Jon Snow and Daenerys Targaryen are genetically similar to full-siblings or mother and son

I’ve posted on this before. So I will post again just to reiterate something: in terms of genes, Jon Snow and Daenerys Targaryen are much closer to being full-siblings than they are to being aunt and nephew.

You get different numbers depending on how deeply you look at the pedigree of the two. But their relatedness is probably above 40% and below 50%. Others have confirmed:

The verbal reason without math and genealogies is simple: Daenerys Targaryen comes from an inbred lineage, and more importantly, two generations of brother-sister marriages. This means that Daenerys Targaryen and Rhaegar Targaryen were genetically much more similar than typical full-siblings. Because of this, Jon Snow and Daenerys Targaryen are much more genetically similar than typical aunts and nephews, because Jon Snow’s father was to a first approximation genetically a male and older version of Daenerys Targaryen.

Open Thread, 04/15/2019

After reading Jared Rubin’s Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not I can say I highly recommend it. Not necessarily because I’m entirely convinced by the thesis, which is quite subtle, but can be reduced to the proposition that religious elites in the Islamic world were never marginalized to the same extent that religious elites in the Christian world were, and so there did not emerge and economic elite which dictated changes in cultural and state amenable to their interests (and therefore, economic growth).

I don’t know if I’m going to fully review Rulers, Religion, and Riches, because I’m still thinking about all the arguments. But, I can recommend it because there are so many interesting subsections. Early on figure 1.1 and 1.2 show the most populous cities in Europe and the Islamic world in 800 and 1300. These data confirm that Europe lagged the Islamic world in 800, but had caught up by 1300. You should have already known this, but Rubin’s focus on data clarifies and solidifies much.

Though I was already sympathetic to the assertion that the timing of the Protestant Reformation was causally connected to the expansion of printing, again Rubin’s quantitative analyses convince me further. As a skeptical of Max Webber’s model, I find Rubin’s argument for why Protestantism was correlated with early modern economic growth much more persuasive (read the book!).

This week on The Insight I’ll be talking to Steve Stewart-Williams, author of The Ape that Understood the Universe: How the Mind and Culture Evolve. Most of the conversation revolves around evolutionary psychology, a topic I haven’t thought about much recently to be honest. The Ape that Understood the Universe is an irreverent, and broad-church, take on the discipline (there is not much mention of “cognitive modules” in the book).

On my other podcast, I dropped two recently that readers of this weblog might be interested in. First, one with Phillipe Lemoine, everyone’s favorite French philosophical “edgelord.” He has a blog post which I recommend to you, Polarization and misrepresentation of the outgroup.

Second, I talked to Zaid Jilani. Along with Leighton Woodhouse, he is behind the Extremely Offline podcast. Zaid is clearly a man of the Left, but he seems to have a traditionally liberal perspective on intellectual discourse. The most recent episode of their podcast featured a discussion between Mike Cernovich and Katie Herzog.

Was Thomas Kuhn Evil? Definitely overrated and not totally coherent, no?

Silicon Valley Housing Crisis Ensnares Stanford. More “cost-of-living porn.” Now I’m reading stories of hairdressers buying houses in Arizona and flying back on Southwest to San Francisco periodically.

Loss-of-function tolerance of enhancers in the human genome.

Genomic selection for lentil breeding: empirical evidence.

John Snow Emails 23andMe About His DNA Results. Genealogically he’s 12.5%. DNA is not magic!

Iran’s Revolution Reconsidered. I always thought it was known that the Iranian Revolution had an element of Platonism? Shia Islam did not turn as definitively against Hellenic thought as the Sunnis did after al-Ghazali.

Origin of elevational replacements in a clade of nearly flightless birds – most diversity in tropical mountains accumulates via secondary contact following allopatric speciation.

Macroevolutionary integration of phenotypes within and across ant worker castes.

Defining the genetic and evolutionary architecture of alternative splicing in response to infection.

By the I, I mentioned this on Twitter. 23andMe says I’m 97% “Broadly South Asian” and my parents are 99% “Broadly South Asian.” That broadly part clearly includes people with substantial East Asian ancestry, as is the norm among most Bengalis, especially those of us from the east. That’s fine, but the method they’re using is masking this from customers. I can see why they do this, but the PCA don’t lie, and we’re off-cline…. The admixture is just “old” (~1,500 years old).

Bayesian Estimation of Population Size Changes by Sampling Tajima’s Trees.

Multiple Deeply Divergent Denisovan Ancestries in Papuans. Many seem skeptical about the recent time estimate for late admixture. But the overall finding of structure is probably right on some level.

New Tides of History on Queen Isabella and the Reconquista.

Last week we dropped a podcast about the “missing heritability” with Alexander Young. He wrote a blog post exploring the issue. I also heard that PLOS has now invited him to write a comment on the topic! In a few weeks, I’ll be talking to John Greally about epigenetics.

Interview with Paul Coates, the father of Ta-Nehisi Coates. In the battle of ideas between the “ancients” and the “moderns”, sometimes the ancients were wiser.

New species of ancient human unearthed in the Philippines.

Coupled MCMC in BEAST 2.

Ritual purity as evoked culture

Jonathan Fast’s novel Golden Fire is set during the height of the Gupta Empire at the end of the 4th century A.D. The novel revolves around the origins and rise of Chandragupta II. But what remains with me after all these years is the depiction of social relations in an India where elite Hinduism as we understand it today is starting to take shape, and Buddhism is abating. Fast depicts a caste society, though not nearly as endogamous as exists today (this is probably correct from what the genetics tell us).

At one point, a former advisor to the king, a Buddhist monk, arrives at court. The current ascendant counselor is a Brahmin. When the monk, his old rival, arrives to address the king, the counselor turns around and faces away from the monk. Not only will he not speak to him, but he will not look at him. He explicitly contends that the rationale for this behavior is to minimize the ritual pollution that entails contact with a Buddhist who lacks caste.

This attitude persists in some ways in India. And South Asia more generally. Even after conversion, many Muslims continued to maintain habits of caste. My father’s mother’s family were converted to Islam from Hinduism in the early 20th century. They had been Bengali Brahmins and continued to maintain habits which reflected their origins without reflecting on or acknowledging their origins. They maintained separate dishes for guests, and would not drink out of other peoples’ cups. My father’s father was an ulem, a religious teacher. So he instructed all his children on the details of Hanafi shariah. But, the children were raised by his wife, and so all maintained the habit into adulthood of never drinking out of other peoples’ cups. Perhaps one way to describe her would be Muslim beliefs, Hindu customs.

I know the details of the origin of these practices (I also internalized my paternal grandmother’s habits in this area, to be honest) because one of my mother’s brothers converted to a reformist and fundamentalist variety of Islam, and he was conscious of the Hindu practices that Bengali Muslims maintained. He was ostentatious about drinking out of other peoples’ cups and eating off their plates because to him that was an important refutation of the separation between classes and castes which Hinduism fostered.

Read More

Tutsis are genetically very similar to Masai

Many years ago, before I used ggplot, I did a little analysis of the genetics of the Tutsi. Actually, it was the genetics of a single Tutsi, or more precisely, someone who was 75% Tutsi ancestry (3 out of 4 grandparents).

I found that the Tutsi individual seemed quite distinct from the Bantu peoples in nearby Kenya. I suggested that it was likely that the Tutsi were then genetically distinct from the Hutu people amongst whom they lived. For many years this was part of the genetics section of the Wikipedia entry on the Tutsi, but recently the reference was removed and the page seems to have been re-edited.

That’s fine. I’m just a random blogger who had one sample. But as it happened recently about a dozen Diasporic Tutsis reached out to me. Over the last decade, the number of people who have been genotyped has increased greatly. So it wasn’t that difficult for interested parties to find these genotypes.

The mission they put before me is simple: “tell us about our genetics”. Over the next few weeks, I’ll do that. As there is no IRB, this won’t be published in a peer-reviewed journal (I am open to putting any researcher in contact with these Tutsis who reached out to me). I’m just going to put what I find out there so that Tutsis who do personalized genetic testing can make sense of what they’re finding out.

I received these genotypes today. A quick merge of samples I have reduced it down to 50,000 markers. I will work on creating a merge with a larger number of markers. But, I’ll report what I have found out so far as a first pass.

As you can see on the PCA plot above the Tutsi overlap almost perfectly with the Masai. Not with the Kenyan Bantu, or the Luo, who are more “African” shifted. But with the Masai. But, they are not as “Eurasian shifted” as the Somali.

Treemix confirms this:

Read More

Open Thread, 04/07/2019

So Kingdoms of Faith: A New History of Islamic Spain is worth it for the first 2/3 of the book. The last 1/3 is a bunch of stuff about the Emirate of Granada that’s hard to keep track of. If you didn’t know that in 1500 most of the Muslim communities of the peninsula outside of Granada were in the kingdom of Aragon, then this book is worth reading, as it explains the reasons for this.

The Brown Pundits podcast is going to release a bunch of stuff in the next few days (already on Patreon page). Readers of this weblog will probably appreciate the conversation with Zaid Jilani the most. We talk about whether Matt Yglesias really believes the stuff he puts out there. Zaid has some insights. The podcast could have gone much longer because it’s interesting to talk to someone who doesn’t have paint-by-the-numbers answers to everything.

Rulers, Religion, and Riches: Why the West Got Rich and the Middle East Did Not is interesting because it’s starting to convince me of the importance of ideas and doctrine in religion in terms of material consequences! Need to think more deeply on this. But recommended.

China’s Hard Edge: The Leader of Beijing’s Muslim Crackdown Gains Influence. “He promoted education in Chinese instead of in Tibetan, and offered financial and other incentives to encourage interracial marriages.” Forced assimilation and demographic absorption have been a past Chinese tactic.

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits.

Gene-level heritability analysis explains the polygenic architecture of cancer.

Genome-wide association study reveals sex-specific genetic architecture of facial attractiveness.

‘There are no black people on Game of Thrones’: why is fantasy TV so white? People criticize Quillette for publishing predictable stuff…but the point that’s not brought up is how ‘respectable’ media regularly publish predictable clickbait to pay the bills.

A Mysterious Infection, Spanning the Globe in a Climate of Secrecy. Maybe we’ll die of infectious diseases rather than heart disease or cancer?

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles.

Genetic Associations with Mathematics Tracking and Persistence in Secondary School.

Genomic Prediction of Depression Risk and Resilience Under Stress.

U.S. Urges Immediate Halt to Military Operations in Libya. What’s going on in Libya again? Another mess we forgot….

This week on The Insight I’m talking to Alex Young about the missing heritability. He’s going to be putting up a blog post this week too.

Selection for and against pigmentation alleles in South Asia

Deepika Padukone

Recently some British friends were asking about what we knew about South Asian historical genetics now. I explained that it does look like there was some migration in from the Central Asian steppe and West Asia into South Asia during the Holocene. To which one friend responded, “that’s obvious though, many Indians look like brown white people.” Setting aside the semantic paradox (if you are brown, you are literally not white), it is clear what he is getting at: due to shared ancestry the facial structure of many South Asians is not that different from West Eurasians.

The Bollywood actress Deepika Padukone is an example of someone who is rather brown-skinned (naturally), but whose facial features are such that if she went with 100% skin-bleaching she would pass as white without too much trouble. For the purposes of this post, I Googled Indian albino…and came up with this family. You can make your own judgments. I don’t know what to think of that!

The reason for this post is a newly accepted paper, Ancestry-specific analyses reveal differential demographic histories and opposite selective pressures in modern South Asian populations:

Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations, and showed our approach to be robust via coalescent simulations.

Our f3 and f4 statistics based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex inter-population relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.

Read More

Unleash the data kraken!

The Reich lab has done a mitzvah and released a huge merged dataset of their modern and ancient populations in a big tarball. Actually, there are two files. One of them is a larger number of individuals with 600,000 SNPs (includes “Human Origins Array”) and the other has 1,200,000 SNPs, but fewer individuals. It is in EIGENSTRAT format.

For the convenience of readers who are more comfortable in PLINK/PEDIGREE format, I’ve converted them, and replaced the family ID column with population labels. The links take to you a zip file that has the three files for the binary format.

You really can’t talk about shariah in 20 minutes

Vox‘s Worldly is a short (less than 30 minute) podcast on world-affairs. I listen to it because American politics is boring, and it’s not a major timesink. But, its brevity is something that has worried me, since this is not a long period of time, and it’s hard to address things in a subtle manner to a general audience in such a short segment.

The most recent one, Brunei just made gay sex punishable by death, illustrated to me a lot of the problems with trying to compress too much into 20 minutes. There are three hosts. A fair portion of the time they discussed Islam, and Islamic jurisprudence (shariah).

Though they didn’t mention it, one of the hosts is a convert to Islam. You can read about her in this article, How a Blonde Tattooed Texas Girl Became an ISIS Twitter Star.

I am a social constructivist when it comes to religion. That is, I don’t have a religion, do not believe in gods, and am willing to accede to a consensus of the believers as to what their religion is, as well as instrumentally taking into account what religious believers as a whole seem to think about their religion.

To give an example of what I mean,

  • I am fine with someone with a non-binary gender identity who rejects a great deal of hadith and is totally fine with apostasy from Islam, calling themselves a Sunni Muslim. I’m not invested in the idea that being a Sunni Muslim means anything more than a particular self-identification. I’m not a Sunni Muslim. I don’t care if you call yourself a Sunni Muslim.
  • But, I also assume that acceptance of non-binary gender identity and apostasy in Islam is not normative among the majority of the world’s Muslims, and as an apostate from Islam I am very cautious about going to Muslim-majority countries and expressing my beliefs. Apostates are still killed by mobs, and it is still against the law in many Muslim-majority nations.

Read More

The growth of human genomics

Citation: Aylwyn Scally

The above figure is from Aylwyn Scally, or as I like to think of him, the Irish Matt Hahn. I’m not going to add any comments as the chart speaks for itself, doesn’t it?

Also, looks like my son is about the 10,000th person in the history of the human race who was whole-genome sequenced. That’s not a shabby record. First prenatal whole-genome sequence of a healthy born individual, and in the first ~0.000125% of the human race alive today to be sequenced.

Sydney Brenner: the passing of a giant

Nobel laureate Sydney Brenner, who helped place Singapore on biotech world stage, dies at 92. If you are in genetics and development you know who Brenner his, and what he meant to these fields. I happened to be in the room with Brenner once, in Berkeley in 2008 I believe. He was already quite an old curmudgeon, and I will say his comments were amusing and awkward!

Long-time readers of this weblog know that about fifteen years ago I dabbled in a little worm-work. At that time I read In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite. As Brenner was involved in promoting C. elegans as a model he occupies a lot of this book. I recommend it. It’s short and packed with historical nuggets that make the 21st-century trajectory of science more comprehensible.