Merry Christmas

Long Live the 28th October, 1940

Human pigmentation mega-study

A great new study on the genetics of human (including African) pigmentation. I would love to see a future study that would reconstruct what ancestral modern humans looked like pigmentation-wise, as this trait is tightly correlated with sun exposure (and thus latitude), and may thus pinpoint a narrow latitudinal zone where ancestral modern humans may have lived.

From a related story:

The most dramatic discovery concerned a gene known as MFSD12. Two mutations that decrease expression of this gene were found in high frequencies in people with the darkest skin. These variants arose about a half-million years ago, suggesting that human ancestors before that time may have had moderately dark skin, rather than the deep black hue created today by these mutations.

Science 12 Oct 2017: eaan8433 DOI: 10.1126/science.aan8433

Loci associated with skin pigmentation identified in African populations

Nicholas G. Crawford et al.

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

Link

Sexual orientation from facial images

This is hardly surprising, as there is an obvious evolutionary advantage for people being able to "read faces" not only for sexuality but also for various cognitive, moral, and personality traits (see, e.g., heroes and villains, wizards and simpletons are often portrayed stereotypically in art).


Deep neural networks are more accurate than humans at detecting sexual orientation from facial images

Description: We show that faces contain much more information about sexual orientation than can be perceived and interpreted by the human brain. We used deep neural networks to extract features from 35,326 facial images. These features were entered into a logistic regression aimed at classifying sexual orientation. Given a single facial image, a classifier could correctly distinguish between gay and heterosexual men in 81% of cases, and in 74% of cases for women. Human judges achieved much lower accuracy: 61% for men and 54% for women. The accuracy of the algorithm increased to 91% and 83%, respectively, given five facial images per person. Facial features employed by the classifier included both fixed (e.g., nose shape) and transient facial features (e.g., grooming style). Consistent with the prenatal hormone theory of sexual orientation, gay men and women tended to have gender-atypical facial morphology, expression, and grooming styles. Prediction models aimed at gender alone allowed for detecting gay males with 57% accuracy and gay females with 58% accuracy. Those findings advance our understanding of the origins of sexual orientation and the limits of human perception. Additionally, given that companies and governments are increasingly using computer vision algorithms to detect people’s intimate traits, our findings expose a threat to the privacy and safety of gay men and women.

Link

Minoans and Mycenaeans

It is great to finally see the first data from the most ancient Greeks (Mycenaeans) and also the Cretan Minoans:

• Ancestrally. both Mycenaeans and Minoans were basically Mediterranean, well outside the variation of most Europeans and Near Easterners and >75% from early European-Anatolian farmers.
• Phenotypically, they were dark-haired/eyed
• They weren't pure Mediterraneans, but also partly "West_Asian". Bronze Age people from S.W. Anatolia were even more "West_Asian".
• Mycenaeans also had some "Ancient North Eurasian" ancestry, which may have come from either the north or east of Greece.
• Two Minoans and a Mycenaean were haplogroup J2, one Minoan was G.
• One high-status Mycenaean female from Messenia was not different from the other three Mycenaeans.

Modern Greeks from Greece are more "northern", more "European", and less "Mediterranean" than the Mycenaeans. Bust, Fst-wise Modern Greeks (and assorted neighbors) are still fairly close to Mycenaeans, more so than other people from Europe and the Middle East:

Nature (2017) doi:10.1038/nature23310

Genetic origins of the Minoans and Mycenaeans

Iosif Lazaridis, Alissa Mittnik, Nick Patterson, Swapan Mallick, Nadin Rohland, Saskia Pfrengle, Anja Furtwängler, Alexander Peltzer, Cosimo Posth, Andonis Vasilakis, P. J. P. McGeorge, Eleni Konsolaki-Yannopoulou, George Korres, Holley Martlew, Manolis Michalodimitrakis, Mehmet Özsait, Nesrin Özsait, Anastasia Papathanasiou, Michael Richards, Songül Alpaslan Roodenberg, Yannis Tzedakis, Robert Arnott, Daniel M. Fernandes, Jeffery R. Hughey, Dimitra M. Lotakis, Patrick A. Navas, Yannis Maniatis, John A. Stamatoyannopoulos, Kristin Stewardson, Philipp Stockhammer, Ron Pinhasi, David Reich, Johannes Krause & George Stamatoyannopoulos

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean1, 2, and most of the remainder from ancient populations related to those of the Caucasus3 and Iran4, 5. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter–gatherers of eastern Europe and Siberia6, 7, 8, introduced via a proximal source related to the inhabitants of either the Eurasian steppe1, 6, 9 or Armenia4, 9. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

Link

Deepest Neandertal mtDNA split

The authors interpret the new result from HST as placing a lower boundary on an introgression from Africans to Neandertals at more than 290kya, which explains why Africans are genomically closer to Neandertals than to Denisovans.

Of course, when one looks at the mitochondrial phylogeny, it has the form:

(Denisovans, (Neandertals, Modern Humans))

Within the Modern Humans, Eurasians are a branch of a tree which is mostly African. This has been interpreted for decades as evidence for the Out of Africa hypothesis for the origin of Modern Humans. But, within the phylogeny as a whole, Modern Humans are a branch of the Eurasian tree. This has not (why?) in general been interpreted as evidence for Out of Eurasia for the common ancestor of Modern Humans and Neandertals.

It seems to me that this hypothesis, that Modern Humans and Neandertals stem from a non-African ancestor (a non-African population of H. heidelbergensis, for example), has much to recommend it.

Eurasia has twice the size of Africa and has been home to hominins for ~1.8 million years. It was inhabited by diverse hominins, and thanks to blind luck we discovered that as late as a few tens of thousands years ago, it also sported two of the populations that split off before anyone else: first H. floresiensis, and second Denisovans.

While a North African source of modern humans is plausible, the data seems to favor a Eurasian origin of the (Modern Human, Neandertal) ancestor.

Nature Communications 8, Article number: 16046 (2017) doi:10.1038/ncomms16046

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens & Johannes Krause

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.

Link

Out of North Africa

I had previously called Irhoud 1 "The Father of Mankind" and proposed a "two deserts" theory of human evolution whereby our species originated in North Africa, and was pumped out of it to both the Middle East (and especially Arabia, the 2nd desert) and Sub-Saharan Africa during periods of Saharan aridity. This Out-of-North Africa theory (together with the secondary Out-of-Arabia expansion ~70kya) is responsible for the spread of Homo sapiens around the world.

The discovery and re-dating of modern human remains from Irhoud of course adds support to this theory and places North Africa as the most probable cradle of our species, with a comfortable 100kya buffer to the next place where modern humans are detected (the Omo remains of East Africa), and another comfortable 100kya buffer to the next place (Israel and the Skhul/Qafzeh hominins).

The interpretation of these findings in terms of Homo sapiens emerging out of a sort of multi-regional evolution involving all Africa is of course wrong. There is no reason to think of a single species evolving across the huge African continent. The early distribution of sapiens remains are in North Africa, East Africa, and the Near East, and such remains are absent in West/Central/South Africa.

The multi-regionalists lost the game in Eurasia, as it turned out that Eurasians only have ~2% archaic admixture, and they are inventing Multiregionalism-in-Africa.

Whatever finds we do have from Sub-Saharan Africa, some of them quite late (such as the Iwo Eleru remains from Nigeria), others of similar age as Irhoud (such as Florisbad and the recently described H. naledi from South Africa) did not belong to our species. The first modern humans appeared in South Africa with the Later Stone Age (probably associated with the migration of Y-chromosome haplogroup E into Africa), and the Hofmeyr skull (which resembled Eurasians and not the eternally romanticized Khoe-San). Even in East Africa the advent of modernity was not clear-cut (see Omo I vs. II and the more archaic later Herto specimen).

It seems that people were misled into thinking of Sub-Saharan Africa as the origin of our species by the genetic observation of greater genetic diversity of Sub-Saharan Africans. But, this diversity could have come about by admixture between people from North Africa and pre-existing people of Sub-Saharan Africa (both early waves of AMH and non-AMH).

It's not certain that North Africa will be the end of the story. Fashions shifted from the Near East to East Africa, to North Africa, with every new find. But, the fact that we do find the earliest modern humans in these areas, while we find non-AMH elsewhere (e.g. Europe or South Africa) is gradually constraining the solution to the problem of our origins. My bet remains North Africa; time will tell.

Younger Dryas comet impact encoded in Göbekli Tepe?

Fascinating if true.

Mediterranean Archaeology and Archaeometry, Vol. 17, No 1, (2017), pp. 233-250


DECODING GÖBEKLI TEPE WITH ARCHAEOASTRONOMY: WHAT DOES THE FOX SAY? 

Martin B. Sweatman* and Dimitrios Tsikritsis

We have interpreted much of the symbolism of Göbekli Tepe in terms of astronomical events. By matching low-relief carvings on some of the pillars at Göbekli Tepe to star asterisms we find compelling evidence that the famous ‘Vulture Stone’ is a date stamp for 10950 BC ± 250 yrs, which corresponds closely to the proposed Younger Dryas event, estimated at 10890 BC. We also find evidence that a key function of Göbekli Tepe was to observe meteor showers and record cometary encounters. Indeed, the people of Göbekli Tepe appear to have had a special interest in the Taurid meteor stream, the same meteor stream that is proposed as responsible for the Younger-Dryas event. Is Göbekli Tepe the ‘smoking gun’ for the Younger-Dryas cometary encounter, and hence for coherent catastrophism?

Link (pdf)

Happy Easter

Long Live the 25th March, 1821

Incipient Mongoloids (or elusive Denisovans) 105-125kya in China?

The authors claim that these archaic humans from China show parallels to both modern eastern Eurasians (Mongoloids) and to Neandertals. The relationship with the Neandertals makes them prime candidates for the elusive Denisovans who were a sister group to Neandertals but are morphologically unknown (since all we've got is a genome, teeth, and a pinky). The relationship with Mongoloids suggest an appearance of Mongoloid morphology pre-dating the transition to sapiens, and brings to mind past claims about incipient Caucasoid morphology in Neandertals. Did aspects of modern Eurasian morphology originate in pre-sapiens archaic Eurasians? Hopefully someone's studying DNA from these crania as we speak.

Science 03 Mar 2017: Vol. 355, Issue 6328, pp. 969-972 DOI: 10.1126/science.aal2482

Late Pleistocene archaic human crania from Xuchang, China 

Zhan-Yang Li et al.

Two early Late Pleistocene (~105,000- to 125,000-year-old) crania from Lingjing, Xuchang, China, exhibit a morphological mosaic with differences from and similarities to their western contemporaries. They share pan–Old World trends in encephalization and in supraorbital, neurocranial vault, and nuchal gracilization. They reflect eastern Eurasian ancestry in having low, sagittally flat, and inferiorly broad neurocrania. They share occipital (suprainiac and nuchal torus) and temporal labyrinthine (semicircular canal) morphology with the Neandertals. This morphological combination reflects Pleistocene human evolutionary patterns in general biology, as well as both regional continuity and interregional population dynamics.

Link

Analytical thinking does not decrease religious belief

It seems to me that psychology would benefit from taking a break from publishing new findings and clean house of all the junk that has accumulated over the years. Junk breeds junk, and if left unchecked can generate entire unwholesome disciplines (as the sad state of the social sciences proves to us daily).

Related:

• Excess Success for Psychology Articles in the Journal Science

PLoS ONE 12(2): e0172636. doi:10.1371/journal.pone.0172636

Direct replication of Gervais & Norenzayan (2012): No evidence that analytic thinking decreases religious belief

Clinton Sanchez, Brian Sundermeier, Kenneth Gray, Robert J. Calin-Jageman

Gervais & Norenzayan (2012) reported in Science a series of 4 experiments in which manipulations intended to foster analytic thinking decreased religious belief. We conducted a precise, large, multi-site pre-registered replication of one of these experiments. We observed little to no effect of the experimental manipulation on religious belief (d = 0.07 in the wrong direction, 95% CI[-0.12, 0.25], N = 941). The original finding does not seem to provide reliable or valid evidence that analytic thinking causes a decrease in religious belief.

Link

Microagressions, debunked

A warning against taking politically-inspired gobbledygook (whose only benefit is to bureaucrats and as a means of virtue signalling by do-gooders) seriously.

Perspectives on Psychological Science Vol 12, Issue 1, 2017

Microaggressions Strong Claims, Inadequate Evidence

Scott O. Lilienfeld

The microaggression concept has recently galvanized public discussion and spread to numerous college campuses and businesses. I argue that the microaggression research program (MRP) rests on five core premises, namely, that microaggressions (1) are operationalized with sufficient clarity and consensus to afford rigorous scientific investigation; (2) are interpreted negatively by most or all minority group members; (3) reflect implicitly prejudicial and implicitly aggressive motives; (4) can be validly assessed using only respondents’ subjective reports; and (5) exert an adverse impact on recipients’ mental health. A review of the literature reveals negligible support for all five suppositions. More broadly, the MRP has been marked by an absence of connectivity to key domains of psychological science, including psychometrics, social cognition, cognitive-behavioral therapy, behavior genetics, and personality, health, and industrial-organizational psychology. Although the MRP has been fruitful in drawing the field’s attention to subtle forms of prejudice, it is far too underdeveloped on the conceptual and methodological fronts to warrant real-world application. I conclude with 18 suggestions for advancing the scientific status of the MRP, recommend abandonment of the term “microaggression,” and call for a moratorium on microaggression training programs and publicly distributed microaggression lists pending research to address the MRP’s scientific limitations.

Link

Dysgenic trend in educational attainment in Iceland

This is a very important study which (if replicated in other countries, with more complex demography, less complete genealogy, but much larger sample sizes) bodes ill for the future. It should also prompt studies of the evolution of cognitive ability at longer time scales (beyond traditional genealogy). Much has been written about genetic differences between the human races, for example, with the "cold winters" theory proposed to explain them as a product of natural selection.

But, this assumes that these differences are long-standing and date to the time that modern humans left Africa for more northern (and colder) latitudes. There is good reason to doubt this explanation: ancient writers of the Mediterranean classical world predictably identified themselves as the optimum, but remarked on the spiritedness and dullness of northerners in contrast to the lack of spirit but intelligence of southerners, which seemingly contradicts present-day cognitive ability distributions. But, it may very well be that cognitive ability has changed dramatically over this time period; certainly the fact that one of its correlates (educational attainment) can change in a small isolated population (Icelanders) over a century does not add to one's confidence that this is a trait that has been stable for millennia (let alone since the time of harsh Ice Age winters). As more markers are discovered to predict cognitive ability in human populations and it becomes easier to study ancient ones, it might be possible to track this trait convincingly.

On the positive side, the pliability of the genetic influences on cognition undercuts arguments that possible differences in this trait among human races and ethnic groups are solidly entrenched and unalterable,. Rather they may be accidents of recent evolution which could, in principle, be reversed.


PNAS doi: 10.1073/pnas.1612113114

Selection against variants in the genome associated with educational attainment

Augustine Kong et al.

Epidemiological and genetic association studies show that genetics play an important role in the attainment of education. Here, we investigate the effect of this genetic component on the reproductive history of 109,120 Icelanders and the consequent impact on the gene pool over time. We show that an educational attainment polygenic score, POLYEDU, constructed from results of a recent study is associated with delayed reproduction (P less than 10−100) and fewer children overall. The effect is stronger for women and remains highly significant after adjusting for educational attainment. Based on 129,808 Icelanders born between 1910 and 1990, we find that the average POLYEDU has been declining at a rate of ∼0.010 standard units per decade, which is substantial on an evolutionary timescale. Most importantly, because POLYEDU only captures a fraction of the overall underlying genetic component the latter could be declining at a rate that is two to three times faster.

Link

Happy New Year 2017

Last year I wished for ancient East Asian DNA and I didn't get my wish. So, I repeat my wish for this year as well.