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.

Link

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.

Link

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.

Link

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.

Link

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.

Link

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.

Link

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.

Link

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.

Link

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.

Link

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.

Link

Mungo Man DNA revisited + first ancient mtDNA from Australia

The authors find that previously published mtDNA from earliest Australians was contamination, and one S2 mtDNA haplogroup in an undated sample of likely Holocene origin.

PNAS doi: 10.1073/pnas.1521066113

Ancient mtDNA sequences from the First Australians revisited

Tim H. Heupink et al.

The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537–542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the “Out of Africa” model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.

Link

May 28, 2016

British Celts have more steppe ancestry than British English

An interesting tidbit in a preprint about blood pressure genes:
We consistently obtained significantly positive f4 statistics, implying that both the modern Celtic samples and the ancient Saxon samples have more Steppe ancestry than the modern Anglo-Saxon samples from southern and eastern England. This indicates that southern and eastern England is not exclusively a genetic mix of Celts and Saxons.
Southeastern England is genetically very homogeneous. If the people there were a mix of ancient Celts and Saxons you'd expect them to be intermediate between modern Celts (who should have more Celtic ancestry than the modern English) and ancient Saxons (who should have more Saxon ancestry than the modern English).

But, it seems that the English have less steppe ancestry than both modern Celts and ancient Saxons, so they're not really intermediate. My guess is that the English have Norman ancestry that the Celts don't. While the original Normans were Scandinavians with presumably lots of steppe ancestry, I'd be surprised if the post-1066 Normans that settled England were not already heavily admixed with the "French" and so had less steppe ancestry than the modern British Celts from Wales and Scotland.

bioRxiv http://dx.doi.org/10.1101/055855

Population structure of UK Biobank and ancient Eurasians reveals adaptation at genes influencing blood pressure

Kevin Galinsky et al.

Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for detecting selection using population differentiation, and enables an analysis of UK population structure at fine resolution. In analyses of 113,851 UK Biobank samples, population structure in the UK is dominated by 5 principal components (PCs) spanning 6 clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses with ancient Eurasians show that populations in the northern UK have higher levels of Steppe ancestry, and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along top PCs identified a genome-wide significant signal of selection at the coding variant rs601338 in FUT2 (p=9.16×10-9). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified new genome-wide significant (p less than 5×10-8) signals of recent selection at two additional loci: CYP1A2/CSK and F12. We detected strong associations to diastolic blood pressure in the UK Biobank for the variants with new selection signals at CYP1A2/CSK (p=1.10×10-19)) and for variants with ancient Eurasian selection signals in the ATXN2/SH2B3 locus (p=8.00×10-33), implicating recent adaptation related to blood pressure.

Link

May 27, 2016

The great migration of African Americans

PLoS Genet 12(5): e1006059. doi:10.1371/journal.pgen.1006059

The Great Migration and African-American Genomic Diversity
Soheil Baharian et al.

We present a comprehensive assessment of genomic diversity in the African-American population by studying three genotyped cohorts comprising 3,726 African-Americans from across the United States that provide a representative description of the population across all US states and socioeconomic status. An estimated 82.1% of ancestors to African-Americans lived in Africa prior to the advent of transatlantic travel, 16.7% in Europe, and 1.2% in the Americas, with increased African ancestry in the southern United States compared to the North and West. Combining demographic models of ancestry and those of relatedness suggests that admixture occurred predominantly in the South prior to the Civil War and that ancestry-biased migration is responsible for regional differences in ancestry. We find that recent migrations also caused a strong increase in genetic relatedness among geographically distant African-Americans. Long-range relatedness among African-Americans and between African-Americans and European-Americans thus track north- and west-bound migration routes followed during the Great Migration of the twentieth century. By contrast, short-range relatedness patterns suggest comparable mobility of ∼15–16km per generation for African-Americans and European-Americans, as estimated using a novel analytical model of isolation-by-distance.

Link

May 19, 2016

35,000 year old mtDNA haplogroup U6 from Romania

I wouldn't be very surprised if many of the markers supposedly signifying recent gene flow Africa and Eurasia were actually quite old in Eurasia. The trouble is that reports of such gene flow were often based on simply observing that marker "X" occurs at a higher frequency in Africa than in Eurasia, so a common sense explanation is that it reflects limited recent gene flow between the continents. But, it is now known that common sense is not always the best guide, as e.g., ancient Europeans had mtDNA haplogroup M (in the past considered evidence of Asian admixture), Y-chromosome haplogroup C (ditto), and now U6.

The same should also apply to the Middle East where there has been admixture with Africans since the Islamic period at least. The existence of such admixture does not mean that every single lineage that occurs at low frequency in the Middle East and high frequency in Africa is diagnostic of this later period of admixture. Some of them could well be relics of old Middle Eastern populations. Who knows what people inhabited the presently inhospitable landscape of the Saharan-Arabian desert zone? The living populations can certainly make no claim to being the first ones there, but the genetic heritage of those earlier occupants may still persist in them in traces.

Similarly for the New World; in that case, there is a better case that European-looking lineages are indeed due to the colonization of the Americas over the last five centuries. However, that does not mean that all of them are, and we should be mindful of the possibility of pre-Columbian contact between the Old and New worlds.

Scientific Reports 6, Article number: 25501 (2016)

The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa

M. Hervella et al.

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

Link