Monday, July 26, 2021

Steven Weinberg Has Passed

Physicist Steven Weinberg, who was born in 1933, died on July 23, 2021.
He was arguably the dominant figure in theoretical particle physics during its period of great success from the late sixties to the early eighties. In particular, his 1967 work on unification of the weak and electromagnetic interactions was a huge breakthrough, and remains to this day at the center of the Standard Model, our best understanding of fundamental physics.

Science News has another nice obituary for him.

The Common Cold Is Old

The common cold virus is much older than modern humans. 

The origins of viral pathogens and the age of their association with humans remains largely elusive. To date, there is no direct evidence about the diversity of viral infections in early modern humans pre-dating the Holocene. We recovered two near-complete genomes (5.2X and 0.7X) of human adenovirus C (HAdV-C), as well as low-coverage genomes from four distinct species of human herpesvirus obtained from two 31,630-year-old milk teeth excavated at Yana, in northeastern Siberia. 
Phylogenetic analysis of the two HAdV-C genomes suggests an evolutionary origin around 700,000 years ago consistent with a common evolutionary history with hominin hosts. 
Our findings push back the earliest direct molecular evidence for human viral infections by ∼25,000 years, and demonstrate that viral species causing common childhood viral infections today have been in circulation in humans at least since the Pleistocene.
From Sofie Holtsmark Nielsen, et al., "31,600-year-old human virus genomes support a Pleistocene origin for common childhood infections" bioRxiv (June 28, 2021).

The Testimony Of The Mandarin

Mandarin citrus fruits were first domesticated in the mountainous regions of Southern China, and spread widely from there. 

Hybridization of these mainland Chinese fruits and some wild species native to Japan's Southern Ryukyu Islands accounts for most important modern varieties of them.

Hunan Province of southern China, which is the center of wild mandarin diversity and the genetic source of most well-known mandarins. When the scientists re-analyzed previously published genomic data, they unexpectedly found that wild mandarins of this mountainous region are split into two subspecies.

"We found that one of these mandarin subspecies can produce offspring that are genetically identical to the mother," said Dr. Guohong Albert Wu, a research collaborator at the Lawrence Berkeley National Laboratory in California. "Like many other plants, wild citrus typically reproduces when the pollen of the father combines with the egg of the mother, mixing the genes from both parents in the seed. 
But we found a subspecies of wild mandarins from Mangshan, in southern China, where the seed contains an identical copy of the mother's DNA without any input from a father. So, the seed grows to be a clone of the mother tree."

From Science Daily.

The body text of the source paper explains that:

We find that the complexity of mandarin relationships is considerably simplified by the discovery of three ancestral lineages which, together with pummelo, gave rise to all extant mandarin diversity by hybridization and introgression. One of these groups is a previously unknown wild species currently found in the Ryukyu islands; the other two are previously unrecognized sister subspecies of mainland Asian mandarin. 
Our analysis leads to a comprehensive revision of the origin and diversification of east Asian citrus, including the elucidation of the origins of apomixis in mandarin and its spread to related citrus including oranges, grapefruits and lemons.

The paper and its abstract are:

The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. 
The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. 
We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.
Guohong Albert Wu, et al., "Diversification of mandarin citrus by hybrid speciation and apomixis." 12(1) Nature Communications (July 26, 2021) (open access). 

Friday, July 16, 2021

Medieval Astronomy

The Syriac Text
The reconstructed sky in the place where the Syriac text was written on May 25, 760 at 2:40 a.m.

Scientists have
analyzed ancient historical accounts from Syria, China, the Mediterranean and West Asia (most critically, the detailed accounts in the hand written Syrian Chronicle of Zuqn¯ın, part of which ended up in the Vatican Library and part of which ended up in the British Museum) to confirm that all of these accounts viewed key parts of the appearance of a particular comet in their skies in late May and early June of the year 760 CE.  

The scientists matched these observations with calculations of where the comet 1P/Halley would have been in the sky at that time based upon its current observed trajectory with key dates pinned down to a margin of error of one to two days for particular events.

This 760 CE fly-by was the comet's last return before a close encounter with Earth in 837 CE. The 760 CE perihelion of the comet that was observed is particularly important for extrapolation further back in time. This study provides one of the longest time frames of confirmed continued observations of the same celestial object. This helps to confirm the accuracy and robustness of astronomy's current gravitational calculations of solar system orbits, and to remind us just how long quite accurate scientistic astronomy observations have been collected and recorded by people.

Historical Context

This was near the end of the period known as the "dark ages" in the former western Roman Empire in Europe, during the life of Charlemagne, eight years before he began his reign as the King of the Franks in what is now France, and forty years after the remarkably wet summer of 720 CE in Europe.

Decisive battles on land and at sea with the Byzantine Empire ended the expansion of the Umayyad Caliphate into the territory of the former Roman Empire fourteen years earlier (746 CE). The Eastern Orthodox Christian Byzantine Empire was the last remnant of the Roman Empire, in what is now most of Turkey, Greece and Italy, and would persist in a gradually diminished form over about three more centuries. The West Asian accounts were written by Byzantine subjects.

As the body text of the new paper explains:
The author of the chronicle was probably the stylite monk Joshua; a stylite is an early Byzantine or Syrian Christian ascetic living and preaching on a pillar in the open air, so that many celestial observations can be expected in his work. The author of the Chronicle of Zuqn¯ın may have lived on a pillar for some time. During the time of writing of the Chronicle of Zuqn¯ın [ed. completed in 775/776 CE], the area was outside the border of the Byzantine empire and already under 푐Abbasid rule.
Thus, the Syrian chronicle entries were written by a Christian monk under the jurisdiction of the Islamic Abbasid Caliphate (750-1517 CE) in areas recently reclaimed by the Caliphate after a brief Byzantine expansion into the territory of the Umayyad Caliphate which preceded it. The Abbasid Caliphate had been formed ten years earlier in the Abbasid Revolution and replaced the Umayyad Caliphate (661-750 CE). The Umayyad Caliphate had been led by an ethnically Arab elite that treated even non-Arab Muslim converts as second class citizens, while the Abbasid Caliphate was led by a multi-ethnic, mostly non-Arab, and eastern oriented Abbasid Caliphate that ruled in a more inclusive manner, whose Caliphs claimed to have descended from an uncle of the Prophet Muhammad (who died about four decades before the comet appeared).

The provenance of the Chronicle was somewhat involved. As the body text explains:
The Chronicle of Zuqn¯ın is not known to be copied and disseminated; sometime during the 9th century it was transferred to the Monastery of the Syrians in the Egyptian desert . . .  Shortly after the manuscript was found and bought for the Vatican, it was considered to be written by the ¯ West Syrian patriarch Dionysius I of Tell-Mah. re, so that this chronicle was long known as Chronicle of Dionysius of ¯ Tell-Mah. re. Dionysius did write an otherwise lost world chronicle, but lived later (died AD ca. 845). Since this mistake was noticed, the chronicle has been called the Chronicle of Pseudo-Dionysius of Tell-Mah. re or, better, the Chronicle of Zuqn¯ın, because the text mentions the monastery of Zuqn¯ın as the living place of the author; Zuqn¯ın was located near Amida, now Diyarbakır in Turkey near the border to Syria. 
The Chronicle of Zuqn¯ın is made of four parts: Part I runs from the creation to Emperor Constantine (AD 272-337), Part II from Constantine to Emperor Theodosius II (AD 401-450) plus a copy of the so-called Chronicle of PseudoJoshua the Stylite (AD 497 to 506/7), Part III from Theodosius to Emperor Justinian (AD 481-565), and Part IV to the time of writing, AD 775/776. The Chronicler used a variety of sources, some of them otherwise lost. The author knew that some of his sources did not provide a perfect chronology; for him, it is more important to convey his message (to learn from history) than to give perfect datings. 
The events reported in the text are dated using the Seleucid calendar; the Seleucid Era (SE) started on October 7, BC 312 (= Dios 1). There are several versions of the Seleucid calendar, including the Babylonian (Jewish), Macedonian, and West Syrian (Christian) ones. The author of our chronicle systematically used the latter version for reports during his lifetime – a solar calendar, in which the year ran from Tishri/October 1 to Elul/September 30, applied since at least the fifth century AD.
This was also two years before the city of Baghdad was founded within the Abbasid Caliphate, near the ancient city of Seleucia, which had been the capitol of the Nestorian Christian Church of the East from 410 CE, until it had to be abandoned to the desert sands when the Tigris River that made it possible to live there shifted, a few decades after Baghdad was founded.

In China, this comet's appearance coincided with the unsuccessful seven year long An Lushan Rebellion against the Tang Dynasty. This rebellion ended with a pair of stunning betrays, first when An Lushan, the leader of the rebellion, was killed by one of his own eunuchs in 757, and then when his successor as leader of the rebellion, Shi Siming, was killed by his own son in 763, which ended the rebellion.

Citizen Science In Astronomy

The actual goal of this project, to find gravitational lensing evidence of a small dark matter halo from a database with tens of thousands of observations, is pretty ordinary as astrophysics goes, and it doesn't yet have any definitive results. Still, it is a worthwhile project that adds incrementally to what we know in a well focused way to expand the margins of our existing knowledge.

It illustrates the reality that the many modern telescopes in multiple frequencies that are now being used can collect a vast amounts of information. But this has made a lot of questions in astrophysics and astronomy "big data" problems.

With a smaller database, a single skilled research could personally review each one. This painstaking pouring over of data by a single highly trained scientist with the PhD in the relevant subfield of astronomy is how this kind of research got started. But it is impossible for a single astronomer to conduct the necessary fairly detailed analysis of each observation required for this kind of study, for such a large collection of data, in a reasonable amount of time. But timely analysis is necessary because the amount of data to review gets larger every month. 

The firehose of incoming data is only getting stronger. For example, a new European Space Agency project targeted for the year 2045 will collect information on 10 to 12 billion new sources of light in the sky that are too faint to discern now.

The citizen science methodology used in this study is remarkable and exciting. It presents an alternative to statistical, machine learning, and supercomputing approaches to sorting through masses of data. Unlike these automated alternatives, this citizen science approach doesn't sacrifice the human judgment element of the process present when a single scientist analyzes a large, but tractable body of data. 

In this case, twenty people, about a quarter of whom were scientists, about quarter of whom were graduate students, and about half of whom were undergraduates, mostly at the University of Crete, worked together to tackle the large dataset to identify 40 strong candidates out of 13,828 (many of which have multiple images at different wave lengths that had to be considered) including two particularly promising needles in the haystack.

It is a kind of project I am familiar with from my day job as an attorney, where, for example, I've had to mobilize similar numbers of people with similar skill levels, to review an entire room full of banker's boxes of not very well organized hard copy business records to locate a handful of key documents in complex securities fraud litigation.

The way this project managed to mobilize so many people to volunteer their time for this somewhat esoteric goal, hearteningly democratized this scientific endeavor and made this task possible to complete.

The paper and its abstract are as follows:

Dark Matter (DM) halos with masses below 108 M, which would help to discriminate between DM models, may be detected through their gravitational effect on distant sources. The same applies to primordial black holes, considered as an alternative scenario to DM particle models. However, there is still no evidence for the existence of such objects. 
With the aim of finding compact objects in the mass range  106 -- 109M, we search for strong gravitational lenses on milli (mas)-arcseconds scales (< 150 mas). For our search, we used the Astrogeo VLBI FITS image database -- the largest publicly available database, containing multi-frequency VLBI data of 13828 individual sources. 
We used the citizen science approach to visually inspect all sources in all available frequencies in search for images with multiple compact components on mas-scales. At the final stage, sources were excluded based on the surface brightness preservation criterion. We obtained a sample of 40 sources that passed all steps and therefore are judged to be milli-arcsecond lens candidates. 
These sources are currently followed-up with on-going European VLBI Network (EVN) observations at 5 and 22 GHz. Based on spectral index measurements, we suggest that two of our candidates have a higher probability to be associated with gravitational lenses.

C. Casadio, et al., "SMILE: Search for MIlli Lenses" arXiv: 2017.06896 (July 14, 2021) (accepted for publication).

Wednesday, July 14, 2021

Is Dark Energy Just Systemic Error?

The authors of this pre-print argue that the redshift estimated age of supernova which is the most important means by which the acceleration of the universe's expansion attributed to "dark energy" is determined may actually be a product of systemic error that does not take into account that the age of the stars that go supernova influences how bright they become. 

If their very plausible analysis is correct, there should be no "dark energy" and the cosmological constant may be zero. 

Supernova (SN) cosmology is based on the assumption that the width-luminosity relation (WLR) and the color-luminosity relation (CLR) in the type Ia SN luminosity standardization would not vary with progenitor age. Unlike this expectation, recent age datings of stellar populations in host galaxies have shown significant correlations between progenitor age and Hubble residual (HR). It was not clear, however, how this correlation arises from the SN luminosity standardization process, and how this would impact the cosmological result. Here we show that this correlation originates from a strong progenitor age dependence of the WLR and the CLR, in the sense that SNe from younger progenitors are fainter each at given light-curve parameters x1 and c. This is reminiscent of Baade's discovery of two Cepheid period-luminosity relations, and, as such, causes a serious systematic bias with redshift in SN cosmology. Other host properties show substantially smaller and insignificant differences in the WLR and CLR for the same dataset. We illustrate that the differences between the high-z and low-z SNe in the WLR and CLR, and in HR after the standardization, are fully comparable to those between the correspondingly young and old SNe at intermediate redshift, indicating that the observed dimming of SNe with redshift is most likely an artifact of over-correction in the luminosity standardization. When this systematic bias with redshift is properly taken into account, there is no or little evidence left for an accelerating universe, posing a serious question to one of the cornerstones of the concordance model.

Monday, July 12, 2021

A Principal Component Analysis Of Major Branches Of Eurasian Population Genetic Diversity


This chart is a two dimensional chart of the relative genetic similarities and relationships of many modern and one group of ancient Eurasian populations from a paper analyzing the genetics of the Saami people of Northern Scandinavia (especially Finland with which they have the strongest linguistic ties), who are now herders and historically were one of the last hunter-gatherer populations of Europe.


Inferring Ancient Arabian Genetics From Modern Populations

Researchers in a preprint earlier this year use modern Arabian and Iranian whole genomes to infer the makeup of ancient Arabian population genetics. 

Their results suggest that the hypothetical ghost population of "basal Eurasians" (who did not experience Neanderthal admixture) may have a real world counterpart in ancient East Arabians and in the ancient Iberomaurusian hunter-gatherers of what is now Morocco, Algeria, Tunisia and Libya, in the period between the Last Glacial Maximum and the Holocene. As Wikipedia describes this an ancient archaeological culture:
The name of the Iberomaurusian means "of Iberia and Mauretania", the latter being a Latin name for Northwest Africa. Pallary (1909) coined this term to describe assemblages from the site of La Mouillah in the belief that the industry extended over the strait of Gibraltar into the Iberian peninsula. This theory is now generally discounted (Garrod 1938), but the name has stuck.

In Algeria, Tunisia, and Libya, but not in Morocco, the industry is succeeded by the Capsian industry, whose origins are unclear. The Capsian is believed either to have spread into North Africa from the Near East, or to have evolved from the Iberomaurusian. In Morocco and Western Algeria, the Iberomaurusian is succeeded by the Cardial culture after a long hiatus.

We know a fair amount about these people genetically from ancient DNA and my own remote Y-DNA E-V13 ancestor is probably from this archaeological culture.

In 2013, Iberomaurusian skeletons from the prehistoric sites of Taforalt and Afalou were analyzed for ancient DNA. All of the specimens belonged to maternal clades associated with either North Africa or the northern and southern Mediterranean littoral, indicating gene flow between these areas since the Epipaleolithic. The ancient Taforalt individuals carried the mtDNA Haplogroup N subclades like U6 and M which points to population continuity in the region dating from the Iberomaurusian period.

Loosdrecht et al. (2018) analysed genome-wide data from seven ancient individuals from the Iberomaurusian Grotte des Pigeons site near Taforalt in north-eastern Morocco. The fossils were directly dated to between 15,100 and 13,900 calibrated years before present. 
The scientists found that all males belonged to haplogroup E1b1b, common among Afroasiatic males. The male specimens with sufficient nuclear DNA preservation belonged to the paternal haplogroup E1b1b1a1 (M78), with one skeleton bearing the E1b1b1a1b1 parent lineage to E-V13, one male specimen belonged to E1b1b (M215*). These Y-DNA clades 24,000 years BP had a common ancestor with the Berbers and the E1b1b1b (M123) subhaplogroup that has been observed in skeletal remains belonging to the Epipaleolithic Natufian and Pre-Pottery Neolithic cultures of the Levant
Maternally, the Taforalt remains bore the U6a and M1b mtDNA haplogroups, which are common among modern Afroasiatic-speaking populations in Africa. 
A two-way admixture scenario using Natufian and modern sub-Saharan samples (including West Africans and the Tanzanian Hadza) as reference populations inferred that the seven Taforalt individuals are best modeled genetically as of 63.5% Natufian-related and 36.5% sub-Saharan ancestry (with the latter having both West African-like and Hadza-like affinities), with no apparent gene flow from the Epigravettian culture of Paleolithic southern Europe. The scientists indicated that further ancient DNA testing at other Iberomaurusian archaeological sites would be necessary to determine whether the Taforalt samples were representative of the broader Iberomaurusian gene pool.
The paper and its abstract are as follows (emphasis mine):
Arabian Peninsula is strategic for investigations centred on the structuring of the modern human population in the three main groups, in the awake of the out-of-Africa migration. Despite the poor climatic conditions for recovery of ancient DNA human evidence in Arabia, the availability of genomic data from neighbouring ancient specimens and of informative statistical tools allow better modelling the ancestry of these populations. 
We applied this approach to a dataset of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. 
The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking west Arabia with Levant, and east Arabia with Iran and Caucasus. East Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for possible bias due to recent sub-Saharan African input in their genomes. Not surprisingly, east Arabians were also the ones with higher similarity with Iberomaurusians, who were so far the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans that diverged from the common European-East Asian pool before 50 thousand years ago, and before the later interbred with Neanderthals. Our results are strong evidence to include the exposed basin of the Arabo-Persian Gulf as possible home of basal Eurasians, to be investigated further on namely by searching ancient Arabian human specimens.
doi: https://doi.org/10.1101/2021.02.24.432678

Saturday, July 10, 2021

Add This To The List Of Problems With Cold Dark Matter Models

Dark matter particle theories have a long string of documented problems. Here is another one. 

Cold dark matter (CDM) has faced a number of challenges mainly at small scales, such as the too-big-to-fail problem, and core-cusp density profile of dwarf galaxies. Such problems were argued to have a solution either in the baryonic physics sector or in modifying the nature of dark matter to be self-interacting, or self-annihilating, or ultra-light. Here we present a new challenge for CDM by showing that some of Milky Way's satellites are too dense, requiring the formation masses and redshifts of halos in CDM not compatible with being a satellite. These too-dense-to-be-satellite systems are dominated by dark matter and exhibit a surface density above mean dark matter cosmic surface density Ωdmρcc/H0200 M/pc2. This value corresponds to dark matter pressure of 1010erg/cm3. This problem, unlike other issues facing CDM, has no solution in the baryonic sector and none of the current alternatives of dark matter can account for it. The too-dense-to-be-satellite problem presented in this work provides a new clue for the nature of dark matter, never accounted for before.
Mohammadtaher Safarzadeh, Abraham Loeb "A New Challenge for Dark Matter Models" arXiv:2017.03478 (July 7, 2021).

Thursday, July 8, 2021

Inbreeding Declined In West And Central Eurasia During The Holocene Era

A new paper published in the journal Cell shows that inbreeding has declined over the last 12,000 years, as demonstrated with 411 ancient DNA samples from West Eurasia (defined as Europe) and Central Eurasia (defined as Southwest Asia, the Caucasus and Central Asia).

Extreme consanguineous matings did occur among agriculturalists but were rare, while inbreeding was more common in hunter-gatherers and declined more gradually as farming societies grow more complex. Modern Europe, which has far more people, has even less inbreeding.



The regressions and images above go from the present on left, to the past, on the right. F(ROH) (for runs of homozygosity) is a measure of inbreeding with a higher number indicating more inbreeding in the lineage of the individual whose DNA is examined.

Essentially, the larger the size of the communities involved, as improving food production technology makes possible, the less inbreeding is found.

The detailed numerical data is summarized in the chart below. The key data points (with median F(ROH)) are:

* Hunter-gathers (N=40) 0.0633
* Simple agriculturalists (N=102) 0.0286
* Early complex agriculture (N=230) 0.0250
* Advanced complex agriculture (N=160) 0.0160
* Modern Central Eurasia (N=309) 0.0156
* Modern Europe (N=139) 0.0039

Central Eurasia is less inbred than Europe among hunter-gathers, simple agriculturalists, and advanced complex agricultural societies, but is modestly more inbred in the era of early complex agriculture, although the statistical significance of the differences in these areas is modest.

In the modern era, Central Eurasia with an inbreeding coefficient of 0.0156 (which is more than in Central Eurasia during the advanced complex agriculture phase) is much more inbred than modern Europe which has an inbreeding coefficient of 0.0039. The combined modern inbreeding coefficient is 0.0066.

Prevalence Of Moderate Inbreeding With Some Cousin Marriage

100% of hunter-gatherers, 95% of farmers prior to the advanced complex agriculture phase, 77% of farmers in an era of advanced complex agriculture, and 14% of modern Europeans are as inbred as the median modern Central Eurasian (0.0117). This is what one would expect to arise from endogamy within a community with some cousin marriage (including remote cousins) that is not predominant.

Prevalence Of Cousin Marriage

93% of hunter-gatherers, 5-15% of ancient farmers, and 2% of modern Europeans are as inbred as 23% of modern Central Eurasian are (0.0391), a level typical for first cousin marriages. According to the paper:
Samples from modern groups like the Balochi, the Bedouin, or the Sindhi from Pakistan have the highest proportions of individuals with FROH > 0.0391 (50%, 41.3%, and 33.3% respectively).
Prevalence Of Highly Inbred Mating

10% of hunter-gathers, 1.9% of simple agriculturalists and modern Central Eurasians, 0.4% of farmers in early complex agriculture, and 0% of farmers in advanced complex agriculture and modern Europeans has an inbreeding coefficient of 0.0932

This is a level of inbreeding in excess of otherwise unrelated double cousin marriages, and similar to that of marriages between an uncle or aunt and that person's niece or nephew, between half-siblings, between a grandparent and a grandchild, or offspring of closer matings. 

Even remote cousin over many generations in a small community, however, can elevate the inbreeding coefficient of mere cousin marriages or of a double cousin marriage, above this threshold. The genetic evidence indicates that this sort of genetic drift was involved in the early hunter-gatherer communities, while cousin and/or closer marriage was a major factor in other genomes studied.


The high inbreeding coefficients in modern "Central Asians" are largely a product of Islamic law's acceptance of cousin marriage and of traditional cultures in some (but not all) Islamic societies, that favor high rates of cousin marriage of 10% to more than 50%, as shown on the map below. 

Cousin marriage is uncommon, however, despite being at least nominally legal under Islamic law, in countries that are predominantly Muslim where Muslims predominantly follow the school of Sunni Islamic jurisprudence that is predominant in Southeast Asia (i.e. the Shafi'i school of Sunni Islamic law).



Some concluding comments of the paper bear repeating in their entirety so as not to lose the nuance of these important caveats to its findings:
Three points further deserve mention regarding mating patterns in human societies. 
One is the seeming contrast between the high levels of drift-driven autozygosity (panmictic inbreeding) we report for ancient hunter-gatherer societies and ethnographic studies showing low levels of inbreeding among modern-day hunter-gatherers. For instance, a comparison of inbreeding patterns in a worldwide sample of contemporary hunter-gatherers with Amazonian horticulturalists reported lower inbreeding in hunter-gatherer groups. Hill and colleagues also report low levels of relatedness within modern-day hunter-gatherer bands. However, the mentioned ethnographic findings rely on genealogies and report the prevalence of inbreeding by consanguinity, not inbreeding by drift. In fact, we also find consanguinity to be rare among early Holocene Eurasian hunter-gatherers relative to agriculturalists, consistent with widespread exogamy in modern-day hunter-gatherers. This raises the possibility that reciprocal exogamy and consanguinity avoidance traditions may have been predominant among human foragers since prehistory (but possibly not in archaic hominins).

Second, our results lend support, albeit with limited data, to the hypothesis that extreme consanguinity may have become more common with farming. This result parallels higher within-group marriages among modern-day horticulturalists than foragers. It is also consistent with singular reports on ancient agriculturalist genomes, such as evidence for consanguinity identified in an early Neolithic farmer from Iran, a first-degree incest case from Neolithic Ireland, as well as a recent report on close-kin unions in the central Andes after 1000 CE. 

In our analysis, among the seven individuals with the highest level of inbreeding (with FROH > 0.125), all four hunter-gatherers appear autozygous by drift, while all three agriculturalists appear autozygous by consanguinity. This appears unlikely to happen by chance (Fisher’s exact test, two-sided p = 0.029). These results are consistent with the view that consanguineous traditions could have thrived in class-based agricultural societies with private property more readily than in more egalitarian hunter-gatherer groups.

Finally, we report higher consanguinity in Central versus West Eurasia in contemporary societies, in parallel with earlier work. This is consistent with widespread first- or second-cousin marriage practices in agricultural societies in Middle Eastern and North African countries and in South Asia, including Muslim and Jewish groups, as documented by ethnographic or genomic studies. We note that cousin marriages were also common among royal dynasties and upper classes of Europe until the 20th century, and many prominent European scientists of that period are known to have married their first cousins, including Charles Darwin and Albert Einstein. These traditions are thought to have arisen through various social factors, including the inheritance of property in class societies.

Interestingly, we do not observe the relatively high rates of consanguineous marriage observed in modern-day Central Eurasia in any of the past societies we studied, in Antiquity or earlier. We naturally prefer to remain cautious, especially given the limited sample size of our advanced complex agriculturalist samples from West and Central Eurasia (n = 9 and n = 30, respectively). Nevertheless, it appears possible that present-day cultural patterns may have emerged relatively late in time.