Razib Khan One-stop-shopping for all of my content

February 14, 2020

The complex origins of our species in Africa

Filed under: Human Evolution,Human Population Genetics — Razib Khan @ 3:37 am

The figure to the right illustrates a model that is put forward in a new paper, Recovering signals of ghost archaic introgression in African populations. This was originally a preprint, Recovering signals of ghost archaic introgression in African populations. So we’ve discussed the implications extensively. Carl Zimmer has covered the story in The New York Times, while Georbe Busby did so in The Conversation.

Broadly, the results are getting at something which plenty of people have been noticing for many years: when it comes to Sub-Saharan Africans, there is something deeply diverged in West Africans vis-a-vis non-West Africans. These results seem to suggest that the divergence between this outgroup lineage and our own is a bit earlier than the modern-Neanderthal/Denisovan split. There are many abstruse statistical inferences and simulations, and it looks like the reviewers made them do a lot of analyses. But the general result is something other groups have seen as well, so I believe it. Additionally, the admixture of this lineage into West Africans seems to have occurred about 50,000 years ago, suspiciously close to the general expansion of modern humans out of Africa (or the most recent expansion).

From the discussion:

The signals of introgression in the West African populations that we have analyzed raise questions regarding the identity of the archaic hominin and its interactions with the modern human populations in Africa. Analysis of the CSFS in the Luhya from Webuye, Kenya (LWK) also reveals signals of archaic introgression, although our interpretation is complicated by recent admixture in the LWK that involves populations related to western Africans and eastern African hunter-gatherers (section S8) (20). Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations. A detailed understanding of archaic introgression and its role in adapting to diverse environmental conditions will require analysis of genomes from extant and ancient genomes across the geographic range of Africa.

This work seems more a question than an answer.

January 26, 2020

Indian ancestry maritime Southeast Asia

Filed under: Human Population Genetics — Razib Khan @ 2:38 pm

In the comments, people keep asking about Indonesia, and Java in particular. The reason is pretty simple: before wholesale conversion to Islam maritime Southeast Asia was dominated at the elite level by Indic social and religious forms. I say “Indic” because unlike mainland Southeast Asia Theravada Buddhism did not supplant other Indian religions, and in fact, while indigenous Buddhism that led to the Borobudur temple complex in the 9th-century went extinct, Hinduism persisted for quite a bit longer and persists to this day. Not only are there long-standing Hindu traditions in Bali, but far eastern Java remained a Hindu kingdom until 1770, and there remain Javanese Hindus (some of them are recent converts).

As several mainland Southeast Asian groups seem to have Indian admixture, what is the evidence for Indonesia? (the Singapore genome data offers up some Malays, and though some show recent Indian admixture, all of them have some Indian admixture). Luckily, there is a paper and data, Complex Patterns of Admixture across the Indonesian Archipelago. It uses the GLOBETROTTER framework, so I decided to reanalyze the data in a simpler manner, adding the Cambodians as a check (since from my previous posts you know a fair amount about that as a baseline).

Three points.

1) Definitely gene flow. But on the whole less than mainland Southeast Asia?

2) Lots of heterogeneity. Not surprising. The Sumatra samples seem to be taken from Aceh. This may matter a great deal.

3) In mainland Southeast Asia east of Burma there hasn’t been lots of colonial migration of Indians, nor a great deal of trade. The opportunities within maritime Southeast Asia for contact with outsiders are far greater. The inspection of results from Malaysia indicates continuous gene flow over a long period of time. In contrast, the results from Thailand and Cambodia indicate an early pulse.

January 25, 2020

The Indian admixture into Southeast Asia is not just a function of distance

Filed under: Human Population Genetics,Southeast Asia — Razib Khan @ 10:41 pm

In the comments to the post below about Indian ancestry in Thailand, some observed that this should not be surprising due to reciprocal gene flow and proximity. Implicitly, I think what is being suggested here is that there is isolation by distance and continuous gene flow. Obviously some of this is true, but there details here which suggest that it is simply not just geography at work.

The reason I was curious about the Dusun people in coastal Borneo is that while Malays all seem to have Indian ancestry, many tribal Austronesian groups in maritime Southeast Asia do not. The Indian admixture into the Malays is not just recent. Some of it seems quite a bit older than the colonial period.

In the context of Southeast Asia, it seems that some of the more ancient Austro-Asiatic people, in particular, the Mon and Khmer, have Indian ancestry, and groups which mixed with Austro-Asiatic substrates, such as Burmans and Thai, also have this.

Additionally, some groups in the northeastern states of India have less “Indian” admixture than the Thai and Khmer. To show this, see this PCA:

The Garo and Naga live in India (some Garo are in Bangladesh). The “East Indian” samples seem to be mostly Mizo. Of course, some of these groups are intrusive to the northeast. But still. Here are admixture and TreeMix:

The issue in Southeast Asia is that ethnolinguistic groups are the product of several syntheses and migrations. Most of what is today “Thailand” was the domain of Mon-Khmer people in 500 AD. Most of the ancestry seems to date to that period, though there was an overlay from Tai people to the north. In Burma the population is a synthesis of Burman elements with connections to northern East Asians, and Austro-Asiatic people such as the Mon in the south. Additionally, a later movement of Tai people also occurred in Burma (the upland Shan). In Vietnam, the Kinh moved south and seem to have replaced the indigenous Chams and Khmer (there is very little Indian-like ancestry in any Vietnamese samples).

When looking at the map the plausible route of gene flow is clearly from the northeastern part of the subcontinent overland. But several people have pointed out to me that this is very difficult terrain. Recently, I have been convinced that a maritime intrusion of Munda languages into Odisha is plausible. One of the potential points of departure for the proto-Munda is the Tanintharyi region of today’s far southern Burma, adjacent to southern Thailand. I propose that the Tanintharyi region served as a cultural and demographic valve, initially mediating overseas expansion by a group of Southeast Asian rice farmers, who eventually established connections across the Bay of Bengal between South and Southeast Asia.

The absorption of lowland Munda domains in Odish by Indo-Aryan speakers did not entail the disruption of the flow of goods and people in the preestablished trade network. Rather, these routes which were preexistent were co-opted by the Kalinga state, and later on by various southern Indian polities facing east on the Bay of Bengal. Inspection of the Y and mtDNA haplogroup profile suggests these were elite Indian males, with few females. This is very different from a folk expansion through Arakan, which would involve both and women.

Thais may have more Indian ancestry than Cambodians and less than Burmese

Filed under: Human Population Genetics,Thai — Razib Khan @ 12:05 am
Click to enlarge

There were some questions about the Indian ancestry of the Thai. The dataset released by the Reich lab has some Thai. I pulled that data, and some other Southeast Asian groups, and Tamils and Tajiks. The merging only left 62,000 SNPs, but that’s probably enough to answer this question. The PCA above shows the West Eurasian shift of some groups. The Thai definitely seem pulled to the Tamils, and are similar to the Cambodians, but with a bit more Indian ancestry and less “southern” Southeast Asian.

Below the fold are admixture and TreeMix plots. Basically you see what I’m talking about but in more detail. The Indian-like ancestry in the Luzon samples is really Spanish. The Ami and Atyal are Taiwanese aborigines. You see that they have the least West Eurasian ancestry. Even southern mainland Chinese seem to have some of that, indicating long-distance gene flow. But groups like Miao, Vietnamese/Kinh, and Dusun (Austronesians from Borneo) don’t the Indian ancestry that Thai/Lao/Cambodians/Malay have.

September 29, 2019

Humans are basically invasive weeds

Filed under: Human Population Genetics — Razib Khan @ 3:14 pm

One of the somewhat surprising things we have learned over the last decade is that massive admixture and homogenization has occurred between distinct human lineages over the last 10,000 years. By this, I mean that we’re not talking simply about continuous gene-flow between neighboring populations, but massive expansions of small groups and assimilation of very different groups from the expanding groups. As a stylized fact, it looks like “Early European Farmers” we as distinct from Mesolithic hunter-gatherers as modern Northern Europeans are from Han Chinese (pairwise Fst ~0.10). The fusion of these two groups later merged in much of Europe with migrants from the east, the western edge of the forest-steppe.

The empirical pattern seems to be that cultural innovations (e.g., agriculture) trigger demographic revolutions, which homogenize and admix vast regions. This is a story of demographic history. Phylogeography.

But there is another aspect, natural selection. Humans are not exempt from this. Selection operates upon genetic variation, which is preexistent (“standing variation”), or, comes from new mutations (de novo).

It seems plausible that cultural innovation has resulted in a great deal of selection over the last 10,000 years. So where did the raw material come from? One argument that has been playing out is between those who argue that it’s from variation within human populations that is ancestral and shared, and new variation. This is where admixture comes into play.

A new preprint on bioRxiv uses the 1000 Genomes data in the New World to suggest that admixture resulted in the introduction of a lot of adaptive alleles into populations of mostly European and Native background from African ancestry. Basically, it seems likely that the American tropics were colonized by African tropical diseases, which entailed adaptations which were already existent within African populations. Admixture-enabled selection for rapid adaptive evolution in the Americas:

Background: Admixture occurs when previously isolated populations come together and exchange genetic material. We hypothesized that admixture can enable rapid adaptive evolution in human populations by introducing novel genetic variants (haplotypes) at intermediate frequencies, and we tested this hypothesis via the analysis of whole genome sequences sampled from admixed Latin American populations in Colombia, Mexico, Peru, and Puerto Rico. Results: Our screen for admixture-enabled selection relies on the identification of loci that contain more or less ancestry from a given source population than would be expected given the genome-wide ancestry frequencies. We employed a combined evidence approach to evaluate levels of ancestry enrichment at (1) single loci across multiple populations and (2) multiple loci that function together to encode polygenic traits. We found cross-population signals of African ancestry enrichment at the major histocompatibility locus on chromosome 6, consistent with admixture-enabled selection for enhanced adaptive immune response. Several of the human leukocyte antigen genes at this locus (HLA-A, HLA-DRB51 and HLA-DRB5) showed independent evidence of positive selection prior to admixture, based on extended haplotype homozygosity in African populations. A number of traits related to inflammation, blood metabolites, and both the innate and adaptive immune system showed evidence of admixture-enabled polygenic selection in Latin American populations. Conclusions: The results reported here, considered together with the ubiquity of admixture in human evolution, suggest that admixture serves as a fundamental mechanism that drives rapid adaptive evolution in human populations.

The period after 1492 is easy for us to think about. But what ancient DNA has shown us is that it’s not as uncommon a phase as we might have thought.

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