Finally some Good News: Tibetan DNA

Hey, we take our good news where we get it.

Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present day Tibetans:

Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau.

Congratulations to the authors. I enjoyed this paper and hope they have more in the works.

Skipping past some of the technical discussion, let’s get down to the nitty-gritty of what it all means:

The haplogroup networks and haplotype–haplogroup sharing demonstrated to us that there was partial matrilineal continuity in Tibetans from 5200 years ago.

That means modern-day Tibetans descended from a mix of peoples, some of whom have been there for over 5,000 years, and some of whom arrived recently.

Under this continuity, some people spread from low-to-high altitudes 4750 to 2775 years ago and some expanded within high-altitude areas 2125 years ago. The timing revolved around the high-altitude agriculture transformed by barley, which appeared 5.2 ka near the northeastern edge of the plateau and moved into high altitudes by 3.6 ka [2].

Farmers. I wonder how difficult it was to get barley to grow up there. Tibet seems like a pretty harsh environment.

That said:

However, based on the 16 haplogroups that have a frequency in Tibetans (a subset of 21 unique haplogroups), D4j1b and M9a1a1c1b1a would represent about 13% (2 out of 6) as the footprint of that event. Thus, our findings did not favour a substantial migration of lowland farmers to the high-altitude areas.

So, farmers did expand into Tibet, but not a ton of farmers (or at least, not a ton of farming women.) Probably because Tibet is a really harsh place–both for people and barley strains that aren’t adapted to living there.

An explanation for the surplus of unaccounted maternal lineages could be that there were earlier waves of populations who settled into higher altitudes and underwent isolation by distance [26]. The earlier settlers were potentially hunters and gatherers who left behind no human fossils, perhaps connected to the blade tool assemblages or fossilized handprints and footprints dating to as far back as 40–30 ka [27] or 13–7 ka [28]. Our results could support a recent diffusion of plateau populations into an otherwise stable population continuous with previous high-altitude populations. A similar point of view has been made from analysing the whole genomes of present-day Tibetans [29].

What would being a hunter gatherer in Tibet have been like?

I figured there was probably some ancient population that has contributed to the modern Tibetan population both because of the aforementioned environmental difficulties, and also because the Tibetans show adaptations to the area, which take time to accumulate. Among those adaptations, Tibetans have some DNA they appear to have picked up from the Denisovans, and Denisovans probably haven’t lived in Tibet in a very, very long time.

Take care and stay healthy, everyone.

The People Who Went Down the Rivers: Origin of the Sino-Tibetan Language Family

I recently received a question from Quas Lacrimas:

“What (if anything) do you make of the fact that Proto-Tibetan and Proto-Sinitic were sister languages, but Tibetans and Han are so genetically disparate?”

My first response was that, assuming the question itself was correct, then one group must have conquered the other group, imparting its language but not its DNA.

On further reflection, though, I decided it’d be best to check whether the question’s initial premises were correct.

Sino-Tibetan, it turns out, is a legit language family:

The Sino-Tibetan languages, in a few sources also known as Tibeto-Burman or Trans-Himalayan, are a family of more than 400 languages spoken in East Asia, Southeast Asia and South Asia. The family is second only to the Indo-European languages in terms of the number of native speakers. The Sino-Tibetan languages with the most native speakers are the varieties of Chinese (1.3 billion speakers), Burmese (33 million) and the Tibetic languages (8 million). Many Sino-Tibetan languages are spoken by small communities in remote mountain areas and as such are poorly documented.

Map of the Sino-Tibetan language family
Red: Chinese; Yellow: Tibetan; Brown: Karen; Green: Lolo-Burmese; Orange: Other

But the claim that Tibetans and Chinese people are genetically disparate looks more questionable. While the Wikipedia page on Sino-Tibetan claims that, “There is no ethnic unity among the many peoples who speak Sino-Tibetan languages,” in the next two sentences it also claims that, “The most numerous are the Han Chinese, numbering 1.4+ billion(in China alone). The Hui (10 million) also speak Chinese but are officially classified as ethnically distinct by the Chinese government.”

But the Chinese government claiming that a group is an official ethnic group doesn’t make it a genetic group. “Hui” just means Muslim, and Muslims of any genetic background can get lumped into the group. I actually read some articles about the Hui ages ago, and as far as I recall, the category didn’t really exist in any official way prior to the modern PRC declaring that it did for census purposes. Today (or recently) there are some special perks for being an ethnic minority in China, like exceptions to the one-child policy, which lead more people to embrace their “Hui” identity and start thinking about themselves in this pan-Chinese-Muslim way rather than in terms of their local ethnic group, but none of this is genetics.

So right away I am suspicious that this claim is more “these groups see themselves as different” than “they are genetically different.” And I totally agree that Tibetan people and Chinese people are culturally distinct and probably see themselves as different groups.

For genetics, let’s turn back to Haak et al’s representation of global genetics:

Haak et all’s full dataset

 

 

 

 

 

 

 

 

 

Just in case you’re new around here, the part dominated by bright blue is sub-Saharan Africans, the yellow is Asians, and the orange is Caucasians. I’ve made a map to make it easier to visualize the distribution of these groups:

Asian, Australian, and Melanesian ethic groups (including Indian, Middle Eastern, and Chinese) from Haak et al’s dataset

This dataset doesn’t have a Tibetan group, but it does have the Nepalese Kusunda, Mongolic Tu (a Mongolic-language speaking people in China), and the Burmese Lahu. So it’s a start.

The first thing that jumps out at me is that the groups in the Sino-Tibetan language family do not look all that genetically distinct, at least not on a global scale. They’re more similar than Middle Easterners and Europeans, despite the fact that Anatolian farmers invaded Europe several thousand years ago.

The Wikipedia page on Sino-Tibetan notes:

J. A. Matisoff proposed that the urheimat of the Sino-Tibetan languages was around the upper reaches of the Yangtze, Brahmaputra, Salween, and Mekong. This view is in accordance with the hypothesis that bubonic plague, cholera, and other diseases made the easternmost foothills of the Himalayas between China and India difficult for people outside to migrate in but relatively easily for the indigenous people, who had been adapted to the environment, to migrate out.[68]

The Yangtze, Brahmaputra, Salween and Mekong rivers, as you might have already realized if you took a good look at the map at the beginning of the post, all begin in Tibet.

Since Tibet was recently conquered by China, I was initially thinking that perhaps an ancient Chinese group had imposed their language on the Tibetans some time in the remote past, but Tibetans heading downstream and possibly conquering the people below makes a lot more sense.

oh look, it’s our friends the Ainu

According to About World Languages, Proto-Sino-Tibetan may have split into its Tibeto- and Sinitic- branches about 4,000 BC. This is about the same time Proto-Indo-European started splitting up, so we have some idea of what a language family looks like when it’s that old; much older, and the languages start becoming so distinct that reconstruction becomes more difficult.

But if we look at the available genetic data a little more closely, we see that there are some major differences between Tibetans and their Sinitic neighbors–most notably, many Tibetan men belong to Y-Chromosome haplogroup D, while most Han Chinese men belong to haplogroup O with a smattering of Haplogroup C, which may have arrived via the Mongols.

According to Wikipedia:

The distribution of Haplogroup D-M174 is found among nearly all the populations of Central Asia and Northeast Asia south of the Russian border, although generally at a low frequency of 2% or less. A dramatic spike in the frequency of D-M174 occurs as one approaches the Tibetan Plateau. D-M174 is also found at high frequencies among Japanese people, but it fades into low frequencies in Korea and China proper between Japan and Tibet.

Also:

It is found today at high frequency among populations in Tibet, the Japanese archipelago, and the Andaman Islands, though curiously not in India. The Ainu of Japan are notable for possessing almost exclusively Haplogroup D-M174 chromosomes, although Haplogroup C-M217 chromosomes also have been found in 15% (3/20) of sampled Ainu males. Haplogroup D-M174 chromosomes are also found at low to moderate frequencies among populations of Central Asia and northern East Asia as well as the Han and Miao–Yao peoples of China and among several minority populations of Sichuan and Yunnan that speak Tibeto-Burman languages and reside in close proximity to the Tibetans.[5]

Unlike haplogroup C-M217, Haplogroup D-M174 is not found in the New World…

Haplogroup D-M174 is also remarkable for its rather extreme geographic differentiation, with a distinct subset of Haplogroup D-M174 chromosomes being found exclusively in each of the populations that contains a large percentage of individuals whose Y-chromosomes belong to Haplogroup D-M174: Haplogroup D-M15 among the Tibetans (as well as among the mainland East Asian populations that display very low frequencies of Haplogroup D-M174 Y-chromosomes), Haplogroup D-M55 among the various populations of the Japanese Archipelago, Haplogroup D-P99 among the inhabitants of Tibet, Tajikistan and other parts of mountainous southern Central Asia, and paragroup D-M174 without tested positive subclades (probably another monophyletic branch of Haplogroup D) among the Andaman Islanders. Another type (or types) of paragroup D-M174 without tested positive subclades is found at a very low frequency among the Turkic and Mongolic populations of Central Asia, amounting to no more than 1% in total. This apparently ancient diversification of Haplogroup D-M174 suggests that it may perhaps be better characterized as a “super-haplogroup” or “macro-haplogroup.” In one study, the frequency of Haplogroup D-M174 without tested positive subclades found among Thais was 10%.

Haplogroup D’s sister clade, Haplogroup E, (both D and E are descended from Haplogroup DE), is found almost exclusively in Africa.

Haplogroup D is therefore very ancient, estimated at 50-60,000 years old. Haplogroup O, by contrast, is only about 30,000 years old.

On the subject of Han genetics, Wikipedia states:

Y-chromosome haplogroup O3 is a common DNA marker in Han Chinese, as it appeared in China in prehistoric times. It is found in more than 50% of Chinese males, and ranging up to over 80% in certain regional subgroups of the Han ethnicity.[100] However, the mitochondrial DNA (mtDNA) of Han Chinese increases in diversity as one looks from northern to southern China, which suggests that male migrants from northern China married with women from local peoples after arriving in modern-day Guangdong, Fujian, and other regions of southern China.[101][102] … Another study puts Han Chinese into two groups: northern and southern Han Chinese, and it finds that the genetic characteristics of present-day northern Han Chinese was already formed as early as three-thousand years ago in the Central Plain area.[109]

(Note that 3,000 years ago is potentially a thousand years after the first expansion of Proto-Sino-Tibetan.)

The estimated contribution of northern Hans to southern Hans is substantial in both paternal and maternal lineages and a geographic cline exists for mtDNA. As a result, the northern Hans are the primary contributors to the gene pool of the southern Hans. However, it is noteworthy that the expansion process was dominated by males, as is shown by a greater contribution to the Y-chromosome than the mtDNA from northern Hans to southern Hans. These genetic observations are in line with historical records of continuous and large migratory waves of northern China inhabitants escaping warfare and famine, to southern China.

Interestingly, the page on Tibetans notes, ” It is thought that most of the Tibeto-Burman-speakers in Southwest China, including the Tibetans, are direct descendants from the ancient Qiang.[6]

On the Qiang:

The term “Qiang” appears in the Classic of Poetry in reference to Tang of Shang (trad. 1675–1646 BC).[14] They seem to have lived in a diagonal band from northern Shaanxi to northern Henan, somewhat to the south of the later Beidi. They were enemy of the Shang dynasty, who mounted expeditions against them, capturing slaves and victims for human sacrifice. The Qiang prisoners were skilled in making oracle bones.[15]

This ancient tribe is said to be the progenitor of both the modern Qiang and the Tibetan people.[16] There are still many ethnological and linguistic links between the Qiang and the Tibetans.[16] The Qiang tribe expanded eastward and joined the Han people in the course of historical development, while the other branch that traveled southwards, crosses over the Hengduan Mountains, and entered the Yungui Plateau; some went even farther, to Burma, forming numerous ethnic groups of the Tibetan-Burmese language family.[17] Even today, from linguistic similarities, their relative relationship can be seen.

So here’s what I think happened (keeping in mind that I am in no way an expert on these subjects):

  1. About 8,000 years ago: neolithic people lived in Asia. (People of some sort have been living in Asia since Homo erectus, after all.) The ancestors of today’s Sino-Tibetans lived atop the Tibetan plateau.
  2. About 6,000 years ago: the Tibetans headed downstream, following the course of local rivers. In the process, the probably conquered and absorbed many of the local tribes they encountered.
  3. About 4,000 years ago: the Han and Qiang are ethnically and linguistically distinct, though the Qiang are still fairly similar to the Tibetans.
  4. The rest of Chinese history: Invasion from the north. Not only did the Mongols invade and kill somewhere between 20 and 60 million Chinese people in the 13th century, but there were also multiple of invasions/migrations by people who were trying to get away from the Mongols.

Note that while the original proto-Sino-Tibetan invasion likely spread Tibetan Y-Chromosomes throughout southern China, the later Mongol and other Chinese invasions likely wiped out a large percent of those same chromosomes, as invaders both tend to be men and to kill men; women are more likely to survive invasions.

Most recently, of course, the People’s Republic of China conquered Tibet in 1951.

I’m sure there’s a lot I’m missing that would be obvious to an expert.

Hey, DNA: What is it good for?

So why do we still have bits of Neanderthal DNA hanging around after so many years? Of course it could just be random junk, but it’s more fun to think that it might be useful.

And the obvious useful thing for it to do is climate adaptation, since Neanderthals had been living in dark, cold, ice-age Europe for much longer than the newly-arrived h. Sapiens, and so might have had some adaptations to help deal with it.

Okay, so here is something related I was reading the other day, that I consider pretty interesting. So it looks like the people who live up on the Tibetan Plateau (like the Tibetans,) are really well-adapted to the altitude. No mean feat, considering that other populations who live at similar altitudes don’t seem to be as well-adjusted, despite living up there for similar lengths of time.

Well, now it appears that the Tibetans have actually been living in Tibet for waaaay longer than expected, because the original h. Sapiens who moved into Tibet intermarried with archaic hominids who had already lived there for hundreds of thousands of years, and so probably picked up their altitude adaptations from those guys.

BTW, “species” is a social construct and you probably shouldn’t bother with it here.

So what kind of useful stuff might we have picked up from Neanderthals?

First I’d like to interject that I still find declarations of “aha, we got this gene from Neanderthals and it does this!” to be speculative and prone to changing. All of the articles I’ve read tend to report the same list of stuff in a similar fashion, so I suspect they’re all workign off one or two sources, which makes everything doubly sketchy. So we’re going in here with a big “if” this is true…

Some of the results are fairly boring, like Neanderthal DNA affecting hair and skin. We already speculate that skin tone helps us deal with sunlight levels, so that’s sensible.

More interesting is the claim that Neanderthal DNA may predispose people to Type-2 Diabetes and depression.

Now why the hell would it do that? It’s probably not *just* random–after all, large stretches of DNA have little to no Neanderthal admixture at all, suggesting that genes in those spots just weren’t useful, so why would we have retained such apparently negative traits?

Maybe, like sickle cell anemia, these things actually have a positive function–at least in the right environments.

I read a fascinating theory a few years ago that Type 2 Diabetes and Seasonal Affective Disorder are actually just part of our bodies’ natural mechanisms for dealing with winter. Basically, you’re supposed to eat plants and get fat all summer long, while plants are available, and then by winter, your ability to absorb more glucose shuts down (there’s no point since the plants are all dead) and you switch over to burning ketones instead and eating an all-mammoth diet.

(Some groups, like the Inuit and Masai, historically [and may today still] survived on diets that included virtually no plants and so ran all of their cellular energy needs through the ketogenic instead of the glucose system.)

During this winter time, humans, like other animals, slowed down and semi-hibernated to save energy and because why the fuck not, it’s dark and no one has invented lightbulbs, yet.

By spring, you’ve lost a lot of weight, the plants come back, and so does your ability to use glucose.

This theory is laid out in the book Lights Out by T. S. Wiley, if you’re curious. I thought it was a really interesting book, but you might just think it’s all crank, I dunno.

Anyway, a big hole in Wiley’s plot is how we actually got this adaptation in the first place, since it’s a pretty complicated one and h. Sapiens hasn’t actually been living in places with winter for all that long. Wiley just claims that it’s a deep internal mechanism that animals have, which always struck me as kinda bunk because why would a species that evolved in Africa, from other animals in Africa, etc., probably going back for million upon millions of years, have some sort of complicated system like this still functional in its genome? A trait that is not undergoing positive selective pressure is probably going to become non-functional pretty quickly. But the theory was cool enough otherwise to ignore this bit, so I’ve kept it around.

Right, so here’s the (potential) answer: h. Sapiens didn’t have this adaptation hiding deep inside of them, Neanderthals had it. Neanderthals had been living in cold places for way, way longer than h. Sapiens, and by inter-breeding with them, we got to take advantage of a bunch of cold-weather adaptations they’d developed over that time frame–thus getting a jump-start on evolving to cope with the weather.

At any rate, if Wiley is correct, and SAD and Type-2 Diabetes are actually part of a dealing with winter complex that benefited our cold-weather ancestors, then that wold explain why these genes would have persisted over the years instead of being bred out.

An easy way to test this would be to compare rates of Type-2 Diabetes and SAD among African immigrants to Europe/other wintery latitudes, African Americans (who have a small amount of Euro admixture,) and Europeans. (Watching out, of course, for Vit D issues.) If the Euros have more SAD and Type-2 Diabetes than Africans living at the same latitude, then those would appear to be adaptations to the latitude. If the Africans have more, then my theory fails.