The Pith: The human X chromosome is subject to more pressure from natural selection, resulting in less genetic diversity. But, the differences in diversity of X chromosomes across human populations seem to be more a function of population history than differences in the power of natural selection across those populations.

In the past few years there has been a finding that the human X chromosome exhibits less genetic diversity than the non-sex regions of the genome, the autosome. Why? On the face of it this might seem inexplicable, but a few basic structural factors derived from the architecture of the human genome present themselves.

First, in males the X chromosome is hemizygous, rendering it more exposed to selection. This is rather straightforward once you move beyond the jargon. Human males have only one copy of genes which express on the X chromosome, because they have only one X chromosome. In contrast, females have two X chromosomes. This is the reason why sex linked traits in humans are disproportionately male. For genes on the X chromosome women can be carriers of many diseases because they have two copies of a gene, and one copy may be functional. In contrast, a male has only a functional or nonfunctional version of the gene, because he has one copy on the X chromosome. This is different from the case on the autosome, where both males and females have two copies of every gene.

This structural divergence matters for the selective dynamics operative upon the X chromosome vs. the autosome. On the autosome recessive traits pay far less of a cost in terms of fitness than they do on the X chromosome, because in the case of the latter they’re much more often exposed to natural selection via males. In the rest of the genome recessive traits only pay the cost of their shortcomings when they’re present as two copies in an individual, homozygotes. A simple quasi-formal example illustrates the process.

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The media has been reporting a lot about Anders Breivik. I’m curious about the tendency of some to label Breivik a “Christian Extremist”. Additionally, there is widespread repetition of the Norwegian official deeming him a “Christian fundamentalist.” I think this is wrong on the specifics, but it also goes toward the general problem of our age where we attempt to fit everything into black-white religious dichotomies. For example, “moderate Muslims” vs. “Islamists.” “Islamic extremists” vs. “Christian extremists.” Because of the salience of notionally religiously motivated Islamic militant movements there has been a shift toward reinterpreting secular nationalist terrorist movements as religious ones. For example, the attempt to frame the Irish Republican Army as Catholic terrorists, or the Tamil Tigers as Hindu terrorists (in reality, both these are nationalist movements, often with a Leftist slant). Or consider the refashioning of Tim McVeigh into a Christian terrorist when he was a lapsed Catholic at best and probably irreligious by the time of his terrorist act. This religionization of all radical movements means that people have a really hard time today digesting the fact that 19th and early 20th century anarchists who committed what seem to be patently suicidal acts were generally atheists, motivated by politics and not religion! Similarly, the shocking raid on Harpers Ferry was executed by a cast of characters of diverse religious views. John Brown was famously Calvinist, but some of his followers, including one of his sons, were free thinkers who did not adhere to religion.

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If you have not read my post “To the antipode of Asia”, this might be a good time to do so if you are unfamiliar with the history, prehistory, and ethnography of mainland Southeast Asia. In this post I will focus on mainland Southeast Asia, and how it relates implicitly to India and China genetically, and what inferences we can make about demography and history. Though I will touch upon the Malay peninsula in the preliminary results, I have removed the Indonesian and Philippine samples from the data set in totality. This means that in this post I will not touch upon spread of the Austronesians.

I present before you two tentative questions:

– What was the relationship of the spread of Indic culture to Indic genes in mainland Southeast Asia before 1000 A.D.?

– What was the relationship of the spread of Tai culture to Tai genes in mainland Southeast Asia after 1000 A.D.?

The two maps above show the distribution of Austro-Asiatic and Tai languages in mainland Southeast Asia. Observe that when you join the two together in a union they cover much of the eastern 2/3 of mainland Southeast Asia. The fragmented nature of Austro-Asiatic languages in the northern region, edging into the People’s Republic of China, implies to us immediately that it is likely that in the past there was a continuous zone of Austro-Asiatic speech in this region. From the histories and mythologies of the Tai people we know that this group migrated from the southern fringes of China around ~1000 A.D. This is obvious when we note that there are still Tai people in southern China, and the expansion of the Tai across what is today Thailand is to some extent historically attested. Between 1000 and 1500 there was a wholesale ethnic reorganization of the Chao Phray river basin. Was that a matter of demographic replacement, or cultural assimilation, or some of both?

Second, what was the impact of Indians upon mainland Southeast Asia? One of the easiest ways to ascertain Indian influence is script. Burmese, Thai and Cambodian scripts all derive from Grantha, an archaic Tamil script (non-Islamic scripts in island Southeast Asia, such as Javanese and Balinese, are also derive from South Indian precursors). The Indian religious influences also are more southern than northern, manifesting in the southern forms of Shaivite Hinduism and Sri Lankan Theravada Buddhism.

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I have posted on the existence of blonde hair amongst some Melanesians before. There are natural chemical treatments as well as extreme malnutrition which can result in blonde hair in dark skinned people. The latter seems unlikely from the photos I’ve seen (the lightening of hair due to lack of food has been reported in African refugee camps). In regards to the former I’m confused as to why chemical treatments would be common among Oceanian people as disparate as Solomon Islanders and central desert Australian Aborigines, and yet not among many other east Eurasian populations.

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Amos Zeeberg, the person you should pester (hopefully ineffectually!) when I’m not being nice to you in the comments, has an interesting opinion piece up lambasting the Shuttle program. Here are the numbers which jumped out at me (I knew the broad outlines, but nice to have precise numbers):

The most important thing to realize about the space shuttle program is that it is objectively a failure. The shuttle was billed as a reusable craft that could frequently, safely, and cheaply bring people and payloads to low Earth orbit. NASA originally said the shuttles could handle 65 launches per year; the most launches it actually did in a year was nine; over the life of the program, it averaged five per year. NASA predicted each shuttle launch would cost $50 million; they actually averaged $450 million. NASA administrators said the risk of catastrophic failure was around one in 100,000; NASA engineers put the number closer to one in a hundred; a more recent report from NASA said the risk on early flights was one in nine. The failure rate was two out of 135 in the tests that matter most.

To take the intangible value of human life out of the question, if we were going on the cheap then a 2 out of 135 failure right might be understandable. But we weren’t. The shuttle cost a lot. To whom much is given (in dollars) much shall be expected. It didn’t live up to the expectations.

In an unrelated vein, I wonder if the aging of the earth’s population is going to put a damper on space exploration in the short term. The explorers of the future are more likely to be de facto intelligent robots.

1) Post from the past: Religion & IQ.

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I don’t give much thought to chimeras, so this editorial in Nature took me unawares (OA): The legacy of Doctor Moreau:

Innumerable mice and other animals have been engineered in past decades to express a human gene and model specific aspects of human disease. They rarely inspire disgust, because they still resemble their own species. But further advances in genetic and stem-cell technologies mean that researchers could, in theory, create animals with quintessentially human characteristics or behaviours. The sight of an animal with shiny, furless ‘human’ skin, for example — exceptionally useful for research into skin disorders — could evoke disgust similar to that created by Moreau’s beast folk, even though the animal itself might be perfectly comfortable. One of the biggest horrors — although technically unlikely — could be a self-aware monkey, a creature with human thought trapped in the body of an animal, unable to express itself.

Perception, the ‘optics,’ matters. I think there are going to be serious issues if chimeras resemble humans. It’s just too good for video not to trigger outrage. More subtle hybridizations which are less phenotypically salient though….

Negrito, Philippines. Credit: Ken Ilio

In the post below I mentioned that the Malaysian and Philippine Negritos seem to be two very distinct populations. This was something I wanted to explore in more detail, so I naturally decided to poke around the Pan-Asian SNP data set. The aims are made somewhat more difficult by the fact that there are only ~56,000 markers in the data set (as opposed to ~600,000 in the HGDP and more than 1 million in the HapMap). Additionally, the intersection with other data sets is small. For example, only ~20,000 SNPs with the HGDP. With all that in mind I hazarded that something is better than nothing. Relatives and HapMap populations were removed from the data set (thanks Zack). Additionally, I beefed up the South Asian populations with the Gujaratis from the HapMap,which had an intersection of ~32,000 SNPs. After a few test runs I decided to remove the Mlabri. They always shook out very early as a separate population from many others nearby, and, their genetic distances were very high. This tribe is only numbered in the hundreds, and I wouldn’t be surprised if they’ve been subjected to a lot of population bottlenecks, resulting in some very distinctive allele frequencies.

But before I move to the results, let’s back up for a moment. Who are the “Negritos”? As suggested by the term Negrito refers to a range of populations which are characterized by small size and African-like features (very dark skin and frizzy hair). In general their distribution is limited to Southeast Asia (there are suggestions that a Negrito population may only recently have gone extinct in Australia’s rainforests, but that’s speculative. On a more antique scale there are records which may be interpreted to suggest the existence of Negritos in Taiwan as late as 1900, and in southern China within the past 1,000 years). So you can bracket their distribution from the Andaman Islands to the Philippines, with isolated groups in the Malay peninsula. Negritos are presumed to be the original inhabitants of Southeast Asia before the arrival of rice farmers from the north. Like the Pygmies of Africa most of the Negritos speak languages whic hare known in other populations. Those of the Philippines speak Austronesian dialects. Interestingly those of Malaysia speak an Austro-Asiatic language, and so have affinities with many groups to their north linguistically, being surrounded by Austronesian speakers. Only the Andaman Islanders have a distinctive language, which makes sense seeing as how they have been relatively isolated from mainland Asian influences.

I ran ADMIXTURE from K = 4 to K = 12. K = 8 seemed the most informative to me (at higher K’s the major dynamic is that the Philippine Negritos start fragmenting into many distinct clusters). I’ve made a few cosmetic changes. With this East and Southeast Asia heavy data set there’s almost no difference between all the various Indian groups, so I amalgamated them together. I also did the same for related populations geographically adjacent which exhibited no genetic difference (e.g., Central and East Javanese).

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I mentioned offhand to Trey of Genomes Are Us that I’d look around for the effect of adoptive environments on criminality (what with the recent concern about studying the genetics of criminal predisposition). Luckily I have Steve Hsu in my RSS, as he posted something of interest just yesterday, pointing me to this paper, The environments of adopted and non-adopted youth: evidence on range restriction from the Sibling Interaction and Behavior Study (SIBS):

Previous reviews of the literature have suggested that shared environmental effects may be underestimated in adoption studies because adopted individuals are exposed to a restricted range of family environments. A sample of 409 adoptive and 208 non-adoptive families from the Sibling Interaction and Behavior Study (SIBS) was used to identify the environmental dimensions on which adoptive families show greatest restriction and to determine the effect of this restriction on estimates of the adoptive sibling correlation. Relative to non-adoptive families, adoptive families experienced a 41% reduction of variance in parent disinhibitory psychopathology and an 18% reduction of variance in socioeconomic status (SES). There was limited evidence for range restriction in exposure to bad peer models, parent depression, or family climate. However, restriction in range in parent disinhibitory psychopathology and family SES had no effect on adoptive-sibling correlations for delinquency, drug use, and IQ. These data support the use of adoption studies to obtain direct estimates of the importance of shared environmental effects on psychological development.

The technical issue here is that there’s long been the assumption that because adoptive families are pre-screened they’re a selection-biased environment which won’t exhibit the same environmental variance as the general population. This matters potentially for behavior genetics studies which use adopted children, as it might underestimate shared environmental effect (a robust behavior genetic finding that puzzles many is that most of the environmental effect is non-shared). I’m not too focused on this specific issue, but rather want to pass along two charts which might interest readers:

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A new paper in PLoS Biology is rather like the last person to leave turning the light off. Evolutionary psychology as we understood it in the 1980s and 1990s is over. Darwin in Mind: New Opportunities for Evolutionary Psychology:

None of the aforementioned scientific developments render evolutionary psychology unfeasible; they merely require that EP should change its daily practice. The key concepts of EP have led to a series of widely held assumptions (e.g., that human behaviour is unlikely to be adaptive in modern environments, that cognition is domain-specific, that there is a universal human nature), which with the benefit of hindsight we now know to be questionable. A modern EP would embrace a broader, more open, and multi-disciplinary theoretical framework, drawing on, rather than being isolated from, the full repertoire of knowledge and tools available in adjacent disciplines. Such a field would embrace the challenge of exploring empirically, for instance, to what extent human cognition is domain-general or domain specific, under what circumstances human behaviour is adaptive, how best to explain variation in human behaviour and cognition. The evidence from adjacent disciplines suggests that, if EP can reconsider its basic tenets, it will flourish as a scientific discipline.

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