May 04, 2015

Ancient mtDNA from Neolithic France

PLoS ONE 10(4): e0125521. doi:10.1371/journal.pone.0125521

When the Waves of European Neolithization Met: First Paleogenetic Evidence from Early Farmers in the Southern Paris Basin

Maïté Rivollat et al.

An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.


Facial reconstruction of Lord of Moken

I wonder when we will start seeing facial reconstructions that make use of ancient DNA. Ancient DNA isn't very good for reconstructing facial features, but it should be quite good at reconstructing pigmentation.

Facial reconstruction for 1,400-year-old 'Lord of Morken'
The man's remains were discovered in 1955 in a Franconian burial ground in Morken, near Cologne. He had been interred around the year 600 AD in a royal burial chamber there. The precious goods within the grave, especially the materials used for his weapons, suggest that the man enjoyed a special status in the population, Elke Nieveler a specialist for the early Middle Ages at the Rheinisches Landesmuseum said.

May 03, 2015

Modern humans, not Neandertals made the Proto-Aurignacian

Science DOI: 10.1126/science.aaa2773

The makers of the Protoaurignacian and implications for Neandertal extinction

S. Benazzi et al.

The Protoaurignacian culture is pivotal to the debate about the timing of the arrival of modern humans in Western Europe and the demise of Neandertals. However, which group is responsible for this culture remains uncertain. We investigated dental remains associated with the Protoaurignacian. The lower deciduous incisor from Riparo Bombrini is modern human, based on its morphology. The upper deciduous incisor from Grotta di Fumane contains ancient mitochondrial DNA of a modern human type. These teeth are the oldest human remains in an Aurignacian-related archeological context, confirming that by 41,000 calendar years before the present, modern humans bearing Protoaurignacian culture spread into Southern Europe. Because the last Neandertals date to 41,030 to 39,260 calendar years before the present, we suggest that the Protoaurignacian triggered the demise of Neandertals in this area.


Structure of Y-haplogroup N

arXiv:1504.06463 [q-bio.PE]

The dichotomy structure of Y chromosome Haplogroup N

Kang Hu et al.

Haplogroup N-M231 of human Y chromosome is a common clade from Eastern Asia to Northern Europe, being one of the most frequent haplogroups in Altaic and Uralic-speaking populations. Using newly discovered bi-allelic markers from high-throughput DNA sequencing, we largely improved the phylogeny of Haplogroup N, in which 16 subclades could be identified by 33 SNPs. More than 400 males belonging to Haplogroup N in 34 populations in China were successfully genotyped, and populations in Northern Asia and Eastern Europe were also compared together. We found that all the N samples were typed as inside either clade N1-F1206 (including former N1a-M128, N1b-P43 and N1c-M46 clades), most of which were found in Altaic, Uralic, Russian and Chinese-speaking populations, or N2-F2930, common in Tibeto-Burman and Chinese-speaking populations. Our detailed results suggest that Haplogroup N developed in the region of China since the final stage of late Paleolithic Era.


Southern origins and recent admixture of Siberian populations


The complex admixture history and recent southern origins of Siberian populations

Irina Pugach , Rostislav Matveev , Viktor Spitsyn , Sergey Makarov , Innokentiy Novgorodov , Vladimir Osakovsky , Mark Stoneking , Brigitte Pakendorf

Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether this area remained habitable during the extremely cold period of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with a recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, since commonly used methods assume a tree-like population history and at most single admixture events. We therefore developed a new method based on the covariance of ancestry components, which we validated with simulated data, in order to investigate this potentially complex admixture history and to distinguish the effects of shared ancestry from prehistoric migrations and contact. We furthermore adapted a previously devised method of admixture dating for use with multiple events of gene flow, and applied these methods to whole-genome genotype data from over 500 individuals belonging to 20 different Siberian ethnolinguistic groups. The results of these analyses indicate that there have indeed been multiple layers of admixture detectable in most of the Siberian populations, with considerable differences in the admixture histories of individual populations, and with the earliest events dated to not more than 4500 years ago. Furthermore, most of the populations of Siberia included here, even those settled far to the north, can be shown to have a southern origin. These results provide support for a recent population replacement in this region, with the northward expansions of different populations possibly being driven partly by the advent of pastoralism, especially reindeer domestication. These newly developed methods to analyse multiple admixture events should aid in the investigation of similarly complex population histories elsewhere.


Eye color and alcohol dependence

American Journal of Medical Genetics Part B: Neuropsychiatric Genetics DOI: 10.1002/ajmg.b.32316

Eye color: A potential indicator of alcohol dependence risk in European Americans

Arvis Sulovari et al.

In archival samples of European-ancestry subjects, light-eyed individuals have been found to consume more alcohol than dark-eyed individuals. No published population-based studies have directly tested the association between alcohol dependence (AD) and eye color. We hypothesized that light-eyed individuals have a higher prevalence of AD than dark-eyed individuals. A mixture model was used to select a homogeneous sample of 1,263 European-Americans and control for population stratification. After quality control, we conducted an association study using logistic regression, adjusting for confounders (age, sex, and genetic ancestry). We found evidence of association between AD and blue eye color (P = 0.0005 and odds ratio = 1.83 (1.31–2.57)), supporting light eye color as a risk factor relative to brown eye color. Network-based analyses revealed a statistically significant (P = 0.02) number of genetic interactions between eye color genes and AD-associated genes. We found evidence of linkage disequilibrium between an AD-associated GABA receptor gene cluster, GABRB3/GABRG3, and eye color genes, OCA2/HERC2, as well as between AD-associated GRM5 and pigmentation-associated TYR. Our population-phenotype, network, and linkage disequilibrium analyses support association between blue eye color and AD. Although we controlled for stratification we cannot exclude underlying occult stratification as a contributor to this observation. Although replication is needed, our findings suggest that eye pigmentation information may be useful in research on AD. Further characterization of this association may unravel new AD etiological factors. © 2015 Wiley Periodicals, Inc.


April 30, 2015

Kalash origins

This is an open access paper.


The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection

Qasim Ayub et al.

The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon's invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.


April 21, 2015

PCA and natural selection

arXiv:1504.04543 [q-bio.PE]

Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data

Nicolas Duforet-Frebourg et al.

(Submitted on 8 Apr 2015)

Large-scale genomic data offers the perspective to decipher the genetic architecture of natural selection. To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis. We show that the common Fst index of genetic differentiation between populations can be viewed as a proportion of variance explained by the principal components. Looking at the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) after removal of recently admixed individuals resulting in 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3X). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and non-coding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). PCA-based statistics retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially in non-model species for which defining populations can be difficult. Genome scan based on PCA is implemented in the open-source and freely available PCAdapt software.



Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia

Kevin J Galinsky et al.

Principal components analysis (PCA) is a widely used tool for inferring population structure and correcting confounding in genetic data. We introduce a new algorithm, FastPCA, that leverages recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using a new test for natural selection based on population differentiation along these PCs, we replicate previously known selected loci and identify three new signals of selection, including selection in Europeans at the ADH1B gene. The coding variant rs1229984 has previously been associated to alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents.


April 19, 2015

mtDNA of Alaskan Eskimos

AJPA DOI: 10.1002/ajpa.22750

Mitochondrial diversity of Iñupiat people from the Alaskan North Slope provides evidence for the origins of the Paleo- and Neo-Eskimo peoples 

Jennifer A. Raff et al.



All modern Iñupiaq speakers share a common origin, the result of a recent (∼800 YBP) and rapid trans-Arctic migration by the Neo-Eskimo Thule, who replaced the previous Paleo-Eskimo inhabitants of the region. Reduced mitochondrial haplogroup diversity in the eastern Arctic supports the archaeological hypothesis that the migration occurred in an eastward direction. We tested the hypothesis that the Alaskan North Slope served as the origin of the Neo- and Paleo-Eskimo populations further east.

Materials and Methods:

We sequenced HVR I and HVR II of the mitochondrial D-loop from 151 individuals in eight Alaska North Slope communities, and compared genetic diversity and phylogenetic relationships between the North Slope Inupiat and other Arctic populations from Siberia, the Aleutian Islands, Canada, and Greenland.


Mitochondrial lineages from the North Slope villages had a low frequency (2%) of non-Arctic maternal admixture, and all haplogroups (A2, A2a, A2b, D2a, and D4b1a–formerly known as D3) found in previously sequenced Neo- and Paleo-Eskimos and living Inuit and Eskimo peoples from across the North American Arctic. Lineages basal for each haplogroup were present in the North Slope. We also found the first occurrence of two haplogroups in contemporary North American Arctic populations: D2a, previously identified only in Aleuts and Paleo-Eskimos, and the pan-American C4.


Our results yield insight into the maternal population history of the Alaskan North Slope and support the hypothesis that this region served as an ancestral pool for eastward movements to Canada and Greenland, for both the Paleo-Eskimo and Neo-Eskimo populations


April 13, 2015

Haplogroup G1, Y-chromosome mutation rate and migrations of Iranic speakers

The origin of Iranian speakers is a big puzzle as in ancient times there were two quite different groups of such speakers: nomadic steppe people such as Scythians and settled farmers such as Persians and Medes.

I am guessing that the story of Iranian origins will only be solved in correlation to their Indo-Aryan brethren and their more distant Indo-European relations.

Clearly, G1 cannot be Proto-Indo-European as it has a rather limited distribution in Eurasia, but it could very well have been a marker of a subset of Indo-Europeans. If it was present in ancestral Iranians, then this would geographically constrain the places where ancestral Iranians were formed.

PLoS ONE 10(4): e0122968. doi:10.1371/journal.pone.0122968

Deep Phylogenetic Analysis of Haplogroup G1 Provides Estimates of SNP and STR Mutation Rates on the Human Y-Chromosome and Reveals Migrations of Iranic Speakers

Oleg Balanovsky et al.

Y-chromosomal haplogroup G1 is a minor component of the overall gene pool of South-West and Central Asia but reaches up to 80% frequency in some populations scattered within this area. We have genotyped the G1-defining marker M285 in 27 Eurasian populations (n= 5,346), analyzed 367 M285-positive samples using 17 Y-STRs, and sequenced ~11 Mb of the Y-chromosome in 20 of these samples to an average coverage of 67X. This allowed detailed phylogenetic reconstruction. We identified five branches, all with high geographical specificity: G1-L1323 in Kazakhs, the closely related G1-GG1 in Mongols, G1-GG265 in Armenians and its distant brother clade G1-GG162 in Bashkirs, and G1-GG362 in West Indians. The haplotype diversity, which decreased from West Iran to Central Asia, allows us to hypothesize that this rare haplogroup could have been carried by the expansion of Iranic speakers northwards to the Eurasian steppe and via founder effects became a predominant genetic component of some populations, including the Argyn tribe of the Kazakhs. The remarkable agreement between genetic and genealogical trees of Argyns allowed us to calibrate the molecular clock using a historical date (1405 AD) of the most recent common genealogical ancestor. The mutation rate for Y-chromosomal sequence data obtained was 0.78×10-9 per bp per year, falling within the range of published rates. The mutation rate for Y-chromosomal STRs was 0.0022 per locus per generation, very close to the so-called genealogical rate. The “clan-based” approach to estimating the mutation rate provides a third, middle way between direct farther-to-son comparisons and using archeologically known migrations, whose dates are subject to revision and of uncertain relationship to genetic events.


Neandertal flutes debunked

Royal Society Open Science DOI: 10.1098/rsos.140022

‘Neanderthal bone flutes’: simply products of Ice Age spotted hyena scavenging activities on cave bear cubs in European cave bear dens

Cajus G. Diedrich

Punctured extinct cave bear femora were misidentified in southeastern Europe (Hungary/Slovenia) as ‘Palaeolithic bone flutes’ and the ‘oldest Neanderthal instruments’. These are not instruments, nor human made, but products of the most important cave bear scavengers of Europe, hyenas. Late Middle to Late Pleistocene (Mousterian to Gravettian) Ice Age spotted hyenas of Europe occupied mainly cave entrances as dens (communal/cub raising den types), but went deeper for scavenging into cave bear dens, or used in a few cases branches/diagonal shafts (i.e. prey storage den type). In most of those dens, about 20% of adult to 80% of bear cub remains have large carnivore damage. Hyenas left bones in repeating similar tooth mark and crush damage stages, demonstrating a butchering/bone cracking strategy. The femora of subadult cave bears are intermediate in damage patterns, compared to the adult ones, which were fully crushed to pieces. Hyenas produced round–oval puncture marks in cub femora only by the bone-crushing premolar teeth of both upper and lower jaw. The punctures/tooth impact marks are often present on both sides of the shaft of cave bear cub femora and are simply a result of non-breakage of the slightly calcified shaft compacta. All stages of femur puncturing to crushing are demonstrated herein, especially on a large cave bear population from a German cave bear den.


April 05, 2015

Biology of Genomes titles

have been announced. A sample of interest is below:

  • Population structure in African-Americans
  • Contrasting patterns in the high-resolution variation of uniparental markers in European populations highlight very recent male-specific expansions
  • Is Sanger sequencing still a gold standard?
  • The time and place of European gene flow into Ashkenazi Jews
  • 65,222 whole genome haplotypes from the Haplotype Reference Consortium and efficient algorithms to use them
  • The expansion of human populations out of Africa might have led to the progressive build-up of a recessive mutation load
  • An early modern human with a recent Neandertal ancestor
  • Great ape Y chromosome diversity reflects social structure and sex-biased behaviours
  • Theoretical analysis indicates human genome is not a blueprint but a storage of genes, and human oocytes have an instruction
  • Modeling population size changes leads to accurate inference of sex-biased demographic events
  • Exploring population structure through large pedigrees
  • Better, faster, stronger—Mixed models and PCA in the year 2015
  • Denisovan ancestry in East Eurasian and Native American populations
  • Measuring the rate and heritability of aging in Sardinians using pattern recognition
  • Dog diversity is shaped by a Central Asian origin followed by geographical isolation and admixture
  • Comparative analysis of the Y chromosome genomes of greater apes
  • Genomic analysis of ‘Paleoamerican relicts’ reveals close ancestry with Native Americans
  • Analysis of genetic history of Siberian and Northeastern European populations

April 04, 2015

In search of the source of Denisovan ancestry


Denisovan Ancestry in East Eurasian and Native American Populations.

Pengfei Qin , Mark Stoneking

Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide SNP data from 2493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.


March 30, 2015

Ice age Europeans on the brink of extinction

Ice-age Europeans roamed in small bands of fewer than 30, on brink of extinction (Horizon magazine)
In some cases, small bands of potentially as few as 20 to 30 people could have been moving over very large areas, over the whole of Europe as a single territory, according to Professor Ron Pinhasi, principal investigator on the EU-funded ADNABIOARC project.

This demographic model is based on new evidence that suggests populations were much smaller than is generally thought to be a stable size for healthy reproduction, usually around 500 people. Such small groupings may have led to reduced fitness and even extinctions.

‘As an archaeologist and anthropologist, I was quite shocked to see how limited, how small the population numbers were. You know, shockingly small,’ said Prof. Pinhasi, based at University College Dublin, Ireland.


Prof. Pinhasi’s team has found that the genomes sequenced from hunter-gatherers from Hungary and Switzerland between 14 000 to 7 500 years ago are very close to specimens from Denmark or Sweden from the same period.

These findings suggest that genetic diversity between inhabitants of most of western and central Europe after the ice age was very limited, indicating a major demographic bottleneck triggered by human isolation and extinction during the ice age.

‘We’re starting to be able to reconstruct the actual dynamics of migrations and colonisation of the continent by modern humans and that’s never been done before the genomic era,’ explained Prof. Pinhasi.

He believes that early humans crossed the continent in small groups that were cut off while the ice was at its peak, then successively dispersed and regrouped over thousands of years, with dwindling northern populations invigorated by humans arriving from the south, where the climate was better.

‘You see a real reduction in population numbers and diversity, so you see the few lineages that probably split or separated before the ice age, and then stayed isolated during the ice age,’ he said. ‘Some time after the ice age, they kind of re-emerge, or disperse, and get together, as we see new contributions to European lineages from Asia and in particular the Near East.’
The last couple of statements are interesting because they hint at post-glacial recolonization of Europe after the Ice Age. So far, we are in the dark about what happened in Europe between the time of Kostenki and 8kya. Hopefully another interesting study is on its way to throw some light into the lattter part of this time interval.

March 28, 2015

Afanasievo, Okunev, Andronovo, Sintashta DNA?

A reader alerts me to this article in Russian, but you can use Google Translate to get the gist of it. Some interesting bits (note that "pit"=Yamna):
I can not ignore the question I now have is particularly exciting - the origin of the Indo-Europeans. Community Indo-Europeists animatedly discussing just appeared as a preprint work of David Raika and his colleagues discovered by studying the genomes of people Neolithic and Bronze Age that a decisive influence on the genetic landscape of Europe has had a migration of people pit culture to the north and west in the middle of the III millennium. BC .e. As a result, according to geneticists, there was a population associated with the Corded Ware culture, and from it are the origin of the later Indo-European. By the same conclusions about the same time came the other team's leading geneticists led by Eske Villerslevom.

A steppe, we thought had long been a special world, and differs sharply from the Middle East, and from the European. Migration from there - so it seemed - were mainly directed not to the west and to the east, along the steppes, in the direction of Central Asia, which the ancient Indo-Europeans, Afanasiev media culture (descendants of the people of the pit culture or their ancestors steppe) reached no later turn IV- III millennium BC. It is now confirmed and the group Villersleva.

By the way, it also happens that paleoanthropologists prompted geneticists way of research - and turned out to be right. As it happens, for example, with native Okunevskaya culture of South Siberia. When 20 years ago, we found that craniologically (by a combination of traditional measurement and we proposed new informative features of the structure of the cranial sutures and holes) okunevtsy - "cousins" of American Indians, few believed us. Firstly, in okunevtsah ever seen Caucasoid-Mongoloid Métis like the Kazakhs, and secondly, the ancestors of the Indians withdrew from Siberia to the New World at least 10 thousand. Before the Yenisey there Okunevskaya culture.

Eske Willerslev Now and his colleagues have fully confirmed our conclusion. They confirmed the close relationship between the carriers and the pit Afanasiev cultures and migration ancestors sintashtintsev and Andronov from Europe in the Urals and further to Siberia - but this is already a long time, few archaeologists and anthropologists doubted.
I hope more details will appear soon on what promises to be a very interesting new study. The author seems to be referring to his theory of a relationship between Okunev and Amerindians, and I'm wondering if this is simply "Ancient North Eurasian" ancestry or an even more specific link. Any Russian readers who can dig up more information are invited to post in the comments.