Populism leads to tyranny

I just listened to the authors of How Democracies Die on NPR. First, the book might well have been titled “The necessity of liberalism.” Basically, democracy without liberalism is clearly not democracy in their judgment.

But second, I was struck by their emphasis on the role of elites in dampening and diminishing the passions of the masses in a functioning modern democratic system. To a great extent, the authors were simply warning about what Fareed Zakaria termed “illiberal democracy” in The Future of Freedom over ten years ago.

Without elites acting as structural guardrails on the atavistic passions of the masses charismatic figures who channel their basest impulses can arise and gain popular approval of their autocratic behavior. The ancient Greeks could have told you that. Some things never change.

The rise of Chinese science and CRISPR

So as of now China is producing more scientific publications than the United States of America. But there’s quality and there’s quantity. I think most people would still American science is more cutting edge than Chinese science. And for cultural reasons that may stay true for a while longer.

But there is one area where China seems to be forging ahead and likely will make advances earlier than the USA: genetics, and genetic engineering in particular. The Wall Street Journal has a long piece, China, Unhampered by Rules, Races Ahead in Gene-Editing Trials. It turns out that Chinese have been doing human trials since 2015. Meanwhile, in the USA the greenlight has still not been given (though it seems close).

Honestly how quickly the Chinese are moving in human trials is alarming. Then again, this is a country with the highest number of executions in the world (some of this is sheer size, but it’s higher per capita than the USA). So we should keep perspective. There are many worse things that the Chinese are doing in relation to human rights that moving too fast in trials with cancer patients.

In any case, this comment jumped out at me:

In traditional drug development, too, human-trial rules can differ among countries. But China’s foray into human Crispr trials has some Western scientists concerned about the unintended consequences of using the wholly new tool—such as harm to patients—which could set back the field for everyone.

Western scientists the Journal interviewed didn’t suggest America’s stringent requirements should be weakened. Instead, many advocate an international consensus on ethical issues around a science that makes fundamental changes to human DNA yet still isn’t completely understood.

As a descriptive matter, I am highly skeptical of the possibility that “international standards” is going to involve the Chinese adhering to Western standards. If a genuine international consensus is going to emerge there has to be a give and take, which means that the very high threshold set for safety in human trials in the West may not apply in China.

The first ethical revolution

My maternal grandfather was born in 1896. He died in 1996. He saw a great many changes in his life. If my children live 100 years what changes will they see? To the same extent? In the biological sciences, I suspect so. In particular, in the domain of stell cells and genetic engineering it strikes me that many revolutions will occur. My confidence when it comes to automation and AI is weaker, but the potential is great.

That being said, there probably won’t be flying cars or day-trips to the moon base.

Why? This may be a function of the nature of the low hanging fruit that we’ve picked in the area of physics with engineering application to technology. If you agree with the work of scholars such as Robert J Gordon there’s been a decrease in technological innovation which changes our lives over the past century so (see The Rise and Fall of American Growth). This isn’t for lack of trying. The institutional structures and organizational effort toward novel innovation are far more directed, conscious and planned than in the past (here’s a Planet Money podcast on how technological change is slower now, though not for lack of trying).

Arguably the only major technological revolution of this century is the smart-phone. And I don’t think that that’s something you can dismiss, the smart-phone has interposed itself today into our lives in some deep and fundamental ways.

But the point of this post is that perhaps human society periodically goes through phases of innovation. And then, there’s nothing.

Fifty years ago Julian Jaynes published The Origin of Consciousness in the Breakdown of the Bicameral Mind. Seventy years ago Karl Jaspers introduced the concept of the Axial Age. Both point to the same dynamic historically.

Something happened in the centuries around 500 BCE all around the world. Great religions and philosophies arose. The Indian religious traditions, the Chinese philosophical-political ones, and the roots of what we can recognize as Judaism. In Greece, the precursors of many modern philosophical streams emerged formally, along with a variety of political systems.

The next few centuries saw some more innovation. Rabbinical Judaism transformed a ritualistic tribal religion into an ethical one, and Christianity universalized Jewish religious thought, as well as infusing it with Greek systematic concepts. Meanwhile, Indian and Chinese thought continued to evolve, often due to interactions each other (it is hard to imagine certain later developments in Confucianism without the Buddhist stimulus). Finally, in the 7th century, Islam emerges as the last great world religion.

It has long puzzled me why all the great institutional faiths arose in about 1,000 years. And then not much since then (numerically Sikhs are marginal, while the fracturing of Christianity in the 16th still left the daughter sects recognizable and possibly reconcilable).

I think here perhaps an analogy to our technological conundrum applies. One reason we don’t have jetpacks and flying cars is that the limitations of physics make it difficult.  Some things may be physically possible, but the engineering costs are prohibitive. The several waves of life-transforming technological revolutions between 1750 and 1950 slowly started to ebb in the past generations. Why? It turns out that going from horse and human power, to fossil fuels, and nuclear power, were huge transitions in terms of gains in power. There may not be much to do at this point (fusion is perhaps the major exception).

Similarly, the reason that modern people can get a lot out of Marcus Aurelius’ Meditations, Confucius’ Analects, and the Bible, is that the ethical low-hanging fruit was picked. Recently there have been advances in domains such as the abolition of slavery, so it isn’t as if no progress has been made. But if you read about the Bronze Age world, you see one where human sacrifice is still routinely practiced, as opposed to being an aberration. The distance between 0 AD and 1000 BC is arguably greater ethically than between 0 AD and 2000 AD.

Living in large complex societies with social stratification posed challenges. A religion such as Christianity was not a coincidence, something of its broad outlines may have been inevitable. Universal, portable, ethical, and infused with transcendence and coherency. Similarly, god-kings seem to have universally transformed themselves into the human who binds heaven to earth in some fashion.

The second wave of social-ethical transformation occurred in the early modern period, starting in Europe. My own opinion is that economic growth triggered by innovation and gains in productivity unleashed constraints which had dampened further transformations in the domain of ethics. But the new developments ultimately were simply extensions and modifications on the earlier “source code” (e.g., whereas for nearly two thousand years Christianity had had to make peace with the existence of slavery, in the 19th century anti-slavery activists began marshaling Christian language against the institution).

We may be living in the 21st century, but we’re still living by Iron Age ethics. And that’s not surprising.

Open Thread, 01/21/2018

Don’t know when I’ll get to Kyle Harper’s book, The Fate of Rome: Climate, Disease, and the End of an Empire, but it looks very interesting (Patrick Wyman interviewed him for his podcast).

One thing though: climate always changes. It’s how organisms react to that change and why that is perhaps more informative. The way the Roman political order reacted the way it did to the exogenous environmental shocks had more to do with the nature of the Roman political order than the sui generis character of the shocks (they were going to happen….).

If you haven’t subscribed to my podcast with Spencer Wells, The Insight, you should (so far it’s on iTunes, Google Play and Stitcher). We’re coming out with episodes every week now. The next one will include Spencer’s recollections of the Paleolithic period of personal genomics, before 2005. We’re also recording a podcast with Gencove’s Joe Pickrell on ancestry testing this week.

DNA Geeks has more Gene Expression themed gear now, including a redesigned “Are you genotyped” shirt.

A new blog, mtDNAwiki.

An Ethnolinguistic and Genetic Perspective on the Origins of the Dravidian-Speaking Brahui in Pakistan. Have not read. Though I anticipated the conclusion over 5 years ago.

I contribute regularly to the Insitome Blog. So, No genetic test will tell you if you are Hispanic or Latino, was written after watching days of DNA-test reveals on YouTube. There’s a lot of education that needs to be done! As the Regional Ancestry product rolls out results expect many more blog posts (and probably explainers in podcast/video format at some point).

The convergences between the racialist Right and the identity politics Left have always been sad. But now that both are the waxing it’s quite sinister. For example, both would agree that science is Eurocentric in some deep way. And, both pay close attention to marriages which are racially mixed to draw broader lessons.

How genetics is unlocking the secrets of ancient human migration. On the Scandinavian hunter-gatherers.

Adaptation is subtle, and that’s the problem

The figure above is from a very important new preprint, Human local adaptation of the TRPM8 cold receptor along a latitudinal cline. A marker in 09TRPM8, rs10166942, seem to be correlated with adaptation to cold.

The abstract:

Ambient temperature is a critical environmental factor for all living organisms. It was likely an important selective force as modern humans recently colonized temperate and cold Eurasian environments. Nevertheless, as of yet we have limited evidence of local adaptation to ambient temperature in populations from those environments. To shed light on this question, we exploit the fact that humans are a cosmopolitan species that inhabits territories under a wide range of temperatures. Focusing on cold perception, which is central to thermoregulation and survival in cold environments, we show evidence of recent local adaptation on TRPM8. This gene encodes for a cation channel that is, to date, the only temperature receptor known to mediate an endogenous response to moderate cold. The upstream variant rs10166942 shows extreme population differentiation, with frequencies that range from 5% in Nigeria to 88% in Finland (placing this SNP in the 0.02% tail of the FST empirical distribution). When all populations are jointly analysed, allele frequencies correlate with latitude and temperature beyond what can be explained by shared ancestry and population substructure. Using a Bayesian approach, we infer that the allele originated and evolved neutrally in Africa, while positive selection raised its frequency to different degrees in Eurasian populations, resulting in allele frequencies that follow a latitudinal cline. We infer strong positive selection, in agreement with ancient DNA showing high frequency of the allele in Europe 3,000 to 8,000 years ago. rs10166942 is important phenotypically because its ancestral allele is protective of migraine. This debilitating disorder varies in prevalence across human populations, with highest prevalence in individuals of European descent, precisely the population with the highest frequency of rs10166942 derived allele. We thus hypothesize that local adaptation on previously neutral standing variation may have contributed to the genetic differences that exist in the prevalence of migraine among human populations today.

The mechanism and adaptive story make sense. They used several methods which corrected/accounted for population structure, and noted that the allele frequency difference was still significantly predicted by variation in latitude (though not temperature).

In the plot above you can see that South Asian populations share allele frequency distributions closer to East Asians, though genetically they are somewhat closer to Europeans. Looking at the haplotype structure this variant looks to be old variation that has been under selection in Eurasia. Additionally if you look at the frequencies it doesn’t look like the sweeps are completing. Since migraines are one correlated side effect that probably makes sense.

The problem I have with this preprint is a simple one. The SNP seems to be in the HGDP browser (it’s in your 23andMe genotype if you have one, I checked). The geographic distribution doesn’t look as clear as it does in the 1000 Genomes data. In particular in the New World populations the latitudinal cline is reversed from what we’d expect.

These sorts of objections are pretty typical. And they authors did do a sophisticated statistical analysis…but sometimes visual inspection of the raw frequencies is still important when the effect is subtle. Over the next decade there is going to be a lot of sophisticated analysis of adaptation, because the low hanging fruit has been picked. But we need to still look over the results with care….

The rich can afford to not steal

Pardis Sabeti has an op-ed in The Boston Globe, For better science, call off the revolutionaries. In it, she contrasts and compares the changes in social psychology and genetics over the past 15 years. In the former, you have had the replication crisis, while in the latter you saw the confirmation that many candidate-gene studies were not robust and replicable.

Sabeti observes that while there has been a great deal of vehemence in the change in social psychology, in genetics people have taken the overturning of the old studies in stride, and not personalized it.

I think we can all agree that personal attacks, vehemence, and Jacobin behavior is counter-productive to what science aims to be. This applies outside of the context of the replication crisis in social psychology. The problem emerges when you ask what the alternative strategy is to overturn an entrenched order.

Though it’s implied in the piece, the reason that geneticists could be more graceful probably has more to do with the situation they were presented with in the 2000s. The rise of genomics and computation generated a surfeit of data and the ability to analyze that data. Repeated gains in power and precision mean that every overturned orthodoxy gave rise to many more research opportunities. An established researcher whose candidate-gene study was overturned had bigger fish to fry than defend turf which was small potatoes set next to the possibilities of the “post-genomic” future.*

In other words, the difference here is situational. I was aware there was a problem in social psychology by the middle-2000s, because I had friends and acquaintances who were graduate students in the field. They complained about all the things that we now know were problems. It was one of those “open secrets” where less powerful people couldn’t speak the truth, and more powerful people who benefited from the status quo had no incentive to change the norms. I really don’t know how this was going to change in a gentle fashion.

* Compare the arguments between selectionists and neutralists in the 1970s vs. now. The reality is most people just want to analyze the data, not argue about theoretical issues. That’s because we have data.

South Asian Genotype Project, update

I’ve been working on the South Asian Genotype Project. Again, if you are interested: send me a 23andMe, Ancestry, or Family Tree DNA raw genotype file to contactgnxp -at- gmail.com.

In the subject please put:

  1. “South Asian Genotype Project”
  2. The state/province your family is from
  3. Ethnolinguistic group
  4. If applicable, caste

I changed the reference populations because the earlier ones were too complicated. You can see the population averages from public data sets for some groups.  The results for project members are here. I re-ran everyone who has sent data in so far. I’ll leave commentary for later.

At this point, I think the easiest way to update project members is to create a mailing list. If you are have submitted genotypes, please join:

Subscribe to the South Asian Genotype Project

* indicates required

From the eastern edge of the sea of grass

A new preprint, Mitogenomic data indicate admixture components of Asian Hun and Srubnaya origin in the Hungarian Conquerors, throws a rather large sample of medieval mtDNA samples at the question of the ethnogenesis of the Magyar people. The context here is that Maygars speak a non-Indo-European language, with a distant relationship to the Finnic ones, but genetically are not much distinguished from their neighbors.

But the differences are not non-zero, ‘best of breed’ methods can pick up a small fraction of exotic ancestry.

The results above are based on samples from cemeteries of the Magyar elite. These are people who identified with a steppe confederacy which coalesced in the 9th century in the Volga region, and in 895 conquered the region of Central Europe which we now term Hungary. In the 10th century, the Magyar tribes were an alien and predatory force within Europe, pagan and exotic. They were, in fact, the latest in a long time of mobile Central Asian horsemen, going back to the Scythian, Sarmatians, Huns, and Avars.

What the data from these results confirm is that a substantial proportion of the maternal lineages of the Hungarian nobility were East Eurasian. Their genetic profiles, in fact, resembled Scythians who had mixed with Altaic peoples, even if they were not descended from those people. What this suggests is that the Magyar conquest elite was part of a broader landscape of ethnolinguistically distinct, but interconnected, steppe confederations. The preprint gives great space to the likelihood that a substantial proportion of the Magyar elite was in fact Turkic in origin.

This leads to one of the major assertions of the paper: the distinctive linguistic identity of modern Hungarians is a legacy of the Hunnic period, and not the Magyar conquest. From what I can tell they didn’t have older DNA, so I don’t know how they came to this conclusion, except that the conquest Magyars were small in number, and seem to have been decimated over time (Mongol invasion, the battle of Mohacs).

The Dravidianization of India

On this week’s The Insight Spencer Wells and I talk about the Indo-Aryan arrival to South Asia. This was recorded very early last summer, and I’m rather unguarded (it’s well before I had the piece published in India Today).

I think 2018 will finally be the year that a lot of South Asia will be “solved.” There has been some foot-dragging on papers and results, but that can only go so long.

All that being said I suppose I should make some suppositions I have arrived at on this topic more explicit, as in a discussion with an Indian friend he admitted had no idea about some of my views, though he reads this weblog when I expressed them. That’s because they are speculative and my confidence in them is weak, though you can infer my opinions if you look very closely.

The figure to the left is from Genomic insights into the origin of farming in the ancient Near East, a paper published about a year and a half ago. You see various South Asian populations being modeled as a mixture of four different source populations. The Onge are an Andaman Islander population (and the closest we can get to the aboriginal peoples of South Asia). Iran_N represents Neolithic Iranians, the canonical “eastern farmer” population. Steppe_EMBA represent Yamnaya pastoralists, who are themselves modeled as a mixture of Eastern European Hunter-Gatherers (EHG) and southern population which has affinities with the Iran_N cluster. EHG in their turn seems to exhibit ancestry from Western European Hunter-Gatherers (WHG), whose heritage dates to the late Pleistocene, and Ancient North Eurasians (ANE), who flourished in Siberia, and contributed ancestry to populations to the west and east (including the ancestors of Native Americans).

When I first saw this specific figure I was incredulous. I had long thought that “Ancient North Indians” (ANI) were a compound of two elements, one related to the farmers of West Asia (Iran_N), and the other steppe Indo-European (Steppe_EMBA/Yamnaya). But the fraction of Yamnaya/Indo-European/Indo-Aryan ancestry seemed far too high.

A few years later I am less certain about my skepticism. The fractions here in the details are debatable. Within the text of the paper, the author admits that the true ancestral populations are probably not represented by the model. But they are close. In most cases, the “Han” ancestry is probably indicative of the fact that the non-ANI component of South Asian ancestry is most closely related to the Onge, but is significantly different nonetheless.

The ratio of Iran_N and Steppe_EMBA is the key. Here is a selection from the paper:

Group Iran_N Steppe_EMBA Ratio
Jew_Cochin 0.53 0.23 2.27
Brahui 0.60 0.30 1.98
Kharia 0.13 0.07 1.97
Balochi 0.57 0.32 1.75
Mala 0.23 0.18 1.25
Vishwabrahmin 0.25 0.20 1.21
GujaratiD 0.29 0.28 1.04
Sindhi 0.38 0.38 1.00
Bengali 0.22 0.25 0.91
Pathan 0.36 0.45 0.81
Punjabi 0.24 0.33 0.72
GujaratiB 0.27 0.38 0.72
Lodhi 0.21 0.29 0.72
Burusho 0.27 0.43 0.64
GujaratiC 0.23 0.37 0.61
Kalash 0.29 0.50 0.58
GujaratiA 0.26 0.46 0.57
Brahmin_Tiwari 0.23 0.44 0.51

Any way you slice it, a group like the Tiwari Brahmins of Northern India have more Onge-like ancestry than most of the groups in Pakistan. But also observe that the ratio toward Steppe_EMBA is more skewed in them than among even Pathans or Kalash.  The Lodhi, a non-upper caste population from Uttar Pradesh in north-central South Asia are more skewed toward Steppe_EMBA than Pathans.

It is important for me to reiterate that the key is to focus on ratios and not exact percentages. Though the Steppe_EMBA fraction did strike me as high, glimmers of these sorts of results were evident in model-based clustering approaches as early as 2010. The population in the list above most skewed toward Iran_N are Cochin Jews. This group has known Middle Eastern ancestry. But next on the list are Brahui, a Dravidian speaking group in Pakistan. There is a north-south cline within Pakistan, with northern populations (Burusho) being skewed toward Steppe_EMBA and southern ones (Sindhi) being skewed toward Iran_N. Additionally, Iranian groups such as Pathans and Baloch likely have had some continuous gene flow with Middle Eastern groups, probably inflating their Iran_N.

Trends I see in the data:

  1. There is a north-south cline within Pakistan with Steppe_EMBA vs. Iran_N
  2. There is a north-south cline within South Asia with Steppe_EMBA vs. Iran_N
  3. There is caste stratification within regions between Steppe_EMBA vs. Iran_N
  4. Though not clear in this table, there are strong suggestions that Indo-European speaking groups tend to be enriched in Steppe_EMBA, all things equal (e.g., the Bengalis in the 1000 Genomes look a lot like the middle-caste Telugus in the 1000 Genomes when you remove the East Asian ancestry…except for a noticeable small fraction of a component which I think points to Indo-European ancestry)

What does this mean in terms of a model of the settlement of South Asian over the past 4,000 years? One conclusion I have come to is that Dravidian speaking groups are not the aboriginal peoples of the subcontinent. Rather, their settlement across much of South Asia is very recent. Almost as recent as Indo-Aryan habitation. In First Farmers the archaeologist Peter Bellwood proposed this model, whereby Indo-Aryans and Dravidians both expanded across South Asia concurrently. Though I think elements of Bellwood’s model that are incorrect, it’s far more correct in my opinion than I believed when I first encountered it.

Why do I believe this?

  1. The Neolithic begins in South India in 3000 BC.
  2. Sri Lanka is Indo-European speaking
  3. The Dravidian languages of South India don’t seem particularly diverged from each other
  4. There is ancestry/caste stratification in South India even excluding Brahmins (e.g., Reddys and Naidus in Andhra Pradesh look somewhat different from Dalits and tribals)
  5. Some scholars claim that there isn’t a Dravidian substrate in the Gangetic plain
  6. R1a1a-Z93, almost certainly associated with Indo-Aryans, is found in South Indian tribal populations
  7. Using LD-based methods researchers are rather sure that the last admixture events between ANI and ASI (“Ancestral South Indians”) populations occurred around ~4,000 years ago

Here is my revised model as succinctly as I can outline it. The northwest fringes of South Asia, today Pakistan, and later to be the home of the Indus Valley Civilization (IVC), was populated by a mix of indigenous populations, a form of ASI, when West Asian agriculturalists arrived ~9,000 years ago from what is today Iran. These were the Iran_N or “eastern farmer” groups. The West Asian agricultural toolkit was serviceable in northwestern South Asia for reasons of climate and ecology, but could not expand further east and south for thousands of years.

There is where the first admixture occurred that led to a population was mixed between ANI and ASI. These people lacked Steppe_EMBA. They were pre-Indo-European. They were almost certainly not all Dravidian speaking. The Burusho people of northern Pakistan, for example, speak a language isolate (in India proper you have Nihali and Kusunda)

By ~3000 BC this proto-South Asian (in a modern sense) population began to expand, while the IVC matured and waxed. Eventually, the IVC waned, fragmented, and disappeared.

Around ~2000 BC, or perhaps somewhat later, Indo-Aryans arrive in South Asia. The situation at this stage in not one of a primordial and static Dravidian India, on which Indo-Aryans place themselves on top. Rather, it’s a dynamic one as the collapse of the IVC has opened up a disordered power vacuum, and a reconfiguration of cultural and sociopolitical alliances.

In the paper above the author alludes to the pervasiveness of both Iran_N and Steppe_EMBA ancestry in South Asia, including in South India. “Indo-European” Y chromosomal lineages are also found among many South Indian groups, albeit at attenuated proportions region-wide. In Peter Turchin’s formulation, I believe that “Indo-Aryan” and “Dravidian” identities became meta-ethnic coalitions in the post-IVC world. Genetically the two groups are different, on average. But some Dravidian populations assimilated and integrated Indo-Aryan tribes and bands, while Indo-Aryans as newcomers assimilated many Dravidian populations.

The reason that the ratio of Iran_N to Steppe_EMBA does not decline monotonically as one goes from west to east along North Indian plain is that Indo-Aryans were not expanding into a Dravidian India.  Dravidian India was expanding only somewhat ahead of Indo-Aryan India, and in some places not all at all. In the northwest fringe of South Asia there had long been a settled population of peasants with West Asian ancestry with Iran_N affinities. In contrast to the east the landscape was populated by nomadic tribal populations with ASI affinities. North Indian Brahmins may have more Steppe_EMBA than some populations in Pakistan and more ASI because they descend from Indo-Aryan groups who absorbed indigenous ASI populations as they expanded across the landscape.

Dravidian groups as they expanded also assimilated indigenous populations. This explains some groups with very high fractions of ASI. Their ASI ancestry is a compound, of an old admixture in Northwest India, and also later assimilation in South India. The presence of R1a1a-Z93 in these populations reflects the integration of some originally Indo-Aryan groups into the expanding Dravidian wavefront.

Where does this leave us?

  1. The Indo-Aryan vs. Dravidian dichotomy is not one of newcomers vs. aboriginals. It is of two different sociocultural configurations which came into their current shape in the waning days of the IVC. That is, it is less than 4,000 years old
  2. The two populations were clearly interacting closely around the time of the collapse and disintegration of the IVC and post-IVC societies. There has been gene flow between the two
  3. ~4000 years ago ANI and ASI populations existed in their “pure” form, but that is because ASI aboriginals still existed to the south and east of the IVC, while Indo-Aryans were a new intrusive presence in the Indian subcontinent

Runs of homozygosity are not good for your functioning

A must read review in Nature Reviews Genetics, Runs of homozygosity: windows into population history and trait architecture. Because it’s a paper on runs of homozygosity, James F. Wilson is on the apper.

If you are the product of a first cousin marriage, you have lots of runs of homozygosity. That’s because some of you will have large sections of the genome where both of the homologous chromosomes come from the same individual and are identical. In populations with small populations, this occurs not through recent inbreeding, as much as the reduced genetic diversity cranking up the frequency of some haplotypes over and above others.

The review covers all the bases, from distributions of runs of homozygosity in modern populations to ancient ones, as well as their functional consequences.

To the left, the plot shows that some populations, such as the Makrani of Pakistan, have fewer numbers of runs of homozygosity, but long ones when they have them. The populations on this part of the diagram are part of the “inbreeding belt.” In contrast, there are other populations with lots of runs of homozygosity, but they’re shorter. These are usually part of the “bottleneck belt,” where bottlenecks and small long-term effective populations have produced greater levels of homozygosity even on the genotype scale.

Perhaps the most interesting point though is that runs of homozygosity strongly correlate with changes in the values of a complex trait. In general, inbreeding is not too good, because recessively expressing deleterious alleles get exposed, and runs of homozygosity are a proxy for that.* This is why more exogamy in the Middle East and India may be such a social good.

* There may be confounds here. More educated and smarter people may marry those more distant from them geographically due to mobility.