February 25, 2017

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).


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.


January 18, 2017

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.


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.


January 01, 2017

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.

August 06, 2016

China's Great Flood and the rise of the Xia dynasty

From a related story: Massive flood may have led to China's earliest empire:
Many cultures trace their origins to the hazy horizon where history meets legend. In China's case, that blurry line occurs sometime between 2200 B.C.E. and 2000 B.C.E., when a legendary hero named Yu tamed Yellow River flooding and earned a mandate to become the founding emperor of the Xia dynasty, the country's first. That’s the story according to texts written long after the fact, and many Chinese believe their civilization started with emperor Yu. But archaeologists have been unable to find convincing evidence for either the flood or the Xia dynasty itself. 
The massive flood “provides us with a tantalizing hint that the Xia dynasty might really have existed," says David Cohen, an archaeologist and co-author at National Taiwan University in Taipei. The devastating flood could have inundated settlements even a thousand or more kilometers downstream, he says, and created chaos from which a new political order emerged. This sequence of events neatly fits the legend of Yu controlling the flooding by dredging channels to confine the Yellow River and its tributaries. This feat, the ancient texts say, allowed him to claim a mandate as the first emperor of the Xia dynasty.  
The timing is curiously coincidental. Around 1900 B.C.E., Cohen says, Chinese society was transitioning from the Neolithic to the Bronze age. The date also correlates with what is called the Erlitou culture, which is known from palace buildings and bronze smelting workshops discovered near Zhengzhou, about 2500 kilometers downstream from Jishi Gorge. Many scholars have argued that Erlitou is a manifestation of the elusive Xia dynasty, but a link is not firmly established.

Science 05 Aug 2016: Vol. 353, Issue 6299, pp. 579-582 DOI: 10.1126/science.aaf0842

Outburst flood at 1920 BCE supports historicity of China’s Great Flood and the Xia dynasty

Qinglong Wu

China’s historiographical traditions tell of the successful control of a Great Flood leading to the establishment of the Xia dynasty and the beginning of civilization. However, the historicity of the flood and Xia remain controversial. Here, we reconstruct an earthquake-induced landslide dam outburst flood on the Yellow River about 1920 BCE that ranks as one of the largest freshwater floods of the Holocene and could account for the Great Flood. This would place the beginning of Xia at ~1900 BCE, several centuries later than traditionally thought. This date coincides with the major transition from the Neolithic to Bronze Age in the Yellow River valley and supports hypotheses that the primary state-level society of the Erlitou culture is an archaeological manifestation of the Xia dynasty.


July 19, 2016

Educational achievement predicted by DNA

Predicting 9% of educational achievement from DNA is quite good. The authors used genotype arrays, so there's obvious room for growth in rare variation that is not covered by such arrays.

I wonder when the public and policymakers will get wind of the fact that educational achievement is highly heritable and can even be somewhat predicted with existing DNA technology.

Genetic egalitarianism is an edifice on which too much has been invested and I doubt that it will go down without a fight. It's of course a great idea to optimize learning for the students you've got. But, at the end of the day there's only so much you can do to foster achievement in a trait that is mostly genetically determined.

Molecular Psychiatry advance online publication 19 July 2016; doi: 10.1038/mp.2016.107

Predicting educational achievement from DNA

S Selzam et al.

A genome-wide polygenic score (GPS), derived from a 2013 genome-wide association study (N=127,000), explained 2% of the variance in total years of education (EduYears). In a follow-up study (N=329,000), a new EduYears GPS explains up to 4%. Here, we tested the association between this latest EduYears GPS and educational achievement scores at ages 7, 12 and 16 in an independent sample of 5825 UK individuals. We found that EduYears GPS explained greater amounts of variance in educational achievement over time, up to 9% at age 16, accounting for 15% of the heritable variance. This is the strongest GPS prediction to date for quantitative behavioral traits. Individuals in the highest and lowest GPS septiles differed by a whole school grade at age 16. Furthermore, EduYears GPS was associated with general cognitive ability (~3.5%) and family socioeconomic status (~7%). There was no evidence of an interaction between EduYears GPS and family socioeconomic status on educational achievement or on general cognitive ability. These results are a harbinger of future widespread use of GPS to predict genetic risk and resilience in the social and behavioral sciences.


July 11, 2016

Y-chromosome haplogroup N phylogeny resolved

AJHG Volume 99, Issue 1, p163–173, 7 July 2016

Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

Anne-Mai Ilumäe et al.

The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3’6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.


June 27, 2016

37,000 year old skull from Malaysia related to indigenous people of Borneo

Front. Ecol. Evol., 27 June 2016 | http://dx.doi.org/10.3389/fevo.2016.00075

Deep Skull from Niah Cave and the Pleistocene Peopling of Southeast Asia

Darren Curnoe et al.

The Deep Skull from Niah Cave in Sarawak (Malaysia) is the oldest anatomically modern human recovered from island Southeast Asia. For more than 50 years its relevance to tracing the prehistory of the region has been controversial. The most widely held view, originating with Brothwell's 1960 description and analysis, is that the Niah individual is related to Indigenous Australians. Here we undertake a new assessment of the Deep Skull and consider its bearing on this question. In doing so, we provide a new and comprehensive description of the cranium including a reassessment of its ontogenetic age, sex, morphology, and affinities. We conclude that this individual was most likely to have been of advanced age and female, rather than an adolescent male as originally proposed. The morphological evidence strongly suggests that the Deep Skull samples the earliest modern humans to have settled Borneo, most likely originating on mainland East Asia. We also show that the affinities of the specimen are most likely to be with the contemporary indigenous people of Borneo, although, similarities to the population sometimes referred to as Philippine Negritos cannot be excluded. Finally, our research suggests that the widely supported “two-layer” hypothesis for the Pleistocene peopling of East/Southeast Asia is unlikely to apply to the earliest inhabitants of Borneo, in-line with the picture emerging from genetic studies of the contemporary people from the region.


June 24, 2016

Population history with physically phased genomes

bioRxiv doi: http://dx.doi.org/10.1101/008367

Modeling human population separation history using physically phased genomes

Shiya Song, Elzbieta Sliwerska, Sarah Emery, Jeffrey M Kidd

Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Massai and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati and CEPH European populations and analyzed population size and separation history using the Pairwise Sequentially Markovian Coalescent (PSMC) and Multiple Sequentially Markovian Coalescent (MSMC) models. We find that statistically phased haplotypes yield an earlier split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation (ABC) approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard Isolation-with-Migration model. We inferred that the separation between hunter-gather populations and other populations happened around 120,000 to 140,000 years ago with gene flow continuing until 30,000 to 40,000 years ago; separation between west African and out of African populations happened around 70,000 to 80,000 years ago, while the separation between Massai and out of African populations happened around 50,000 years ago.


June 21, 2016

Panorama of African admixture

I remember how in the early days of online discussions of anthropology a constant topic of contention was whether African variation was the result of admixture, some of it within Africa, some of it from Caucasoids, or whether it was the result of climatic adaptation manifested in gradual clines (as opposed to clusters corresponding to physical types).

Well, I won't dismiss the role of climate altogether, but it's hard to argue for it much anymore now that we know that the two big fish in the African ocean of human diversity were the spread of Niger-Congo languages (from the west), and of Caucasoids (from the east) over the last few thousands of years, with a healthy seasoning of minor admixtures before and after. Once again it seems that old-style anthropology was right and the more fashionable and trendy attempts to dismiss it as "typology", "imposition of European colonialism through science" and the like were wrong.

eLife 2016;5:e15266

Admixture into and within sub-Saharan Africa

George BJ Busby et al.

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.


June 08, 2016

700 thousand year old ancestors of H. floresiensis

Nature 534, 245–248 (09 June 2016) doi:10.1038/nature17999

Homo floresiensis-like fossils from the early Middle Pleistocene of Flores

Gerrit D. van den Bergh, Yousuke Kaifu, Iwan Kurniawan, Reiko T. Kono, Adam Brumm, Erick Setiyabudi, Fachroel Aziz & Michael J. Morwood

The evolutionary origin of Homo floresiensis, a diminutive hominin species previously known only by skeletal remains from Liang Bua in western Flores, Indonesia, has been intensively debated. It is a matter of controversy whether this primitive form, dated to the Late Pleistocene, evolved from early Asian Homo erectus and represents a unique and striking case of evolutionary reversal in hominin body and brain size within an insular environment1, 2, 3, 4. The alternative hypothesis is that H. floresiensis derived from an older, smaller-brained member of our genus, such as Homo habilis, or perhaps even late Australopithecus, signalling a hitherto undocumented dispersal of hominins from Africa into eastern Asia by two million years ago (2 Ma)5, 6. Here we describe hominin fossils excavated in 2014 from an early Middle Pleistocene site (Mata Menge) in the So’a Basin of central Flores. These specimens comprise a mandible fragment and six isolated teeth belonging to at least three small-jawed and small-toothed individuals. Dating to ~0.7 Ma, these fossils now constitute the oldest hominin remains from Flores7. The Mata Menge mandible and teeth are similar in dimensions and morphological characteristics to those of H. floresiensis from Liang Bua. The exception is the mandibular first molar, which retains a more primitive condition. Notably, the Mata Menge mandible and molar are even smaller in size than those of the two existing H. floresiensis individuals from Liang Bua. The Mata Menge fossils are derived compared with Australopithecus and H. habilis, and so tend to support the view that H. floresiensis is a dwarfed descendent of early Asian H. erectus. Our findings suggest that hominins on Flores had acquired extremely small body size and other morphological traits specific to H. floresiensis at an unexpectedly early time.


Nature 534, 249–253 (09 June 2016) doi:10.1038/nature17663

Age and context of the oldest known hominin fossils from Flores

Adam Brumm, Gerrit D. van den Bergh, Michael Storey, Iwan Kurniawan, Brent V. Alloway, Ruly Setiawan, Erick Setiyabudi, Rainer Grün, Mark W. Moore, Dida Yurnaldi, Mika R. Puspaningrum, Unggul P. Wibowo, Halmi Insani, Indra Sutisna, John A. Westgate, Nick J. G. Pearce, Mathieu Duval, Hanneke J. M. Meijer, Fachroel Aziz, Thomas Sutikna, Sander van der Kaars, Stephanie Flude & Michael J. Morwood

Recent excavations at the early Middle Pleistocene site of Mata Menge in the So’a Basin of central Flores, Indonesia, have yielded hominin fossils1 attributed to a population ancestral to Late Pleistocene Homo floresiensis2. Here we describe the age and context of the Mata Menge hominin specimens and associated archaeological findings. The fluvial sandstone layer from which the in situ fossils were excavated in 2014 was deposited in a small valley stream around 700 thousand years ago, as indicated by 40Ar/39Ar and fission track dates on stratigraphically bracketing volcanic ash and pyroclastic density current deposits, in combination with coupled uranium-series and electron spin resonance dating of fossil teeth. Palaeoenvironmental data indicate a relatively dry climate in the So’a Basin during the early Middle Pleistocene, while various lines of evidence suggest the hominins inhabited a savannah-like open grassland habitat with a wetland component. The hominin fossils occur alongside the remains of an insular fauna and a simple stone technology that is markedly similar to that associated with Late Pleistocene H. floresiensis.


June 07, 2016

Neolithic Aegean genomes

I had covered this paper when it went on the bioRxiv, but the final version has been published in PNAS in open access.

PNAS doi: 10.1073/pnas.1523951113

Early farmers from across Europe directly descended from Neolithic Aegeans

Zuzana Hofmanová, Susanne Kreutzer et al.

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.


Ancient DNA and human history

A very useful review of the field c. mid-2016. The only major addition would be the study on Upper Paleolithic Europeans that appeared recently.

The lack of East Asian DNA validates my New Year's wish for some. Hopefully my wish will be granted in the second half of 2016.

PNAS doi: 10.1073/pnas.1524306113

Ancient DNA and human history

Montgomery Slatkin, and Fernando Racimo

We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.