Jan 142013

Genome-wide data substantiate Holocene gene flow from India to Australia

PNAS online publication January 14, 2013; doi: 10.1073/pnas.1211927110
Irina Pugach, Frederick Delfin, Ellen Gunnarsdóttir, Manfred Kayserd, and Mark Stoneking

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.


At K = 5, the proportion of Australian ancestry not shared with the New Guineans most closely resembles the ancestry profile of the three Indian populations [Chenchu and Kurumba (tribal Dravidian speakers) plus nontribal Dravidian speakers from south India] at this value of K.

Additionally, at K = 7, six runs with the highest log-likelihood scores ascribe 11% of Australian ancestry to India, whereas an additional 9% is shared with the Mamanwa

Pugacha et al. (2013) Fig. S5B&C
Figs. S5B and S5C

The graph that best fits the data has four inferred migration edges: Chenchu to CHB (weight, 4%), Onge to India (17) (weight, 6%); one of the edges captures shared ancestry between NGH, AUA, and MWA (5, 23) (weight, 15%); and one of the edges provides evidence for the gene flow from India to Australia. The weight for this migration edge is estimated to be 11%, in agreement with the admixture proportion obtained in the ADMIXTURE analysis.

Pugacha et al. (2013) Fig. 4C
Fig. 4C

… our study includes 11 populations from island SE Asia [Borneo: Land Dayak; Sumatra: Besemah and Semende; Philippines: Manobo and (negrito) Mamanwa; Nusa Tenggara: Alor, Flores, Roti, Timor; Moluccas: Hiri and Ternate], but there is no signal whatsoever of recent gene flow from India into these populations or from these populations into Australia (Fig. S8), which renders this scenario of Indian ancestry via SE Asia unlikely.

Pugacha et al. (2013) Fig. S8B
Fig. S8B

Quick thoughts

The aboriginal Australian samples in this study were obtained from individuals in “a broad geographical area of the Northern Territory” — as the authors acknowledge, it can’t be presumed that this 11% “Indian” contribution is uniform across all aboriginal Australian populations, and broader sampling would be desirable. (Now, what would really be interesting would be genomic data from historic Tasmanian aborigines.)

This “Indian” element is evident neither in contemporary insular SE Asia (granted, the present-day non-Negrito inhabitants of the region seem to be, to a large extent, replacement populations) nor in (highland) New Guinea. (How about lower elevations?)

Chenchu to Beijing Han: Indian subcontinental admixture in China (but not Bornean Dayaks)?

That “Mamanwa”-modal component showing up in Australian aborigines — but not NGH — at K = 7: again something that made it into Australia while skirting (highland) New Guinea? Shades of Birdsell’s first-wave “negritos”?  Let’s remember that the Mamanwa were found previously to derive almost three-quarters of their ancestry from an East Asian-like source…

In closing … some remarks by Jonathan Morris, writing of Alfredo Trombetti and his early-20th-century precursor to Greenberg’s “Indo-Pacific”:

While my primary aim is an accurate portrayal of Trombetti’s ideas and data rather than an assessment of their merits, we may note in passing that the revision of his hypothesis to include Dravidian has the anomaly of showing better matches with Australian than with Andamanese or Papuan.

[...] Viewed from a modern perspective, I wonder whether Trombetti’s link to Dravidian is not demonstrating something else, i.e. evidence of a much later migration from India to Australia during the Mesolithic/Neolithic… [...] If so, then the implications of Trombetti’s work are that the South Indian populations which migrated to Australia were Dravidian speakers, even if he was probably wrong to include this family in his Andamanese-Papuan-Australian phylum.

Nov 182012

Unsupervised 44-population ADMIXTURE analysis (K=9) using the Genographic Project’s new “GenoChip” SNP array, from the Geno2.0 poster at ASHG 2012. No photographs of the poster were permitted, but a scaled-down version was made available by the presenters as a handout (scanned in full here).

Quick impressions: Nothing looks too out of the ordinary (save that “South East Asian” has to be a composite of both “ASI” and southern East Asian proper). Those “Northern Indians” could only be Ladakhis or something similar. “Native American” shows up everywhere in Eurasia that you’d expect it, with greatest pronouncedness in the Altaians, next the Mongolians, and then the Tatars, the Finns, and so on. Somewhat interesting that the Mexico Amerindians (wonder what their specific identity is), have a small “North East Asian” element close to negligible in the Andeans. Like I said, no big shocks.

Nov 082012

Journal of Human Genetics advance online publication 8 November 2012; doi: 10.1038/jhg.2012.114

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

Japanese Archipelago Human Population Genetics Consortium: Jinam et al.

The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

[Rough first take follows, updates to come.]

Death knell of the “Caucasoid hypothesis”:

No obvious affinities between the Ainu and West Eurasians, not even a little tug towards the CEU pole.

Sans YRI this time. Obvious gradient of admixture (more below on those supposed Ainu right in the middle of the regular Japanese cluster).

A “strange drop of oil” still:

Are they Mongolian? If they are, they have none of the characteristics of that race; and if they are not Mongolian, then they are something like a strange drop of oil in the ocean, being surrounded by Mongols, yet not of them. — Royal Navy Captain H.C. St. John’s 1880 impression of the Hokkaido Ainu.

Lonely leaf on a long branch. Ryukyuans come out quite stably as their nearest sisters, but they’re still not all that close.

Northern vs. southern origin debate clearly not going to be solved by a straightforward crumbling out into “Siberians” or “southeast Asians”. The Ainu are a very differentiated kind of East Eurasian unto themselves.

Internal structure and outliers:

Authors suggest five individuals in red circle on PCA graph (which break out as all-purple at k=4 in the admixture chart) were potentially Sakhalin Ainu, some of whom relocated to the study locality following WWII. Component potentially related to Okhotsk Culture (northern maritime complexes pushing south).

As for the (supposed) Ainu inside Mainland Japanese cluster: there were some Mainland Japanese individuals who married Ainu people in Biratori Town when blood collection was conducted. These genetically non-Ainu people might have been included in the ‘Ainu’ samples we used. The well-known practice of adopting wajin infants could perhaps also account for this.

Either way, sounds like these samples could have benefitted from some better curating.

Admixture plot puzzles:

What accounts for those upticks of dark blue, if they’re actually meaningful, at k=4 and k=5 in Dai, Lahu, and Uyghur? Suspicion that something southerly’s afoot > “ASI”-Ainu connection?

Where to go from here:

It should be noted that Omoto conducted a pioneering study on the phylogenetic relationship of the Ainu population considering various degrees of admixture. When a 60% admixture with the Mainland Japanese was assumed for the modern Ainu population, the ancestral Ainu population was clustered with Sahulian (Papuan and Australian). This sort of simulations based on the real data is needed. Seconded.

What ought to be next: admixture analyses with Australian aboriginal and Papuan (wondering about “Australoid” and more specifically “Murrayian” connections), negrito (particularly Andamanese), Tibetan Plateau (Y-hg D … but keeping expectations low given what Wang et al. (2011) found re: Tibetans and non-Ainu Japanese), Indian subcontinental, and New World references. (Does the Amerindian-like component showing up in northern Europeans seem to be present in the Ainu as well?) “Paleoasiatic” Siberians (especially from Kamchatka and thereabouts), not just Turkic, Mongolic, and Tungusic ones, ought to be included too.

Archaic hominid ancestry values vis-à-vis other East Eurasians?

Future sampling: modern DNA from Nivkhs and other Amur-Sakhalin peoples; aDNA from various localities and time depths in Japanese archipelago (especially those Okinawan cave remains) of course, but also Korean peninsula and Russian Far East. Still more ambitiously, Paleoamerican aDNA (one wonders about all those Jomon-like Kennewick types). Just for kicks, Valdivia-era coastal Peru too.

Adaptive stories? EDAR and co. — wondering about basis of Ainu hirsuteness (and interesting combination of wavy yet very coarse hair), non-sinodont tooth patern. (And what’s going on with proportionally tiny teeth?) ABCC11 and wet earwax, apocrine gland development. Pigmentation alleles. Alcohol dehydrogenases.

Nov 072012

Readers of GNXP may remember a straw poll Razib took somewhat over a year ago asking which undersampled or unsampled populations people would like to see genotyped. The Ainu, who have heretofore really only been analyzed for Y- and mtDNA, were a frequent mention. As some of my previous posts probably made clear, the Ainu would have been my top choice, too.

Today, it looks like the wait’s up. As soon as the current issue of the Journal of Human Genetics (Volume 57, Issue 11) comes online, the world will see what 36 Ainu individuals look like at 900,000 SNP resolution. These are evidently coming from stored materials collected around 30 years ago. To accompany them will be 35 native Okinawan and, from Honshu and elsewhere — which hopefully includes Hokkaido — 243 Yamato Japanese samples.

Here’s what I’ve pieced together from the general news sites that’ve picked up this story so far (Asahi Shimbun article in English here, Nikkei article translation here):

Ancestry of all Japanese well-approximated by a two-way mix of “Yayoi” and “Jomon”; “Jomon” component bimodal, albeit still somewhat diluted relative to pre-Yayoi epochs, in far south (Okinawans) and far north (Ainu); Ainu closest, in decreasing order, to Okinawans, Yamato Japanese, Koreans, and Han Chinese; Kanto Japanese rather similar to Koreans, less so to Han Chinese (some of the articles suggest even closer to Koreans than to Okinawans, though that remains ambiguous).

None of this comes as a surprise. Physical-anthropological, archeological, and textual data (i.e., accounts of warfare with and enslavement of Ainu-like hostile emishi on Honshu as well as the more peaceable co-opting of friendly or pacified emishi into the Japanese world-system) have long indicated as much, and the last point in particular has been fairly undeniable since the 2010 Jung et al. study — no matter how much Japanese and Koreans alike have sidestepped it. (And continue to sidestep … look at what the Asahi Shimbun chose to highlight instead.)

It’s just the first time this story’s being told with an Affymetrix 6.0 array, and the first time we have any autosomal Ainu references whatsoever.

(Left from the Asahi Shimbun, right from the Chugoku Shimbun.)

It’s nice timing that this comes hot on the heels of the Loh et al. ALDER paper, which estimates the Japanese — using CHB Han Chinese as the Yayoi proxy — to have admixed 45 +/- 6 generations/1,300 years ago and a genome-wide lower bound “(likely very conservative)” of 41 +/- 3% “Yayoi” ancestry.

More thoughts about this for sure, but I’m going to first wait and see what else the actual paper holds in store. Until then, some funny early receptions: here or here, as suits your taste.

Apr 302012

A footnote in Christopher Beckwith’s The Tibetan Empire in Central Asia (1987: 142):

Then, on December 16, 755, the Turco-Sogdian military governor An Lu-shan rebelled against the T’ang and shook “all under Heaven.”212

212 CTS, 104:3213; HTS, 135:4570; TCTC, 216:6916. These three sources quote a conversation that took place between An Lu-shan and his bitter enemy Qośu Khan that took place prior to the rebellion in the presence of Hsüan-tsung. Trying to placate Qośu, An said: “My father was an Indo-European, my mother a Turk; your father was a Turk, your mother an Indo-European.” Qośu Khan’s father was indeed a Türgiś. (Cf. Des Rotours, 1962:1-2.) In An Lu-shan’s case, the word hu [胡] (“Indo-European, especially Sogdian”) almost certainly identifies him as a Sogdian because his surname (An) was commonly used to refer to Sogdians originally from Bukhara. Hu did not mean just “Serindian” during the T’ang period, but anyone of Indo-European race (p. 1[n. 3]).

I’m sure this last line raised some eyebrows (the sin of brachycephalic grammar and all that), but those who would berate Beckwith should cluck their tongues too at the Pashtuns and Taimannîs, for “Aryan” in present day Afghan parlance means simply Afghano-Iranoid (Schurmann, 1962: 66) — if not in the exact same sense of Carleton Coon’s “Irano-Afghan” type, then nonetheless in a more-than-linguistic one (for what do the Hazaras speak?).

See also this earlier post on historical use of *arya as an Indo-Iranian self-designation.

Works Cited:

Beckwith, C.I. (1987). The Tibetan Empire in Central Asia: A History of the Struggle for Great Power among Tibetans, Turks, Arabs, and Chinese during the Early Middle Ages. Princeton, New Jersey: Princeton University Press.

Schurmann, H.F. (1962). The Mongols of Afghanistan: An ethnography of the Moghôls and related peoples of Afghanistan. ‘s-Gravenhage: Mouton.

Nov 132011

Members of the New York-based Cacibahagua Taino Cultural Society performing at the “Drums Along the Hudson Festival,” May 2009. (Photo credit: M. Sague.)

The end of October saw Nature News subjected to the electronic rage of dozens of self-proclaimed latter-day Taínos — modern Puerto Ricans who, long after the extinction of the Taíno language, and long after the slave trade and trans-Atlantic European migrations had reduced Taíno ancestry on that island to a relatively thin substrate, decided to assert an Amerindian identity.

The casus belli? Susan Young, reporting on Carlos Bustamante’s efforts to genomically “reconstruct” the Taíno from the fragmentary inheritance of some of their substantially admixed descendants (Puerto Rican participants in the 1,000 Genomes Project), had spoken of this people as “extinct.” Instantly, the comment section was flooded with remarks like that of one Cheyenne Velazquez (contemporary “Taíno” self-conception’s debt to various North American Indian iconographies is wondrous indeed):

How Dare You. I think you have violated several your own guidelines by publishing this article: It is offensive, presents misinformation, it discriminates against 20,000 plus Taino People and Families the list goes on and on. […] Apologize. I stand here arm in arm with my Sisters and Brothers and I say I AM ALIVE, WE ARE ALIVE,WE ARE STRONG, WE BREATH, WE ARE TAINO.

Won over, no doubt, by the inarguable eloquence of these critiques, Nature News reworded and retitled the article — from Breathing life into an extinct ethnicity to Rebuilding the genome of a hidden ethnicity (not extinct, just in occultation, like the Twelfth Imam, you see) — and appended an apology to the end:

Corrected: This article originally stated that the Taíno were extinct, which is incorrect. Nature apologizes for the offence caused, and has corrected the text to better explain the research project described.)

Bustamante stepped in with his own heart-felt clarification:

I am writing to thank the members of the Taino community who wrote here for their response and to apologize for any offense our work and the media coverage has caused. It was a mistake to refer to the Taino people as “extinct” given the large number of people who self-identify as Taino. We, too, are committed to the message you state loud and clear: El Taino Vive / The Taino Live On.

One wonders how all this could have conceivably slipped his mind while he was preparing his presentation for the 2011 International Congress of Human Genetics. Perhaps his epiphany came just after the abstract revision deadline.

Genomic Reconstruction of an Extinct Population from Next-Generation Sequence Data – Insights from the Taìno [sic] Genome Project.

J.K. Byrnes1, J.L. Rodríguez-Flores2, A. Moreno-Estrada1, C.R. Gignoux3, S. Gravel1, W. Guiblet4, F. Zakharia1, J. Dutil5, E.G. Buchard3, T.K. Oleksyk4, J.C. Martínez-Cruzado4, C.D. Bustamante1, The 1000 Genomes Project Consortium. 1) Department of Genetics, School of Medicine, Stanford University, California 94305, USA; 2) Department of Biological Statistics and Computer Science, Cornell Univeristy, New York 14853, USA; 3) Institute for Human Genetics, University of California San Francisco, California, USA; 4) Department of Biology, University of Puerto Rico at Mayagüez, Puerto Rico 00680; 5) Ponce School of Medicine, Puerto Rico 00732.

The first Native American people encountered by Europeans across the Caribbean were given the collective name “Taìnos” by the arriving Spaniards. One hundred years after this initial contact, the Taìnos were effectively extinct due to war, slavery, suicide, hunger, and disease. Today, the ancestral legacy of the Taìnos is found in traces of their genomes still present in the inhabitants of the islands. […] Although the Taìno admixture proportion is small (0.09 ± 0.01 S.E.) relative to the African (0.13 ± 0.03 S.E.) and European (0.77 ± 0.03 S.E.) proportions, greater than 85% of the genome is covered by five or more chromosomes of Taìno origin. Looking at the ancestry tract length distribution, we can infer various aspects of the demographic history. For example, Taìno ancestry tracts follow an exponential distribution suggesting a single pulse of indigenous Taìno ancestry incorporation consistent with historical records of rapid extinction of the Taìnos. Given our ancestry inference, we can use the high-throughput sequencing data to measure heterozygosity, estimate time to most recent common ancestor between maternal and paternal lineages, and construct the site frequency spectrum in an ancestry-specific way. This provides further information on demographic history including effective population size estimates of the source populations contributing to the admixture event. Finally, we identify Taìno specific genomic variation cataloging what remains of this lost ancestral lineage. […] This is the first known reconstruction of the genomic variation of an extinct human population using modern data.

I was planning a more extensive post, but Dienekes (The Taíno are extinct) and Razib (The perils of human genomics) rather took the wind out of my sails. However, I’ve recently noticed that versions of the original Nature News report mirrored on other sites were being altered, too — at the gentle suggestion (one assumes) of levelheaded Caribbean Indigenes like Cheyenne — and I’m accordingly revisiting the matter.

For posterity’s sake, I’ll present the major points of discrepancy. At left, selections from a facsimile of the original that was hosted at Caribbean Business — itself subsequently bowdlerized — and, at right, the corresponding portions of the Nature News article as it presently stands:

The Taínos were the first Native Americans to meet European explorers in the Caribbean. They soon fell victim to the diseases and violence brought by the outsiders, and today no Taínos remain.

But the footprints of this extinct ethnicity are scattered throughout the genomes of modern Puerto Ricans, according to geneticist Carlos Bustamante at the Stanford University School of Medicine in California. On average, the genomes of Puerto Ricans contain 10 percent to 15 percent Native American DNA, which is largely Taíno, says Bustamante.

The small size of the ancestral segments fits with our understanding of the history of Puerto Rico, says Marc Via, a molecular anthropologist at the University of Barcelona, Spain, who was not involved in the study. “The admixture took place suddenly, so most of the population mixed with the African slaves and European settlers in the very early colonization of Puerto Rico.” But the Taínos quickly died out, so with every generation, the segments of Taíno genome would become smaller and smaller, he says.

The Taínos were the first Native Americans to meet European explorers in the Caribbean — and they soon fell victim to the diseases and violence brought by the outsiders. Today, the genomes of most if not all descend[a]nts of Taínos now contain few of the unique markers that characterized their ancestors.

But the genetic footprints of these ancestors are scattered throughout the genomes of modern Puerto Ricans, according to geneticist Carlos Bustamante at the Stanford University School of Medicine in Stanford, California. On average, the genomes of Puerto Ricans contain 10–15% Native American DNA, which is largely Taíno, says Bustamante.

The small size of the ancestral segments fits with our understanding of the history of Puerto Rico, says Marc Via, a molecular anthropologist at the University of Barcelona, Spain, who was not involved in the study. “The admixture took place suddenly, so most of the population mixed with the African slaves and European settlers in the very early colonization of Puerto Rico.” With every generation, the segments of Taíno genome would become smaller and smaller, he says.