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

May 17, 2020

Knanaya & Kerala: perhaps there is some different down south?

Filed under: Human Population Genetics — Razib Khan @ 2:03 am


Over the past few months I have been getting together some samples from people from Kerala, with a focus on Knanaya Christians. A subset of the brother St. Thomas Christian community, two things have jumped out in my analyses:

– they are quite endogamous

– they are shifted off the ‘India-cline’

More precisely, like Cochin and Mumbai Jews, they are often shifted toward Middle Eastern populations. This is relevant because the Knanaya believe themselves, like most St. Thomas Christians, descended in part from Jews or Christians from the Middle East.

All that being said, looking more deeply into the data I’m not quite as sure. One of the reasons is that Kerala may not be as “structured” as other parts of India. Some of this is well known. The Nair samples I have are shifted toward South Indian Brahmins, which is plausible in light of connections between Nairs and Brahmins.The Brahmin-adjacent Ambalavasi seem quite similar to Brahmins. These are not surprising. But, Kerala samples I have as a whole seem notably shifted on the India cline more toward the “north” than I would have expected. This could be due to gene flow from without and within Kerala, in a way that is not typical in other parts of the subcontinent.

I say this because even the Ezhava, who were basically what we’d call a Dalit community (no longer today), show a shift.

Instead of talking, let me post some admixture plots (unsupervised):

Now, supervised:

Now TreeMix:

Here is an admixturegraph (using the Narasimhan et al. right-populations):

Test_PopSteppeAHGIndusValley
Bengali0.1520.4130.435
Cochin_Jews0.2120.1880.6
K_Bunt0.1970.3070.496
K_Ezhava0.1470.2810.572
K_Iyer0.2710.1640.565
K_Knanaya0.1490.1860.665
K_Mapilla0.1410.2930.565
K_Nair0.1720.2440.584
K_Nambudiri0.2480.1830.569
K_Nasrani0.1340.270.596
K_Poduval0.20.2760.524
K_Vaniya0.2150.1390.646
K_Varma0.2130.1160.67
Brahui0.236-0.1810.945
Mumbai_Jews0.271-0.1340.863
Patel0.1670.270.562
Pulliyar0.050.5750.375
TamilBrahmin0.1910.2620.547
UP_Brahmin0.2930.2230.484
Velamas0.1010.2980.601

I ran f3-stat. Here it is filtered of any z-scores that are > -2.

Thoughts?

April 4, 2020

Hard sweeps and natural selection obscured by Bronze Age admixture

Filed under: Human Population Genetics,Selection — Razib Khan @ 10:48 pm

The above is the map from the Online Ancient Genome Repository. You can see the variation by region. There’s a lot of ancient DNA in Europe. Very little in Asia. And only moderate amounts elsewhere.

The map is from a new preprint, Ancient human genomes reveal a hidden history of strong selection in Eurasia:

The role of selection in shaping genetic diversity in natural populations is an area of intense interest in modern biology, especially the characterization of adaptive loci. Within humans, the rapid increase in genomic information has produced surprisingly few well-defined adaptive loci, promoting the view that recent human adaptation involved numerous loci with small fitness benefits. To examine this we searched for signatures of hard sweeps – the selective fixation of a new or initially rare beneficial variant – in 1,162 ancient western Eurasian genomes and identified 57 sweeps with high confidence. This unexpectedly extensive signal was concentrated on proteins acting at the cell surface, and potential selection pressures include cold adaptation in early Eurasian populations, and oxidative stress from carbohydrate-rich diets in farming populations. Critically, these sweep signals have been obscured in modern European genomes by subsequent population admixture, especially during the Bronze Age (5-3kya) and empires of classical antiquity.

So the “big thing” that they found here is that admixture obscures signals of selection. More precisely, it obscures signals of hard selective sweeps, the classical variant where a single position in a single haplotype rises up in frequency rapidly due to positive selection.

If you read further into the paper you note that they believe admixture, due to the mixing of backgrounds, attenuates the signal of hard sweeps, and may even imply that these hard sweeps are soft sweeps through the mixing of distinct genetic backgrounds. I honestly didn’t follow that too closely, but I guess it depends on the selection coefficient and rate of mixing. They are reporting lots of selection events of >1%, and I wonder about how credible this is (Haldane’s dilemma?).

That being said, the functional significance of these selection events is important. Basically, they look like adaptations to climate and changes in diet. What authors seem to be suggesting here is that the shift in lifestyle and expansion of farmers in the early Holocene was a pretty big deal, and the mixing between various divergent streams during the Bronze Age muddled the signals.

If the authors are right, that means that ancient DNA is going to be very big for understanding the trajectory of selection, because it’s not just going to be subtle polygenic changes.

March 17, 2020

Blood group A at greater risk from COVID-19 (maybe)

Filed under: coronavirus,Human Population Genetics — Razib Khan @ 10:26 am

To a great extent much of the population genetics of humans in the 20th-century that doesn’t involve external traits is the population genetics of blood groups. A, B, and O, along with Rhesus factor. Read L. L. Cavalli-Sforza and William Bodmer’s The Genetics of Human Populations, the first edition of which was written in the 1960s. The emergence of more genetic markers, and Y, mtDNA, and genome-wide analysis has marginalized the exploration of population genetic variation of ABO. But it’s still useful. And it’s still functionally important (there’s a reason that A and B groups evolved!).

Many years ago while reading Alan Templeton’s Population Genetics and Microevolutionary Theory I stumbled upon the fact that spontaneous abortion (miscarriage) is associated with blood group differences between mother and fetus on the ABO blood groups. Basically, women who are O (and so genotype OO) have issues with fetuses that express A or B antigen. This isn’t deterministic, just a change in probabilities (I’m A, my wife is O, and our children are a mix, as my genotype is AO).

ABO has also been associated with different risks to different diseases (e.g., it is well known that those who express blood group B are more at risk for Hepatitis B).

So with that, a new preprint, ABO blood group and susceptibility to severe acute respiratory syndrome:

…The ABO group in 3694 normal people in Wuhan showed a distribution of 32.16%, 24.90%, 9.10% and 33.84% for A, B, AB and O, respectively, versus the distribution of 37.75%, 26.42%, 10.03% and 25.80% for A, B, AB and O, respectively, in 1775 COVID-19 patients from Wuhan Jinyintan Hospital. The proportion of blood group A and O in COVID-19 patients were significantly higher and lower, respectively, than that in normal people (both P < 0.001). Similar ABO distribution pattern was observed in 398 patients from another two hospitals in Wuhan and Shenzhen. Meta-analyses on the pooled data showed that blood group A had a significantly higher risk for COVID-19 (odds ratio-OR, 1.20; 95% confidence interval-CI 1.02~1.43, P = 0.02) compared with non-A blood groups, whereas blood group O had a significantly lower risk for the infectious disease (OR, 0.67; 95% CI 0.60~0.75, P < 0.001) compared with non-O blood groups. In addition, the influence of age and gender on the ABO blood group distribution in patients with COVID-19 from two Wuhan hospitals (1,888 patients) were analyzed and found that age and gender do not have much effect on the distribution…

It looks like from their data that A individuals were:

1) more likely to get infected
2) more likely to have severe responses

The individual difference is modest. You aren’t invulnerable if you are O. But, this might impact the course and severity of COVID-19 as it runs through populations…

Here is the table:

Here are blood group distributions:

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.

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