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September 19, 2018

Hawaii: complicated a journey to paradise

Filed under: anthropology,Genetics,hawaii,science — Razib Khan @ 7:11 pm
The extent of Austronesian Diaspora

Ask any American what they think when you say the word “Hawaii,” and certain words will no doubt reoccur from person to person. That’s because certain images, feelings, come to mind. A gentle breeze, beaches, and volcanoes. The 50th state has been the byword for paradise on the mainland. A certain sense of Hawaii is part of American popular culture.

But Hawaii is a real place with real people. It isn’t a dreamland. Rather, it is one of the most isolated large islands in the world. Over 2,500 miles from the nearest continent, there is only a single terrestrial mammal native to the islands: predictably, a bat!

Obviously, the island is crawling with mammals today. Nearly 1,000 years ago voyagers from the lands of the western Pacific landed on the Society Islands, which includes famed Tahiti, and then sailed northward to the Hawaiian archipelago. When the ancient Polynesians settled Hawaii they did not arrive alone. They brought with them pigs, chickens, and dogs. Naturally, rats tagged along as unwanted passengers.

Humans arrived in Hawaii in catamarans

But the settlement of Hawaii by humans was the end of a long journey which began thousands of years earlier in the mists of prehistory. Six thousand years ago a small group of stone-age seafarers, who we call Austronesians, journeyed south from Taiwan and settled the northern Phillippines.

But they did not stop there. Over a period of thousands of years, these ancient mariners spread out over Southeast Asia, sometimes introducing intensive forms of rice agriculture and their distinctive language. But they did not stop there. For whatever reason, these were a people who wondered what was over the horizon, even if it was the deep blue ocean. They moved on west and east. Over 1,000 years ago their descendants reached the western Indian Ocean, mixing with the Bantu farmers of eastern Africa and occupying the island of Madagascar. In the other direction, Austronesians moved into Oceania, abandoning rice and adopting taro from Melanesians. Less than 1,000 years ago the Pacific expansion finally crested, as Polynesians settled in New Zealand, off the coast of Australia, Easter Island, 2,300 miles west of South America. And of course, they ventured north to Hawaii, an isolated ecologically rich and unique jewel in the midst of the Pacific.

In Southeast Asia, the Austronesians merged with native populations of farmers which migrated out of southern China earlier. But as they moved west and east they encountered very different populations, whether it be African farmers and pastoralists, on the one hand, or Melanesians in the case of the ancestors of the Polynesians.

Citation: Kim SK, Gignoux CR, Wall JD, Lum-Jones A, Wang H, Haiman CA, et al. (2012) Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study. PLoS ONE 7(11): e47881

And just as the people of Madagascar, despite speaking a language closest to those spoken in Borneo, have a blended with nearby populations. Polynesians carry signatures of interactions with the peoples of Near Oceania, which includes New Guinea, Australia, and Melanesian islands in the western Pacific, such as the Solomon Islands and New Caledonia.

As genomics began to illuminate all the relationships between human populations, in 2012 a paper was published that surveyed the genomes of many native Hawaiians. The results were clear: the indigenous peoples of Hawaii had a dominant signature of ancestry shared with mainland Asian peoples, but also a minority component that had more affinities with the peoples of Near Oceania.

Lapita culture sites

This result was relevant to what traditionally had been termed the “express train vs. slow boat” models of the settlement of Polynesia. The “express train” hypothesis implies that the Austronesian Lapita culture rapidly pushed out of maritime Southeast Asia, with minimal interaction with local Papuans and other Melanesians. In contrast, the “slow boat” model meant that the expanding proto-Polynesians mixed with Papuans and Melanesians as they spread eastward more gradually, creating a fused culture which pushed onward into the far Pacific.

The results above, along with maternal and Y chromosomal lineages seem to support the “slow boat” model. Not only are all Polynesians, including Hawaiians, descended from Southeast Asian farmers, but their ancestors also include the people who first pushed to the edge of the Pacific. These were the ancestors of Oceanians who settled New Guinea, Near Oceania, and Australia more 40,000 years ago with the first “Out of Africa” migration.

Citation: Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., … & Fu, Q. (2016). Genomic insights into the peopling of the Southwest Pacific. Nature, 538(7626), 510.

So case closed? Not exactly. Science and history are often more complex than our elegant human imaginings. Over the past few years, the field of ancient DNA has come upon the scene to disturb hypotheses and provoke the development of new ones. Now researchers can see snapshots of the past with much crisper detail than would have been the case in the past.

Two papers have helped reshape our understanding of the peopling of Polynesia. First, a 2016 paper showed that samples of ancient Lapita people don’t show any admixture from Melanesians. This is in accordance with the “express train” model, which the genetic heritage of modern Polynesians presumably refuted!

An immediate solution to this conundrum is that the old models were too simple. That there wasn’t just a simple migration outward, but rather several, and that Melanesian ancestry arrived later. Within the last 2,000 years.

A paper published in 2018 added more nuance and clarity to what may have been going on. Today the island of Vanuatu is considered to be Melanesian and is settled by people of predominant Oceanian heritage. But ancient DNA from 3,000 years ago yielded individuals of nearly total Asian heritage. But by about 2,000 years ago these people were replaced, by the ancestors of modern Melanesians, as later samples show overwhelming Oceanian heritage.

Poke is a melange of flavors and ingredients from the four corners of the world

Where does this leave us? Appropriately, a paper appeared with the title “Human Genetics: Busy Subway Networks in Remote Oceania?” was penned as a response to all this uncertainty and confusion. The title says it all, doesn’t it?

These findings may actually be consonant with recent archaeological results that eastern Polynesia and New Zealand were subject to a massive demographic expansion and radiation beginning around ~1,000 years ago.

Today modern Hawaii is a melange of peoples, reflected in its cuisines, such as Poke, which has been inflected and modified by new ingredients brought by immigrants from the mainland and Asia. And yet perhaps this was always so, as paradise was never as serene and eternal as we may dream in our imaginings. Rather, Hawaii and the Hawaiians were products of daring voyages generation after generation, and the waxing and waning of peoples and cultures, bringing together diverse and disparate threads of the human expansion out of Africa.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Hawaii: complicated a journey to paradise was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

September 12, 2018

Season 2, Episode 1: The Legacy of L. L. Cavalli-Sforza

Filed under: anthropology,Evolution,Genetics,History — Razib Khan @ 1:15 pm
L. L. Cavalli-Sforza, 1922–2018

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we discussed the life and legacy of L. L. Cavalli-Sforza, who died on August 31st, 2018. See the Stanford obit. From John Hawks, The man who tried to catalog humanity on Medium is probably the most thorough review of his life and works.

Cavalli-Sforza’s magnum opus

We discussed the popularization of PCA and phylogenetic trees by Cavalli-Sforza and his colleagues, outlined in his magnum opus The History and Geography of Humans. The methods of analysis developed in the 20th century prepared us for the avalanche of data we confront into the 21st century.

Also, Cavalli-Sforza’s collaboration with Marcus Feldman that laid the seed for the field of cultural evolution. See the book Cultural Transmission and Evolution. Today the field of cultural evolution is being pushed by researchers such as Joe Henrich.

Cavalli-Sforza was also instrumental in synthesizing the application of formal demographic models to archaeology. See The Neolithic Transition and the Genetics of Populations in Europe.

L. L. Cavalli-Sforza remained active into the 21st century. See this interview from 2012.

After his retirement, several labs have carried on the project of exploring population genetic history. David Reich’s lab’s publications. Also, see Eske Willerslev’s work.

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. A 2008 study that uses the HGDP sample on a SNP-array, bringing The History and Geography of Humans into the 21st century!

Finally, the cultural anthropologist wrote a full-length biography of L. L. Cavalli-Sforza’s life, with a focus on his scientific contributions, A Genetic and Cultural Odyssey.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Season 2, Episode 1: The Legacy of L. L. Cavalli-Sforza was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

August 15, 2018

The Insight Show Notes: Episode 32, So you want to be a geneticist…

Filed under: anthropology,Archaeology,Genetics,science — Razib Khan @ 5:45 pm
Drosophila

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we talk to an “early career” geneticist, Austin Reynolds. A graduate of Indian University and University of Texas-Austin, he is currently a post-doctoral fellow at University of California-Davis.

Alfred H. Sturtevant in his own “fly lab”

As a field, genetics is officially a bit over a century old. Though Gregor Mendel made his key discoveries fifty years before. Since the year 2000 genetics has undergone a revolution driven by sequencing technology and more powerful computing. Around 2010, a different revolution began, which Austin has been a part of, involving the synthesis of archaeology and genetics with the field of ancient DNA.

The first ancient whole-genome analysis, Ancient human genome sequence of an extinct Palaeo-Eskimo. Also, the Neanderthal paper which revolutionized our understanding of our relation to this lineage.

An excellent review of the state of the current research, Ancient Human Genomics: The First Decade. And a preview of the future, Tales of Human Migration, Admixture, and Selection in Africa.

David Reich’s book Who We Are and How We Got Here is a good primer on ancient DNA and population genetics. Highly accessible to the lay audience without sacrificing any of the scientific content.

Loci associated with skin pigmentation identified in African populations.

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.

On career issues, Track the fate of postdocs to help the next generation of scientists.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The Insight Show Notes: Episode 32, So you want to be a geneticist… was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

June 8, 2018

On the rectification of names and religion

Filed under: anthropology,Religion — Razib Khan @ 3:30 pm

A major influence on my thinking about human social phenomenon is Scott Atran’s In Gods We Trust: The Evolutionary Landscape of Religion. Atran, along with other scholars such as Dan Sperber and younger researchers such as Harvey Whitehouse, work within a “naturalistic” paradigm, as opposed to the more interpretative framework currently ascendant within American anthropology.

The interpretive framework emphasizes “thick description,” and avoids generalities (unless they are convenient ones!), as well as exhibiting a suspicion of synthesis with the natural sciences. Ways of thinking such as post-colonialism are part of the umbrella of paradigms which are consonant with interpretive anthropology’s premises.

Both naturalistic and interpretive frameworks are useful. But I believe in modern discourse the latter is given almost monopolistic power to adjudicate on factual matters, even though in other contexts those who engage in interpretation are wont to say that facts are fictions!

Let’s start with the idea that the idea of religion qua religion is Protestant, Christian, or Abrahamic. I’ve seen all three flavors of the argument using a narrow definition of religion. It’s hard to deny that Christianity, and often in particular Protestantism, have resulted in a reorganization and reimagining of non-Christian religions. For example, the “confessionalization” of South Korea after World War II, and the transformation of Won Buddhism into an institution which resembles Protestantism would be a case in point. Or the emergence of Arya Samaj in the 19th century, and its relationship to the stimulative effect of evangelical Protestantism.

It is hard to deny confessional Protestantism is a very particular form of religion, and a clear and distinct one. The emphasis on individual volition in this view of religion makes it such that identity is clear and distinct through adherence to a precise formula and community. Practitioners are self-conscious in their identity. They come to it, it is not given to them.

But is it fair to say that religion by necessity must follow the outlines of confessional Protestantism? Or that it has to be a congregational faith with exclusive boundaries, as the Abrahamic faiths tend to be?

Not necessarily. A Ju/’hoansi tribesman in the Kalahari does not follow any of the organized world religions. He or she surely does not have the word for religion in their language, unless he or she is in extensive contact with missionaries. But the Ju/’hoansi have a rich supernatural world in which they believe, and which is seamlessly woven into their lives.

Do the Ju/’hoansi  have a religion or not? If you asked them they might not know what you are talking about. The Ju/’hoansi lack many of the institutions which modern societies have, so they don’t need all the labels of modern societies. Do the Ju/’hoansi have “daycare”? Again, they would look at you in a very confused manner. But the do have  Ju/’hoansi some alloparenting. It’s just something implicit, tacit, and taken for granted. It might not be labelled daycare, but that’s what it is. Functionally they have daycare, even it’s not institutionalized.

To bring it back to the central focus of this weblog, there has been some assertion that Hinduism as such was invented/defined by the British. That Hinduism as a coherent ideology is a very distinct and novel thing from the welter of beliefs and practiced of Indians more generally.

It is clear there is some truth in this. The Hinduism of a Brahmin expositor of Sanatana Dharma is distinct from the local spirituality of a adivasi group, and both differ from something like Gaudiya Vaishnavism.

But the reality is that Hinduism is not particularly unique. American Presbyterians exhibit self-conscious identity and adherence to elite-mediated belief and practice. This sort of individualistic confessional Christianity is arguably the apotheosis of a modernist conception of religion. But this is a relatively new development in the West among Christians.

The vast majority of the European peasantry did not exhibit this sort of Christian self-consciousness before the later medieval centuries, and much of it did not become self-conscious until after the Reformation period. This is one reason that some Reformed Protestants argue that Europe was not Christianized until after the Reformation. Peasants may have had a sense that they were Christians, and others were heathens, but the full liturgy and deep catechism were not necessarily a part of their lives (in contrast to the elite).

And yet it seems ridiculous to assert in the context of the Crusades, the rise of Gothic cathedrals, and the conversion of Northern and Eastern Europe by missionaries, that Europe was not Christian before the late medieval period. Individual Europeans may not have been self-conscious confessional Christians, but everyone around them was at least nominally a Christian. Additionally, the Christian Church, whether West or East, saw itself as bringing salvation to everyone within the society, high or low, poor or rich, and devout or ignorant. Many Europeans were not Christian in the individual way modern evangelical Protestants would understand, but European civilization was Christian.

I think this is the best way to understand what Hinduism was, and what it became. Indian civilization was long seen to be distinct by the ancients. It was not a random and disparate collection of peoples, but a civilization with various centers, and jostling competition between aspirant elites.

It is well known in the pre-modern period “Hindu” seems to have bracketed people who lived in India. From the Muslim perspective all non-Muslims who lived in the subcontinent. It was a geographical designation more than a religious one as such. But it is clear that already by the time of the arrival of Muslims in the Sindh in the 8th century, and definitely by the era when Al-Biruni wrote his well known ethnography of South Asia around 1000 AD, that Indian religion had taken on some distinctive forms and outlines, even if it was not self-consciously termed Hinduism. It is clear because outsiders describe normative Indian religious practices and beliefs that we would recognize today (e.g., reincarnation).

There are two other elements to this broader issue. First, it curious that the British had to define Hinduism, when it seems Muslims had been doing so for the whole period after the initial incursions. Al-Biruni made the most thorough early attempt, and his writings on India would make an Orientalist proud. And I say that not as a dismissal, but a description. Al-Biruni seemed rather clear-eyed that Indian hostility to Muslim was due to the predatory character of the warlords who also patronized his scholarship. The focus on the British reflects the recency-bias in post-colonial studies, where the only colonialism and conquest of interest is tht which is executed by Europeans.

Additionally, I am  convinced by the arguments in Buddhism and Islam on the Silk Road, Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane, and Warriors of the Cloisters: The Central Asian Origins of Science in the Medieval World, that Turanian Buddhism was essential and instrumental in shaping Islam as we understand it from the Abbassid period onward (in particular, the emergence of madrassa and the hadith traditions). Though Turanian Buddhism is clearly not Hindu, connections to India to the south and China to the east were part of a broader “Buddhist international” which flourished in the 4th to 7th century.

This is not to deny the distinctiveness of the Islam Al-Biruni used as a contrast to Indian religious thought. But, by his life Central Asian Buddhism was extirpated, and he would not have been able to see the influence of that Indian-influenced tradition on Islam because it had become thoroughly integrated.

Second, Indian religious civilization was successfully exported to the east so it was not constitutively associated with being Indian. The Balinese of Indonesia and the Cham of Vietnam are recognizably Hindu. It would be curious to tell them that the British defined Hinduism in the early modern period…when they were practicing Hinduism 1,000 years ago. The Ankgor temple complex was built in the 12th century, when Hinduism was Cambodia’s dominant elite religion.

Finally, an addendum to my post on caste and genetics. I read Castes of Mind many years ago. I think many of the arguments in that book aren’t necessarily invalidated by the genetic data. But, we need to think hard about whether we really expected the genetic data given the thesis that British colonialism was highly determinative in shaping the hierarchy and structure of South Asian society.

In fact, the genetic data makes it clear that most South Asian communities have been distinct and endogamous for several thousand years. That the genetic differences between castes groupings and jati within regions are closer to what you could expect of from differences between antipodes of a continent. And, within a given region ancestry which is closer to West/Central Eurasian tends to be enriched in groups “higher” up the modern caste ladder, across the subcontinent (at least if there is a correlation).

Additionally, this is not well known, but the genetic structure seems to exist even if you remove Indo-Aryans from the picture. Groups such as the Reddys and Nadars in South India who do not have any northern/western affinity at all are still genetically quite distinct from adivasis and scheduled castes in the local region. They also tend to have more West/Central Eurasian ancestry than adivasis and scheduled castes in the local region.

March 31, 2012

Post-Neolithic revenge of the foragers

Filed under: anthropology,Culture,Farmers vs. Foragers,History — Razib Khan @ 10:18 am

If I have something to share, why not share it? Over the past few weeks I’ve been ruminating on some of the possible intersections between historical population genetics and anthropology, especially in light of the discussion that I’ve had in the past with Robin Hanson about ‘farmers vs. foragers’. Entering into the record that such a dichotomy is too stark, and only marginally useful (i.e., I think it is important to separate farmers and foragers in to their own sub-classes, as some farmer types may share more with some forager types, and so forth), it may be that after the first wave of the Neolithic expansion the descendants of the foragers “bounced back” in many regions of the world. It does seem that ancient European hunter-gatherers have left modern descendants. They were not totally swamped out. Using autosomal patterns some genome bloggers have inferred the same pattern, and perhaps even a counter-reaction by “Mesolithic” populations which adopted some aspects of the “Neolithic” cultural toolkit.

But here let me come back to the Turks. Are they the descendants of farmers who expanded out of the valleys of eastern ...

December 12, 2011

Out of the agricultural hearths

Filed under: Agriculture,Anthroplogy,anthropology,Genetics,Genomics — Razib Khan @ 2:34 pm

Dienekes has an important post up, The womb of nations: how West Eurasians came to be. He outlines a scenario where a rapid expansion of a farming population has overlain much of Western Eurasia, atop aboriginal substrata. A few years ago you’d have laughed at such a model, mostly due to the authority of archaeologists and phylogeographers relying on mtDNA lineage distributions. No longer. This is not necessarily an orthodoxy, and the details of the model vary, but here is my verbal rendering of the simplest scenario:

1) ~50 thousand years hybridization between Eurasian hominins and “Out of Africa”

2) ~40-10 thousand years before the present, crystallization of the Paleolithic order of human population structure, derived from groups seeded in the original migration

3) ~10 thousand to a few thousand years before the present, the Paleolithic order is replaced and assimilated by farmers expanding from a few hearths

Below the fold is a stylized tree representation of what I have in mind.


October 13, 2011

Australia on fire

Fascinating, Orbital cycles, Australian lake levels, and the arrival of aborigines:

But the other big feature is that the lake-filling events that occurred after 50,000 years ago were much smaller than those which occurred before. Climactically, the conditions 10,000 years ago should have been the same as the conditions 115,000 years ago. But the lake was only a fraction of the size. The authors find no natural causes which can explain this. So they suggest that the aridity starting around 50,000 years ago is related to the reduction in forest and increase in grasslands which occurred at this time. This vegetation change was a result of a huge increase in the frequency of fire in central Australia, which allowed fire-adapted plants to prosper at the expense of moisture-retaining forest. The increase in fire at this time is generally associated with the arrival of the first people on the Australian continent. It is known that of Australia’s megafauna went extinct at this time, but Magee et al. (2004) show that even the tropical rains were effected by human migration, with drastic changes to the continent’s largest river basin.

If you read some of the academic literature on fire ecology you have a hard time not coming to the conclusion that modern humans terraformed the planet Earth! The hallmark of modern H. sapiens seems to be extinction of large organisms, a propensity to go where no hominin has gone before, and copious utilization of the “red flower.”

September 22, 2011

Out of Africa onward to Wallacea


There are two interesting and related papers out today which I want to review really quickly, in particular in relation to the results (as opposed to the guts of the methods). Taken together they do change our perception of how the world was settled by anatomically modern humans, and if the findings are found to be valid via replication (I think this is likely, in at least some parts) I was clearly wrong and misled others in assertions I made earlier on this weblog (more on that later). The first paper is somewhat easier to parse because it is in some ways a follow up on the paper from 2010 which documented admixture into Near Oceanian (Melanesian + Australian Aboriginal) populations from a distant hominin lineage, the Denisovans.

In this paper in The American Journal of Human Genetics they extend their geographic coverage. Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania:

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.


In some ways the result is not too surprising. There’s a rather clear cline of declining Melanesian admixture as one moves west across the Indonesian archipelago. Intriguingly the Denisovan admixture seems restricted on the western boundary to Wallacea, though the story is made more complex by the existence of the Philippines. The latter archipelago was connected to Sundaland during the last Ice Age, not Sahul, or isolated such as the isles of Wallacea.

The more complex aspect of the paper is that Denisovan admixture is not just a function of admixture with Near Oceanians. Obviously the proportion for Polynesians is elegantly explained by this model, because there is a well known cline of admixture amongst various Polynesian groups with Melanesian populations. And as I noted earlier there is also a Melanesian cline in Indonesia. But the story is not neat for the Philippines due to geography and other genetic results.

A simple model would be that Philippine Negrito admixture with the Denisovans is also a function of admixture with Near Oceanians. An event which we have no record of or reason to suspect, but may have occurred. But they did not find evidence for this. To the left is a figure which shows some of the phylogenetic relationships which they report from their analysis of SNP data. First, you see the admixture of Neandertals with all non-Africans. Second, you see the admixture of Denisovans with the very distant common ancestors of the Philippine Negritos and Near Oceanians. Next, you see an admixture of what I term “Western Negritos” (Andaman Islanders + Malaysian Negritos) with the ancestral Near Oceanian population, but not with the Philippine Negritos. Then you see admixture of an East Asian element, probably Austronesian, with various Negrito groups. The distinction between Philippine and Malaysian Negritos from each other is not that surprising if you look at PanAsian Consortium SNP data. It is a nice result though that the Andaman Islanders seem to be related to the Malaysian Negritos. The geography of the Ice Age implies the origin of this group on western mainland Southeast Asia, in close proximity to the domains of the Negritos of southern Thailand and peninsular Malaysia.

Probably the most tantalizing element to me is that the ancestry and genesis of what we term Near Oceanians may be a more complex affair than we had previous thought. This brings me to the next paper, An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia:

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

This figure distills the model down to its essence:

The main technical issue which is straightforward when comparing the previous paper to this one is that here they sequenced a whole genome of an Australian Aboriginal man who lived 100 years ago. So while the previous paper was working with tens of thousands of markers, this paper could play with millions of SNPs (though do recall that the previous paper had a much wider set of populations covered, which isn’t trivial). The top line finding seems to be that Europeans and East Asians are closer to each other than either is to the Australian Aboriginal. I’ve seen this result before. But, a major issue which is resolved here with their methods is that Aboriginals are closer to East Asians than they are to Europeans! This is the major problem I’ve always had with the idea that there were “two waves” of migration Out of Africa. If this was so, why isn’t it that Australian Aboriginals exhibit equal distance from East Asians and Europeans? The answer here is simple: admixture between the two waves, but only amongst those going east.

In other words I was confused by excessive “tree” thinking, and neglected the possibility of admixture. The first paper also hints as a possible candidate source for the admixture event: the same source population of the Western Negritos! From what I can gather this population falls into the “eastern” branch Eurasian humanity. Not quite close to East Asians, but definitely closer to them than West Eurasians. Therefore the affinity of East Asians to Aborigines may be due to this broader global “East Eurasian” heritage, which was injected into the Aboriginal man’s genome at some point in the past. Interestingly the authors found no difference in admixture from Neandertals between the populations, in line with earlier results. This implies to me, though does not prove, that the Aboriginals are a basal outgroup to other non-Africans, who all underwent the same rough admixture dynamic with Neandertals as they pushed out of Africa. Instead of two waves Out of Africa, perhaps two pulses just outside of Africa?

Finally, the fact that the gene flow seems to pre-date the separation of Native Americans from East Eurasians serves as a “peg” on the populating of Australia. The authors conclude that at a minimum we’re talking 15-30,000 years before the present. The distinctiveness of Australian Aboriginal mtDNAs, as well the localization of Denisovan admixture amongst Near Oceanians, in addition to the archaeology, makes me credit this early founding event. The populations of Sahul may have avoided being swamped out by newcomers by and large since their arrival ~50,000 years ago. I will speculate that this may explain their relatively high quantum of “archaic” ancestry. It may be that in pre-agricultural Eurasia there were many groups with higher fractions of Neandertal ancestry on the margins of the wave of anatomically modern human advance, which were only later assimilated by the demographic swell of the farmers.

There’s a lot more one could say, but I’ll leave it to readers….

September 5, 2011

Horses, not people (sort of)

Filed under: Anthroplogy,anthropology,History,Pots not People — Razib Khan @ 2:16 am
I have criticized the “pots not people” paradigm on this weblog before. In short, the idea is that material cultural changes reflected in the archaeological record are an indicator of memetic, not genetic, evolution. So a shift from pottery style X to pottery style Y informs you of an cultural switch. This is not implausible [...]

July 25, 2011

War in Pre-Columbian Sumeria

Filed under: Anthroplogy,anthropology,History,War — Razib Khan @ 11:05 pm

For most of my life I have had an implicit directional view of Holocene human culture. And that direction was toward more social complexity and cultural proteanism. Ancient Egypt traversed ~2,000 years between the Old Kingdom and the fall of the New Kingdom. But it s rather clear that the cultural distance which separated the Egypt of Ramesses and that of Khufu was smaller than the cultural distance which separates that of the Italy of Berlusconi and the Italy of Augustus. Not only is the pace of change more rapid, but the change seems to tend toward complexity and scale. For most of history most humans were primary producers (or consumers as hunter-gatherers). Today primary producers are only a proportion of the labor force (less than 2% in the USA), and there are whole specialized sectors of secondary producers, service workers, as well as professionals whose duty is to “intermediate” between other sectors and smooth the functioning of society. The machine is more complex than it was, and it has gotten more complex faster and faster.

This is a accurate model as far as it goes, but of late I have ...

June 18, 2011

Grain, disease, and innovation

I just finished reading a review of the literature since 1984 on the bioarchaeology of the transition to agriculture. Stature and robusticity during the agricultural transition: Evidence from the bioarchaeological record:

The population explosion that followed the Neolithic revolution was initially explained by improved health experiences for agriculturalists. However, empirical studies of societies shifting subsistence from foraging to primary food production have found evidence for deteriorating health from an increase in infectious and dental disease and a rise in nutritional deficiencies. In Paleopathology at the Origins of Agriculture (Cohen and Armelagos, 1984), this trend towards declining health was observed for 19 of 21 societies undergoing the agricultural transformation. The counterintuitive increase in nutritional diseases resulted from seasonal hunger, reliance on single crops deficient in essential nutrients, crop blights, social inequalities, and trade. In this study, we examined the evidence of stature reduction in studies since 1984 to evaluate if the trend towards decreased health after agricultural transitions remains. The trend towards a decrease in adult height and a general reduction of overall health during times of subsistence change remains valid, with the majority of studies finding stature to decline as the reliance on agriculture increased. The impact of agriculture, accompanied ...

May 17, 2011

There was scale and structure before history

Filed under: Anthroplogy,anthropology,Culture — Razib Khan @ 1:56 pm

Until relatively recently the spread of agriculture in Europe, and to some extent the whole world, was pigeon-holed into two maximalist models: cultural or demographic diffusionist. Neither of these models were maximalist in that they denied the impact of culture or demographics in totality, but they tended to be rhetorically brandished in a manner where it was clear which dynamic was the dominant mode of explaining the nature of cultural and genetic variation and their origins. Here are two representative headlines from the BBC:

- Most European males ‘descended from farmers’.

- Genetic roots of Europe, “New DNA evidence suggests that a few hundred Stone Age hunter-gatherers were the ancestors of many modern day northern Europeans.”

For whatever reason archaeologists themselves haven’t been able to resolve these issues. To me it seems that ultimately even if genetics is not determinate or even fundamentally specially insightful, it will at least sharpen the discussions, and move scholars away from arguments of rhetorical excess.

One of the broader issues which I’ve been coming to greater consciousness of is the idea whereby all pre-literate societies were diffuse to the point of being in a state of ...

May 6, 2011

How the “fierce people” came to be

The pith: there are differences between populations on genes which result in “novelty seeking.” These differences can be traced to migration out of Africa, and can’t be explained as an artifact of random genetic drift.

I’m not going to lie, when I first saw the headline “Out of Africa migration selected novelty-seeking genes”, I was a little worried. My immediate assumption was that a new paper on correlations between dopamine receptor genes, behavior genetics, and geographical variation had some out. I was right! But my worry was motivated by the fact that this would just be another in a long line of research which pushed the same result without adding anything new to the body of evidence. Let me be clear: there are decades of very robust evidence that much of the variation in human behavior we see around us is heritable. That the variation in our psychological dispositions, from intelligence to schizophrenia, is substantially explained by who our biological parents are. This is clear when you look at adoption studies which show a strong concordance between biological parents and biological children on many metrics as adults, as opposed ...

April 24, 2011

South Asian endogamy predates the British

Filed under: Anthroplogy,anthropology,Genetics,Genomics,India — Razib Khan @ 10:36 pm

One of the things that happens if you read ethnographically thick books like Nicholas Dirks’ Castes of Mind: Colonialism and the Making of Modern India is that you start to wonder if most castes were simply created by the British and for the British. Granted, even Dirks would not deny the existence of Brahmins prior to the British period, but those who work within his general paradigm might argue that a group like Kayasthas were the product of very recent developments (e.g., the uplift of a non-Brahmin literate group willing to serve Muslim and British rulers). The emergence of genomics complicates this sort narrative, because you can examine relationships and see how plausible they would be given a particular social model.

Zack Ajmal is now at 90 participants in the Harappa Ancestry Project. He’s still undersampling people from the Indo-Gangetic plain between Punjab and Bengal, but that’s not his fault. Hopefully that will change. He posted K = 4 recently for the last 10 participants, but I notice K = 12 in his spreadsheets. So this is what I did:

1) I aligned the ethnic identification information with the K = 12 results.

2) I removed relatives and those who ...

March 18, 2011

Foragers to farmers: a tale of collective action?

Filed under: Anthroplogy,anthropology,Culture,Farming,Neolithic Revolution — Razib Khan @ 12:46 am

The economist Samuel Bowles recently had a paper out in PNAS which caught my attention, Cultivation of cereals by the first farmers was not more productive than foraging. This naturally begs the question: why did farming conquer foraging as a lifestyle? First, let’s look at the abstract:

Did foragers become farmers because cultivation of crops was simply a better way to make a living? If so, what is arguably the greatest ever revolution in human livelihoods is readily explained. To answer the question, I estimate the caloric returns per hour of labor devoted to foraging wild species and cultivating the cereals exploited by the first farmers, using data on foragers and land-abundant hand-tool farmers in the ethnographic and historical record, as well as archaeological evidence. A convincing answer must account not only for the work of foraging and cultivation but also for storage, processing, and other indirect labor, and for the costs associated with the delayed nature of agricultural production and the greater exposure to risk of those whose livelihoods depended on a few cultivars rather than a larger number of wild species. Notwithstanding the considerable uncertainty to which these estimates inevitably are subject, the evidence is inconsistent with ...

February 8, 2011

Why Some Like It Hot: Food, Genes, and Cultural Diversity

Link to review: Slow and diverse food.

February 4, 2011

Empires of the Word: A Language History of the World

Link to review: Empires of the Word & anti-Babel

February 3, 2011

Pandora’s Seed: The Unforeseen Cost of Civilization

Link to review: Pandora’s Seed: The Unforeseen Cost of Civilization

Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present

Link to review: Who’s the barbarian now? Empires of the Silk Road

Dragon Bone Hill: An Ice-Age Saga of Homo erectus

Link to review: Dragon’s Battles

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