The International Union for Conservation of Nature (IUCN) announced the positive change to the giant panda’s official status in the Red List of Threatened Species, pointing to the 17 per cent rise in the population in the decade up to 2014, when a nationwide census found 1,864 giant pandas in the wild in China.
“For over fifty years, the giant panda has been the globe’s most beloved conservation icon as well as the symbol of WWF. Knowing that the panda is now a step further from extinction is an exciting moment for everyone committed to conserving the world’s wildlife and their habitats,” said Marco Lambertini, WWF Director General.
But we need to keep perspective. Something similar is happening with tigers, whose census sizes are finally increasing after a century of continuous decline. But we’re talking bounce back to 4,000! This is still a small and vulnerable population. Genetically, depending on the details of the structure, 100 to 1,000 are probably enough for viability. But genetics isn’t everything. Some random stochastic event (e.g., look at what happened to the Tasmanian devil) could wipe out a few thousand quickly, and we’d be up against our heels.
Excited to be going to ASHG 2016. Is Vancouver really part of Canada? Isn’t it like Seattle with a queen? In any case, the abstracts aren’t online yet. They should drop this week….
As a change of pace I’ll be checking out Christie Wilcox’s new book, Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry. It’s often joked that geneticists don’t know real biology, and despite an undergrad background in biochemistry that’s probably somewhat true for me.
5 racist stereotypes that historically were the opposite of what they are today. Vox is doing well because they’re very cautious about challenging the preconceptions of their readers. Often they reinforce them. Too easy to deconstruct, but please note that stereotypes which might be held about Asians may not be common for certain types of Asians. This sort of banal observation is difficult to make when you are experiencing an orgasm because of the smug-saturation.
It is too much to assert to say that the Indian ocean is “our sea,” writ large as a species. But it does certainly seem to be the case that this body of water does punch above its weight. It is likely that anatomically modern humans emerged not too far from its shores, while the first, second, and third civilizations arose arose along its fringes (civilization being defined as having cities and some basic level of literacy). As humanity developed complex societies at the antipodes of Eurasia, in Europe and China, the focus on the Indian ocean basis became somewhat attenuated, but its centrality as a nexus between these two dynamic loci of economic and cultural activity persisted. In addition, both the world of Islam and Southeast Asia were deeply connected to the ocean, while for India it was the ocean.
Sanjeev Sanyal’sThe Ocean of Churn: How the Indian Ocean Shaped Human History is a panoramic narrative which surveys the lands around this ocean, and how wrapped up they’ve been in human history. There are two broad themes which undergird The Ocean of Churn. First, Sanyal seems to (mostly) reject the Great Man theory of history, as well as deterministic Marxist models. Rather, he posits that historical processes are a complex adaptive system. This is probably true, but honestly I don’t see that it looms very large in The Ocean of Churn, which is mostly a descriptive narrative on the macroscale. If you deleted this nod to the theoretial framework it could be read perfectly fine. The second major theme, that the flow of ideas and peoples is bidirectional, rather than a sequential branching processes, permeates the book. In fact, it’s hard to ignore, because Sanyal begins by recounting how the Pallava dynasty of South India was refounded by a collateral branch from Cambodia!
The map to the left is a stylized representation of humanity’s expansion out of Africa. To a first approximation it gets a lot right. But because it only depicts unidirectional migration it misses a lot in the detail. The same could be said for culture. For example, the narrative of Islam is that it spread from Arabia, to the west and the east. But works such as Lost Enlightenment and Warriors of the Cloisters both argue that there was a massive reflux from the east after the transition between the Umayyads and the Abbasids. The Abbasid power base, and many of their courtiers, were from Khorasan in the northeast of modern Iran, and Transoxiana. While 7th century Islam crystallized in the matrix of a post-Roman Late Antique world, with the Umayyad center of power being in Syria, the Abbasids emerged from a milieu where Muslims, Christians, Zoroastrians, Buddhists, and even Hindus, mixed freely and exchanged ideas.
Like Empires of the Silk Road and Facing the Ocean: The Atlantic and Its Peoples 8000 BC-AD 1500, the The Ocean of Churn is a historical geography with a broad view and lacking a tight focus. It’s not a bug, it’s a feature. Additionally, Sanyal’s style is quite conversational and informal…dare I say, almost bloggish? He admits very early that he’s not writing an academic work. Rather, The Ocean of Churn is part travelogue, part historical commentary, and part review of the academic literature. Additionally, there is arguably somewhat of an Indo-centric bias, insofar as in a book which runs less than 300 pages India and its role at the center of events take up disproportionate space. This is somewhat ironic in light of the author’s conscious observation that previous histories of the Indian ocean were quite Eurocentric, but somewhat justified by the fact that India’s long history, relative influence around the basin of the Indian ocean, and demographic heft, probably warrant extra attention.
Sometimes this focus gets the better of Sanyal. The voyages of Zheng He somehow get drafted into the shift within maritime Southeast Asia from affiliation with the Dharmic set of cultures rooted in Hinduism and Buddhism toward that of Islam, where the machinations within the Chinese court were geared toward breaking the Indic affinities of this region to increase Chinese cultural hegemony.
There are two major problems I see with this. First, the swing from Hinduism and Buddhism to Islam in maritime Southeast Asia was a centuries long process, and occurred first in the Arabian sea, before shifting to the eastern regions of the Indian ocean. One can make the case that it was the rational thing to do for maritime facing Southeast Asian polities to realign their culture focus from Dharmic religions to Islam.
Second, there were longstanding dynamics at the court of the Ming dynasty which could explain much of the rationales for the voyages of Zheng He’s fleet, dynamics which can be traced as far back as the Song dynasty as to the proper role of the state in society and the world. This is a case where Sanyal’s narrative is too geographically and historically delimited to flesh out the more complex and messy dynamics at the heart of which was a civilizational pivot in Southeast Asia and sui generis maritime voyages out of the heart of the Chinese world.
But in general The Ocean of Churn does not suffer from narrowness. Rather, the footnotes and citations are a testament to Sanjeev Sanyal’s catholic tastes; they are wide-ranging, and warrant closer attention and follow-up. I did not, for example, know that the native Malagasy had retained a custom of boat burial even after they had to retreated to the highlands and become farmers with little experience of the sea. The Ocean of Churn is packed with many interesting details of this sort. It’s a gold-mine for those looking for more to read.
And yet in the course of inter-disciplinary work sometimes you’ll miss the trees from the forest. This occurs in Sanyal’s survey of the historical genetics literature. He gets most right, but gets some wrong. The first case is that Sanyal refers a few times to the 2013 paper, Genome-wide data substantiate Holocene gene flow from India to Australia. It came out in PNAS, a reputable journal, and includes an author, Mark Stoneking, which some prominence in the field. Additionally, the timing was such that it aligned well with a contemporaneous cultural change in humans, and the arrival of dingos. Unfortunately, the paper was certainly wrong. First, the data was not open, so I could not replicate, to see how robust the statistics were. I complained about this at the time. Second, several prominent statistical geneticists told me privately that they were very skeptical of the statistics. Third, recent research suggests that Aboriginal paternal lineages are very deeply rooted, Deep Roots for Aboriginal Australian Y Chromosomes. Indian Y chromosomes are very distinctive. There is evidence for them in Southeast Asia in regions without colonial era Indians, in particular Cambodia. Of course, it could be that only the female lineages persisted, but there is the reality that there’s been no evidence for recent Indian mtDNA in Australia to my knowledge (the divergences are very deep), and, no other paper which has access to Australian genome data has replicated this finding. Finally, from what I am hearing a new autosomal paper will come out soon and definitively render judgment against this paper’s result (this is why the Y chromosome paper came out).
But the above is pretty small-ball. The major issue in the citation of historical genetic papers in The Ocean of Churn is that there are references to older works, as in five years old, that are totally out of date, and interpretations based on consensus understandings of the late 2000s that have been overturned.
Let’s start with R1a1a. This a male Y chromosomal lineage which is very common in South Asia, Central Asia, and West-Central Eurasia (Eastern Europe). When it comes to Y chromosomal lineages whole genome analyses have changed our understanding a lot of the phylogenetics of this topic. The earliest work uses highly mutable microsatellites, while later work focused on single nucleotide polymorphisms. Using these patterns of variation researchers created phylogenies, most of which have stood the test of time, and calibrated divergence times, many of which have not. Basically the Y chromosome doesn’t have enough SNP diversity to allow good calibration of divergence, while because of their high mutation rate microsatellites are not good for temporal inference.
The plot above shows the R1a1a males in the 1000 Genomes data (it’s from Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences). The green are South Asians, the blue are Europeans. Because the 1000 Genomes data is biased toward West Europeans, there are far fewer R1a than R1b in the data from that continent. What they confirm is that South Asian and European R1a are two different clades. The South Asian clade is often termed Z93 because of a particular mutation. Z93 is overwhelming in South Asia, very rare in Europe, and relatively common among the R1a individuals in Central Asia (e.g., the Altai sample from the 1000 Genomes). The pattern of genetic diversity shows that there isn’t much, and, that the diversity is relatively shallow. That is indicative of two things. R1a went through a very recent massive population expansion. It’s a “star-shaped phylogeny.” Contrast that with J2, which has also undergone expansion since the rise of agriculture, but exhibits far more internal structure. J2 probably started expanding earlier, and, it’s expansion was never at any moment as explosive as that of R1a and R1b. Earlier work suggesting R1a diversification ~10,000 years ago does not hold up.
The second issue in relation to R1a is that now have ancient DNA . Both R1a and R1b are very rare before 4,000 years ago. Here’s a section from a paper published in 2015 out of David Reich’s lab:
Further evidence for a connection between the Srubnaya and populations of central/south Asia—which is absent in ancient central Europeans including people of the Corded Ware culture and is nearly absent in present-day Europeans…is provided by the occurrence in four Srubnaya and one Poltavka males of haplogroup R1a-Z93 which is common in present-day central/south Asians and Bronze Age people from the Altai…(Supplementary Data Table 1). This represents a direct link between the European steppe and central/south Asia, an intriguing observation that may be related to the spread of Indo-European languages in that direction.
The Srubna people seem to have flourished between the Dnieper and Volga, and south toward the Caucasus, about ~3,500 years ago. But the Srubna are not simple solution to the problem of Indo-Aryan origins. From the supplements of Genomic insights into the origin of farming in the ancient Near East:
The analysis in this section reconciles the evidence presented in the first paragraph regarding the origin of the ANI by showing that is may be related both to “southern” populations related to Iran and the Caucasus and to “northern” steppe populations. Our results do not resolve the relationship between ANI and the origin of Indo-European speakers in South Asia, in the sense that they reveal that South Asian populations have ancestry both from regions related to the Eurasian steppe and ancient Iran, which is compatible with alternative homeland solutions…
…
While the Early/Middle Bronze Age ‘Yamnaya’-related group (Steppe_EMBA) is a good genetic match (together with Neolithic Iran) for ANI, the later Middle/Late Bronze Age steppe population (Steppe_MLBA) is not. Steppe_MLBA includes Sintashta and Andronovo populations who have been proposed as identical to or related to ancestral Indo-Iranians…as well as the Srubnaya from eastern Europe which are related to South Asians by their possession of Y-chromosome haplogroup R1a1a1b2-Z935. A useful direction of future research is a more comprehensive sampling of ancient DNA from steppe populations, as well as populations of central Asia (east of Iran and south of the steppe), which may reveal more proximate sources of the ANI than the ones considered here, and of South Asia to determine the trajectory of population change in the area directly.
Basically, the Reich lab has used ancient DNA to confirm what genome bloggers started noticing around 2010: the “ANI” component of South Asian ancestry is itself a composition with different streams. In the initial analyses the division between ANI and ASI (“Ancestral South Indian”) dropped out so easily because the two groups were very genetically distinct. In contrast, the West Asian and Bronze Age Steppe streams of the ANI ancestry are rather genetically similar in comparison, making them harder to differentiate. Ancient DNA has been particularly useful because the differences were starker in the past.
All good so far. Much of this aligns with The Ocean of Churn and its thesis of bidirectionality. The problem I have is that Sanyal seems to be implicitly assuming that an “Out of India” theory for the emergence of Indo-Aryans is the correct position when there’s a lot of legitimate debate about this, and good reason to hold that this is not plausible. He refers to the Indo-Aryan Mitanni as “Indian,” when it fact this is likely to be an anachronism. Similarly, if it is found that a Dravidian language was spoken in southern Iran during the Bronze Age, I suspect that terming them “Indian” would also be an anachronism.
When I told Sanyal I was going to bring this up on Twitter he told me that I needed to cite peer-reviewed literature. This is reasonable, in light of the fact that when you’re navigating different disciplines you can’t familiarize yourself totally with the landscape…but, it highlights a problem with his citation pattern: he’s not a human population geneticist, and so hasn’t kept up with the field, nor does he know what papers are of high quality in retrospect and what papers are not. I suggested to him that I could actually run many of the analyses myself since the data is open, but he responded that this would be “he said/she said.” This is fair because most people do not have much familiarity with population genomics. But, it is unfair because I actually have familiarity with the field and can actually do the work myself, so perhaps my opinion should be weighted a bit higher?
Ultimately all this is going to be forgotten commentary when sites like Rakhigarhi start yielding ancient DNA. I have already made a bunch of predictions relating to that research. There have already been leaks in the Indian press, such as ‘Descendants of Harappans still living in Rakhigarhi’. I’m pretty sure that what they’ll find is that the people who inhabited the Northwest quadrant of South Asia at that point were already admixed. They simply lacked the Bronze Age Steppe component of ancestry, which probably arrived with the Indo-Aryans.
Of more interest to me is Sanyal’s assertion of Southeast Asian influences India. The 1000 Genomes data makes clear that there is substantial admixture from Southeast Asian populations in Bengal. But there is no historical record of this, but its impact has been significant. The Ocean of Churn makes much of matrlineal customs, and their diffusion from Southeast Asia to India through the vector of migration. I’m not so sure that migration (cultural diffusion) is the only explanation of this phenomenon, but it is certainly plausible. One quibble I would make here is the same as above in regards to India: a lot of the population dynamics of Southeast Asia date to the later Holocene. Not the Holocene-Pleistocene boundary, when Sundaland would have been inundated.
There is clearly recent gene flow from South Asia to Southeast Asia. The genetic data from Cambodia suggest it is even, which means it was a demographic movement which affected the whole people. The cultural connections between Indic Southeast Asia and India have long been known, but it has long been assumed that this was mostly a matter of ideas, not people. But clearly enough people went so that ~5% of Cambodian ancestry seems to be Indian! The question then proceeds about reverse migrations. The movement into Bengal was relatively recent, and my own analyses have shown that it can’t be explained as purely an Austro-Asiatic event. Rather, the Tai migrations which reshaped the cultural and to some extent demographic landscapes of mainland Southeast Asia seem to have had a spillover effect into Bengal, which was at that time rising to prominence under the Pala dynasty.
Ultimately The Ocean of Churn lives up to its name. The authors explores connections between Madagascar and the East African coast, the Indus Valley Civilization and Mesopotamia, and Southeast Asia and India. It is fertile ground, and despite my quibbles and concerns with portions of the book, it is an excellent place to start. If you want to continue in a more narrow and academic vein, I’d recommend The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies, a book which traces connections between the two civilizations, and also looks further as to deeper influences from Mesopotamia on both of them.
The map to the left is a stylized representation of humanity’s expansion out of Africa. To a first approximation it gets a lot right. But because it only depicts unidirectional migration it misses a lot in the detail. The same could be said for culture. For example, the narrative of Islam is that it spread from Arabia, to the west and the east. But works such as 
