Five to three thousand years ago cuneiform was state of the art. And if you want permanence, look no further. The tablet to the left dates to 2400 BC! With the decline in cuneiform there is something of a lacunae in our understanding and memory of the literary production of ancient societies. Scrolls of papyrus can certainly keep, but only under ideal conditions (e.g., very dry climates, such as Egypt). The codex, the technology which we know as the book, is more recent than the scroll. But it too relies on relatively perishable materials in comparison to cuneiform.

How is it that we have so much of ancient literature then? First, we don’t. There are constant mentions of great works of Greek and Roman antiquity which were obviously widely circulated judging by the references to them in the works we do have. These background elements of the ancient canon were never copied down to our present era. Why is the copying so important? Shouldn’t we have the originals? The Epic of Gilgamesh was retrieved from the remains of the library of the Assyrians (later literature mentions Gilgamesh, but for these earlier cuneiform copies we wouldn’t have the full work from what I know). This is where the perishable aspect comes in. There are classical-era works whose original production dates back to late antiquity, but from what I have read our modern distillation of the ancient canon is almost entirely filtered through three great bursts of copying at the nexus of late antiquity and the early medieval period:.

- The Arab effort during the early years of the Abbasid Caliphs in the 9th century.

- The Carolingian Renaissance of the late 8th and early 9th centuries.

- And a burst of activity as Byzantium recovered from its assaults by the Arabs in the 9th and 10th century, in particular under the patronage of Constantine VII.

These endeavors were somewhat complementary. The Islamic transmission of great philosophical works is well known, but there was little interest from them in preserving the corpus of ancient Greek humanism, such as the works of the great playwrights. Rather, we have the Byzantines to thank for this. From this, combined with the Carolingian preservation of many Latin works, a reasonable picture of antiquity comes down to us today because of these three independent efforts. But only through the grace of contingency do we have this continuity. The literature of pre-Islamic Persia is lost to us. Why? Perhaps it never was. Or perhaps unlike the Greeks and Romans they did not generate cultural heirs who would patronize the perpetuation of their great works.

Franzen’s concern about the lack of permanence of digital formats has a real basis. But it’s not a vague one predicated on some sapping of the Weltgeist. Rather, there is a chance technological civilization will collapse or retrench at some point in the future. Old fashioned concrete physical mediums not reliant on the “grid” may be necessary backups in that case to preserve memory of the past. Instead of fixating on the death of print, people who worry genuinely about the potentially ephemeral aspect of digital medium should start thinking like the Long Now foundation. Shakespeare on platinum cuneiform anyone?

The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins.

The new view is fast supplanting the traditional idea that modern humans triumphantly marched out of Africa about 50,000 years ago, replacing all other types that had gone before.

Instead, the genetic analysis shows, modern humans encountered and bred with at least two groups of ancient humans in relatively recent times: the Neanderthals, who lived in Europe and Asia, dying out roughly 30,000 years ago, and a mysterious group known as the Denisovans, who lived in Asia and most likely vanished around the same time.

Their DNA lives on in us even though they are extinct. “In a sense, we are a hybrid species,” Chris Stringer, a paleoanthropologist who is the research leader in human origins at the Natural History Museum in London, said in an interview.

First, for reasons of novelty we are emphasizing the exotic tendrils of the human family tree. Even Chris Stringer, the modern paleontological father of “Out of Africa,” is claiming we’re hybrids! But let’s not forget that non-Africans are the product of a very rapid radiation out of the margins of the Afrotropic ecozone within the last ~50-100,000 years. I am not entirely sure that this is as true of Africans (recall how extremely basal Bushmen are to the rest of humanity; they seem to have diverge well before the “Out of Africa” pulse).

Second, the old model was way easier to write about, even if there were confusions like the idea that mtDNA Eve was our only female ancestor from 200,000 years ago in the past. The new paradigm leaves one with awkward and unhelpful turns of phrase. For example:

But Dr. Reich and his team have determined through the patterns of archaic DNA replications that a small number of half-Neanderthal, half-modern human hybrids walked the earth between 46,000 and 67,000 years ago, he said in an interview. The half-Denisovan, half-modern humans that contributed to our DNA were more recent.

How to make sense of this gibberish? I suspect that the author didn’t have a good idea how to translate a particular population genetic statistic, and its importance to assessing time since admixture, into plainer prose. I have no idea either!

In other news, i09 has an interesting interview up with Rebecca Cann and Mark Stoneking. These two were heavily involved in the mtDNA Eve controversies of the 1980s. Nice capstone to an era. Like Stringer, even they admit the likelihood of a necessity to modify the simple “Out of Africa” with replacement model.

The title is rather loud and non-objective.  But that seems to me to be the upshot of Henrich et al.’s The puzzle of monogamous marriage (open access). In the abstract they declare that “normative monogamy reduces crime rates, including rape, murder, assault, robbery and fraud, as well as decreasing personal abuses.” Seems superior to me. As a friend of mine once observed, “If polygamy is awesome, how come polygamous societies suck so much?” Case in point is Saudi Arabia. Everyone assumes that if it didn’t sit on a pile of hydrocarbons Saudi Arabia would be dirt poor and suck. As it is, it sucks, but with an oil subsidy. The founder of modern Saudi Arabia was a polygamist, as are many of his male descendants (out of ~2,000). The total number of children he fathered is unknown! (the major sons are accounted for, but if you look at the genealogies of these Arab noble families the number of daughters is always vague and flexible, because no one seems to have cared much)

So how did monogamy come to be so common? If you follow Henrich’s work you will not be surprised that he posits “cultural group selection.” That is, the advantage of monogamy can not be reduced just to the success of monogamous individuals within a society. On the contrary, males who enter into polygamous relationships likely have a higher fitness than monogamous males within a given culture. To get a sense of what they mean by group selection I recommend you read this review of the concept by David B. A major twist here though is that they are proposing that the selective process operates upon cultural, not genetic, variation (memes, not genes). Why does this matter? Because inter-cultural differences between two groups in competition can be very strong, and arise rather quickly, while inter-group genetic differences are usually weak due to the power of gene flow. To give an example of this, Christian societies in Northern Europe adopted normative monogamy, while pagans over the frontier did not (most marriages may have been monogamous, but elite males still entered into polygamous relationships). The cultural norm was partitioned (in theory) totally across the two groups, but there was almost no genetic difference.  This means that very modest selection pressures can still work on the level of groups for culture, where they would not be effective for biological differences between groups (because those differences are so small) in relation to individual selection (within group variation would remain large).

From what I gather much of the magic of gains of economic productivity and social cohesion, and therefore military prowess, of a given set of societies (e.g., Christian Europe) in this model can be attributed to the fact of the proportion of single males. By reducing the fraction constantly scrambling for status and power so that they could become polygamists in their own right the general level of conflict was reduced in these societies. Sill, the norm of monogamy worked against the interests of elite males in a relative individual sense. Yet still, one immediately recalls that elite males in normatively monogamy societies took mistresses and engaged in serial monogamy. Additionally, there is still a scramble for mates among males in monogamous societies, though for quality and not quantity. These qualifications weaken the thesis to me, though they do not eliminate its force in totality.

In the end I am not convinced of this argument about group selection, though the survey of the empirical data on the deficiencies of societies which a higher frequency of polygamy was totally unsurprising.  I recall years ago reading of a Muslim male who wondered how women would get married if men did not marry more than once. He outlined how wars mean that there will always be a deficit of males! One is curious about the arrow of causality is here; is polygamy a response to a shortage of males, or do elite polygamist make sure that there is a shortage of males? (as is the case among Mormon polygamists in the SA)

Finally, I do not think one can discount the fact that despite the long term ultimate evolutionary logic, over shorter time periods other dynamics can take advantage of proximate mechanisms. For example, humans purportedly wish to maximize fitness via our preference for sexual intercourse. But in the modern world humans have decoupled sex and reproduction, and our fitness maximizing instincts are now countervailed by our conscious preference for smaller families. Greater economic production is not swallowed up by population growth, but rather greater individual affluence. This may not persist over the long term for evolutionary reasons, but it persists long enough that it is a phenomenon worth examining. Similarly, the tendencies which make males polygamous may exist in modern monogamous males, but be channeled in other directions. One could posit that perhaps males have a preference to accumulate status. In a pre-modern society even the wealthy usually did not have many material objects. Land, livestock, and women, were clear and hard-to-fake signalers to show what a big cock you had. Therefore, polygamy was a common cultural universal evoked out of the conditions at hand. Today there are many more options on the table. My point is that one could make a group selective argument for the demographic transition, but to my knowledge that is not particularly popular. Rather, we appeal to common sense understandings of human psychology and motivation, and how they have changed over the generations.

Addendum: When I say polygamy, I mean polygyny. I would say polygyny, but then readers get confused. Also, do not confuse social preference for polygyny with lack of female power. There are two modern models of polygynous societies, the African, and the Islamic. The Islamic attitude toward women shares much with the Hindu monogamist view, while in African societies women are much more independent economic actors, albeit within a patriarchal context. The authors note that this distinction is important, because it seems monogamy (e.g., Japan) is a better predictor of social capital than gender equality as such, despite the correlation.

Citation: Joseph Henrich, Robert Boyd, and Peter J. Richerson, The puzzle of monogamous marriage, Phil. Trans. R. Soc. B March 5, 2012 367 (1589) 657-669; doi:10.1098/rstb.2011.0290

Image credit: 1, 2, 3

The papers are The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa and Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Dienekes has already commented on the first paper. I am not going to take a detailed position on either, but I have to add that we need to be very careful of extrapolating from maternal or paternal lineages, and, assuming that population turn over is low enough that we can make phylogeographic inferences about the past from the present. For example, if you look at mtDNA South Asians as a whole strongly cluster with East Asians and not Europeans, while if you look at Y chromosomes you see the reverse. The whole genome gives a more mixed picture. Additionally, ancient DNA analyses in Northern Eurasia are showing strong discontinuities between past and present populations. So coalescence back to last common ancestor between two different lineages in two different regions may actually be due to diversity in a common source population more recently, which entered into demographic expansion and replaced other groups.

If you need the papers, email me. Some of you know the alphabet soup of haplogroups better than I do. Below are two figures which I think give the top line results.

We are no longer talking just about African mtDNA Eve and her husband Y chromosomal Adam. I’m going to consciously avoid the term “revolutionize,” because the broad outlines of the old story certainly hold. Rather, as we are wont to do it seems that we became a bit too bold with some of our brush strokes, and elided fascinating and subtle elements of the landscape on the margins. There were Crebs, and other assorted Oogas and Boogas. And the painting is not completed yet. As such we can’t really draw any conclusions as to “what it all means,” aside from the fact that it’s fascinating.

Addendum: Someone in the comments observes in relation to a depiction of Eve in the story that “She’s awfully pale for an East African.” This is true on the merits, but the logic is kind of dumb. Why exactly do we think that people ~150,000 years ago looked anything like modern East Africans? It is very likely that Europeans ~35,000 years ago did not look like Daryl Hannah.

Another interesting aspect to this phenomenon is that it looks like the three populations respond to adaptive pressures differently. Their physiological response varies. And the more recent work in genomics implies that though there are similarities between the Asian and American populations, there are also differences. This illustrates the evolutionary principle of convergence, where different populations approach the same phenotypic optimum, though by somewhat different means. To my knowledge there has not been as much investigation of the African example. Until now. A new provisional paper in Genome Biology is out, Genetic adaptation to high altitude in the Ethiopian highlands:

We highlight several candidate genes for involvement in high-altitude adaptation in Ethiopia, including CBARA1, VAV3, ARNT2 and THRB. Although most of these genes have not been identified in previous studies of high-altitude Tibetan or Andean population samples, two of these genes (THRB and ARNT2) play a role in the HIF-1 pathway, a pathway implicated in previous work reported in Tibetan and Andean studies. These combined results suggest that adaptation to high altitude arose independently due to convergent evolution in high-altitude Amhara populations in Ethiopia.

The main shortcoming about this paper for me is that it does not highlight the evolutionary history of this adaptation. In the paper the authors compared the Amhara (a highland population) to nearby lowland populations. But did not explore the nature of the population structure and how it might have influenced the arc of adaptation. Are these very ancient adaptations? Or new ones? It seems that hominins have been resident in Ethiopian for millions of years. If this is so presumably there have been adaptations to higher elevations from time immemorial. But what if these adaptations are new?

More pointedly the Ethiopians can be modeled as a compound of an Arabian population with an indigenous East African one. If this is a genuine recent admixture event, then one might be able to ascertain via haplotype structure whether the adaptive variants derive from ancient African genetic variation, or whether they’re novel mutations. It seems that this paper is a good first step, but there’s a lot more to see here….

Citation: Genome Biology, doi:10.1186/gb-2012-13-1-r1

Image credit: Wikipedia

It’s been a while since I’ve gone looking for genotypes of particular ethnic groups. The results were rather good for the Tutsi and Malagasy. So I thought I’d venture out again, despite being a bit busy. Here’s what I want: the genotype of an Afrikaner (or several). A few years ago South African geneticist J. M. Greeff did an analysis of his own pedigree, and estimated that he had ~6 percent non-European ancestry (he did validate this with some genetic markers; e.g., his father’s mtDNA is of the M haplogroup, which is almost always Indian). This is in line with other genealogists who have estimated, about 5 percent non-European heritage. How much should we trust these non-biological studies? The genomic estimates of African American ancestry being ~20 percent European were anticipated by analyses of family histories from text records, so we certainly shouldn’t dismiss them (in fact, it seems possible that these analyses will underestimate non-European ancestry because of cryptic individuals in the pedigrees).

And we have plenty of records of people of non-European ancestry contributing to the Afrikaner population in any case. Greeff found the records for his own pedigree, but the first Governor of the Dutch Cape Colony was himself of mixed-race (his mother was Eurasian). The question is is a matter of degree. Are Afrikaners like American whites, with hardly any non-European ancestry (~1 percent or less), or like Latin American whites, with significant non-European ancestry (~5 to 20 percent)? My own bet is that they’ll be in the middle. The proportion of non-European ancestry is low enough that individuals such as Sandra Laing are very rare indeed. But if the 5 percent estimate is valid, and almost of all these ancestors were women, then a larger proportion of the mtDNA is going to be non-European.

So how do we do this? Well, I need an autosomal genotype. I’ll take it anyway I can get it. But, if you don’t have one, but are willing to let me analyze your own genotype, and, are of 100 percent known Afrikaner descent, then we can probably figure out a way to purchase you a kit.

Why does this matter? I guess you could ask why any science matters. I’m a little confused as to why no one has done this before. There’s plenty of work on the cultural cousins of the Afrikaners, the Cape Coloureds. My working assumption is that except for the initial decades of the Cape Colony, when women were in severe shortage and the color line was not as strict, most of the non-European gene flow into the Afrikaners is going to be from the Cape Coloureds. This means that like the Cape Coloureds the Afrikaners carry within them the genetic variation of a huge swath of the world’s population. The non-European ancestry of the Afrikaners is naturally part African. Bantu and Khoisan. But there is also considerable Asian, from South and East Asia. Though this leaves out the Middle East and the New World, you have here most of extant genetic variation in human populations.

There are approximately 3 million Afrikaners in South Africa. What if these were the only human beings left on earth? At 5 percent that’s 150,000 non-Europeans, with a mix of Southeast Asians, Chinese, Indians, Khoisan, and Bantu. Because of diminishing returns you’ll actually have enough variation in just a few thousand individuals of any given ethnic group to capture most of its genetic character. In other words you could in theory reconstitute the Chinese and Khoisan from these Afrikaners.

Addendum: The paper, Complete Khoisan and Bantu genomes from southern Africa, has one “South African European.” But I suspect that this individual is author Vanessa M Hayes, and she is not an Afrikaner to my knowledge.

Image credit: Wikipedia

A new paper on archaic adaptive introgression among Melanesians has been discussed elsewhere. But I think it is worth reviewing, because it’s probably a foretaste of what’s to come. Researchers are combing through the human genome, as more and more genomes come on line, in the search of weird and unexpected variation. The paper is in Molecular Biology and Evolution, and is titled Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations (why is it that this journal doesn’t even allow supplemental information to be free to the public?). The two primary figures from this paper do a good job of illustrating the main result.

The first figure is a phylogenetic tree of haplotypes at the OAS1 locus, with pie charts showing the proportion of individuals from a set of populations which contribute to the total number for that haplotye. So you see above that the “deep lineage” is relatively distant from a cluster of other haplotypes (as measured by mutational differences which are proportional to depth of common ancestry), and, that deep linage is exclusively found in Papuans in this set. The second figure shows the frequency of the deep lineage haplotype over a larger set of populations. I cut off the section which shows that Africans are at zero percent. The haplotype is found almost exclusively in Melanesian populations, except for the fact out of over 200 South Asians they sampled, 3 of them carried it (2 Pakistanis, 1 Sri Lankan). There is aspect though not evident in the figures above, but which is clear in the abstract that you need to know:

Recent analysis of DNA extracted from two Eurasian forms of archaic human show that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. While these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene, OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We re-sequenced a 7 kb region encompassing the OAS1gene in 88 individuals from 6 Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5′ region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 million years, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

There there is “more genetic diversity within Africa” is a cliche rooted in reality. But, this is not true at all genes. For example, at MC1R Africans have less genetic diversity than Europeans. Why? MC1R is implicated in pigmentation, and this locus is subject to strong functional constraint at low latitudes. In other words, there is more at work than just demographic history. When you see more diversity at a locus outside of Africa than within there is a strong suspicion that natural selection or admixture may be at play, because your null expectation is that the dominant “Out of Africa” event will imply more Africa diversity or modern humans. So at OSA1 you have a genetic variation which is very diverse, and very divergent, from the modal human variant. When you take away the deep lineage you also see a pattern which is constant with genome wide expectations. Africans are distributed across the unrooted tree, while non-Africans seem to be nested within a subset of nodes.

But if this was published in 2008 it might not be as notable, because the human genome is big, and there are going to be random patterns here and there. This might have been dismissed. The key is that the authors matched this divergent haplotype to the variant found in the draft Denisovan genome. Naturally it’s going to be harder to dismiss as a statistical fluke when you actually have concrete evidence in this form that the ancient lineage was shared with an archaic hominin group.

There are two scientific points that jump out at me. First, the authors don’t discuss adaptation or selection in very much detail (except to dismiss balancing selection). But if this is due to archaic admixture its fraction in Melanesians is far higher than the genome wide average. Again, some loci will naturally deviate from expected values, but those that do are excellent candidates for being targets of adaptation. And, this gene has a clear functional role related to immune response. Second, the presence of this haplotype in South Asians is strongly suggestive of the location of the admixture event between archaic humans and the ancestors of modern Melanesians. This sort of information needs to be synthesized with the two papers last fall that came out on Australian evolutionary genomics.  One of the interesting aspects of the Denisovan admixture analyses is that it doesn’t seem that any South Asian group, including Andaman Islanders, exhibit it. And yet a few South Asians here carry a haplotype similar to the Denisovan variant. Interestingly, the authors present a rather unbelievable large value for the common ancestor between the deep lineage and other modern haplotypes, ~3 million years, which is an order of magnitude more than the divergence of Denisovans from modern humans.

How to resolve this confused situation? In the conclusion they point to the possibility that this haplotype may have introgressed into both the Denisovans and modern humans from H. erectus! The most recent genomics on Melanesians implies that their own history is relatively complex. On the one hand they may be some of the earliest distinct migrants out of Africa, and secondarily, they themselves may be successive compounds between those early migrants, archaic humans, and a second wave of Eurasians. All that being said, I think there is some hope in the combination of full genome sequencing of modern populations as well as the same of ancient populations via DNA from subfossils. The main qualification is that I doubt we’ll ever get good samples of ancient DNA from the tropics.

Citation: Fernando L. Mendez, Joseph C. Watkins, and Michael F. Hammer,
Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations, Mol Biol, doi:10.1093/molbev/msr301

Image credit: Wikipedia

The main lacunae in the above analysis is that it does not cover results from autosomal studies. Some of that has been performed by Dienekes, but more is necessary for a region characterized by as much ethnographic diversity and density as the Caucasus. One peculiarity that emerges in analyses of autosomal data sets is that the Caucasus looms relatively large in a wide array of dispersed populations. For example, there is a genetic signature which ties Indo-Aryan and Caucasian populations together, and others which seem to connect the latter to some Balkan groups.

These are possible hints that the Caucasus is the “mother of nations,” and that the old idea of the “Caucasian race” may have some reality to it. But I would bet on something else: the Caucasus is not the mother of nations, but the repository of forgotten peoples. The Ossetes themselves are presumed to be just such a population. I offer up the hypothesis that one reason that disparate Caucasian populations have diverse and wide-ranging connections has less to do with outward expansion, and more to do with the fact that on the margins of the Caucasus a great range of historic genetic diversity erased by later demographic events (e.g., the Slavic and Turkic expansions from two directions in on the North Iranian peoples) is preserved, as the defeated take refuge.

In this way, Mr. Romney’s Mormonism may end up being a critical advantage. Evangelicals might wring their hands over the prospect of a Mormon president, but there is no stronger bastion of pre-civil-rights-America whiteness than the Church of Jesus Christ of Latter-day Saints.

Yes, since 1978 the church has allowed blacks to become priests. But Mormonism is still imagined by its adherents as a religion founded by whites, for whites, rooted in a millenarian vision of an America destined to fulfill a white God’s plans for earth.

There is something to this. The ancient leadership of the present day Mormon church grew up in a very different America, and they sometimes reflect that America in their pronouncements. For example, despite the fact that plenty of Mormons are in interracial marriages (I know this from my Facebook friends), there is still some literature floating around in the Mormon church discouraging the practice. Now, granted most Americans’ revealed preferences indicate that they aren’t too into interracial marriage personally, but the social norm is strongly against expressing disapproval in the abstract against the practice.

All that being said, one needs to be careful about overemphasizing the whiteness of Mormons. First, remember that most Mormon males are missionaries abroad at some point in their life, so it isn’t as if they are unfamiliar with societies where non-whites are the majority. And, it is probable that around half of Mormons in the world today are not white (the claims vary on this issue). But it is also notable that Mormons in the USA today are far less white than they were just a generation ago. To illustrate this point I’ve replicated some religious data from the Pew survey. I’ve highlighted in blue some historical mainline/liberal Protestant denominations, and in red some of their evangelical/conservative counterparts.

Some of the results are not surprising. The Lutheran churches in America have become the ethnic religions of people whose ancestors immigrated from Germany or Scandinavia (and those who marry into these families, who are invariably white because white people have a strong revealed preference of marrying other white people). What is perhaps more interesting is that the list of very white American churches seems somewhat overloaded with liberal establishment denominations. Methodists, Presbyterians, and Episcopalians. These movements have fewer blacks than the Southern Baptists, whose origins are rooted in part in the Southern system of racial segregation! When you compare liberal and conservative divisions of the same church (e.g., Evangelical vs. Missouri Synod Lutherans, United vs. Free Methodists, Presbyterian USA vs. America), there does seem to be a pattern where the proportion of whites is generally higher in the more liberal denomination.

Finally, let’s go back to the Mormon issue. Turns out that Mormons are about as white as Unitarians. This is not too surprising if you’ve ever been to a Unitarian church (I’ve been to several). Mormons are also as white as atheists or agnostics. This will not surprise. But what may surprise is that the denomination into which Barack Obama is baptized has a higher proportion of white members than the Latter-day Saints!

My main point with this post is that you should be careful of toting up numbers, and using that to buttress your position. Mormons in America are proportionally a white denomination. But they’re arguably no whiter than Unitarians, and far less white than Jews. The fact that Unitarians are just as white as Mormons does not imply that they are equivalent in racial sentiments and attitudes with Mormons. Mormonism’s “race problem” is a feature of its history, and a strain of its modern culture, which is independent from its contemporary demographics. Therefore, the demographics should be set to the aside. No one minds that Evangelical Lutherans are overwhelmingly white because there’s nothing about that religion which is particular racist. If there was, then perhaps one could focus on the demographics as a consequence, rather than a suspicious feature.

The idea of a “folk wandering” was once a well accepted idea in history, in particular for the phase of the Late Roman Empire, and the subsequent fall of the Western Empire. It’s a rather simple concept: the collapse of the Pax Romana occurred simultaneous with a mass ethnic reordering of Europe, primarily via the migration of Germanic peoples across its frontiers and beyond. The most extreme depictions of this can be found in the works of the British cleric Gildas: German hordes literally drove the British into the sea, until they only retained their redoubts around the “Celtic Fringe.”

This was an extreme understanding of the dynamics of post-Roman Europe. It was, and has been, succeeded by another extreme model: that the ethnic change in the post-Roman world was more illusion than substance, a manner of shifting nomenclature, than lineage. For example, I have commonly read in this literature that the Germanic tribes which crystallized as “federates” to the Romans, or on occasion as antagonists (or vassals to hostile powers such as the Huns) were ad hoc collections of mercenaries who created an identity de novo.  In some cases it is posited that masses of Romans simply assimilated to the identity of a small cadre of warriors whose demographic impact was trivial. This is the scenario that is posited for the transformation of Celtic Britain into Germanic England. But let’s shift away from that extreme case, and look at another one: the 5th and early 6th century kingdom of the Vandals in Norh Africa.

The Vandals were a German tribe with a rather unsavory reputation (perhaps undeserved, but it is what it is). Originally after breaking into the Roman Empire they were junior partners in Spain to a confederation of Iranian tribes, the Alans. But in a series of conflicts the Spanish Alans were reduced to a shadow of their former selves by Romans or Roman federates (e.g., Visigoths), and they allowed themselves to be assimilated into the Vandal power structure. When the Vandals moved into North Africa, they took the Alans with them. And just as the monarchs of England were monarchs of Scotland distinctly, in the 17th century, so the king of the Vandals was separately a king of the Alans.

What does this have to do with genetics? Easy. A few years ago the historian Peter Heather came out with a book, Empires and Barbarians, where he attempted to resurrect the idea of a folk wandering. Instead of the idea of post-Roman Europe being dominated by the rapid emergence of ethnic identities from a small platoon of warriors, he posits that there were general transfers of the freeborn caste of whole Germanic tribes across Northern Europe. The women and children moved with the men. Heather’s thesis is more modest than that of Gildas. He does not suggest there was total, or even wholesale, replacement. Rather, the Franks, Visigoths, Anglo-Saxons, etc., were not rapid social constructions on a chaotic cultural landscape, but peoples which were organic developments out of a broader Germanic cultural milieu who were transplanted in toto across the post-Roman world. The kludge of a dual monarchy in the case of the king of the Vandals and Alans does not make much sense if ethnic identity was so fluid as to be purely instrumental in a proximate sense. Rather, even in extremis the Alans insisted upon retaining their identity as a people in the face of the more practical option of total assimilation into the Vandal horde. If ethnic identities are purely ephemeral labels given to political coalitions of mercenaries this behavior makes no sense. On the other hand if these identities carry with them the weight of history, of cultural memory, then these actions and baroque compromises are rendered understandable.

The Vandal kingdom of North Africa in some ways is probably the most least plausible case for a folk wandering, in that the wandering was quite extensive, and the Vandal kingdom seems to have been the least culturally robust its long term impact (suggesting perhaps a superficiality of their hegemony). And I have read scholarly literature which does argue that the concept of “Vandal” and “Alan” were simply constructs, which post-Roman elites easily took upon when the circumstances suited them. There is something to the idea that individuals can acculturate, but I think what the idea of radical social constructionism in post-Roman Europe misses is that you need a culture to assimilate to, and that culture can only exist in the first place due to a critical mass. Could a small number of German and Iranian warriors, without any women or other elements of their freeborn population replicate their tribal culture over thousands of miles? I think not. Single elements of culture are replicable, but whole cultural systems often exhibit more integrity and contingency than is obvious from the outside.

To explore the possibility of Germanic ancestry in North Africa I decided to use the Henn et al. data set. I merged it with the Utah white sample from the HapMap. I then had 188,000 markers. My goal was to find runs where Southern and Northern Europeans were distinct. Below are two sets of runs where Northern and Southern Europeans were distinct. The first are supervised, and the second unsupervised.

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K = 8, unsupervised

K = 8, Algerians, Andalucians, N. Moroccans unsupervised

K = 8, supervised

K = 8, Algerians, Andalucians, N. Moroccans supervised

I don’t really see any good evidence of the impact of specifically a German element in this. The Vandals seem to fail the test of long term demographic impact in these samples. To really explore this issue I’d have to look at the ancestry at the chromosomal level, and look for matching haplotypes and segments identical-by-descent. Perhaps I will in the future.

Image credit: Wikipedia

The Fulani (Fula) people of the western Sahel seem to have a relatively old West Eurasian component which has distinct affinities with the “Maghrebi” element discerned by Henn et al. In fact, the non-Sub-Saharan African ancestry of the Fulani is almost exclusively of this origin. To me this serves as a peculiar mirror of what you see in the Cushitic and Ethiopian Semitic peoples of the far east of the Sahel-Sudan latitudinal region. These populations also seem to be compounds of a Sub-Saharan Africa element with a West Eurasian one, but in their case the admixture is almost exclusively from a Southwest Eurasian (Arabian) component. Geographically these two symmetric admixture events make sense, but the exclusivity is still a bit surprising. Additionally, in both the case of the Fulani and the Ethiopian and Cushitic groups the admixture is widely distributed and even enough to imply that they are old events. I also assumed this because in some admixture runs a “pure” Fulani cluster partitions out, which is not unexpected for stabilized hybrid populations (all human populations are stabilized hybrids if you go back far enough).

To give you a flavor of what I’m talking about here are some screen shots of a run which is currently going. It has 180,000 markers. I removed Tunisians and many African populations from the Henn et al. data set, and included in the Utah whites from the HapMap. The individual plots show the ancestral proportions for each Fulani in the data set:

So what can we see here? First, let’s reiterate something: as in the case of the populations of the Horn of Africa the West Eurasian element in the Fulani is difficult to find in “pure” form in the populations from which it putatively derived. What does that imply? I think that that means that the Fulani have an origin in relatively recent historic time, on the order of 2,000, not 10,000, years. That is because I am skeptical that the Fulani would be able to maintain genetic distinctiveness for ~10,000 years from other populations around them. In contrast, the last 2,000 years have seen the rise of various cultural institutions, from trans-Saharan nomadism to Islam, which might slow down admixture sufficiently to maintain the differences between the Fulani and their neighbors. It also implies to me that the non-Maghrebi “Near Eastern” element which Henn et al. discerned is relatively a recent phenomenon in northwest Africa, else the Fulani should also carry it. How recent? Probably from Classical Antiquity down to the Muslim period. Observe that many North Africa groups have a red “European” element. This may be from Near Eastern populations, but I suspect that the fraction here is just too high to be explained by that. Also, you can see above that some groups in Morocco have nearly as much of this as Egyptians, but far less of the more genuine Near Eastern components.

In all likelihood the West Eurasian component came to the Fulani via the Tuareg or a related or antecedent population. So if you typed the Tuareg you would probably get a better sense of the “pure” “Maghrebi” genetic profile. These genetic results also can serve as fodder to understanding the ethnogenesis of the landscape of the Sahel. In the map above it is interesting to observe that the Hausa speak an Afro-Asiatic language, even though their West Eurasian component is far lower than the Fulani, who speak Niger-Congo dialects. What gives? I suspect that the difference here is that the Hausa are a case of elite emulation of a cultural complex which was much more integrated and elaborated by the time it arrived on the West African scene. This explains how there could be language shift, while in the case of the Fulani there was none. Another hypothesis is that Afro-Asiatic derives from Sub-Saharan Africa itself, and the Chadic (Hausa) group are basal to the phylogeny. I’ll let readers explore the implications of that. A final aspect, I put the quotations in the title because perhaps the Berber dialects spread via elite emulation, and the original Maghrebi ancestors of the Fulani spoke a different language, which has been lost? As they say, for every answer there bloom a thousand questions….

Image credit: Wikipedia, Wikipedia.

For me the simplest option is to look at relatives. Each of my grandparents happens to have had siblings, so there are many sets of relatives related to just each of those individuals of interest. I also have many cousins, so pooling all the genotypes together and using the information of a pedigree one could ascertain which chromosomal segments are likely to derive from a particular grandparent. To give a concrete example, my mother has a maternal cousin to whom she is quite close. By typing my mother and her cousin one could infer that the segments shared across the two individuals derive from the common maternal grandparents. Of course there’s a problem that cousins have a coefficient of relatedness of only 1/8th, so there is going to be a lot of information missing. But, if you had lots of cousins you could presumably reconstruct the genotypes far better.

But what if you didn’t have any of this? I came up with a crazy idea, and I want to throw it out there to see how crazy it is. The issue from the perspective of you, the indivdual without grandparental information, is that for either your mother or your father you don’t know which homologous chromosomes come from which parent (your grandparents, their parents). As it happens, everyone has a male parent and a female parent. So if you can assign a a chromosomal region as having come from the male, and another as having come from the female, then you can reconstruct some of your grandparents’ genotypes because you know their sexes. How can you make this determination?

Genomic imprinting. This is a phenomenon where genes from a given parent, often of a particular sex, are expressed, while those of the other sex are repressed (often it manifests in terms of methylation or lack of methylation). Therefore, if you have a gene, A, which is usually expressed if inherited from a male parent and repressed if it is inherited from a female parent then the state of that gene within a chromosomal region can be a “tag” for the sex of the parent of origin. With enough of these imprinted genes you can create a mosaic of the genome of the individual in terms of sex of origin. Obviously genomic regions from different sexes are from different parents. If you have enough children of these two parents you should be able to infer the whole genomes of these individuals.

The big reason this probably won’t work is that there just aren’t enough imprinted genes in the human genome. But what do readers think?

For some scholars of human history in Amazonia, the geoglyphs in the Brazilian state of Acre and other archaeological sites suggest that the forests of the western Amazon, previously considered uninhabitable for sophisticated societies partly because of the quality of their soils, may not have been as “Edenic” as some environmentalists contend.

Instead of being pristine forests, barely inhabited by people, parts of the Amazon may have been home for centuries to large populations numbering well into the thousands and living in dozens of towns connected by road networks, explains the American writer Charles C. Mann. In fact, according to Mr. Mann, the British explorer Percy Fawcett vanished on his 1925 quest to find the lost “City of Z” in the Xingu, one area with such urban settlements.

In addition to parts of the Amazon being “much more thickly populated than previously thought,” Mr. Mann, the author of “1491,” a groundbreaking book about the Americas before the arrival of Columbus, said, “these people purposefully modified their environment in long-lasting ways.”

…

“If one wants to recreate pre-Columbian Amazonia, most of the forest needs to be removed, with many people and a managed, highly productive landscape replacing it,” said William Woods, a geographer at the University of Kansas who is part of a team studying the Acre geoglyphs.

“I know that this will not sit well with ardent environmentalists,” Mr. Woods said, “but what else can one say?”

There are two descriptive models which have to be interpreted in different normative frames. First, there is the model whereby before the arrival of the Europeans the New World was lightly populated by indigenous groups which had a minimal impact upon the environment. This is the description. Before the 1960s this was viewed by the mainstream culture as a rationale for the justified conquest of the New World by Europeans, who put the land to productive economic usage, whereas before it had been fallow and under-untilized. After the 1960s many, especially in the environmental movement, inverted the moral valence of the description. Instead of being primitive savages, the native peoples were at balance with the environment. Rather than an outmoded way of life to be superseded, they were a potential model for the future.

The second descriptive model is the one that Charles C. Mann outlines in 1491: New Revelations of the Americas Before Columbus. It posits that in fact the New World was much more heavily populated and its environment more impacted by humanity than we had thought previously. Rather, it suggests that the introduction of Old World diseases resulted in massive population crashes, subsequent to which there was a “re-wilding” of much of the Americas. Mann focuses more on the period before the arrival of Europeans, but if you read the scholarship on the arrival of Paleo-Indians there is a fair amount of evidence that even their appearance resulted in a massive change in the suite of fauna which characterized the New World (e.g., the gray wolf and American bison are also Holocene newcomers, just like man).

Some have argued tat Mann has taken a maximalist position (in fact, some readers have lied and stated that Mann argued that the Amazon was as populated as Bangladesh!). But even granting that Mann may be sampling from the more revisionist tail of the scholarship, I think it is creditable that we need to move away from the extreme position of the first descriptive model. There is a fair amount of circumstantial evidence that New World civilizations had not attained the same level of sophistication and complexity as Old World civilizations (see Guns, Germs, and Steel for some of the reasons why). But it is also likely that the Aztecs and Incas were not sui generis aberrations, but rather one point along the spectrum of social complexity which characterized the New World.

This is a subtle point though, because the new model also has normative ramifications. I state above that New World civilizations were not as complex or developed as Old World ones, and that is not a position that many are comfortable with. Rather, they may want to assert that the New World societies were just as complex and sophisticated as the Old World civilizations, that fundamentally all civilizations have equal value and similar character. Therefore, these partisans are particularly enthusiastic about the model which Charles C. Mann popularizes in 1491, as it reverses the narrative of noble simple savages, projecting the indigenous as highly cultured, and only brought down by the biological weapons which Europeans brought.

Where does that put those who wish to construct a plausible model of reality, rather than a mythic history for purposes of ideology? It is lazy to simply pick the position in the middle, but in this case that’s probably the most prudent unless you want to dive into the primary literature yourself. I don’t accept the old model anymore for a variety of reasons, not just having to do with the natural history of the New World. But, I can’t personally assess in detail the magnitude of the numbers that some of the scholars Mann relies upon to revise upward population estimates. So I take the revision with a grain of salt and some caution.

I would conclude that there is one reason I can think of why the Amazon basin might have been more suitable for human habitation that some other wet tropical zones in the Old World: the relative lack of disease. Many wet lowland zones which would otherwise be suitable farmland are lightly populated due to malaria, but this was not an issue in the New World before 1492.

There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with just one group. The first author on this new paper is Brenna Henn, who was also first author on another paper with a diverse African data set. Importantly the data was posted online. Unfortunately though most of the populations didn’t have too many markers. This isn’t an issue in an of itself, but it becomes a big deal when trying to combine it with other data sets. If you limit the markers to those which intersect across two data sets you start to thin them down a lot, to the point where they’re not useful. Though the the results of the paper are worth talking about, the authors claim that they’ll be putting the data online. This is important because they used a large number of markers, so the intersections will be nice (I can, for example, envisage exploring the relationship between the North Africans and the IBS Iberian sample in the near future).

As for the paper itself, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations:

Proposed migrations between North Africa and neighboring regions have included Paleolithic gene flow from the Near East, an Arabic migration across the whole of North Africa 1,400 years ago (ya), and trans-Saharan transport of slaves from sub-Saharan Africa. Historical records, archaeology, and mitochondrial and Y-chromosome DNA have been marshaled in support of one theory or another, but there is little consensus regarding the overall genetic background of North African populations or their origin and expansion. We characterize the patterns of genetic variation in North Africa using ~730,000 single nucleotide polymorphisms from across the genome for seven populations. We observe two distinct, opposite gradients of ancestry: an east-to-west increase in likely autochthonous North African ancestry and an east-to-west decrease in likely Near Eastern Arabic ancestry. The indigenous North African ancestry may have been more common in Berber populations and appears most closely related to populations outside of Africa, but divergence between Maghrebi peoples and Near Eastern/Europeans likely precedes the Holocene (>12,000 ya). We also find significant signatures of sub-Saharan African ancestry that vary substantially among populations. These sub-Saharan ancestries appear to be a recent introduction into North African populations, dating to about 1,200 years ago in southern Morocco and about 750 years ago into Egypt, possibly reflecting the patterns of the trans-Saharan slave trade that occurred during this period.

The model outline here is straightforward:

- A population of West Eurasian provenance migrated across the fringe of the southern Mediterranean >10,000 years B.P. (Maghrebi)

- This was later overlain by a later West Asian migration (Near Eastern)

- A third major element here seems to be Sub-Saharan African admixture, which these authors claim is rather new (post-Roman)

Two of the methods used will be familiar to readers of this weblog. They used ADMIXTURE to generate barplots which fractionate putative ancestral components given K number of components. Second, they also use PCA to visualize the largest components genetic variation within the samples on a plane.

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As you “move up” the K’s you note that Maghrebi populations “split” from the Near Eastern reference, the Qataris. This is supported by the PCA, which shows that there is a dimension of variation which separates Near Easterners & Europeans from Maghrebis. The authors note that this dimension is orthogonal to the Sub-Saharan African vs. Eurasian component. That suggests that the putative Maghrebi component is likely to be part of the set of “Out of Africa” populations, rather than an African population which simply experienced continuous gene flow with West Eurasians.

They also estimate a Fst, a statistic which partitions genetic variation within and between groups. The value between Sub-Saharan Africans and Europeans is ~0.15 using HGDP SNP data, and between Europeans and East Asians ~0.10.  Using the Tuscans and Qataris as European and West Asian references against the North African populations along their east-west cline they estimate Fsts from ~0.03 to ~0.06. The higher end values are from populations which are less admixed with Near Eastern elements, and the colored polygons illustrate the domain generated by ADMIXTURE Fsts across inferred ancestral components. You also see in the chart estimated time of divergence. I won’t get into the assumptions in the model, but the authors do note that ~12,000 years B.P. seems to be the low bound estimate for when the Maghbrebis diverged from other West Eurasians. This is important, because it predates agriculture.

The final set of methods outlined in this paper looked at ancestry on a more fine-grained genomic scale. To the left you see a plot where each horizontal bar represents an individual’s chromosome 1 (among a set of North Africans). Each color in that bar indicates a component of ancestry (except the black, which are centromeres). This sort of information is important, because saying someone is 50% X and 50% Y summarizes information to the point of eliding it. An individual who is a first generation product of a Chinese-European marriage is going to have the same ancestral proportions as someone who is a Uyghur for those respective populations. But a fine-scale mapping of the genomic ancestry would look very different, because the history of the admixture is very different.

There are many inferences in the paper which I won’t address. Rather, let me focus on this one assertion:

After accounting for putative recent admixture (Figure 1), the indigenous Maghrebi component (k-based) is estimated to have diverged from Near Eastern/Europeans between 18–38 Kya (Figure 3), under a range of Ne and k values. We hence suggest that the ancestral Maghrebi population separated from Near Eastern/Europeans prior to the Holocene, and that the Maghrebi populations do not represent a large-scale demic diffusion of agropastoralists from the Near East.

This is not implausible on the face of it. The component of ancestry modal in the Mozabite HGDP sample tends to have a relatively high Fst in relation to other West Eurasian groups. I had wondered if this was due to ancient Sub-Saharan African admixture which had produced a particular stabilized hybrid, but these results indicate that the component is no closer than other West Eurasians. What I’m confused and skeptical about are the range of divergence times which different papers are producing which seem somewhat implausible taken together.

There are papers which posit that East Asians separated from Europeans ~25,000 years B.P. This is in the same range as the divergence between Maghrebis and West Eurasians, but the Maghrebi genetic distance (Fst) is about 1/2 as great. Also, these sets of results which generate a “bunching” together of the separation of many extant non-African lineages in the 20-40,000 year range imply very rapid differentiation after the “Out of Africa” event, if that event did occur ~50,000 years ago (at least for most Eurasians, even assuming a revised model whereby Australian Aboriginals derive from an earlier wave). One at a time any given divergence estimate may be broadly plausible, but the literature is just not particularly coherent on this matter, and it often seems archaeologically implausible.

Citation: Henn BM , Botigué LR , Gravel S , Wang W , Brisbin A , et al. 2012 Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397

Image Credit: Raphaël Labbé

The image above come from John Hawks’ weblog. I was thinking today about the resettlement of Europe since the Last Glacial Maximum. It is clear that much of northern Europe was not habitable until the Holocene, after the Ice Age. And those regions which were habitable were often marginal. But, there were zones of southern Europe which remained relatively clement. One model of how Europe was settled after the warming is that hunter-gatherers expanded north out of these southern refuges. This can explain the lower heterozygosity of northern populations (see map to left). They may have lost their genetic diversity to some extent through population bottlenecks or simply drift on the wave of demographic advance. And yet something jumped out at me on this map: the southwest portion of Portugal is reputedly the zone with the highest African admixture in continental Europe (for historical reasons). The heterozygosity may simply be a function then of the fact that southern Europe has been in greater contact with other regions of the world because of geographic proximity.

There is also a second pattern which has always elicited curiosity in me: why is it that the largest component of genetic variation in Europe separates north vs. south, as opposed to east vs. west? This does not seem to comport well with a model of expansion from southern refuges. Should not the west-east genetic variation of Ice Age Europeans who faced the tundra and ice be represented among modern populations as they expanded their range northward simultaneously? Something is wrong with the model.

First, it seems clear that a lot has changed since the Last Glacial Maximum. As recently as the late aughts authors were claiming that by ~20,000 years before the present the general shape of genetic variation we see around us had been set. I’d be willing to bet $5,000 dollars that that’s wrong. In the specific case of Europe there may be many explanations for the set of patterns we’re seeing. It may be that the original populations of the refuges were later replaced. Northern Europeans may be legitimate descendants of those groups, but the original patterns of genetic variation in southern Europe were washed away due to being overwhelmed by Neolithic populations from Anatolia. Or, it may be that modern people in the north of Europe descend from a group which moved laterally, and replaced and assimilated the original inhabitants of the continent.

There are many plausible models, and combinations of models. From what I have read people in the Reich lab are now attempting to construct a scenario for the ethnogenesis of Europeans analogous to that of South Asians. In other words, modern Europeans are a compound of the descendants of the Paleolithic hunter-gatherers with an intrusive population. The same lab seems to be positive that Indo-Europeans did have a substantial effect on genetics of South Asians. If so, then I see no reason why the same would not be so in Europe.

In any case, interesting times. We’ll know a lot more in exceedingly great detail soon enough (I’d be willing to bet money on that too!).

It’s just not that big of a deal anymore. But take a look at the order articles in The New York Times. There was a day that peopel were very worried about what “test tube babies” entailed. The end of the world as we know it? If that happened I don’t see anymore complaining.

The Globe & Mail in Canada has a very long piece on PGD, Unnatural selection: Is evolving reproductive technology ushering in a new age of eugenics? I do think it is ushering in a new age of eugenics, though it doesn’t go by that name. Many of the issues I’ve brought up on this weblog, such as the incentive for governments which fund national healthcare to take a deep interest in sifting through the range of future taxpayers and consumers of services, are explored. My basic instinct here is much more libertarian than most people. As a practical matter I’m rather close to a maximalist in terms of the amount of latitude I think parents should be given in selecting the nature of their offspring. But, I’m not a libertarian in an absolute philosophical sense, and I think a broader discussion in a society where the state and majority have coercive power over individuals is warranted.

There are two minor technical angles that I do want to bring up though:

- PGD seems to be ideally tailored already for people who marry their cousins. It would be relatively good at screening for the many recessive diseases which are common in the children of cousins. Also, it might even be able to reduce the fraction of runs of homozygosity through judicious selection. So, in the near future Muslim nations might be major consumers of PGD (Muslims as a whole are moderately anti-abortion, but they take a much more pragmatic line on these issues than the Roman Catholic church).

- PGD for trait selection runs into some statistical genetic difficulties. But, I wonder if perhaps PGD for decreased mutational load might be useful? With high coverage full genome scans could not one ascertain with good precision which genes have been subject to inherited or de novo deleterious mutations? It is generally assumed that loci where there is a major deleterious mutation masked by a normal functional copy still induce some fitness drag on the individual. The range in outcomes in siblings may be part of the natural variation in the mutational load. Parents may be tempted to lop off the asymmetrical-faced end of this.

I’m reflecting upon the post for a second time because it is very rich in ideas, and lays out may different general concepts and specific propositions. The bottom line from what I can gather is that Johnson agrees with those thinkers who believe that agriculture and the Neolithic revolution to a great extent reshaped social relations, and give us a skewed perception of “normal” human societies. I’m not going to rehash all of the points in the piece, but will focus on just a few which I think I can extend upon fruitfully.

Long time readers of this weblog know that I tend to accept that something radical shifted during the Neolithic revolution. I’m of the opinion that like most animals humanity’s state was Malthusian during the age of hunter-gatherers, and of farmers. That is, gains in population eventually absorbed productivity increases due to technology (e.g., bow and arrow) or surplus land (e.g., settlement of the New World by humans). But different forms of Malthusianism can obtain different stable states. The rhythm of life of a Chinese peasant and a Bushmen are very different, despite the fact that both may operate on the Malthusian subsistence margin. Malthusianism is a end point, it does not specify the dynamic by which one proceeds toward it.

Johnson relays the idea that prior to agriculture humanity had a matrifocal and de facto polyamorous bias. For the purposes of my thought here we need to separate the social and biological. In the social sense matrifocality simply means that males move between focal groups, while females remain in their natal groups. Polyamory implies that males and females may have multiple sexual relationships. In a genetic sense matrifocality should imply that Y chromosomes flow between groups (lower Fst), and mitochondrial lineages exhibit greater geographical constraint (higher Fst). In the longer term equitable pure polyamory would not be genetically distinguishable from pure equitable momogamy (because of more combinations in the former case there may be more diverse autosomal haplotypes, but I’m not sure this is very relevant for this discussion).

It isn’t innovative or surprising for someone to assert that agriculture was a major rupture in human history. Major public intellectuals routinely take a shot at characterizing what made it so special, and it’s a lively area of scholarship. Rather, I will reiterate here what I have held for many years: the “traditional” and normative social systems common among civilized societies since the rise of agriculture and the emergence of mass society are cultural adaptations which serve to constrain impulses which are deeply hard-wired within our species. Elite lineages the world over arranged the pair bonds of their offspring for many generations, and yet this often meets resistance, or at least resignation. The tales of adulterous lovers subject to a tragic fate are common literary motifs. This is I suspect an aspect of evoked culture, the inevitable tension between our deep impulses driven by individual preferences, and the social obligations which many have to had fulfill as part of extended kinship networks which had accrued prestige and capital. Both of these are human universals, as are the consequences. The high culture literature records this tension, and elaborates upon it so as to model proper and correct behavior for elites so as to avoid tragedy.

I have no doubt that hunter-gatherer societies had lineages which accrued prestige and capital. The modern hunter-gatherer societies which Eric Michael Johnson highlights are not representative of the human past. They have been relegated to marginal land. In the past hunter-gatherer societies drew upon lands with greater primary productivity, so the chasm between themselves and their farming successors in terms of physical capital and social stratification was often less than we may expect using the modern relics as references. But, agriculture clearly signaled a shift in scale and quantity. Super-male lineages, such as that of Genghis Khan, are possible only due to the contingent conditions of civilization, in particular all the elements necessary for globalism. Agriculture was likely an amplification of a “winner take all” dynamic in the game of social positioning. And not surprisingly these societies also developed complex belief systems and institutions to moderate and dampen these tendencies, likely due to their innate instabilities, as well as a human bias toward egalitarianism (i.e., land redistribution and opposition to inequality is a tendency in many societies at the commanding heights, while world religions all exhibit an anti-Nietzschean bent, for lack of a better term).

The reason that “Western culture” with its individualist ethos is so attractive, and threatening, is that in many ways it is a purer reflection of the impulses which were operative in the ancestral environment. I am not here talking about the most extreme manifestations of Western liberality in sexual mores, such as gay marriage or formal polyamory (most people do not crave homosexual relations). Rather, a modicum of personal choice and sexual egalitarianism, are out of keeping with the norms which were necessary to maintain social order in the period between small-scale hunter-gatherer societies and the rise of the mass consumer society. On the margins of subsistence in a world of farmers individual action may redound very negatively upon the broader kinship group, so personal norms of honor and propriety may be highly developed.

And yet if these cultural norms were so strong why did humans not evolve their way out of their hunter-gatherer ethos? There are two primary reasons for this. First, for much of human history the norms outlined in high culture texts and religions were applicable only to elite lineages. This is history recorded in the texts, but it may not be most of lived human history. For example, religious marriages in much of medieval Europe were obligate for noble families, but may not have been for peasants, who made recourse to common law relationships. Bastardy is less of a concern in scenarios where property divisions are of no consequence. There’s no property to inherit. But, this phenomenon is probably moderated by the fact that over much of history elite lineages may have been more fecund than the masses. Lived history may be more ephemeral than we realize in a genetic sense.

A second explanation though is that the very tendencies which make adherence to traditional norms somewhat discomforting on an individual level are necessary in other contexts. Love is an inconvenience when it comes to arranging marriages for your offspring optimally on a social dimension, but it may be necessary for men and women to invest in their offspring due to the love they feel for them so that they live and flourish. In other words, psychological impulses which were inconvenient in one domain were necessary and adaptive on others. Phenotypically I’m implying that there was functional constraint, and genetically it would manifest as pleiotropy. I suspect that a strong tendency toward developing loving bonds with children is a much more important characteristic in these elite lineages than dampening the initial discomfort that may occur when one is paired off with someone with whom one is not particularly enamoured. In a social and biological evolutionary sense romantic love is less important than we might think in our individualist age. But, romantic love remains hard-wired within us because it is biologically impossible to suppress its manifestation so long as we need the emotion of love more importantly to bind us together with children.

Finally, let’s go back to Johnson’s treatment of the disjunction between idealized polyamory and realized polygyny in the ancient environment (at least to a mild extent). By this, he points to the reality that some of the Y chromosomal data point to a reproductive skew, where a few males tend to give rise to a disproportionate number in the next generation. In extreme polygyny you have a Genghis Khan situation, where males of one narrow lineage have an enormous reproductive advantage. The scenario sketched out in Johnson’s post is that females may have had relationships with several males (and the inverse), but there was a tendency toward favoring reproduction with one focal male or female. This does not seem to negate the reality of jealousy and drama. We see this among common chimpanzees, who have a classic mating system in the extreme sense outlined by Johnson (this species has huge testicles to generate viscous sperm the competition is so extreme). And modern polygamorists who have formal relationships all tell tales of enormous time investments necessary to maintain proper relationship equilibrium. This is I think the reason that elite lineages in mass agricultural societies turned toward simpler relationship networks. The older model was simply not sufficiently stable for the purposes of maintaining the social and cultural systems necessary for the proper functioning of the older Malthusian civilizations. This is evident when conflicts within elite lineages are often rooted in questions of paternity and maternity (half siblings; Charles Martel was the bastard son of his father, who superseded the legitimate line), or accusations of false paternity (the first Chinese Emperor was subject to this rumors due to his bad reputation in later generations).

Where does this lead us? I think it’s complicated. Many social conservatives would argue that you can’t just dispense with the whole cultural toolkit which has organically evolved over the last 10,000 years, and revert back to the more primal state of affairs before agriculture. Social liberals point out that the forms of the past are no longer necessary in the present. But though affluence has removed many necessary social constraints, we have not warped ourselves back to the Paleolithic either. The balance between our instincts, which evolved in small groups thousands of years ago, and our notional cultural mores, which crystallized during the Axial Age, is still a work in progress. I believe that the world religions were version 1.0 in regards to formalizing workable compromises between our basic natures and the realities of the aristocratic world. What we need is a version 2.0, where we balance the needs of the common person on the street, with their basic impulses. The great compromise between our biology and our current social complexity will continue. But it is a dynamic parameter, not a static element.

We’ve got the lineage of the hobbit, ‘Homo floresiensis’ (in quotation marks because its human status in not yet clear), perhaps diverging more than two million years ago, evolving in isolation in southeast Asia, and apparently going extinct about 17,000 years ago.

We’ve got Homo erectus, most likely originating in Africa, giving rise to lineages which continue in the Far East in China and Java, but which eventually go extinct. In Europe, it perhaps gave rise to the species Homo antecessor, “Pioneer Man,” known from the site of Atapuerca in Spain. Again, going extinct.

In the western part of the Old World, we get the development of a new species, Homo heidelbergensis, present in Europe, Asia and Africa. We knew heidelbergensis had gone two ways, to modern humans and the Neanderthals. But we now know because of the Denisovans that actually heidelbergensis went three ways—in fact the Denisovans seem to represent an off-shoot of the Neanderthal lineage.

North of the Mediterranean, heidelbergensis gave rise to the Neanderthals, over in the Far East, it gave rise to the Denisovans. In Africa heidelbergensis evolved into modern humans, who eventually spread from Africa about 60,000 years ago, but as I mentioned, there’s evidence thatheidelbergensis populations carried on in Africa for a period of time. But we now know that the Neanderthals and the Denisovans did not go genetically extinct. They went physically extinct, but their genes were input into modern humans, perhaps in western Asia in the case of the Neanderthals. And then a smaller group of modern humans picked up DNA from the Denisovans in south east Asia.

We end up with quite a complex story, with even some of this ancient DNA coming back into modern humans within Africa. So our evolutionary story is mostly, but not absolutely, a Recent African Origin.

Now, I know that Milford Wolpoff has still not totally buried the hatchet with Stringer, but their views are actually converging a great deal. What does that tell us? Well, paleoanthropology most definitely is a science, reality and results are dictating to the intellectual antagonists.

(Via Ruchira Paul)

Now, however, comes evidence that India may in fact be succeeding. In a pair of articles in the Indian Express, Surjit Bhalla, an economist, and Ravinder Kaur, a sociologist, use a different set of figures to get a different result. On the basis of the national sample surveys (NSS), they calculate that India’s sex ratio at birth swung from 924 females per 1,000 males in 2004-05 to 977 in 2011, a stunning turnaround in favour of girls.

I hear about the problem of sex bias through selection (either abortion or greater neglect of female babies) a lot in the press. There are a few issues which the mainstream seems rather ignorant of, both theoretical and empirical. First, there is the Trivers–Willard hypothesis. It offers a strong theoretical rational for why high status lineages are going to exhibit a preference for males over females. It also is a reason to expect a shift toward male preference with economic development and elite emulation! Second, South Korea is not the only East Asian nation to switch from male to female preference of late. Japan has also done so, though nearly 15 years earlier. The fact that South Korea has followed the same social and economic track as Japan is highly suggestive that this is not a coincidence.

The issue of sex-selection is a big one. But before we talk about it I wish we could integrate the best theoretical models and empirical evidence. As it is, I hear constant “surprise” that economic development many lead to sex-selection, because of the prejudices that many have that economic wealth leads to greater sexual egalitarianism. In the long run this may be true, but as they say, in the long run we’re all dead.

Economic forecasting is a mug’s game. There are simply too many unknowable factors that affect “the economy” for anyone to make accurate predictions. The Fukushima earthquake and nuclear disaster, for instance, had a noticeably negative macroeconomic impact around the world, and nobody knows what lurks inside the hearts of central bankers. Plus, if I did possess the secrets to the future, I’d be making a fortune as a speculator, not telling you about it.

There are plenty of financial types who have funds where investment is contingent upon expectation of macroeconomic conditions. You know what they think because you know how they invest, and they’ll tell you what they think as well. What’s the point of journalists and academics even offering predictions if they don’t have “skin the game”? You can basically just say anything to be contrary, perhaps like in a publication such as Slate.

Here’s another anti-pessimism piece from Slate, No Pessimists Allowed! America’s economic recovery will be twice as big as experts predict. Date: January 2nd, 2010. With hindsight this was obviously unwarranted optimism. But how sure was the author, Dan Gross, about his prediction? It would be nice to get a sense if Gross had some put real money down on his predictions and made the values transparent. The amount of money would have given you a sense of the individual’s confidence in their proposition.

Of course, as Matt Yglesias says above why would he even publish his predictions instead of investing them? As Yglesias has said explicitly and implicitly he’s not a blogger for the money, he likes his job a great deal. He likes making predictions and performing rapid analyses. So that’s one reason why a Harvard grad with a degree in philosophy didn’t go to law school or into finance to make more money. But another issue here is that most journalists are probably not big enough individually to move the market. Therefore, their “small bets” would be a good gauge at least of how seriously to take any given prediction for their readers. Though obviously most readers aren’t interested in this stuff for truth. They just want to be entertained….