One aspect of human demographic expansions seems to be the fact that we often model them as a constant diffusion process, when in reality there were likely pulses (economic historians can conceive of this as the periodic gaps between land and labor factor inputs). I don’t know much about the human movements prior to H. sapiens sapiens, and from what I can gather the fossil remains are too sparse to be too wedded to a specific model, but it seems clear that anatomically modern human expansion occurred through a series of rapid outward sweeps which would periodically reach a “natural barrier.” Modern humans reached the Solomon Islands ~30,000 years ago, after which there was stasis for ~25,000 years. Only with the Austronesian expansion did humanity push past the Solomons. And this was no baby-step, ultimately the Austronesians went as far as the Hawaiian islands and Easter Island.

The New World is similar. The initial migration out of Africa by modern humans resulted in the range expansion of the human lineage into a region which had been untouched by earlier hominins, Australasia. But after that point tens of thousands of years passed before our species pushed into virgin territory, in this case North America. The when and the how of this though is still up for debate. A new paper PLoS One attempts to construct a plausible scenario by taking archaeological data points and inputing them into a diffusion model. Archaeological Support for the Three-Stage Expansion of Modern Humans across Northeastern Eurasia and into the Americas:

We use diffusion models…to quantify these dynamics. Our results show the expansion originated in the Altai region of southern Siberia ~46kBP , and from there expanded across northern Eurasia at an average velocity of 0.16 km per year. However, the movement of the colonizing wave was not continuous but underwent three distinct phases: 1) an initial expansion from 47-32k calBP; 2) a hiatus from ~32-16k calBP, and 3) a second expansion after the LGM ~16k calBP. These results provide archaeological support for the recently proposed three-stage model of the colonization of the Americas….Our results falsify the hypothesis of a pre-LGM terrestrial colonization of the Americas and we discuss the importance of these empirical results in the light of alternative models.

It’s an interesting paper because it seems to have been triggered in part by inferences made from the genetic data. I don’t know how confident archaeologists are about their radiometric dates, but I think some of the molecular clock results from the genetics of Amerindians need to be taken with a grain of salt (I don’t see many people repeating some of the really ancient coalescence dates for Amerindian Y lineages at this point).

These data seem to indicate that modern humans made it no further than previous hominin groups for several tens of thousands of years. But something happened within the last 20,000 years, and our species made the leap across Beringia. The bottleneck here is certainly not the Bering Strait, which was spanned by land much of the time in any case. Rather, our species didn’t have the biological or cultural capacity to survive in extremely frigid environments. I’ve read modern humans pushed the boundaries of their range in northern Europe further than Neandertals ever did, indicating our flexibility and plasticity. Since the human lineage had been resident in Eurasia for at least one million years that suggests to me that it was behavioral modernity that was key. In particular, how quickly our cultures evolve and shift. Though that flexibility itself may be a function of our biological competencies.

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Last spring two very thorough papers came out which surveyed the genetic landscape of the Jewish people (my posts, Genetics & the Jews it’s still complicated, Genetics & the Jews). The novelty of the results was due to the fact that the research groups actually looked across the very diverse populations of the Diaspora, from Morocco, Eastern Europe, Ethiopia, to Iran. They constructed a broader framework in which we can understand how these populations came to be, and how they relate to each other. Additionally, they allow us to have more perspective as to the generalizability of medical genetics findings in the area of “Jewish diseases,” which for various reasons usually are actually findings for Ashkenazi Jews (the overwhelming majority of Jews outside of Israel, but only about half of Israeli Jews).

Just as the two aforementioned papers were deep explorations of the genetic history of the Jewish people, and allowed for a systematic understanding of their current relationships, a new paper in PNAS takes a slightly different tack. First, it zooms in on Ashkenazi Jews. The Jews whose ancestors are from the broad swath of Central Europe, and later expanded into Poland-Lithuania and Russia. The descendants of Litvaks, Galicians, and the assimilated Jewish minorities such as the Germans Jews. Second, though constrained to a narrower population set, the researchers put more of an emphasis on the evolutionary parameter of natural selection. Like any population Jews have been impacted by drift, selection, migration (and its variant admixture), and mutation. Teasing apart these disparate parameters may aid in understanding the origin of Jewish diseases.

The paper is open access, so you don’t have to take my interpretation as the last word. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population:

The Ashkenazi Jewish (AJ) population has long been viewed as a genetic isolate, yet it is still unclear how population bottlenecks, admixture, or positive selection contribute to its genetic structure. Here we analyzed a large AJ cohort and found higher linkage disequilibrium (LD) and identity-by-descent relative to Europeans, as expected for an isolate. However, paradoxically we also found higher genetic diversity, a sign of an older or more admixed population but not of a long-term isolate. Recent reports have reaffirmed that the AJ population has a common Middle Eastern origin with other Jewish Diaspora populations, but also suggest that the AJ population, compared with other Jews, has had the most European admixture. Our analysis indeed revealed higher European admixture than predicted from previous Y-chromosome analyses. Moreover, we also show that admixture directly correlates with high LD, suggesting that admixture has increased both genetic diversity and LD in the AJ population. Additionally, we applied extended haplotype tests to determine whether positive selection can account for the level of AJ-prevalent diseases. We identified genomic regions under selection that account for lactose and alcohol tolerance, and although we found evidence for positive selection at some AJ-prevalent disease loci, the higher incidence of the majority of these diseases is likely the result of genetic drift following a bottleneck. Thus, the AJ population shows evidence of past founding events; however, admixture and selection have also strongly influenced its current genetic makeup.

The sample size of Ashkenazi Jews was ~400, and they looked at ~700,000 SNPs. As I said, how Jews relate to other populations really isn’t at the core of this paper as it was in the earlier ones from the spring, but there were the PCA plots (sorry Mike), a frappe bar plot, and a phylogenetic tree derived from Fst statistic. Again, remember that PCA is showing you the largest independent components of genetic variation within the data. The bar plot has a set of ancestral populations of which individuals are composites of. And finally, Fst measures between population component of genetic variation. The larger the Fst across two populations the bigger the genetic distance.

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PCA + frappe

PCA with labels

Fst & tree

Using the Druze & Palestinians as the ancestral Middle Eastern reference the authors estimated that the European admixture into Ashkenazi Jews is on the order of 30-55%. This is in the same ballpark as the previous studies, so no great surprise. As I stated in earlier posts the authors can spin the same results in very different ways. From what I can tell these authors are inclined to emphasize the strong possibility that in terms of genetic distance Ashkenazi Jews are somewhat closer to Europeans than they are to Levantine Arabs. Of course these sorts of assertions need to be handled with care. The genetic distance between Ashkenazi Jews and Tuscans is less than half that between Ashenazi Jews and Russians, while the Jewish-Russian value is about 50% larger than the Jewish-Palestinian one. Remember that there’s a fair amount of circumstantial evidence that Tuscans may themselves be a relatively recent hybrid population between indigenous residents of the Italian peninsula and Near Easterners.

One thing that this paper does do is rebut any strong assertion that Ashkenazi Jews are a genetically homogeneous population which went through a powerful bottleneck. Basically, the idea that Jewish diseases are just an outcome of the operational inbreeding that occurs when genetic variation is expunged from a population through low effective population size. The clincher seems to be comparison of heterozygosity of Ashkenazi Jews and gentile Europeans. The former are actually somewhat more heterozygous than the latter. There’s been a bit of evidence from previous research that the long term effective population size of Ashkenazi Jews was not necessarily very small, so this isn’t a total surprise. Remember that heterozygosity simply means the fraction of individuals heterozygous at a locus.

One way you can become heterozygous is naturally admixture. Remember that populations differ across many genes. As an example, there’s a pigmentation gene, SLC24A5, where all Europeans are at one state, and all West Africans in another. Naturally African Americans exhibit much more heterozygosity on this locus than the ancestral populations. The Ashkenazi Jewish case is less extreme because the two parental populations are genetically closer, but the principle still holds.

A consequence of recent admixture between genetically different populations are high levels of linkage disequilibrium, non-random associations of alleles at different loci across the genome. Why? There are many genes where two populations may be very different. Offspring inherit half their genome from one parent, and half from the other, and the parents pass along to their offspring particular associations of alleles. There may be a set of European distinctive alleles on a chromosome, and an African distinctive set of alleles, so that in a hybrid individual the alleles are strongly correlated across loci. These associations are broken down over time by recombination. The regularity of this process can serve as a clock with which to measure the period since admixture. African Americans were used to calibrate the time since admixture for the Uyghur people of western China, who are mixed from West and East Eurasian populations. The authors did not do this in this paper, I assume because the ancestral populations were genetically rather close in comparison to the two above examples, so there’d be less linkage disequilibrium to break down in the first place.

In the Ashkenazi Jewish population they found more linkage disequilibrium than in Europeans as well as longer haplotypes. This could be the result of a population bottleneck where drift could drive up the frequency of blocks of the genome, but as they note in the paper that should probably reduce heterozygosity. The natural inference then is that admixture between distinct populations can explain both data points.

But let’s cut to the chase. What genes exhibit signatures of natural selection in Ashkenazi Jews? More precisely, what distinctive regions of the genome exhibit signatures of natural selection? They used the standard haplotype type based methods. Basically you’re looking for regions of the genome where there are long blocks of correlated alleles, signs of a selective sweep due to a favored variant which dragged along flanking genomic regions as it rose rapidly in frequency, more rapidly than recombination could break apart the associations. Because recombination does breaks up associations over time, you need the selective sweeps to be relatively recent to detect them with these methods. Since the Jewish people, and Ashkenazi Jews more particularly, are relatively recent historically timing shouldn’t be an issue for Jewish specific sweeps. But another factor is that the two primary tests they used, EHH and iHS, are not good at picking up sweeps which are just starting. EHH is geared toward sweeps which are almost complete, so the frequency of the selected allele is near 100%. iHS is better are mid-range values. Using a combination of these two techniques they found that six genes which are implicated in diseases characteristic of Ashkenazi Jews have the hallmarks of natural selection. Natural selection is self-evident, so what seems to have been going here is that the disease was simply a side effect or byproduct of adaptation.

The strongest signal they found was in ALDH2. The strongest signal in Europeans, LCT, was not found in Ashkenazi Jews. But is LCT a strong signal in Europeans? Many Southern European populations have low frequencies of the derived LCT allele, indicating that they haven’t been subject to strong selection for lactase persistence. These are the same populations genetically close to the Ashkenazi Jews. The authors suggest that the Jewish-European admixture occurred before the sweep of the derived LCT allele, but it seems more plausible that the Ashkenazim simply admixed with a European population, such as Italians, which do not exhibit much lactase persistence. As for ALDH2, the association between genetic variation on this locus and alcoholism is well known, and has been used to explain the low Jewish rates of the disease. In this case, the authors posit that protection from alcoholism is a positive side effect of natural selection:

The mechanism driving selection of the ALDH2 locus is unknown, but a plausible target of selection also within this selected region is the TRAFD1/FLN29 gene, which is a negative regulator of the innate immune system, important for controlling the response to bacterial and viral infection (49). TRAFD1/FLN29 may have conferred a selective advantage in the immune response to a pathogen, perhaps near the time that the Jews returned to Israel from their Babylonian captivity. Despite the unclear selective mechanism, this remains a remarkable example of a putatively selected region accounting for a known population phenotype.

Many of the other loci naturally did not show signatures of natural selection. But this sort of work is exploratory, and there are limits to the power of their techniques. As it is, it seems that we’re very far along on understanding the phylogenetic tree of the Jewish people, and we’re finally getting a grip on the exogenous parameters which might prune the branches.

Citation: Steven M. Bray, Jennifer G. Mulle, Anne F. Dodd, Ann E. Pulver, Stephen Wooding, & Stephen T. Warren (2010). Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population PNAS : 10.1073/pnas.1004381107

Related: John Hawks, New data on Ashkenazi population history.

Image Credit: Wikimedia

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The autosomal genome of Ötzi the Austrian “Iceman” is apparently in the pipeline (from what I can tell they’re doing the analysis right now). What can we learn from one sample? Ann Stone, who was a graduate student on the original team which recovered his body, says:

A specialist in anthropological genetics, Stone is excited by the recent news but also cautious. “It is a sample of one. For us to really say something about that period, you need a sample of 25 to 50 individuals,” she explained during an interview with Deutsche Welle, Germany’s international broadcaster.

This is fine as it goes. Worries about sample size are pretty generic and if the practicalities permitted who wouldn’t want a bigger N? But whether you should worry about sample size is partly conditional on how much the findings deviate from what you’d expect. Imagine for example that ~25% of Ötzi’s genome was of Neandertal origin. Obviously it would be great to have 25 to 50 representative individuals from this region to know whether Ötzi was atypical…but the very finding itself would be of such large effect that an N = 1 would tell us quite a bit. Similarly, one genome of a Sub-Saharan African would be very informative if you had several hundred non-African genomes as a point of comparison (because Sub-Saharan Africans have so much genetic variation which is outside of the distribution found among non-Africans).

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In my post Pakistan ~10 years on I alluded to the fact that despite India’s robust economic growth of the past ~15 years or so in the aggregate there is a wide range of state-by-state variation. It is conventional in the media to point out the massive caste/class divisions in India, but because of the lack of familiarity with the geography of that nation there’s less reference to the regional gulfs. But if you look at the state-level data they’re rather large. The total fertility in the northern gangetic states of Uttar Pradesh and Bihar is ~4, while that in the southern states of Kerala and Tamil Nadu is ~2. Uttar Pradesh and Bihar are not trivial states, rather, they’re the two most populous! Additionally, they’re a meaty portion of the South Asian “Cow Belt”, the cultural heart of the subcontinent. The first great historic polities of South Asia, that of the Maurya and Gupta, had their focus in what is today Bihar, while later on the Muslim dynasts famously operated from a base around the region of Delhi in Uttar Pradesh. In the Indian cultural geography these states are the heart of Āryāvarta.

Wikipedia has a set of pages which rank the states of India by various metrics. The tables themselves are illuminating, but for non-Indian readers I thought a series of thematic maps would be better. Additionally, I added one scatterplot.

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electricity

gdp-per-capita-usa

literacy

tfr-vs-gdp-per-capita

total-fertility-rate

underweight-females

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To the left you see a map of the distribution of languages and language families in Europe. Language is arguably the most salient cultural feature of our species, as well as one of the most obviously biologically embedded. The trait of language is a human universal, to the point where even those without hearing can create their own gestural languages de novo. But the specific nature of language as it is instantiated from region to region varies greatly. Language in the generality is a straightforward utility with which you communicate with your fellow man. But language also separates you from your fellow man.

European nationalism in the 19th and 20th centuries was in large part rooted in the idea that language defined the boundaries of a nation. During the Reformation era some German-speaking Roman Catholic priests declaimed the value of the bond of language against that of religion, praising those non-Germans who adhered to the Catholic cause against German speaking heretics (in the specific case the priest was defending Spanish tercios brought in by the Holy Roman Emperor to put down the rebellion of Protestant German princes). In the long centuries between the Reformation and the Enlightenment the idea of a Western Christian Commonwealth slowly melted in the face of the rise of vernacular, but even after the shattering of Western Christianity with the explosion of Reformations the accumulated capital of a unified Christian European elite persisted. Hungarian Protestant students at Oxford could make do with Latin even if they were totally innocent of English (see The Reformation). Newer lingua francas, French and later English, lack the deep unifying power of Latin in part because they are also living vernaculars. They may resemble Latin in some particulars of function, but eliding the differences removes far too much from the equation to be of any use. Linguistic diversity is a fact of our universe, but how it plays out matters a great deal, and has mattered a great deal, over the arc of history.

This is the subject of Empires of the Word: A Language History of the World. Nicholas Ostler, the author, tackles an enormous subject here. He acknowledges the Herculean nature of his task in the introduction. And yet he does avoid some of the more intractable controversies within historical linguistics by constraining his subject matter to the period of history. That is, where we have some written records. This means that Ostler does not address the origins of the Indo-European language family, or the more recent expansion of the Bantus. Despite being separated by thousands of years these are both in the domain of pre-history, because we have no written records of proto-Bantu or proto-Indo-European. This does not mean that the book is not ambitious all the same. On the contrary, Empires of the Word takes on the “thicker” and messier tangle which is the association between language and fine-grained historical processes, social, cultural, economic and political. How history has shaped the nature and distribution of languages which we see extant in our world today is a labyrinth with many doors. Ostler doesn’t come close to opening the majority of those doors, but those he selects in Empires of the Word yield a rich number of surprises and insights, though he does not in the end seem to be able to generate a Grand Unified Theory of linguistic diversity and change from the welter of details.

There are two parallel threads throughout Ostler’s narrative: description and prediction. The latter is not prediction as a physicist would predict, rather, it is as a historical scientist might. Taking the data and producing models which can plausibly explain the phenomena we describe. Let’s take a look at the top 20 languages in the world. It seems that there are two primary ways that the speakers of a language can become numerous: rice & empire. Such a generalization is a bit glib, as many Mandarin speakers do not live by the “rice bowl,” but the big picture is that some languages gained adherents through “brute force,” pushing inexorably against the Malthusian possibilities of primary production and reproduction and assimilating smaller groups on the wave of advance of the speakers. The Asian languages on this list fall into that category. In contrast, you have the languages which spread with empire, exploration, and colonialism. English and Spanish are the exemplars of this class. Of the hundreds of millions of English and Spanish speakers a majority can not be accounted for simply by demographic expansion of the home countries. Rather, these languages colonized new lands, and acquired new speakers, rather rapidly over the past 500 years. Turkish is almost certainly in this category, though the transition from Greek, Armenian and Kurdish speech in Anatolia is less clearly understood because of thinner textual records of the process.

Of course the distinction between the two is somewhat artificial. The expansion of Mandarin, let alone the Chinese dialects, was almost certainly a synthesis of demographic expansion & migration, and linguistic assimilation of “barbarians.” Han Chinese are a genetically far less homogeneous than the Koreans or Japanese, in large part because the expansion of Han identity occurred over  a diverse group of populations which were resident within China proper 2,000 years ago. Similarly, it seems implausible that the Vietnamese ethnically cleansed all the Malay and Khmer speaking populations along the Annamese coast as they pushed toward the Mekong delta. The genetic data in fact hint to a large scale assimilation of Malay Chams by the Vietnamese. Inversely, the rise of English was partially accompanied by the demographic explosion of British peoples, while Spaniards contributed a great deal genetically to the mestizo populations of the New World. So it is not rice or empire, but rice and empire. Albeit with different weights on a case-by-case basis.

“Rice” really refers to social, cultural and economic forces which bubble up from below and swallow up the numerous islands of linguistic diversity. “Empire” connotes the political and military structure which allows for the trickle down from above of imperial values and mores. But the two are also intimately connected. The Chinese state under the Ching Dynasty saw a rapid rise in population, and that rise was enabled in large part due to political stability. That stability fostered long term projects which increased the land under cultivation as well as public works infrastructure which could distribute grain so as to dampen the effect of local shocks. The Greek historian Polybius attributed the resiliency and strength of the Roman state in to its assimilative capacity, turning barbarians into citizens. The military and political resiliency of the Roman Empire through the Crisis of the Third Century was probably conditioned on the expansion of Romanitas from the the Atlantic to the Black Sea (the military core of the revival drew from the Latin speaking regions south of the Danube in the Balkans).

Just as the Roman Catholic Church is sometimes referred to as “the ghost of the deceased Roman Empire,” so the distribution of modern languages are tells of political, social and economic events of the past. Social and economic forces almost certainly loom large in language family explosions which Ostler did not cover, that of the Bantus, the Polynesians and Indo-Europeans. In the first case it seems that the Bantu peoples brought with them a new mode of production to east and south Africa. This was then a rice expansion, along with some genetic assimilation. The case of the Polynesians is more difficult, but the existence of a similar group in Madagascar, attests to the power of long distance seafaring techniques in scattering obscure peoples. Without the existence of Malagasy, both their genetic and linguistic uniqueness, the written record would not clue us in to the existence of an organized community of long distance seafaring Southeast Asians across the Indian ocean basin. Finally, the Indo-European expansion is more mysterious because it is so much further back in time, but it is also the most significant as nearly half the world’s population speaks an Indo-European language. David Anthony in The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World makes the case that a shift toward nomadic pastoralism enabled by the horse is the critical catalyst for the sweep of this language group from the Atlantic to the Bay of Bengal.

Though the Indo-European case is likely an ancient one Empires of the Word actually begins its story earlier. Ostler’s in depth knowledge of ancient Near Eastern linguistic history is frankly mind-blowing, and is arguably the most insightful and novel spin on the topic I’ve ever encountered. The extent of detailed and subtle grasp of the facts is awe inspiring. I did not know, for example, that the Elamites of southwest Iran once had their own writing system, which they eventually abandoned for Akkadian cuneiform. Ostler recounts the life-after-death which Sumerian experienced for over 1,000 years because of the nature of cuneiform itself, which was fitted to the Sumerian language, a linguistic isolate with no known relatives. For the last thousand years of cuneiform it was written in Akkadian, the first great Semitic language in the world, later to be succeeded by Aramaic, Punic, Hebrew, and Arabic. Parallel to the waxing and waning of these antique Semitic languages was the ebb and flow of ancient Egyptian, with its own peculiar form of writing.

One aspect of these ancient societies and their languages is the almost cold-blooded torpidity with which change occurred. Sumerian persisted as a liturgical language in what became Babylonia down to the Roman and Parthian period, 3,000 years of written history. The social-political entity which we term ancient Egypt arguably spanned 2,500 years, up until the final Persian conquest. Egyptian culture in a sense that the Pharaohs would recognize persisted for another 1,000 years, until the closure of the Temple of Philae under the orders of the Christian Emperor Justinian in the 6th century. This cut the last link with the literature and religion of ancient Egypt. Consider that the time between our own era and that of Jesus Christ is equivalent to that between the rise of the Egyptian polity and its decline in the late Bronze Age. Though there are certainly similarities between Paul of Tarsus and a modern Western man, a great many disruptions have broken chains of cultural continuity.

There may be one exception to this, and that is another language which arose just as Egypt went into decline, and that is Chinese. Classical Chinese in its written form remained relatively static between the ancient period of the first dynasties, and the early 20th century. This continuity is telling insofar as Western scholars never had to “discover” the history of the Chinese, they had always remembered it. The continuity of language, culture values, and political and ethnic identity, dovetailed together so that despite the reality that the architecture of China is ephemeral, its stories are not. In contrast, much of the literary corpus of the ancient Western world comes down to us only because of three intense periods of copying: the Carolingian Renaissance, 10th century translations in the Byzantine Empire, and the Abbasid translation project in the 9th century. The history of the societies before Greece was perceived only obliquely through the Bible and the classical authors. Modern archaeology and linguistics eventually unlocked the secrets of both hieroglyphics and cuneiform, but the reality that we did not know of the significance of the Hittites in the ancient world attests to the poverty of knowledge which lack of cultural continuity imposes (the great disruption between the Indus civilization and pre-Maurya India means that the script of the former remains lost to us).

The distribution and continuity of dead languages also is a signpost for that other aspect of human culture which is very powerful and ubiquitous: religion. Today most of the Latin spoken is “Church Latin,” and that is because of the languages sacred role within the Roman Catholic Church. Though Hebrew is the spoken language of the secular state of Israel thanks to a modern revival, for nearly 2,500 years it was a language of religion only, as the Jews adopted the languages of the people amongst whom they lived, Aramaic, Greek, Persian, Arabic, Latin, German, etc. The ancient languages of the Near East, Coptic from ancient Egyptian, and Syriac from Aramaic, persist as liturgical languages. It seems that so long as the gods do not die in the minds of believers the tongues of the ancients persist down the ages. So next to the language of rice and empire, you have languages of the gods.

As I indicated above Empires of the Word is rather thin on robust generalizations. But one point which the author mentions repeatedly is that the rise and fall of languages of great expanse and utility is the norm, not the exception. In particular, Nicholas Ostler takes time out to emphasize that languages which spread via trade often do not have long term staying power. Portuguese, Aramaic, Punic and Sogdian would fall into this category (the later success of Portuguese was a matter of rice and empire in Brazil). It seems that mercantile communities are too ephemeral, that successive historical shocks inevitably result in their decline when there isn’t a peasant demographic reservoir or imperial power which imposes it by fiat. Even those languages which eventually spread beyond traders and gain cultural and political cachet may fall from grace. Greek is the best case of this. It was the dominant language of the Roman East, and spoken as far as modern Pakistan, and studied in Dark Age Ireland. By the early modern period it was a strange and foreign language in the West, and with the rise of Islam in the east it lost its cultural glamor, and even those Christians in Arab lands who were Melkite, Greek Orthodox who adhered to the theological position of Constantinople, became Arab in speech and identity (in greater Syria the Greek Orthodox have been instrumental in the formulation of Arab nationalism).

And yet to some extent one must be cautious about over-reading the recession of Greek in the face of Arabic after the rise of Islam. Ostler repeats the conventional wisdom that the predominant vernacular in the Roman East was never Greek, but rather Semitic dialects descended from Aramaic. This is manifest in the fact that the Oriental Orthodox churches do not use Greek in their liturgy, but forms of Syriac. Their root is in an alternative intellectual tradition from that of the Greek Church. The transition to Arabic was then predominantly from a closely related Semitic language, not from Greek. One of the theses to explain the spread of Arabic across North Africa, but not into Persia, is that Arabic found it easier to replace other members of the Afro-Asiatic language family. I can accept that people can intuitively perceive differences of language family without a deep knowledge of said languages. In Sons of the Conquerors: The Rise of the Turkic World it is recounted that an ambassador to the court of the Hapsburg Emperor in Vienna communicated to the Sultan that apparently the locals spoke a dialect of Persian! Persian and German are of course both Indo-European languages, and set next to Turkish they may sound vaguely similar.

This thesis is plausible to me, and I have long held to it in regards to Arabic’s replacement of Aramaic. I have been told by a friend who is familiar with both languages (in addition to Hebrew) that they are rather close, and if not intelligible close enough to make language acquisition much easier. But Ostler extends the argument much further, suggesting that genetic affinity also explains the replacement of Egyptian and Berber dialects in North Africa. These are Afro-Asiatic languages, but they are not Semitic. I assume linguists do perceive similarities of character which can connect these languages, but what features span the Afro-Asiatic languages which would make language acquisition easier even at this remove of relationship? The Afro-Asiatic theory for the spread of Arabic is somewhat convenient in that it does explain the data well: Arabic has spread widely only in regions of other Afro-Asiatic languages, the exception being in Spain. And in Spain the Mozarab dialect had a stabilized existence with the Romance language of the rural areas, which eventually came back in the form of Castilian, Portuguese, etc. What Nicholas Ostler seems to be proposing is that the world of language acquisition is not flat. This is clearly true for closely related languages, but I think the thesis needs to be explored for distantly related languages from the same family. Does a native speaker of Marathi have a leg up on a Hungarian when it comes to learning Gaelic? I remain skeptical of the affirmative in that case.

So Empires of the Word outlines some broad generalizations of how languages grow, which seem born out by the record of history, and offers some more speculative theories about the importance of the cultural terrain upon which languages can flow and spread. But the narrative also lingers long on the future of the current lingua franca of our age, English. Nicholas Ostler does nothing to dismiss the omnipresence of English at the commanding heights of international culture. He reports for example that in 1994 50% of international telephone calls were between English speakers. 45% were between English speakers and those who were not English speakers! That means only 5% of international calls in 1994 were cases where people neither spoke English as their native language. I suspect that the numbers have changed a bit since then, but if that study is correct then it points to the awesome international spread of the English language. But Nicholas Ostler does not think that it will last, and his rationale seems to be the record of history, where such universal languages always fall. His next book, The Last Lingua Franca: English Until the Return of Babel outlines his thesis in detail.

And yet contra Ostler I have to suggest that perhaps this time it’s different. I do not believe that English in a unified form will dominate all. Already there has been considerable dialect drift. But the past 200 years are qualitatively different from what has come before, and there is already a revolution in communication technology. It may be that in the future languages do not crystallize as a function of geography, but perhaps more as a function of class and occupation. It does seem historically that trade lingua francas have been ephemeral in impact, and English, the language of McWorld, is the language of capital. But the modern world is much more dependent on flows of capital and commerce than the pre-modern world, the Sogdians and Portuguese were primarily vectors for high value luxury goods. Pre-modern capitalism had the air of a parlor game between the high and mighty, and was quite often in bad odor among rentier elites themselves. It is with reason that I observed above that the pace of cultural change in the past was less than what it is today. Positive feedback loops may be much more powerful than they once were, so that a “Globish” derived from English may quickly sweep away all comers, before it diversifies again.

But really I should wait for Ostler’s new book. The arguments I make here may be addressed, or I may misunderstood what I gleaned from Empires of the Word. It is as I said a story with rich and vibrant detail, much of which I glossed over, or did not address. For that Ostler’s tale is worth the time it takes to complete it. But there is I must say a lack of theoretical punch and heft. Perhaps this is just a function of the subject domain, which has too much complexity to distill down to any model of elegance or tractability. But I suspect a more rigorous analytical framework could squeeze some juice out of the enormous pile of detail which Nicholas Ostler has at his disposal. Perhaps he should read Replicated Typo.

Image Credit: Wikimedia, Ethnologue

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Most readers of this weblog are aware that the United States is in a mission of “nation building” in Afghanistan. I know that we probably deny that, but that’s what it is. Going through Google data explorer I’m struck by what an exceptional nation we’ve decided to intervene in. Below is a chart which has infant mortality rate on the y-axis and life expectancy on the x-axis. I’ve allowed the bubbles to be defined by their regions in terms of color, and labelled the South & Central Asian nations to give a sense of the change in vital statistics for the “peers” of Afghanistan over the past generation. Observe that Sub-Saharan Africa is pulling away from Afghanistan in the last 10 years!

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“…the occupation of Australia/New Guinea is momentous in that it demanded watercraft and provides by far the earliest evidence of their use in history. Not until about 30,000 years later (13,000 years ago) is there strong evidence of watercraft anyway else in the world, from the Mediterranean.

Initially, archaeologists considered the possibility that the colonization of Australia/New Guinea was achieved accidentally by just a few people swept to sea while fishing on a raft near an Indonesian island. In an extreme scenario the first settlers are picture as having consisted of a single pregnant young woman carrying a male fetus. But believers in the fluke-colonization theory have been surprised by recent discovers that still other islands, lying to the east of New Guinea, were colonized soon after New Guinea itself, by around 35,000 years ago….”

- page 42 of Guns, Germs and Steel

The settlement of Australia is a breakthrough in the “human story.” Very soon after anatomically modern humans began to replace (and to some extent assimilate) other lineages of our genus in Eurasia we pushed beyond the previous outer limits of the domains of humankind. The ancestors of Australian Aboriginals swept past the Wallace Line, and quickly settled the Ice Age continent of Sahul, consisting of Australia and Papua New Guinea. The biogeography of Australia is well known. Aside from bats and some endemic rodents the continent was free of placental mammals before modern humans arrived.

As for when these humans made landfall, there is some debate as to that particular issue. The oldest remains from Australia, Mungo Man, has been dated to anywhere between 70,000, and 30,000, years before the present. If we took the older date then Australia would have been settled almost immediately after the expansion of non-African modern humanity. If we accepted the younger date, then the settlement of Australia would have been concurrent with the final replacement of Neandertals by modern humans in Europe. The current consensus seems to be that Mungo Man dates to approximately 46,000 years before the present. As the first dating of a particular individual from a species in a region is liable to miss earlier individuals who were not fossilized it seems likely that Australia was settled by anatomically modern humans on the order of 46,000 years before the present, but somewhat earlier than that date. That would imply that Australia was populated by anatomically modern humans at least 10,000 years before Europe. One should probably not be too surprised by this. Out-of-Africa humans were probably initially tropically adapted so lateral migration would have been easier, but also, there were no hominin competitors in Australia.

But how do these archaeological insights relate to the current Aboriginal population of Australia? Such questions are fraught with politics, but let’s put that to the side. We know that Australia was not totally isolated from the rest of the world. The dingo arrived from Southeast Asia within the last 4,000 years. The Aboriginals of northern Australia were certainly familiar with the idea of agriculture, because they traded with the Torres Straits Islanders, who were farmers and seafarers, and who had contacts with New Guinea (see After the Ice). Some anthropologists, such as Joseph Birdsell, proposed that modern Aboriginals were a compound of multiple migration events, and had undergone a great deal of evolution in situ. Additionally, classically trained physical anthropologists in the early 20th century noted morphological parallels between Australian Aboriginals and the peoples of India, giving rise to the construct of the Australoid race (a term still used by Indian anthropologists). As I noted earlier the connection between South Asia and Australia genetically seems likely to be distant and tenuous at best, inferring from what we know of uniparental markers (genetic variants passed only through the mother or father, the mtDNA and Y). The genetic data tentatively seem to reject Birdsell’s model, and favor a more parsimonious one of a single original settlement on Sahul, and subsequent diversification and isolation (Australia, Tasmania and Papua New Guinea were separated only ~10,000 years ago with rising sea levels).

But there’s only so much that uniparental lineages can tell us. There are limits to the information one can glean from relatively short sequences of mtDNA and Y, and, these gene lineages are subject to their own particular dynamics. Not only do human mating patterns exhibit sex-specific biases, but the neutrality of these lineages from an evolutionary perspective has been questioned. And, the haploid nature of these loci also mean that the effective population size is small (i.e., only copy of each per person, instead of two as in the case of most genes) and stochastic fluctuations may be more extreme than in the rest of the genome. On the one hand more random variation could allow for the emergence of greater between population differences which might be informative, but on the other hand it can also swamp out the past history too quickly and result in convergences which tell us nothing about phylogenetic connections.

All this is why a new paper looking at the broader genomic patterns of variation in Australian Aboriginals is important for clarifying and adding more precision to our evolutionary historical assumptions, which would frame more specific inferences about this population. There are, and were, difficulties in obtaining the data for historical and political reasons. But now that the barrier has been breached, I assume that we’ll be seeing more in the near future. Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry:

Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region. The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent’s unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues.

The sample consisted of 38 individuals, 30 females and 8 males, from the Riverina region of New South Wales. The sample size may be small, but for the broad-brush and relatively coarse questions being asked in this paper they’re sufficient. Consider that genomic sequencing of one Native American and one Bushman could tell you that the latter is likely to come from a far more genetically diverse population than the former. If you constructed a phylogenetic tree with half a dozen individuals of each of the populations you’d see that the Native Americans are a subset of the Bushman genetically, so to speak. If you’re trying to distinguish between questions such as, “did the last common ancestor of Australian Aboriginals and Javanese live 5,000, or 50,000, years before the present”, then this is a sufficient sample. A bigger issue is that the sample has substantial European admixture through the paternal lineages. From what I have heard attempts were made to get a more “pure” Aboriginal group, but the logistics were too difficult in the end. Science is the art of the possible.

They used an Affymetrix chip with nearly 1 million SNPs (out of 3 billion base pairs), but filtered it down even further for this analysis. Most of the work used a data set of ~160,000 SNPs, arrived via quality controls, as well as the intersection with HapMap3 and HGDP SNP sets. Again, in light of the coarse questions asked 160,000, let along 16,000, should probably suffice. Remember they’re trying to move beyond what we can infer from classical autosomal markers and uniparental lineages. This is a big step in that direction.

The figure to the left shows two phylogenetic trees (note: I may reedit these figures for ease of display or clarity). The utility of the trees is obvious: they’re showing you how populations relate to each other. So you throw all the individuals in each given population into a pot, average out their genetic character, and perform pairwise calculations on them. The other groups are from the HGDP data set. The statistic they’re using is F_st; basically a measure of between population genetic variation. Alleles, genetic variants, vary in frequency from population to population, as well as the fact that different individuals within populations have different genotypes, and this is just capturing the component which is varying across populations. So as an example, if the allele x in two populations is at frequency 0.5 for both, then the F_st is 0. There’s no difference. If x is at 1 in one population and 0 in the other, then F_st = 1. All the variation is between the populations, since there is none within the populations.

The trees illustrate visually the relationships in an F_st matrix of pairwise population comparisons. Populations which are genetically close are not very distant from each other along the length of the tree, while those which are genetically very different are farther from each other terminus-to-terminus. But remember that these visualizations don’t tell us anything necessarily in a concrete manner before we interpret them through the filter of what we already know. For example, the Mozabites, “MOZ”, are outside of the main clusters. Why? Without knowing anything about their history we might assume that they were isolated from the original African population at an early point in time (though observe the minimal distance from the trunk, peculiar). But we know their history, and the topology in that region of the network is an outcome of admixture. The Mozabites have a substantial amount of recent Sub-Saharan African ancestry. Similarly, two of the groups near the root of the East Eurasian cluster are actually relatively recent admixtures between West and East Eurasian populations, the Uyghurs and Hazaras.

The Australian Aboriginals are similar to the Mozabites, Uyghurs and Hazaras. Their position in the first panel is near the root of the Oceanian cluster. This is due to their substantial European admixture, which we know is present through their oral history, recorded history, and, the physically composite nature of many modern Australian Aboriginals. To generate the second tree the authors reconstructed the allele frequencies of the Australian Aboriginals by subtracting the European component of admixture. They did this by noting that they had Western European populations in HapMap3, and the offspring population between these groups which they knew, and the unknown Aboriginal parent population.  Using the Structure program they simply performed the algebra, whereby Aboriginal = Admixed Aboriginal – European (OK, not “simply”). And as you can see, by using the reconstructed Aboriginal allele frequencies the tree now places this group, AuR*, firmly within the Oceanian cluster.

The clustering of the Oceanian groups itself alone gives us strong evidence that the settlement of Sahul was by one population which later diversified, rather than separate independent groups. But let’s back up a bit, and look at the admixture aspect again. To the left you see the PCA plots of the HGDP data set which you should be familiar with. Each axis represents and independent dimension of genetic variation.  For the first panel the x-axis, PC1, is the separation between Africans and non-Africans. This is the biggest dimension of variation, and points to the Out-of-Africa event. The second dimension seems to map well onto the east-west axis, more or less. Remember that each PC is rank ordered in terms of the proportion of the total genetic variation which it can explain independently. Interestingly PC3 and PC4 allow for the separation of Oceanians and Amerindians from other groups. In isolation-by-distance and serial bottleneck models it shouldn’t be too surprising that these two groups on the geographic margins of the traditional human range would exhibit some genetic peculiarities due to their history after separation from Eurasian groups. This is why the Kalash of Pakistan are also outliers, this non-Muslim tribe remained isolated in their mountain valley and so accumulated their own genetic distinctiveness.

And yet note the position of Amerindians and Oceanians in the first panel, they’re somewhat closer to West Eurasians than East Asians. In the case of Amerindians there has long been the model whereby the ancient Beringian population which expanded into the New World had a component of ancestry which was closer to West Eurasia. This is true today among Siberian groups such as Yakuts, but differentiating the more recent introgression of Russian ancestry with an ancient West Eurasian substratum is difficult.

But admixture is surely part of the puzzle too. Compare the linear topology of Aboriginals and Amerindians with African Americans. The PCA plot is putting the focus on between population differences, so these sorts of distributions, so cleanly linear, are indicative of possible recent admixture between two distinct populations. The populations of the New World and Australia were relatively small and thin in terms of distribution, so it should not be too surprising that a substantial uptake of European ancestry has occurred in both cases. Isolated cases of individuals “going native” probably illustrate a bigger trend. The 2002 film Rabbit-Proof Fench was a dramatization of the reality that quite often children of mixed heritage will identify with one culture and parent. This is not an atypical disjunction between genes and culture in terms of their mode of inheritance. Both parents contribute equally genetics to the autosome, but cultural contribution is more of a contingent matter.

To further explore the admixture within Aboriginals the authors performed a frappe and Structure analysis. These two methods differ in the details but perform basically the same operation; they take individuals and assign components of their genome to K putative ancestral groups. So K = 2 would indicate 2 ancestral groups, while K = 10 would indicate 10. Here’s we’re looking at K = 5. Again, proper caution is warranted with these methods because without context we may not be able to interpret the results. But in this case the ends are clear and distinct: what is the extent and range of European ancestry in this Australian Aboriginal sample? Both the frappe and Structure programs paralleled each other in outcome; the Aboriginal sample varied quite a bit in ancestral quanta. The Papuans and Melanesians serve as appropriate Oceanian references. The Melanesians have a residual component (shaded orange and yellow top to bottom) which is similar to East Asians. This is a marker of the Austronesian expansion into the Pacific. The Papuans and Aboriginals generally lack this, which stands to reason considering their greater cultural isolation from the Austronesians.

The frappe and Structure results dovetail perfectly with the PCA plots. Both suggest that the Aboriginal population is admixed, with the parental populations being West Eurasian (European) and Oceanian, and, that that admixture varies from individual to individual.  The F_st also suggested this, though at a coarser population wide scale, and only with prior knowledge of the possibility of admixture. Not only that, but the mtDNA and Y chromosomal results on these individuals also comes out to the same inferred proportion. Recall that there were only 8 males, so the Y sample is small. But they calculate that ~40% of the Y lineages are not Aboriginal, while nearly ~100% of the female ones are. This sort of disjunction is common in the New World among Mestizo and African American populations, as well as the mixed Cape Coloured population of South Africa. The proportional of autosomal ancestry inferred from these uniparental markers is about what was calculated with their SNP-chip, suggesting the persistence of this sex-biased admixture pattern over the past two centuries. Remember that if something more complex demographically had occurred we may not have been able to infer admixture from uniparental lineages. Imagine if the Aboriginal tribes in New South Wales which were admixed were decimated by an unadmixed group, so that only the females from the admixed group survived. After that event both mtDNA and Y chromosomal lineages would have been Aboriginal, but the European ancestry would persist in the autosome.

To the left is an estimate of individual-to-individual ancestral quanta. The mode, the most frequent value, is near the total genome estimate of the whole population, around ~2/3 Aboriginal. There is clearly a wide range of variation in admixture. It looks like that within this Australian Aboriginal community 20% of this sample are 50% or more European in ancestry. Interestingly one man is ~100% Aboriginal. The authors do remark that their estimates are probably low balling the Aboriginal ancestral quantum; the SNP-chip was constructed with European genetic variation as a baseline, so it is missing Australian variation on loci where Europeans are monomorphic. But even with that taken into account the  Aboriginal group here is substantially admixed. This prompts me to ask: is it possible that there is more distinctive indigenous genetic material in the ~20 million white citizens of Australia than within the indigenous groups themselves? I’ve already suggested that this dynamic is exactly what is operative in Brazil, but the analogy is only rough a best. Many Australian whites derive from recent waves of migration and may not have any ancestors with roots back to the 19th century (i.e., all their grandparents and/or parents may have been born in Europe or the British Isles). But that must be balanced against the fact that Australian Aboriginals are much more European in ancestry than Brazilian Amerindians likely are. The rapid growth of indigenous Australians can’t be a function purely of high fertility. Rather, many people of mixed heritage are identifying as indigenous. The outmarriage rates for urban Aboriginals in some of the literature is estimated to be in the 70-90% range.

So far we’ve covered aspects of Australian Aboriginal genetics relevant to paleoanthropology and historical population genetics. But as I have observed many a time, one of the primary reasons for this sort of population analysis is to clarify background parameters for medical genetics. The life expectancy gap between indigenous and non-indigenous Australians is on the order of 10 years. It also seems plausible that the same disease-driven population crash which occurred in the New World after contact with Europeans was also driving population changes in Australia around the time of European settlement. Since Aboriginals were generally hunter-gatherer groups many infectious diseases which required higher densities could only be incubated among Europeans. Aboriginals near European settlements, or those who settled within them, would naturally be exposed to these infections and suffer greater morbidity and mortality. One wonders if some of the diseases which Aboriginals suffer from are due to genetic differences between the populations in regards to immunity, as well as the “diseases of civilization” (e.g., type 2 diabetes).

As noted in the paper admixed populations present both pitfalls and opportunities when it comes to elucidating risk alleles:

Whereas the admixture present in the AuR [the Riverina Aboriginals -Razib] sample presents a potential challenge in conducting traditional association methods for disease gene discovery…it opens the possibility of using admixture mapping…Admixture mapping is most suitable for traits, like CKD, that differ in frequency between the two parental populations of an admixture group. The approach essentially looks for genomic regions with an excess of higher-risk population ancestry relative to other regions or controls..A set of markers, spread across the genome, that are highly informative as to ancestry (ancestry informative markers or AIMs) is an essential requirement for admixture mapping.

CKD above refers to chronic kidney disease, which Aboriginals suffer at ~10 times greater rates than non-Aboriginals. To the left is a figure which shows the distribution of SNP rs12458349, a derived allele which has the highest F_st value between AuR* and HapMap3 populations. The genomic region which rs12458349 is embedded within has been implicated in diabetic nephropathy, a major cause of CKD. Derived here means that the SNP is evolutionarily novel in relation to the ancestral state, which all other human populations exhibit.

So why is this derived variant at a high frequency in Aboriginals (and other Oceanians), but not other human populations? It could be random genetic drift. As populations migrated out of Africa they may have gone through bottlenecks and isolations in a step-wise fashion and each group down the spatial and temporal sequence would accumulate their own unique variants. Or, it may have been adaptation, which drive up frequencies through positive selection around that genomic region. But this is where limitations of sample size and representativeness crop up, as these are not quite the coarse questions which we were focusing on earlier. From the the text:

Genetic drift, or random changes in allele frequencies, is expected to be a major force in a population, like Aboriginal Australia, that has been relatively small and/or isolated for a long period of time. Differentiation could also be explained by natural selection. The presence of several highly differentiated SNPs in the region, spanning nearly 0.5 Mb in length, hints at the presence of a long common haplotype that might be indicative of genetic hitch-hiking and recent positive selection. However, it is difficult to distinguish between possible explanations because the sample is small, with extensive admixture hampering phasing and direct investigation of linkage-disequilibrium-based selection signals.

Note however the presence of the derived allele in Papuans and Aboriginals, but not Melanesians. In the phylogenetic network the Aboriginals are the outgroup, and yet on this character the Melanesians are. This is a locus which will no doubt be explored in the future, because the patterns here will be fascinating to tease apart, and, of possible medical relevance.

Overall this paper has confirmed much of what we know, or at least solidified our background assumptions. The contemporary peoples of Melanesia, New Guinea and Australia have a common ancestral heritage. Coalescence times back to the last common ancestor between these populations and non-Oceanian groups suggest that their residence in their current locations is antique, and possibly back to the first settlement. One should be duly cautious about extrapolating from contemporary patterns to variation to the past, but I think on this scale we’re on more solid ground. Parts of southern Australia and Tasmania may have an equitable climate where ancient DNA samples may have been preserved, so that could resolve the issues with more certainty in the future.

But aside from phylogeny, a closer study of Australian Aboriginal genetics may also give us insights into the impact which agriculture and higher population densities had upon our species’ genomes. The Australian Aboriginals were aware of agriculture because of contacts with the peoples of the Torres Straits, but they never seem to have adopted it. In contrast to Australia the highlands of New Guinea developed a relatively high population density with the spread of a gardening mode of production. So here you have two populations which were in contact ~10,000 years ago, and have diverged in mode of production subsequent to that period. A comparison in allele frequencies between these two populations would then be instructive as to the power of drift and selection to drive evolutionary change over 10,000 years.

Obviously there needs to be more work done, and extrapolating from one sample will not do. The north coast Aboriginals were certainly in contact with sailors from Southeast Asia before Europeans arrived, and they speak a different group of languages from those in the rest of the continent. The existence of tribes with non-trivial numbers of blonde individuals in the western deserts despite no other apparent European admixture also demands to be explored. From what Joseph Birdsell documented about the Mendelian inheritance patterns of blondism among these tribes it seems likely that the genetic architecture is very different from that in Europeans.

Over the past generation we’ve begun to really understand how the human tree of life branched out and flourished. Now it’s time to fill in the gaps, and with whole genome sequencing around the horizon many of the technical limitations will be removed. But what about the social and political ones? The consent given by this Aboriginal group has now opened a window into the evolutionary genetic history of all Australian Aboriginals, imperfect as that is. But what will happen when many more people in developed nations get sequenced, and so know their own genetic history with great detail? If a non-trivial proportion of Aboriginal ancestry is found across the old stock white population of Australia could a collaborative project just “reconstruct” the Aboriginal genome from these individuals, and so do an end-around the socio-political minefields? I suppose we’ll see soon enough.

Image credit: Aboriginal cricket team, 1868, Wikimedia Commons

Citation: McEvoy, Brian P., Lind, Joanne M., Wang, Eric T., Moyzis, Robert K., Visscher, Peter M., van Holst Pellekaan, Sheila M., & Wilton, Alan N. (2010). Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry The American Journal of Human Genetics : 10.1016/j.ajhg.2010.07.008

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Readers might find these responses of interest. Mostly I just laughed, though some of you may be a bit more serious than I, so if anthro-gibberish drives you crazy, don’t follow the links. As I told “ana” below a lot of the discussion we had was basically just talking past each other. I kept telling her she was vacuous because she was assuming presuppositions which I simply did not share as empirical background descriptions of the world (e.g., a strong form of linguistic relativism where the specific nature of a language shapes cognition). Though at least she was concise. On the other hand, see this small section of Creighton’s response:

I think this is what bothered me the most about Khan’s piece. No discussion of what poverty means, what it is, how it’s defined. I could be completely wrong, but that led me to feel that there was a high degree of Eurocentric neo-colonialism behind Khan’s proposition. Who is saying to who what “median human utility” means? Are we assuming that homeownership, vehicle ownership, and other tangible measures of economic prosperity are involved? Is access to fresh food and water part of this measurement? Khan didn’t discuss poverty at all and he didn’t acknowledge that the neo-colonial policies of certain nations are at least partially responsible for the long-term economic suffering of many of the people he is referring to. I just got the feeling that he was telling the people who belong to small language communities to accept defeat and learn English. It incited me even more that his justification for making this decision was in purely economic terms. Abandoning your heritage will pay out in the end. But will it?

Dhaka smells like human shit. That’s poverty. Most people think that to get rich is glorious, and an understanding of wealth is cross-cultural. Many anthropological types problematize too much for my taste. They confuse the nuance and shading which vary between societies, for the core truths, which are relatively culture-free. For almost all of human history most people lived at the poverty line, because Malthusian conditions were operative. The possibility for wealth, and consumer society, is new. Those who opt-out in modern societies do so for explicit ideological reasons and are aware of the trade offs (e.g., the Amish, Hasidic Jews, people who live in communes).

The point which I tried to emphasize a few times, but generally ignored by my interlocutors, is that people as individuals, and communities, make rational decisions in a world of constrained choices. Quite often, and especially today, language change does not occur from on high (in fact, the top-down imposition of standard national languages on the masses is more a recent feature of post-Enlightenment nationalism; Latin spread in the Roman Empire over centuries among the western peasantry). Most Africans who adhere non-world religions are shifting to Islam or Christianity. There is little explicit coercion in this (though a fair amount of social pressure from elites who find Vodun and other native traditions backward). The moral panic that many Westerners have over the extinction of small-scale societies is not shared by many members of those small-scale societies, who wish to opt-out, often for material reasons. And by material, I’m not talking McMansions, I’m talking having income above subsistence. The level of wealth of a Chinese factory worker, not that of an academic adjunct.

As for my critics, note that I don’t really engage them directly, because the theoretical frameworks we use are so distinct. They misunderstand me, and I misunderstand them (honestly, I have no idea what they’re saying most of the time in the broad sense, aside from the fact that they’re offended). I have as much respect for most American cultural anthropology as I do for Talmudic scholarship; I’m sure they’re bright individuals, but they aren’t doing anything which I think relates to a world outside of the minds of the practitioners.* Contrast that with Jared Diamond, who I think is positively wrong in many of his models (not to mention recent ethical controversies which have erupted), but, who I can understand in terms of what he is saying. Being wrong, and asserting things which turn out false, are essential in the process of building a better model of the world. Extreme projects in cultural relativism, and fixation on semantics, tells us more about the psychology of WEIRD people than anything else.

For a better understanding of how I approach anthropology, and the study of human culture, the first half of D. Jason Slone’s Theological Incorrectness describes it almost perfectly. If you continue to read this weblog, you’ll note that I have a deep interest in culture and history. But, my treatment is not going to resemble much of what would find in cultural anthropology in the United States. In fact, I’ll drive you crazy, and perhaps an r-squared here and there will strike as you positivist gibberish. No one’s paying you to read though.

Oh, and yes, I am Euro-centric. Some things can be stated as objective facts, but obviously where you start from impacts how you judge the import of particular facts. Though I think Epoche is methodologically useful. Or at least the attempt.

* To be fair, a large number of people do take the Talmud seriously, and so the scholarship does have an impact because people take the scholarship seriously. But I don’t think this is like mechanical engineering, where the reason to take it seriously from the outside is not dependent on a normative view of the importance of mechanical engineering. As for cultural anthropology, I don’t think it matters too much, aside from intellectual types who think that it is a form of scholarship with non-trivial empirical basis. I think most American cultural anthropology is about as empirically robust as astrology.

Related: Also see my post Knowledge is not value-free.

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How we perceive nature and describe its shape are a matter of values and preferences. Nature does not take notice of our distinctions; they exist only as instruments which aid in our comprehension. I’ve brought this up in relation to issues such as categorization of recessive vs. dominant traits. The offspring of people of Sub-Saharan African and non-African ancestry where the non-African parent has straight or wavy hair tend to have very curly hair. Therefore, one may say that the tightly curled hair form is dominant to straight or wavy hair. But, it is also the case that there is some modification in relation to the African parent in the offspring, so the dominance is not complete. When examining the morphology of the follicle, which determines the extent of the hair’s curl, the offspring may in fact exhibit some differences from both parents. In other words our perception of the outcomes of inheritance are contingent to some extent on our categorization of the traits as well as our specific focus along the developmental pathway.

Or consider the division between “traits” and “diseases.” The quotations are necessary. Lactose intolerance is probably one of the best cases to illustrate the gnarly normative obstructions which warp our perceptions. As a point of fact lactose intolerance is the ancestral human state, and numerically predominant. It is the “wild type.” Lactose tolerance is a relatively recent adaptation, found among a variety of West Eurasian and African populations. A more politically correct term, lactase persistence, probably better encapsulates the evolutionary history of the trait, which has shifted from the class of disease to that of genetic trait when we evaluate the bigger picture (obviously diseases are simply “bad” traits”).

Sometimes though the issues are more cut & dried. No one would doubt that sickle-cell anemia is a disease. It has a major fitness impact in a colloquial sense, as well as evolutionarily. It kills you, and it kills your potential genetic lineage. But, it is also a byproduct of adaptation to endemic malaria. Sickle-cell disease one of the classical illustrations of heterozygote advantage, whereby those who carry one copy of the mutation on the gene have increased fitness vis-a-vis those who carry two normal copies of the gene. The increase in frequency of the mutant gene though is balanced by the fact that mutant homozygotes have decreased fitness.

We can then construct a narrative of the long term evolutionary dynamics from this initial condition. When a new exogenous stress hits a population mean fitness drops immediately (take a look at the biographies of the Popes, and observe how many died of malaria in the Dark Ages when that disease was new to Italy). Natural selection quickly increases in frequency any alleles which confer protection against the exogenous stress. But, baked into the cake of how genetics in complex organisms usually works, one allele may often have multiple downstream consequences. This is pleiotropy. This means that if a change at a locus increases aggregate fitness, it may nevertheless destabilize long established biochemical pathways. In the short term evolution simply takes the net fitness impact into account. Over the long term one assumes that “better solutions” will emerge which do not have so high a fitness drag, perhaps through the evolution of modifier genes which mask the deleterious outcomes of the initial mutant. This sort of ad hoc trial and error and “duct-taping” of kludges is part and parcel of how adaption works in situations where shocks out of equilibrium states are common.

In many cases the byproducts of a genetic change may be benign. To my knowledge no one knows major negative consequences of carrying the alleles which confer lactase persistence (excepting some studies indicating higher obesity, but this seems a marginal fitness impact which has only come to the fore in the past century in all likelihood). But in other cases the outcomes may not be as serious as that of sickle-cell anemia, but may rise above the level of significance where one must note the existence of a disease which is a secondary consequence of adaptation to meet a new challenge.

Yesterday I pointed to a paper which illustrates just this phenomenon, Association of Trypanolytic ApoL1 Variants with Kidney Disease in African-Americans:

African-Americans have higher rates of kidney disease than European-Americans. Here, we show that in African-Americans, focal segmental glomerulosclerosis (FSGS) and hypertension-attributed end-stage kidney disease (H-ESKD) are associated with two independent sequence variants in the APOL1 gene on chromosome 22 {FSGS odds ratio = 10.5 [95% confidence interval (CI) 6.0 to 18.4]; H-ESKD odds ratio = 7.3 (95% CI 5.6 to 9.5)}. The two APOL1 variants are common in African chromosomes but absent from European chromosomes, and both reside within haplotypes that harbor signatures of positive selection. Apolipoprotein L-1 (ApoL1) is a serum factor that lyses trypanosomes. In vitro assays revealed that only the kidney disease-associated ApoL1 variants lysed Trypanosoma brucei rhodesiense. We speculate that evolution of a critical survival factor in Africa may have contributed to the high rates of renal disease in African-Americans.

In its implementation the paper has a lot of moving parts, but the outcome is straightforward. If you haven’t, you might read Genomes Unzipped and its post How to read a genome-wide association study. This is a case where the original association studies were not reporting false results, but, it seems that one had to take a further step to really understand the likely molecular genetic and evolutionary underpinnings of what was going on. These results suggest that the original signals of association for variants within the MYH9 gene were actually signals from within APOL1, which happened to be next to MYH9. The region around MYH9 had already showed up in tests to detect natural selection through patterns of linkage disequilibrium (non-random associations of alleles at different loci within the genome, in this case the relevant consideration are adjacent loci across continuous regions of the genome which come together to form haplotype blocks). Since the footprint of natural selection on the genome is often wide that did not imply that MYH9 was the target of natural selection per se, opening the likely possibility for other causal associations. A convenience in light of the difficulty of establishing a plausible functional relationship between renal failure and MYH9.

To explore the possibility of nearby functional candidates the researchers focused on a number of alleles within this genomic region which exhibited maximal European-African frequency differences in the 1000 Genomes Project. Once they ascertained the between population differences they then looked at differences in allele frequencies in cases and controls within the African American population for the two diseases in question (those with the trait/disease vs. those without). Table 1 has the top line raw results:

WT = “Wild Type,” the ancestral allelic variant found in most populations. G1 and G2 are two haplotypes, associated alleles across the locus of the APOL1 gene. G1 consists of the two derived non-synonymous coding variants rs73885319 (S342G) and rs60910145 (I384M) within an exonic region of APOL1. Non-synonymous simply means that a change at that base pair alters the amino acid coded, and exons are the genomics regions whose information is eventually translated into proteins. In other words, these are non-neutral functionally significant genomic regions which do something. G2 is a 6 base pair deletion, rs71785313, close to G1 in APOL1.

To more formally model the relationship between the alleles which are found to differ between cases and controls they performed a logistic regression. The alleles serve as independent variables which can predict the probable outcome of the dependent variable, the probability of FSGS or H-ESKD in this case (renal failure). Figure 1 to the left has a summary of some of the results of the regression in graphical form for FSGS. I’ve rotated it so it can fit on the screen. Basically the strong signals are to the right of the chart (from your perspective). The y-axis displays (horizontal from your perspective) negative-log of p-values for a signal at a particular marker, which is defied by the x-axis (vertical for you). The labels show the particular gene at that genomic position. The smaller the p-value, the more probable that the signal is real and not random. This produces huge spikes in the negative-log values (in the body of the paper they present p-values on the order of 10^-35).

You can see that it is in APOL1 that the biggest signals reside. The first panel, A, throws all the SNPs into the mix. On MYH9 they highlight a few SNPs which combine to form the E-1 haplotype, which is strongly associated with cases (this is where the association between disease and genetic variants on MYH9 are coming from). This haplotype is found in conjunction with G1 and G2 on APOL1. E-1 is present in 89% of haplotypes carrying G1 and in 76% of haplotypes carrying G2. A classic illustration of likely correlation but not causation. The second panel controls for the effect of G1. In other words, this is showing you the variation in the dependent variable that remains after you take the largest independent variable, G1, into account. The G2 haplotype is the largest effect independent variable after G1 is taken into account; in other words, it explains most of the residual variation in FSGS probability. Finally, the last panel controls for both G1 and G2. As you can see there aren’t any major signals left; the distribution is relatively flat. Logically once you account for the variables which produce change in an outcome you shouldn’t see any impact of other variables. And that’s what happens here. They also performed controls where MYH9 was held constant, and that does not eliminate the signals in APOL1. MYH9 is conditional on its correlation with APOL1. This was the correlation which showed up on the original association studies. The exact same pattern of signals within the logistic regression model was replicated for H-ESKD. G1 had the strongest signal, then G2. The markers within MYH9 was not significant once one controlled for the variants in G1 and G2.

It is important to remember though that these markers are segregating within a human population where individuals have three potential genotypes. Ancestral homozygote, homozygote for the mutants, and heterozygote. They found that a recessive model of expression of disease is most appropriate in the case of these risk alleles. That is, most of the increased risk is accounted for by the change from one risk allele, the heterozygote state, to two risk alleles, the homozygote state. One risk allele increased odds of renal failure by 1.26, but two by 7.3. The odds ratio of two risk alleles compared to a base rate of one risk allele was 5.8. They report that the results for FSGS were broadly similar. This matters because the frequency of the trait/disease in a random mating population is conditional on the homozygotes if it has a recessive expression pattern. G1 was present in 40% of Yoruba HapMap data set, but in none of the two Eurasian groups, Europeans and East Asians. G2 was found in three Yoruba, but in none of the Eurasian groups. Assuming Hardy-Weinberg equilibrium the Yoruba should have 16% of the population at sharply elevated risk for FSGS and H-ESKD because they’d be homozygotes for the G1 allele.

Once they established which markers seem to implicated in this phenotypic variation, they wanted to focus on how the frequencies of those markers came to be. Specifically, G1 and G2 seem to be derived haplotypes which arose out of the ancestral background. In plain English 20,000 years ago Africans should have looked like all non-Africans genomically, at least on the functionally relevant segments, but within the last 10,000 years it looks like new variants rose in frequency driven by natural selection to new environmental stresses. The region has already broadly been surveyed by linkage disequilibrium based tests, which basically look for regions of long haplotypes, homogenized zones of the genome where many individuals have the variation removed because one gene rose so rapidly in frequency that huge adjacent sections hitchhiked up in frequency. Presumably this may have happened with the MYH9 haplotype correlated with the traits under consideration here; G1 and G2 dragged up the E-1 haplotype as a secondary consequence of their own rise to prominence among some Sub-Saharan African populations.

So next authors turned to tried & tested techniques and focused on the risk markers which they had discovered earlier in their research, G1 and G2. Specifically, EHH, which is best at detecting selection where sweeps have nearly completed (e.g., the derived variant is at frequency 0.95 within the population), iHS, which is best at detecting sweeps which have not completed (e.g., the derived variant is at frequency 0.6), as well as ΔiHH, which I am less familiar with but is reputedly similar to iHS but uses absolute haplotype length as opposed to relative haplotype length. Figure 2 show the results of these tests:

The resolution isn’t the best, but G1 and G2 seem to be outliers on all three tests to detect natural selection by using patterns of linkage disequilibrium. The first panel is EHH, the second and third show iHS and ΔiHH respectively, with the position of the markers being outliers among the distribution of values for the genome within the Yoruba. This is not proof of adaptation, but it changes our weights of possibilities. Additionally, they note that Europeans exhibit no such patterns on these markers. Visually the position of the markers in the latter two panels would be closer to the mode of the distribution in Europeans.

To review, first they confirmed a causal relationship between a particular set of markers, haplotypes, and the traits of interest. Second, they confirmed that said markers seem to bear the hallmarks of genomic regions subject to natural selection. We know that focal segmental glomerulosclerosis (FSGS) end-stage kidney disease (H-ESKD), the traits whose relationship to the G1 and G2 haplotypes seem confirmed, are unlikely to be targets of positive natural selection. To get a better sense of that we need to look at Apol1, the protein product of APOL1, and what it does. At this point I’ll quote the paper:

ApoL1 is the trypanolytic factor of human serum that confers resistance to the Trypanosoma brucei brucei (T. brucei brucei) parasite…T. brucei brucei has evolved into two additional subspecies, Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense, which have both acquired the ability to infect humans…T. brucei rhodesiense is predominantly found in Eastern and Southeastern Africa, while T. brucei gambiense is typically found in Western Africa, though some overlap exists…Since these parasites exist only in sub-Saharan Africa, we hypothesized that the APOL1 gene may have undergone natural selective pressure to counteract these trypanosoma adaptations. As an initial test of this hypothesis, we performed in vitro assays to compare the trypanolytic potential of the variant, disease-associated forms of ApoL1 proteins with that of the “wild-type” form of ApoL1 protein that is not associated with renal disease.

We’re talking about sleeping sickness. Here’s a description:

It starts with a headache, joint pains and fever. It is the kind you would expect to get over quickly. But after a while, things get worse. You fall asleep most of the time, are confused and get intense pains and convulsions.

If you do not get treatment, your body begins to waste away. Eventually, you slip into coma and die. This is human African trypanosommiasis, better known as sleeping sickness. If untreated, it kills 100% of its victims in a very short time.

Cheery. I think we have a plausible reason for natural selection to kick into overdrive! Or more specifically, we have a plausible external selection pressure which will drive fitness differentials which correlate with genetic variation. Increased probability of kidney disease seems preferable to this. In terms of the molecular genetics it looks like a factor, serum resistance-associated protein (SRA), produced by T. brucei rhodesiense binds to a specific location of Apol1, and that mutations at G1 and G2 change exactly that location within the protein. So these mutants may block the ability of T. brucei rhodesiense to turn off the body’s defenses against trypanosomes.

To test this they examined the in vitro lytic potential of serum produced by individuals carrying the G1 and G2 haplotypes against the three subspecies of of Trypanosoma. T. brucei brucei, which normal Apol1 can lyse, and T. brucei rhodesiense and T. brucei gambiense which can infect humans (endemic to eastern and western Africa respectively, though the former extends into west Africa as well).

- All 75 samples lysed brucie brucie

- None lysed brucie gambiense

- 46 samples lysed SRA-positive brucie rhodesiense, all 46 samples were from G1 or G2 carrying individuals

- The potency of G2 seemed higher than G1 against SRA-positive samples of brucie rhodesiense, though not SRA-negative samples, where G1 seemed as potent

- Recombinants of Apol1 which had only one of the two SNPs of the G1 haplotype were less effective against brucie rhodesiense than those which had both (G1 haplotype)

- Recombinants with G1 and G2 were not more effective against brucie rhodesiense than those with G2 alone

- Recombinants with G1 alone were more potent against SRA-negative brucie rhodesiense than those with G2 alone

- G2 was necessary and sufficient to block SRA binding to Apol1 and allow lysing of brucie rhodesiense. G1 did not block SRA binding to Apol1, but was still sufficient to lyse brucie rhodesiense, but far less potent against SRA-positive brucie rhodesiense than G2

It seems that the G1 and G2 haplotypes utilize different mechanisms to enable the lysing of invasive pathogens, and so prevent the development of sleeping sickness. Their means differ, but the ends are the same. The authors note that even minimal amounts of plasma serum produced by G2 individuals seems potent enough to block the binding of SRA to Apol1 and so enable lysis. And introduction of such plasma into the bloodstreams of individuals who do not have resistance may then be highly efficacious as a preventative treatment against sleeping sickness. They do note that they did not explore in detail the mechanism by which the G1 and G2 variants result in suscepbility to kidney failure, but that’s presumably for the future.

Finally, the second to last paragraph where they bring it all together:

It will be interesting to determine the distribution of these mutations throughout sub-Saharan Africa. In present-day Africa, T. brucei rhodesiense is found in the Eastern part of the continent, while we noted high frequency of the trypanolytic variants and the signal of positive selection in a West African population. Changes in trypanosome biology and distribution and/or human migration may explain this discrepancy, or resistance to T. brucei rhodesiense could have favored the spreading of T. brucei gambiense in West Africa. Alternatively, ApoL1 variants may provide immunity to a broader array of pathogens beyond just T. brucei rhodesiense, as a recent report linking ApoL1 with anti-Leishmania activity may suggest…Thus, resistance to T. brucei rhodesiense may not be the only factor causing these variants to be selected.

This is a very long review already. But, while I have your attention, I think I need to point to another paper on the same topic which has a slightly different twist. I won’t dig into the details with the same thoroughness as above, but rather I’ll highlight the value-add of this group’s contribution. It’s an Open Access paper, unlike the one above, so you can review it in depth yourself. Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene:

MYH9 has been proposed as a major genetic risk locus for a spectrum of nondiabetic end stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes Project to identify two western African-specific missense mutations (S342G and I384M) in the neighboring APOL1 gene, and demonstrate that these are more strongly associated with ESKD than previously reported MYH9 variants. The APOL1 gene product, apolipoprotein L-1, has been studied for its roles in trypanosomal lysis, autophagic cell death, lipid metabolism, as well as vascular and other biological activities. We also show that the distribution of these newly identified APOL1 risk variants in African populations is consistent with the pattern of African ancestry ESKD risk previously attributed to MYH9. Mapping by admixture linkage disequilibrium (MALD) localized an interval on chromosome 22, in a region that includes the MYH9 gene, which was shown to contain African ancestry risk variants associated with certain forms of ESKD…MYH9 encodes nonmuscle myosin heavy chain IIa, a major cytoskeletal nanomotor protein expressed in many cell types, including podocyte cells of the renal glomerulus. Moreover, 39 different coding region mutations in MYH9 have been identified in patients with a group of rare syndromes, collectively termed the Giant Platelet Syndromes, with clear autosomal dominant inheritance, and various clinical manifestations, sometimes also including glomerular pathology and chronic kidney disease…Accordingly, MYH9 was further explored in these studies as the leading candidate gene responsible for the MALD signal. Dense mapping of MYH9 identified individual single nucleotide polymorphisms (SNPs) and sets of such SNPs grouped as haplotypes that were found to be highly associated with a large and important group of ESKD risk phenotypes, which as a consequence were designated as MYH9-associated nephropathies…These included HIV-associated nephropathy (HIVAN), primary nonmonogenic forms of focal segmental glomerulosclerosis, and hypertension affiliated chronic kidney disease not attributed to other etiologies…The MYH9 SNP and haplotype associations observed with these forms of ESKD yielded the largest odds ratios (OR) reported to date for the association of common variants with common disease risk…Two specific MYH9 variants (rs5750250 of S-haplotype and rs11912763 of F-haplotype) were designated as most strongly predictive on the basis of Receiver Operating Characteristic analysis…These MYH9 association studies were then also extended to earlier stage and related kidney disease phenotypes and to population groups with varying degrees of recent African ancestry admixture…and led to the expectation of finding a functional African ancestry causative variant within MYH9. However, despite intensive efforts including re-sequencing of the MYH9 gene no suggested functional mutation has been identified…This led us to re-examine the interval surrounding MYH9 and to the detection of novel missense mutations with predicted functional effects in the neighboring APOL1 gene, which are significantly more associated with ESKD than all previously reported SNPs in MYH9.

Table one has the top line results. Focus on the first two rows, they’re “G1″ from the earlier study (that is, the two SNPs which combine to form the G1 haplotype).

Here’s a difference between the previous paper and this one: the table above uses cases and controls from African Americans and Hispanic Americans. The original paper which the genomic data on this sample is drawn from calculates the average ancestry of African, European and Native American in the two groups is as follows (I did some rounding to keep the values round):

African American – 85%, 10%, 5%
Hispanic American – 30%, 55%, 15%

Not surprisingly the Hispanic American sample here is mostly Puerto Rican and Dominican, explaining the greater African than Native American ancestry. Nevertheless, it is a sufficiently different genetic background to test the effects of the same marker against different genes. They confirmed the association of the markers of large effect in African Americans within the Hispanic cohort. The risk allele frequency in the African American control group is 21% vs. 37% in the cases. For Hispanic Americans are 6% and 23% for the same categories.

OK, now to the most interesting point in this short paper:

HIVAN has been considered as the most prominent of the nondiabetic forms of kidney disease within what has been termed the MYH9-associated nephropathies…We have reported absence of HIVAN in HIV infected Ethiopians, and attributed this to host genomic factors (Behar et al. 2006). Therefore, we examined the allele frequencies of the APOL1 missense mutations in a sample set of 676 individuals from 12 African populations, including 304 individuals from four Ethiopian populations…We coupled this with the corresponding distributions for the African ancestry leading MYH9 S-1 and F-1 risk alleles. A pattern of reduced frequency of the APOL1 missense mutations and also of the MYH9 risk variants was noted in northeastern African in contrast to most central, western, and southern African populations examined…Especially striking was the complete absence of the APOL1 missense mutations in Ethiopia. This combination of the reported lack of HIVAN and observed absence of the APOL1 missense mutations is consistent with APOL1 being the functionally relevant gene for HIVAN risk and likely the other forms of kidney disease previously associated with MYH9.

Bingo. The previous paper focused on African Americans (along with the HapMap Yoruba). But the pattern of variation within Africa is interesting as well. Ethiopians are not quite like other Africans, having a great deal of admixture with populations from Arabia (many of the languages of highland Ethiopia are Semitic). But the majority of their ancestry remains similar to that of other Sub-Saharan Africans. As a point of contrast the ecology of Ethiopia differs a great deal from the rest of Sub-Saharan Africa because of its elevation, and concomitant frigidity. The mean monthly low in Addis Ababa is around 10 (50 for Americans) degrees and mean high 20-25 (high 60s to mid 70s for Americans). There isn’t much variation from month to month because of the low latitude, but the high elevation keeps the temperatures relatively moderate. Different environments result in different selection pressures, and Ethiopia has a very unique environment within Africa. The tsetse fly which serves as a vector forTtrypanosomes does not seem to be present in the Ethiopian highlands. The map above shows the distribution within Africa of one the markers which defines the G1 haplotype in the previous paper. Note that the modal frequency is in the west of Africa, and the frequency drops off to the east (though the geographic coverage leaves a bit to be desired if you look at the raw data which went into generating this map, which smooths over huge discontinuities).

One of the points I want to reemphasize from the tests of natural selection in the first paper is that these genetic adaptations are likely to be new, otherwise recombination would have broken up the long haplotypes and reduced linkage disequilibrium. New as in the last 10,000 years. It is interesting that a particular subspecies of Trypanosome which is immune to these genetic adaptations is endemic to west Africa. We may be seeing evolution in action here, or at least the arms race between man and pathogen where man is always one step behind. In contrast, the subspecies which is effectively diffused by the genetic adaptations reviewed here is present in higher numbers precisely in the regions where the resistance mutations are extant at lower proportions. Perhaps there are different mutations in these regions of Africa, not yet properly identified. Or perhaps the we’re seeing humans in this region at an earlier stage of the dance, so to speak.

Citation: Giulio Genovese, David J. Friedman, Michael D. Ross, Laurence Lecordier, Pierrick Uzureau, Barry I. Freedman, Donald W. Bowden, Carl D. Langefeld, Taras K. Oleksyk, Andrea Uscinski Knob, Andrea J. Bernhardy, Pamela J. Hicks, George W. Nelson, Benoit Vanhollebeke, Cheryl A. Winkler, Jeffrey B. Kopp, Etienne Pays, & Martin R. Pollak (2010). Association of Trypanolytic ApoL1 Variants with Kidney Disease in African-Americans Science : 10.1126/science.1193032

Citation: Tzur S, Rosset S, Shemer R, Yudkovsky G, Selig S, Tarekegn A, Bekele E, Bradman N, Wasser WG, Behar DM, & Skorecki K (2010). Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene. Human genetics PMID: 20635188

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This isn’t The New Yorker, and I’m not writing twenty page essays which flesh out all the nooks and crannies of my thought. When I posted “Linguistic diversity = poverty” I did mean to provoke, make people challenge their presuppositions, and think about what they’re saying when they say something.

I think knowledge of many languages is awesome. I am weak at language acquisition myself, but, as someone with an interest in Bronze Age Near Eastern history I’m obviously invested in people having some comprehension of Sumerian and Akkadian (not to mention Hittite or ancient Egyptian). And I’m not someone who has no interest in the details of ethnographic diversity. On the contrary I’m fascinated by ethnic diversity. Like many people I enjoy reading monographs and articles on obscure groups such as Yazidis (well before our national interest in Iraq) and the Saivite Chams of Vietnam. Oh, wait, I misspoke. I actually don’t know many people who have my level of interest in obscure peoples and tribes and the breadth of human diversity. If you’re the type of person who reads monographs on Yazidis not because it pertains to your scholarly specialty, but because you’re interested in a wide range of facts and topics, and would like to have discussions with someone of similar disposition (me), contact me with your location and if I swing through town we can have coffee or something. I’m interested in meeting like minds who I can explore topics with (and here I’m not talking about someone who is a Hakka and so knows a lot about the history of the Hakka; I’m not Hakka and I know something about the Hakka and I’m not an Oirat I know something about the Oirat, and so forth). All things equal the preservation of linguistic diversity is all for the good, and not only does it enrich the lives of humanity as a whole, it enriches my life in particular because of my intellectual proclivities. But all things are not equal.

First, let me digress and admit that I do not adhere to a plain utilitarianism which does not value the cultural accretions and symbolic residues of history. For a concrete example, consider the destruction of the Buddhas of Bamyan in 2001 by the Taliban. On a concrete material level this was simply the rearrangement of molecular aggregations. We even have the visual sensory representation of the Buddhas before their destruction in the form of photographs. Why the outrage? Naturally Buddhists were outraged because the images of the Buddha had a sacred valence for them. But the world in general was outraged, Buddhist and non-Buddhist. The local Shia Muslims who live in the region, the Hazaras, were aghast at the cultural destruction, as they considered the Buddhas to be part of their heritage. At the time the Hazaras were being subjected to genocidal persecution from the Taliban, who considered them racially alien due to their Mongolian heritage and also heretics because of their Shia faith, so they were in no position to interpose themselves between the Taliban and the Buddhas.

As for the Taliban their concept of the Buddhas of Bamyan is that they were plain stone. Additionally, the Taliban perceived that the Buddhas were blasphemous because they were idolatry, drawing upon a long line of iconoclasm which goes back to the legendary Abraham. Unlike the atheist the Taliban may have perceived in the stone something more than material, rather, the stone may have been an expression of demonic or devilish forces in the world. Even if it lacked malevolent spirit forces, if they were objects of worship by human beings then that naturally violated their conception of the proper order of things.

But there’s a more nuanced context to the destruction of the Buddhas: Afghanistan was suffering through a famine during that period. Though the proximate cause for their destruction seems to have been the influence of the Arabs who were a power in Afghanistan at the time, Arabs who had no cultural affinity for Afghanistan’s pre-Islamic heritage, I have read that one aggravating issue may have been that the leadership of the Taliban was offended that the world seemed more focused on the potential destruction of statues than on the suffering of flesh & blood people. You can extrapolate this sort of objection pretty easily; at the same time that the Buddhas of Bamyan were under threat, tens of thousands were dying weekly in the Congo.

Here is where I must admit that my actions suggest that I am no simple utilitarian, who prioritizes the suffering of flesh and blood above stone and symbol. At the time in 2001 I specifically remember being very concerned about the destruction of the Buddhas, though I did not imbue them with spiritual value. I do not imbue the pyramids of Giza with spiritual value in a deep metaphysical sense, but I would be concerned about their destruction. I am not the only one. How many Egyptians would have to die in local violence to obtain the same world-wide media coverage as a terrorist detonation of a series of devices which destroyed the pyramids? I estimate on the order of millions (and even here, I am not so sure, as the genocide of millions in Africa receives far less coverage than I believe that a destruction of the pyramids would entail).

Human life and suffering are balanced against the aesthetic of life itself, which is more than bread and water. How many millions could have been fed with the funds which went to the Apollo mission? And yet what dollar value could we put on the photo of the pale blue dot? What dollar value on the reality that a human being has stepped foot on another planet? These are difficult questions in some ways because assessments of value and worth need to get the root of one’s implicit calculations. I know many people from the biological sciences who have little use for space exploration. And yet I know many people of marginal academic inclination who perceive much of biological research to be esoteric and without direct utility.

And it is here that biologists can respond that the domain of knowledge leads directly to discoveries in medicine and technology which will enable greater human happiness and well being, no matter what one thinks of the millionth beetle cataloged. On the margin some of these justifications for research based on plausible utility are as ludicrous as the justifications for a manned space mission. But the attempt must be made. Whether the quest for knowledge is worthy or not is not evaluated by some objective abstract criteria; even if researchers sit on granting committees the funds must ultimately come from elsewhere.

Which brings me back to the extinction of languages. The Lousy Linguist is skeptical of my contention that very high linguistic diversity is not conducive to economic growth or social amity. I outlined the theoretical reasons previously. If you have a casual knowledge of history or geography you know that languages are fault-lines around which intergroup conflict emerges. But more concretely I’ll dig into the literature or do a statistical analysis. I’ll have to correct for the fact that Africa and South Asia are among the most linguistically diverse regions in the world, and they kind of really suck on Human Development Indices. And I do have to add that the arrow of causality here is complex; not only do I believe linguistic homogeneity fosters integration and economies of scale, but I believe political and economic development foster linguistic homogeneity. So it might be what economists might term a “virtuous circle.”

A more on point response came from John Hawks:

I’m sympathetic to recognizing the real loss that accompanies the disappearance of a language from the world of speakers. The “unique oral history” and “lost in translation” ideas are true as far as they go — the value of folk art and oral history is that they enable social relationships.

But most communities of a few hundred speakers don’t have a Beowulf. Unique perspectives and unique history, to be sure — just as every Rembrandt is unique. But every Rembrandt is not the Night Watch. Most unique perspectives are about the speaker’s life. At some point we can’t learn the stories of all our ancestors anyway, because there are simply too many of them. Obviously I think we should enable people to learn about their history, yet we can’t keep communities pinned like butterflies in a cabinet of curiosities.

Human language communities in prehistory had a few hundred to a few thousand speakers. Those communities shared the same basic social lives and needs. Ninety-five percent or more of all those languages were lost — and those remaining have mostly come from a handful of languages less than 10,000 years ago.

I read in the Rijksmuseum that art historians figure more than 95% of the work of artists from the Dutch golden age had been lost or destroyed over the last 300 years.

John says it with more sensitivity and sympathy for the issue than I did, but I agree 99% with what he is saying here. The only point I might quibble over is that perhaps all groups do have their Beowulf. And yet it doesn’t matter. If the speakers of the language decided to shift to another language, then they are making the choice which increases their own flourishing. Speakers of a few hundred languages are not always in the circumstances of Native or Aboriginal peoples in North America, where they can gain sympathetic hearing for preservation of their folkways from the government and majority population. They need to make the best decision for themselves at the time, and often assimilation is the best of all choices, because the sample space of choices is limited. It is correct that bilingualism, or resistance to linguistic assimilation can persist. Hasidic Jews in New York City have communities where English is a second language and adults, of the third generation born and raised in the United States, have strong accents. But this community’s insulation comes at a cost, their relative poverty.

But for most communities the level of poverty of Hasidic Jews, or the material deprivation of the Amish, is wealth indeed. Many groups in Africa, South Asia and Australasia have not moved far up on Maslow’s hierarchy of needs. Many of these groups live in grotesque poverty, experience radical marginalization, and some of them fear for their individual survival, not just tribal or ethnic coherency. If those in the developed world do value the preservation of these groups and the richness which they add to the world by their very existence, then a concrete program has to be offered. Perhaps a massive direct wealth transfer to targeted ethnic groups which are being assimilated (in India and Southeast Asia conversion to Christianity has been the most efficacious manner in which to preserve ethnic and linguistic identity, so perhaps one should donate to evangelical missionary groups). Or, the selective sponsored immigration of whole tribes and ethnic groups to the West, with an agreement that these groups have a sort of spatial sovereignty similar to Native Americans. In this way they wouldn’t be subject to the same dynamics as they were in their nation of origination.

I don’t care about linguistic diversity enough to support either of these programs. But that’s an expression of my values. And, I think it’s an expression of the values of most humans (granted, most humans do not value knowledge, but they do pay taxes which fund social engineering projects so their opinion counts). For those who do value linguistic diversity, to be taken seriously you need to present more than what it offers you and your own interests when you bear none of the costs of marginalization. Aggregate intangible utility may be maximized by this diversity, but it is simply unjust for that aggregate utility to be gained at the expense of the ones adding the diversity at the cost of their exclusion from the nation-states in which they’ve found themselves.

Addendum: Spencer Wells has noted that there is somewhat the same issue with genotypic diversity, as small groups are absorbed into larger groups. By analogy, one might offer up a program whereby tribal members are encouraged to marry only their own ingroup so as to preserve genetic lineages which may be of intellectual interest, and add diversity to the world. This is naturally the sort of argument many racialists present, though with a slightly different spin.

Image Credits: Wikimedia, CNN, Glenn Fleishman

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