Open Thread, 2/29/2016

I’m reading . Incredible how well it anticipated the behavior of the Cultural Revolution. Yes, I’ve read , and have just purchased .

The New York Times has a two part series on the decision to overthrow Gaddafi and Hillary’s involvement in it: Hillary Clinton, ‘Smart Power’ and a Dictator’s Fall, and A New Libya, With ‘Very Little Time Left’. I’m not a big fan of Barack Obama, but I appreciate his cautious and indecisive pattern in foreign policy. If we learn anything from George W. Bush’s presidency it’s that boldness can have long term consequences which we can’t foresee. It seems likely that Hillary will be president at this point, so we’re going back to neocon-lite liberal internationalism in all likelihood.

Paper of the week, Sex speeds adaptation by altering the dynamics of molecular evolution.

Interview with Nick Patterson on a machine learning podcast.

The American Quran Pissing Off the Saudis, referring to . It’s 2,000 pages. But the is still only ~$20. Pretty good.

I was talking to Justin Loe, and he admitted that Full Genomes might have more visibility in China than in the United States. Though their 30x sequences are $1,650, their 2x is $280. Now 2x may seem useless, but 35% of my readers have already done genotyping, so perhaps they can squeeze more juice out of combining the two data? The world we live in in terms of options….

I’m going to finally try and push out some non-blog content in the near future, so please remember to subscribe to my or follow me on .

is a much more compact book than . Recommended, though I’m not that convinced by the thesis proffered in the subtitle, there’s a lot of interesting information in the book which will be fodder for a future post. Also got Valerie Hansen’s , but who knows when I’m going to get to that?

Google searches for the secret sauce of asabiyyah

What Google Learned From Its Quest to Build the Perfect Team:

As the researchers studied the groups, however, they noticed two behaviors that all the good teams generally shared. First, on the good teams, members spoke in roughly the same proportion, a phenomenon the researchers referred to as ‘‘equality in distribution of conversational turn-taking.’’ On some teams, everyone spoke during each task; on others, leadership shifted among teammates from assignment to assignment. But in each case, by the end of the day, everyone had spoken roughly the same amount. ‘‘As long as everyone got a chance to talk, the team did well,’’ Woolley said. ‘‘But if only one person or a small group spoke all the time, the collective intelligence declined.’’

Second, the good teams all had high ‘‘average social sensitivity’’ — a fancy way of saying they were skilled at intuiting how others felt based on their tone of voice, their expressions and other nonverbal cues. One of the easiest ways to gauge social sensitivity is to show someone photos of people’s eyes and ask him or her to describe what the people are thinking or feeling — an exam known as the Reading the Mind in the Eyes test. People on the more successful teams in Woolley’s experiment scored above average on the Reading the Mind in the Eyes test. They seemed to know when someone was feeling upset or left out. People on the ineffective teams, in contrast, scored below average. They seemed, as a group, to have less sensitivity toward their colleagues.

Google also found that shared norms matter, but the details of the norms vary a great deal across high performing teams. Combine this with a modicum of a relatively flat egalitarian structure and enough social feedback mechanisms for the team to operative like an organism, and you have a “hive mind.” Of course, teams at a firm like Google are already selected for much more intelligent than average individuals, so there might be reasons why these factors loom so large, as the sum-of-the-parts are roughly equivalent across the company.

The last 10,000 years and the rise of patriarchy

In light of David Reich’s interview I have been thinking about how genetics will shed light on many questions in the near future, and what my particular expectations are. The interview prompts me to collect some of my thoughts into one place, and outline a tentative thesis that I’ve been pointing to for the past few years. My friend Greg Cochran wrote in the late aughts, and some of his predictions have come to pass (e.g., Neanderthal admixture, and likely adaptive introgression according to many analysts of the data).

Others have not, and one of those that needs to be heavily modified was the idea that a mutation for lactase persistence allowed for the Indo-European expansion. That is, the original Indo-Europeans were simply biologically superior at extracting calories from the land, and so succeeded due to that advantage (at least in large part). The ancient DNA tells a different story; the Indo-Europeans may have originated the mutation, but it came to be at higher frequency after their demographic replacement and absorption of the European first farmer populations. That is, genetics post-dated the cultural shift, rather than initiating it.

Though understanding the biological basis of human behavior remains important to me, over the past decade or so I have become more and more convinced that the missing piece of the puzzle of the last 10,000 years is about how cultural evolution produced civilization and altered patterns of human genetics, rather than the other way around. This is somewhat a change in tack for me. One of the reasons I refer to Richard Klein’s so much is that ten years ago the book’s thesis that a biological change in our cognitive architecture allowed for the “Out of Africa” expansion was moderately persuasive (also see Steven Mithen’s ). My acceptance was probably inadvertently tempered by the fact that Klein seemed to have only a rudimentary idea as to the details of formal evolutionary theory, appealing as he did to punctuated equilibrium.

It may be that anatomically modern humans changed in some fundamental way 50,000 years ago. But the bigger picture seems just too complicated to reduce in this fashion right now. Rather than focus how human culture was shaped by the genes, I am now more curious about how genes were shaped by human culture.

Last year a paper was published, A recent bottleneck of Y chromosome diversity coincides with a global change in culture, which reported that it seems that a major recent change had occurred in the composition of Y chromosomes of humans. These are basically records of paternal transmissions across the generations. Ancient DNA shows that many of the very common lineages only appear to have risen in frequency ~4,000 years ago. This was of course thousands of years after agriculture. One can’t reduce this simply to a shift in mode of production, and the demographic excess of farming societies.

I’m sure most of you can anticipate where I’m going here. The rise of pastoralism, and the emergence of a mobile arms-bearing males changed civilization. It wrecked civilization, but it also created civilization as we know it. If you read , you would already suspect that (or, books going back to the early 20th century). But even the author of that book was shocked by the demographic impact of the Indo-Europeans as evident in ancient DNA. And, anyone who looks at star-shaped phylogenies such as that for R1a1a would have a hard time explaining what might have caused such an explosion in anything but the vaguest detail.

My answer comes from Peter Turchin in . In  Azar Gat reports that more numerous armies are more likely to win any pairwise conflicts. But in Peter notes that Lanchester’s laws indicate that superiority with long range weapons on flat territory gives a much greater likelihood of victory to those groups who are more numerous than with simple near engagement on foot. The combination of this with horses to aid in mobility, and I believe you had a revolution on the Eurasian steppe where the outcomes of inter-group competition between coalitions of males became “winner-take-all” affairs.

Because of the inevitability of the drafting of the horse as a beast of burden and transport it was inevitable that the early adopters would undergo a cultural revolution, and trigger a high stakes series of inter-group competition. The winners of that elimination tournament are the Y chromosomes we see around us.* But between 2000 BC and 0 AD the winners decided to cash out, as a new stable equilibrium emerged. “Higher religion,” a shift toward monogamy, and reduced inter-group warfare due to the emergence of state monopoly on violence, was an exit strategy from the melee of the transition between the Neolithic and Iron Age (again, Peter Turchin has discussed this at length). The patriarchy forged on the steppe at the tip of the spear and on the chariot now decided to mature and accrue more cultural adaptations to prevent itself from eating its own young.

* Something similar happened between 1650 and 1850 in Europe. Who have guessed that by the 20th century English would have been the international language? First the British vanquished their Dutch commercial competitors, and slowly ground down preeminence of French political, military, and cultural power on the continent. A dynamic Europe was engaged in competition on a massive scale, and the victorious British obtained the empire upon which the sun never set.

A Portrait of the Blogger as a Young Man

artistAt the moment I am taking a break between non-internet related professional obligations. No real time to write something interesting, though I now plan to write a post with the tentative title of “the pagan kafir origins of Islam.” This, inspired by my quick reading of . I figured I should read this book before getting to . All part of my attempt to practice what I preach in obtaining a wide portfolio of quasi-competencies.

I have probably posted the picture to the left before. I don’t know. I was four years old in it. I’ve been revisiting old pictures of myself as my own children have been maturing. I can see my daughter particular right now when I look at these images. It’s all rather strange.

(for those of you curious as to my severe mien, it’s a cultural norm not to smile too much in pictures in Bangladesh, at least during that period)

Eugenics: the problem is coercion

f91f1ec3f20d34989c512b18aeed47caThe Washington Post has an op-ed up right now titled: What’s the difference between genetic engineering and eugenics? I will be frank and state that it’s not the clearest op-ed in my opinion, though to be fair the is a generalist, not a science writer. As I quipped on Twitter, the issue with eugenics is simple: the problem is coercion, and the rest is commentary. I understand that the public is wary and skeptical of CRISPR technology and preimplanation genetic diagnosis. The problem is that the public is also suspicious of food which has DNA in it. Genes are not magic, but that is hard to convince the person on the street. Whereof one does not know, thereof one must be suspicious.

I believe for there to be a clear discussion, one needs to take coercion off the table, and abolish its specter by stating that it just isn’t an option. Then we can have a real dialogue that gets beyond the superficiality induced by the shadow of genocide. For example, consider sentences such as the following from the op-ed above “editing genes for frivolous purposes such as increasing intelligence.” There are many technical reasons that it may not be possible to increase intelligence in the near future through genetic engineering. But would increasing one’s intelligence be frivolous? I don’t think so. Whether you agree with this project or not, it is a serious matter, and gets to the heart of what we value as human beings (or at least some of us). But the specter of genocide casts a pall on exploring these nuanced questions, and that is because of the past record of coercion in eugenics.

Erika Check Hayden, a science journalist, has a much more nuanced piece in Nature, Should you edit your children’s genes? Here are some passages that jumped out at me:

In January, Ruthie’s dad Ethan asked her whether she wished that her parents had corrected the gene responsible for her blindness before she was born. Ruthie didn’t hesitate before answering — no. Would she ever consider editing the genes of her own future children to help them to see? Again, Ruthie didn’t blink — no.

The answer made Ethan Weiss, a physician–scientist at the University of California, San Francisco, think. Weiss is well aware of the rapid developments in gene-editing technologies — techniques that could, theoretically, prevent children from being born with deadly disorders or with disabilities such as Ruthie’s. And he believes that if he had had the option to edit blindness out of Ruthie’s genes before she was born, he and his wife would have jumped at the chance. But now he thinks that would have been a mistake: doing so might have erased some of the things that make Ruthie special — her determination, for instance. Last season, when Ruthie had been the worst player on her basketball team, she had decided on her own to improve, and unbeknownst to her parents had been practising at every opportunity. Changing her disability, he suspects, “would have made us and her different in a way that we would have regretted”, he says. “That’s scary.”

Sandy Sufian, a historian of medicine and disability at the University of Illinois, agrees with MacArthur that CRISPR has the potential to become widely adopted, both because of the perception that it would save money that would otherwise be spent caring for disabled people and because of people’s fear of disability. But she questions the idea that eliminating such conditions will necessarily improve human life. Sufian has cystic fibrosis, a disease caused by mutations that render her lung cells more vulnerable to infection and disease. She spends 40 hours a week inhaling medicine to clear her lungs of mucus, exercising and undergoing physical therapy; others have to quit their jobs to make sufficient time for treatments. Yet given the option to edit cystic fibrosis out of her bloodline, Sufian wouldn’t do it. “There are some great things that come from having a genetic illness,” she says.

Garland-Thomson echoes that sentiment; she has one and a half arms and six fingers because of a condition called limb-reduction disorder. She says that she values traits in herself that she may have developed as adaptations to the condition: she is very sociable and wonders if that is because she’s had to learn to work hard to make others feel comfortable around her. “Any kinds of restrictions or limitations have created the opportunity for me to develop work-arounds,” Garland-Thomson says.

450px-FlagellantsThe great thing about taking coercion off the table is that people can have differing opinions. We can differ as to eudaimonia. But, to not put too fine a point on it, I think the world would be fine without cystic fibrosis, even if some great things come of it. We humans are good at making lemonade out of lemons, but Mendelian diseases are definitely low hanging fruit. The people who now have cystic fibrosis are made who they are by their experience of the disease, but if I had the power of the gods I would would abolish cystic fibrosis from their past and their children’s future. You can call me abominable to admit to such a thing, but it’s true. Greatness can come out of adversity, but defeating misery is not a reason to welcome its appearance in our midst. There’s a reason the cult of flagellants isn’t particularly popular.

Yes, having a disease can alter your life. The singer Bobby Darin knew that his life expectancy was short, so he operated in a sort of frenzy when not in poor health because he wanted to accomplish something before he passed on. But with all due respect to Splish Splash, I wouldn’t be sad if Darin had lived a more sedate and relaxed life because the Sword of Damocles wasn’t always hanging over him.


There is a common saying among people in the disability-rights community: “Nothing about us without us.” People with disabilities argue that scientists, policymakers and bioethicists should take steps to ensure that the CRISPR debate reflects what is best for patients and their families, to ensure its most humane use now and for future generations.

We can disagree on what is, and isn’t, humane. I think a future with far fewer Mendelian diseases, such as cystic fibrosis, is humane. If some consider me a monster for admitting this, then bring on the monstrosity I say! In the long run I think the we’ll win the argument.

David Reich interview on Edge

David Reich has a interview (with video) up at Edge. If you see someone featured on Edge, it’s usually because you’ll hear from them in the future.

There’s not too much that close readers of this weblog will find surprising. But it was interesting to see David explicitly assert that West Eurasian ancestral input into modern Indians was male mediated. This is clear if you compare the frequency of West Eurasian Y lineages (e.g., R1a1a) and the India specific M haplogroup. But I suspect that they’ve looked closely at X chromosomes, which spend 2/3 of their time in females, and these are probably enriched for Ancestral South Indian (ASI).

David emphasizes the admixture event that occurred on the order of ~3,000 years ago between Ancestral North Indians (ANI) and Ancestral South Indians (ASI) in the ethnogenesis of the genetic landscape of South Asia. But as I’ve stated here before I believe that the West Eurasian admixture pre-dates this. In particular, I believe that the Dravidian languages probably have a West Asian provenance. So here’s a revised model of what happened in South Asia. First, the West Asian intrusion resulted in a mixed population during the period of the Indus Valley civilization. But this was limited to the northwest corner of the subcontinent. It was with the arrival of the Indo-Aryan cultural toolkit that the rest of India, inhabited by predominantly ASI populations, was opened up to demographic expansion from the Northwest. Note that this does not mean that most of the ancestry was derived from the steppe.* Just that the intrusion for the steppe may have triggered a cultural shift which reshaped the landscape, rather like how the arrival of Huns on the Roman frontier triggered folk wanderings by German and Iranic (Sarmatian) peoples.

* I don’t know if David misspoke, but he stated that Ancient North Eurasians contributed a lot of ancestry to Indians.

Open Thread, 2/22/2016

A debate broke out in the comments as to the natures of Western and Chinese culture over the long run. There is a problem in any of these discussions because very few people are conversant in both sides of the coin, so to speak. When it comes to cross-cultural comparisons outside of a very narrow set of people mostly you deal in the true but superficial or trivial. E.g., China has had less of a focus on a synthesis between confessional religious cults that encompassed all of society from the top to the bottom than the West and Islam (and Indian culture depending on how you define what became Hinduism). But the deeper question is what does this really mean and what are the implications? To work that out requires more than what you might learn on Wikipedia. One might say, for example, that the Chinese are less religious than Westerners. This is a assertion about deep and consequential aspects of culture. But it can be easily problematized. In particular, what does “religious” mean? Certainly institutional and monopolistic organized religion is less salient a characteristic of the Chinese, and East Asian landscape more generally. But it is often stated that in contrast that the Chinese are quite “superstitious.” If you define religious as indicative of a bundle of deep intuitions about the universe the Chinese may be just as religious as Westerners.

Ultimately there’s really no way around getting at these issues but muddling through the scholarship and expanding one’s own personal experiences. Obviously most of us have only a minimal ability to digest monographs steeped in assumptions about familiarity with primary sources, but works such as Harold Tanner’s are essential to bridge the gap between academicians and those who dabble on Wikipedia. Another way to fill the gap is theory. For example, on a priori grounds I’m skeptical of those who make broad and grand assertions about cultural differences now because cognitive science tends to tell us that such differences are often subtle, and, highly situational.

I’ll be posting on 1000 Genomes data more soon time permitting.

Dienekes’ post, Are living Africans nested within Eurasian genetic variation (?) is worth a read. Probably my main question is how to account for the fact that most of non-African ancestry does seem to date to an expansion 60,000 years ago. The idea that pre-Out of Africa modern humans left little genetic impact is not totally implausible. But I’m not sure it is probable.

Been rather busy last week or so, so that’s it for now.

South Asians in the 1000 Genomes

brownFor a while I’ve been playing around with 1000 Genomes South Asian data. It’s an interesting exercise, because unlike other South Asian data set it’s relatively generic with minimal ethnic/caste labels. This is important because unlike other population groups that the 1000 Genomes has sampled, such as in Africa, Europe, and East Asia, the South Asian data exhibit genetic structure beyond their ethno-linguistic identity. For example, the “Telugu” and “Tamil” data in the 1000 Genomes both contain individuals who are clearly Brahmins. This is obvious because these individuals are positioned on the margins of northern South Asian groups, not their ethno-linguistic compatriots. So using a combination of Estonion Biocentre data, the HGDP, and some friends and my own family, I’ve partitioned the 1000 Genomes South Asians more finely than is presented in the raw downloads.

The PCA above is hard to make out because there are so many groups I relabeled. But I’ve put the pedigree file (with my friends removed) with new labels on Dropbox. The Gujurati and Punjabi populations I separated by “ANI-ness,” from most to least numerically (Gujurati_ANI_1 is the most ANI for example). The large number of Patels I labeled separately, as they are pretty obvious (Zack Ajmal found that Patels for the Harappa project land right in the middle of this cluster of related individuals). Additionally, the Tamil and Telugu and Bangladeshi population had individuals who seem likely to have been scheduled caste or Dalit. I broke them out. I also removed a few outliers (e.g., one of the Telugu individuals was probably mixed caste, half-Brahmin and half non-Brahmin, so I removed them, and one of the Bangladeshis was likely a Bengali Brahmin or some such thing).

Some surprises for me in the 1000 Genomes. The “Punjabis” sampled from Lahore were very diverse. Many were clustering with Pathans in the HGDP (by the way, there were two Pathan clusters, so that I suspect that one of them is “Pathanized,” and I removed these). But there were others, such as Punjabi_ANI_4, who were not that different from more generic South Asians. I suspect these are Muhajirs who have become ethnically assimilated more or less (or, the 1000 Genomes just labeled everyone from Lahore as Punjabi). The Bangladeshis were ancestrally very homogeneous. Unlike the Tamils or Telugu speakers there wasn’t much of a separation of lower caste individuals, and not many were Brahmins either (I found one). There were a few individuals who were very distinct in the Bangladesh sample…they clustered with scheduled castes, and didn’t have much East Asian ancestry. I believe these people descend from migrants from India in the past few centuries because of the last fact and likely remain Hindu and maintain caste endogamy (two of them had adjacent IDs, so were probably sampled together?).

IndiaTree3To the right is a representative TreeMix (you see all the rest on Dropbox). The Bangladeshi scheduled caste individuals are in the tree next to Chamars, Dalits from North India. The Telugu sample in the 1000 Genomes is most similar to Velamas, who I got from the Estonian Biocentre data set. Velamas are middle castes from Andhra Pradesh, so probably representative of the group that the 1000 Genomes Telugus are sampled from. The Bangladeshi samples are somewhat near the Patels or Gujurati_AN_4 in most of the runs, but have substantial East Asian ancestry. On the PCA above my parents, who are both from an eastern region of East Bengal, Comilla, are among the most East Asian of the Bangladeshis sampled. I also projected a friend whose family has deep roots in West Bengal and are Kayasthas. You can see that he is exactly between the Bangaldeshis and other South Asians. This suggests that the East Asian cline in Bengal is very sharp. It does not really persist outside of that region. Additionally, the idea that there is widespread Austro-Asiatic ancestry in South Asia does not seem to be supported by these data…only Bengalis and Burusho, both with notable East Asian ancestry, are shifted toward East Asians. The ANI-ASI cline is really sufficient for everyone else.

inbreed1Finally, I wanted analyze inbreeding in the South Asian samples. I used plink’s default run of homozygosity feature. The raw results are in the first Dropbox link. I invite you to check them out yourself. Looking to the left you see total runs of homozygosity in KB units across the genome. Notice that the Gujurati Patels are shifted to the right, but they have a narrow window. In contrast, the Bangladeshis are to the left, but have a few outlier individuals. The Patels are an endogamous Hindu group, and so likely have lots of medium length IBD tracts. But they don’t engage in marriage between close relations. In contrast, the Bangladeshis don’t seem to have practiced much endogamy at all, presumably because they’re Muslims and caste consciousness is weak among Bangladeshis from what I can tell (my family has very vague awareness by surnames what castes they were from, but no one really cares), but some of them engage in marriage between close kin.

ibreedThe second shows average length of the run of homozygosity, so is more informative of recent inbreeding. You can see that the Tamils have a flat distribution, because of lots of people who have long runs. Cousin marriage and uncle-niece marriage has been practiced by South Indian Hindus historically. The Punjabi samples also have long runs of homozygosity. One difference between Muslims in Pakistan and Muslims in Bangladesh seems to be that the Middle Eastern pattern of cousin marriage is much more ubiquitous in Pakistanis. I have no idea why there is this difference. Also, unlike Hindus in much of South Asia Bangaldeshis seem to exhibit little community level genetic structure. The thesis of , that the strength of Islam in this region of Bengal was due to its relatively recent settlement and organization during the Muslim period, and that it was a unstructured frontier society, seems roughly supported by these genetic results.

A final thing I should note is that I appreciate the Estonian Biocentre releasing it raw data, but many of the samples seem to exhibit little co-ethnic association. I’m not sure whether this is a labeling problem or something else, but I discarded a lot of individuals (e.g., a Uttar Pradesh Brahmin placed among non-Brahmin South Indians). But for the South Asians people should be cautious about using this data set without double checking (in contrast, the non-South Asians have never caused me this problem from that data set).

Anyway, please download the data and use it if useful. The IDs are the same you would recognize in the 1000 Genomes and HGDP etc. I put an ADMIXTURE file in there too for K = 4. Nothing surprising.

Why I still lean toward a Sub-Saharan African origin for modern humanity

Dienekes argues:

Yes, it’s possible that the divergence event happened in Africa. It’s also possible that it happened in Asia. I see no reason to prefer one or the other. After all, the main piece of evidence in favor of Out-of-Africa is that Eurasians are nested within African genetic variation.

If this paper is right, this is no longer the case: Africans are nested in Eurasian variation as a whole, inclusive of both modern Eurasians and the mystery population.

I’m not sure that this is the main piece, though it was a major reason. Here are two other reasons:

1) Anatomically modern humans show up in Africa first.

2) The deepest divergences in the mtDNA, Y chromosomes, and autosomes, are all found within Africa (in particular, between hunter-gatherer African populations and everyone else).

Let’s consider the alternative models in terms of the genetics.

Near Eastern origin of modern humanity: Rapid expansion of humans out of this area. The deep divergences within Africa are happenstance; all the deep lineages outside of Africa were replaced by the “Out of Africa” population.

African origin of modern humanity: Rapid expansion of “Out of Africa” humans 60,000 years ago, with deep structure within Africa that dates back to 200,000 years ago.

Both views match the data. But the latter model seems more parsimonious to me. And as I stated above I’m to understand it is more well aligned with the archaeology. But time will tell. The first view may be true.

Ancient structure and interbreeding in Africa

The figure in Ewen Callaway’s piece in Nature, Evidence mounts for interbreeding bonanza in ancient human species, does a good job at relaying what we know about admixture between different human lineages informed by ancient DNA. But is that all there is? Before ancient DNA in large quantities came online there were attempts to infer admixture based on the available data (mtDNA, modern populations) and model building and simulations. There were two natural conclusions.

First, admixture happened. Second, it did not. Here’s a paper from 2004, Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe, in PLOS BIOLOGY. And from 2006, Possible Ancestral Structure in Human Populations, in PLOS GENETICS (the first paper has 100 more citations, ~250 vs. ~150, as was in the more mainstream journal). The relatively tentative title of the second paper as opposed to the bold aspect of the first publication does I think reflect the strength of the two positions across academia as a whole at the time (I grant that many population geneticists in particular were skeptical at “Out of Africa” with-total-replacement triumphalism, which was evident in Richard Dawkins’ , published at about that time).

Screenshot from 2016-02-18 09-16-07Ancient DNA has changed things. But it has not changed everything, because ancient DNA has been retrieved predominantly from northern Eurasia, for various reasons. I was careful to state above that Callway’s piece was informed by ancient DNA, because I think it omits the likelihood of archaic admixture within Africa. A group associated with Jeff Wall and Michael Hammer have been arguing for gene flow between highly diverged lineages within Africa for many years (and archaic admixture more generally going back to the mid-2000s), and yesterday they came out with two papers in Genome Research.

First, Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies:

Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.

And, Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection:

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba farmers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

I have to say that sometimes I think that selection scans in population genomics are a bit little neuroscience. Neuroscience tells us that stuff happens in the brain. Selection scans tell us that adaptation targets a bunch of functional regions of the genome. Though I’m sure you would feel different in “your gene” shows up on the laundry list.

In any case, two points that I want to emphasize. Haplotypes which seem introgressed from an archaic lineage are underrepresented in genic regions. The same sort of purifying selection you see in archaic admixture in Eurasians (and now in the Altai Neanderthal) seem to be at work here. Second, the divergence between western Pygmies and African farmer populations is nearly double the time of the “Out of Africa” event. And, the results from this group seem consistent that admixture continued to occur after it had ceased to occur in Eurasians because the archaics outside of Africa had been absorbed by then (at least to our knowledge, I would not be surprised if there was later in some groups detectable at very low levels). This reinforces the idea that we need to update and complexify our idea of how modern humans came to be.