Spencer Wells’ Journey of Man, Bryan Sykes’ Seven Daughters of Eve, and Steve Olson’s Mapping Human History. The way this method worked involved taking the distributions and diversity of particular Y and mtDNA lineages present in the world today, and inferring back to the past routes of human expansions assuming that the tree-like model of genetic fission reflected a serial founder process of human migration. On the largest scale this work did confirm and extend previous research which implied a dominant signal “Out of Africa,” as well as broad geographic racial clusters. But on a finer scale the method likely led us astray, in large part because it seems that the model of human expansion and diversification was just too simple. Empirically, the rise of whole-genome analysis via SNP-chips in the middle years of the 2000s and today ancient DNA has revolutionized and clarified our understanding of the human past. Many of the inferences made from Y and mtDNA turn out to be wrong, even if the original results are broadly robust.

And that is a key point, because the original Y and mtDNA results are correct, and there has been an enormous body of research already in this area, they can be leveraged in understanding the human past when slotted into the framework sculpted on the edges by autosomal SNP data and ancient DNA. A serial founder model where the tree-like phylogeny was recapitulated spatially and temporally always had “anomalies.” In light of new results those anomalies may actually make much more sense. In particular, the common lineages which span Sub-Saharan Africa and western Eurasia (e.g., R1b above) are less perplexing in light of a model of periodic Eurasian back migration after the initial Out of Africa event. Admixture between long distinct lineages resolves issues relating to haplogroups with discordant geographic distributions. As long a the results are correct and methodologically sound, more data is better.

• Category: Science • Tags: Historical Population Genetics 
Jalkh, Nadine, et al. "Genome-wide inbreeding estimation within Lebanese communities using SNP arrays." European Journal of Human Genetics (2014).

Jalkh, Nadine, et al. “Genome-wide inbreeding estimation within Lebanese communities using SNP arrays.” European Journal of Human Genetics (2014)., SH = Shia, MA = Maronite, GO = Greek Orthodox, SU = Sunni

The term “eugenics” has very negative connotations today. Nevertheless, in some ways society is moving in a direction which results in “eugenical” outcomes, insofar as allele frequencies and genotypes are skewed from what would otherwise be the case if natural processes operated without human volition.* Probably the most obvious case in modern medicine is the high rate of abortion of fetuses which are inferred to carry the genetic profile of an individual with Down Syndrome. In the future this sort of instance will be more general, as high quality prenatal genome sequencing along with progress toward understanding of the basis of inheritance of Mendelian diseases will avail parents of many choices. This will naturally result in a lot of discussion and debate about ethics and values.

But there is a less high-tech and ethically fraught form of eugenics, which is nevertheless culturally controversial. One of the overlooked aspects of the 2009 paper Reconstructing Indian population history is that it found that many Indian populations had an excess of homozygosity, likely due to long standing endogamous practices encouraged by the caste system. This, despite customs which enforce exogamy for Hindus across much of India, in particular the North. Within the abstract the authors suggest then that “there will be an excess of recessive diseases in India.” Recently I spoke to a young woman of Jat background whose parents are very traditional. I told her the issue relating to homozygosity, and communicated that to gain the benefits of masking genetic load one need not go genetically and culturally very far. An individual of the same ethnicity and religion would be sufficient, so long as they were not of the same caste (jati).**

This is not only a South Asian issue, as evident in a recent paper in The European Journal of Human Genetics, Genotyping of geographically diverse Druze trios reveals substructure and a recent bottleneck. Following up on earlier work it confirms some structure within the Lebanese Arab population. This should not be surprising, as the distribution of ethno-religious groups within Lebanon is not geographically arbitrary. Whether they live in Beruit today, the Maronite Christians for example often have a ancestral background from around Mount Lebanon. Additionally, the Muslim groups within Lebanon have been subject to a proportion of admixture with foreign populations over the past ~1,000 years. Nevertheless, it does seem that overall the Lebanese of all sects derive from a common ancestral group, and exhibit more affinities with each other on the whole than with non-Lebanese populations (the Druze have been subject to a stronger bottleneck than the other sects, explaining why they are distinct genetically).

In any case, the major finding in these results is that there are elvated levels of homozygosity in individuals who are Lebanese who are the product of marriages between “unrelated” parents. Additionally, individuals of Muslim background who are the product of first cousin marriages show evidence of being descended from common ancestors recently across multiple paths, suggesting a more ubiquitous practice of cousin marriage within this group. This mean that “first cousins” in the Muslim community often exhibit a relatedness greater than that of idealized first cousins because they are part of an extended inbred lineage.

ROH In the figure to the right you can see the distribution of runs of homozygosity for different Lebanese sects comparing individuals who are the product of unrelated parents and those who are first cousin offspring (against a reference set of Europeans). You note that in the 0.5 to 1 Mb range of homozygosity tract length Europeans are highly enriched in comparison to Arab Lebanese. This is almost certainly due to the bottlenecks that Europeans have been subject to over the past ~50,000 years. Most Middle Eastern populations a priori should have a higher long term effective population size assuming a serial founder effect, as well as the ecological context of the Ice Ages. But at 1-2 Mb you see that long term inbreeding shows up in all the Lebanese groups. Notice that the further you go up in tract length the more unequal the ratio between the first cousin offspring (FCO) and those who are the products of “unrelated individuals” (URO). This is what you expect. But even at greater than 16 Mb you see that Lebanese who are unrelated still have many more of these segments than Europeans. This is a major tell that cryptic relatedness is a bigger issue within the Lebanese population than among Europeans.

Shakira, half-Lebanese

Shakira, half-Lebanese

The recommendation here then would be simple: Lebanese Arabs should marry individuals who are culturally aligned with them (e.g., Greek Orthodox Lebanese marrying Greek Orthodox Palestinians, Maronites with individuals from other Arab Christian groups in alignment with Rome, etc.), but have a different genetic history. This shouldn’t be controversial, but it can be (e.g., warning about the dangers of cousin marriage in terms of birth defects has resulted in accusations of Islamopobhia in Britain because of the power of identity politics in a multicultural society). Yet to some extent I believe that first cousin marriages will decline throughout the Middle East because of the demographic transition. If you don’t have many first cousins, then the potential for first cousin marriages declines greatly. But as I noted above in many Indian Hindu groups exogamy is normative, but there is still an issue with elevated homozygosity, so even without first cousin marriages there could be some gains in utility on the margin from outbreeding further than just near relatives.

Finally, aside from the straightforward genetic issues, there may be social benefits to the breakdown of clan structures which are the driving force behind population wide elevated homozygosity. Keeping it “all in the family” may not be conducive to broader national trust and cohesion. Readers probably know enough about the modern Middle East so that I don’t need to elaborate on this issue angle….

* In a narrow sense eugenics should actually result in allele frequency changes, but in modern practice this is not always the case. E.g., the screening for individuals with Tay-Sachs carrier alleles changes the genotype frequency in the population so it is not in Hardy-Weinberg Equilibrium.

** Another thing that might be feasible to be to attempt to infer potential enrichment of homozygosity by looking at genotypes of pairs of potential mates within the same caste.

• Category: Science • Tags: Arab genetics, Inbreeding 

Nice review, Advances and limits of using population genetics to understand local adaptation. In particular the focus here is on the insights one can derive from new genomic methods (e.g., think of SFS analysis). But they on a cautious, perhaps even down, note:

Many of the important questions in local adaptation being pursued with population genetics approaches begin – rather than end – with identifying loci responsible for variation. It is therefore important to realize that a full accounting of local adaptation at the molecular level goes beyond having high-quality data to analyze and statistical methods to identify causative genes. The crux of the challenge is that most ecologically important traits responsible for local adaptation are quantitative, and identifying all of the genes responsible for variation in quantitative traits is likely not possible. Even the cumulative explanatory power of individual loci identified in human genotype–phenotype association studies, which often involve tens of thousands of individuals, is generally only a small percentage of the phenotypic variation….

But I want to note that they cite a paper from 2012, and the work in capturing the fraction of phenotypic variation from genomic variation for height has gotten much better since then. So perhaps in that way that is a reason for optimism. Though, as they note, humans are a best case scenario since the sample sizes are enormous. Just a nice reminder of the limitations of the ‘post-genomic’ era.

• Category: Science • Tags: Population Genetics 

9780226520438 A very fertile area of evolutionary science is the understanding and modeling of human culture. But it’s hard, which is why my aspiration is to be an evolutionary geneticist in a more classical sense. Not only is it hard, but people don’t appreciate it, because they think they understand “culture.” Robert Boyd and Peter Richerson’s The Origin and Evolution of Cultures is an excellent introduction (with Not by Genes Alone for a more popular audience), but Alex Mesoudi’s Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences is a more recent survey which I think is very worthwhile. 0226712842 Complementary to the modelers, who draw from classical genetic frameworks (going back to Cultural Transmission and Evolution by Cavalli-Sforza and Feldman), are the cognitive anthropologists, represented by Dan Sperber and his colleagues (Explaining Culture: A Naturalistic Approach). Another way to look at this is that it is cultural anthropology without the Post-Modern Voodoo. In other words, it strives for disciplinary relevance through a fidelity to reality, rather than political and social impact.

This is all to highly recommend you read an excellent post on cultural evolution, Why Cultural Evolution Is Real (And What It Is). I don’t link to blogs much because it is usually more useful to read the paper, or the book, but in this case I think the writer really reduced the essentials of the field down to a manageable extent. Hopefully it will encourage readers to pursue their own avenues of inquiry.

• Category: Science • Tags: Cultural Evolution 

Adapted from Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

It is common for strong results from population genetics to be confused when it is translated for public consumption. The best example is that of “mtDNA Eve.” Despite the big warning label that mtDNA Eve is one of many female ancestors, the public has gained the impression that she is the female ancestor. A similar problem is cropping up with the Khoisan paper which reports that they went through a relatively mild bottleneck in comparison to other modern human populations. There’s a reason I titled the post The Least Bottlenecked Humans of All. It’s a defensible reduction of the results. In contrast many popular treatments are translating the results into the conclusion that “the Khoisan had the largest population of all human groups at some point in the past.” The reason I avoided this formulation is that plainly stated I doubt that at any time the Khoisan as we understand them, a genetically-culturally coherent group in southern Africa, had the largest population of all. Humans of various sorts have been common across Afro-Eurasia for over a million years. Is it plausible that ancestors of the Khoisan had the largest populations of all? Anne Gibbon’s somewhat cautiously stated piece in Science, Dwindling African tribe may have been most populous group on planet, relays the sentiment which I share:

Other researchers agree that it’s likely that the Khoisan descend from a large population. But because sampling of African genomes is still so spotty, not everyone is yet convinced that the Khoisan “was the largest population on Earth at some point,” says evolutionary geneticist Pontus Skoglund of Harvard University. “Many African populations are not included for comparison,” he says, so it is possible that some of the diversity seen in the Khoisan was inherited from recent interbreeding that cannot yet be detected.

Either way, the study makes it clear that even though the Khoisan are genetically diverse by today’s standards, even they carry just a fraction of our ancestors’ genetic legacy over the past 120,000 years. “It is quite staggering how much extraordinary genetic variation and ethnic diversity was present but is now lost,” Skoglund says. The Khoisan, retaining more than the rest of us, offer a rare window to look back in time at some of that diversity.

The biggest gap in the current study is that many extinct lineages were not included. Obviously they couldn’t be included, because they’re extinct, though at some point in the future ancient DNA or (more likely in the African context) reconstruction of ancient genomes from extant populations which have absorbed them, might allow for a better understanding of Pleistocene human population sizes. Population genomics is powerful, but it has limits. We need to be cautious about assuming that what we can illuminate with current methods is all that can be conceived in our natural philosophy.

• Category: Science • Tags: Genetics, Khoisan, Population genomics 
Citation: The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades

Citation: The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades

There’s a new open access paper on human Y chromosome phylogenies, The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades, which is just as interesting because of a reference than the paper itself. The paper cited is “Batini, C, P Hallast, D Zadik, et al. submitted. Large-scale recent expansion of European patrilineages shown by population resequencing. Nature Comms.” As I’ve mentioned earlier it was clear from several posters at ASHG that whole genome sequencing of larger sample sizes is making much more clear how recent and rapid the expansion of several of the common lineages across Eurasia was. In particular I’m thinking of R1a and R1b. We know this already from earlier work, but these latest results just confirm it. The truth is visually obviously. Notice in the figure above how R1b fans out in an instant from a single node. This reflects recent rapid population expansion.

The_Journey_of_Man_-_A_Genetic_Odyssey But when The Journey of Man and The Seven Daughters of Eve were being written in the early 2000s it was assumed that Y and mtDNA phylogenies could tell us about human prehistory in totality. In hindsight that was probably asking for too much. But because they are sex specific these two lineages can inform us a great deal about social structures. In particular, rapid expansion of Y chromosomal lineages in the recent past may indicate the rise of patriarchy, as powerful males began to see polygyny as a viable strategy due to their monopolization of the resources of whole societies.

If I had to predict, I believe that female lineages tend to be characterized by isolation by distance dynamics. In contrast, male lineages are pruned periodically by rapid expansions and admixtures by groups which are able to marginalize or exterminate competitors over vast swaths of territory. The Genghis Khan effect is just the most prominent of this sort of phenomenon. It is certain that in prehistory this occurred as well, as new technologies such as agricultural triggered social revolutions, and the rise of specialization and stratification among humans.

• Category: Science • Tags: Y Chromosome 
Razib Khan
About Razib Khan

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