New preprint papers on Finland’s population history and disease, skin pigmentation in Africa, and genetic variation in Thailand hunter-gatherers

finland-genetics

New and interesting research these days in BioRxiv:

Haplotype sharing provides insights into fine-scale population history and disease in Finland, by Martín et al. (2017):

Finland provides unique opportunities to investigate population and medical genomics because of its adoption of unified national electronic health records, detailed historical and birth records, and serial population bottlenecks. We assemble a comprehensive view of recent population history (≤100 generations), the timespan during which most rare disease-causing alleles arose, by comparing pairwise haplotype sharing from 43,254 Finns to geographically and linguistically adjacent countries with different population histories, including 16,060 Swedes, Estonians, Russians, and Hungarians. We find much more extensive sharing in Finns, with at least one ≥ 5 cM tract on average between pairs of unrelated individuals. By coupling haplotype sharing with fine-scale birth records from over 25,000 individuals, we find that while haplotype sharing broadly decays with geographical distance, there are pockets of excess haplotype sharing; individuals from northeast Finland share several-fold more of their genome in identity-by-descent (IBD) segments than individuals from southwest regions containing the major cities of Helsinki and Turku. We estimate recent effective population size changes over time across regions of Finland and find significant differences between the Early and Late Settlement Regions as expected; however, our results indicate more continuous gene flow than previously indicated as Finns migrated towards the northernmost Lapland region. Lastly, we show that haplotype sharing is locally enriched among pairs of individuals sharing rare alleles by an order of magnitude, especially among pairs sharing rare disease causing variants. Our work provides a general framework for using haplotype sharing to reconstruct an integrative view of recent population history and gain insight into the evolutionary origins of rare variants contributing to disease.

finland-migration-haplotype
Migration rates and haplotype sharing within Finland and between neighboring countries. A) Map of regional Finnish, Swedish, and Estonian birthplaces Purple triangle indicates St. Petersburg, Russia. Hungary not shown. 1 Finnish, Swedish, and Estonian region labels are shown in Table S3. B) Principal components analysis (PCA) of unrelated individuals, colored by birth region as shown in A) if available or country otherwise. C-D) Migration rates inferred with EEMS. Values and colors indicate inferred rates, for example with +1 (shades of blue) indicating an order of magnitude more migration at a given point on average, and shades of orange indicating migration barriers. C) Migration rates among municipalities in Finland. D) Migration rates within and between Finland, Sweden, Estonia, and St. Petersburg, Russia. Available under a CC-BY 4.0 International license.

Interesting to understand this paper is the whole research published by the Institute for Molecular Medicine Finland (FIMM): their website contains detailed research on Finland’s recent genetic history.

NOTE: The featured image of this article contains three figures from the FIMM (License CC-BY 4.0). Left: Position of the points represents the locations of 1042 Finnish individuals. By clustering the individuals into two groups based on genome data we see a split between eastern (blue) and western (red) parts. Individuals who show considerable relatedness to both groups have been colored with cyan. Both parents of each individual were born close to each other and based on the parents’ birth years we can infer that we are looking at the genetic structure present in Finland before 1950s. Center: An estimated borderline of the Treaty of Nöteborg on top of the map from the left. The border line is drawn between Jääski (28.92 N, 61.04 E) and Pyhäjoki (24.26 N, 64.46 E). Right: The settlement border divides Finland into the early settlement region (to west and south of the border) and the late settlement region (to east and north of the border) (Jutikkala 1933, s. 91). We see that Southern Savo (in south-eastern part of the early settlement) is among the only parts of the early settlement region that is dominated by the eastern genetic group. Information from Matti Pirinen and Sini Kerminen, 24.5.2017.

An Unexpectedly Complex Architecture for Skin Pigmentation in Africans, by Martin et al (2017):

Fewer than 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed with genetic architecture varying by latitude. We investigate polygenicity in the Khoe and the San, populations indigenous to southern Africa, who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but that known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13 using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand, by Kutanan et al. (2017):

The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non-recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely-related group.

Related:

Iberian Peninsula: Discontinuity in mtDNA between hunter-gatherers and farmers, not so much during the Chalcolithic and EBA

iberia-mtdna

A new preprint paper at BioRxiv, The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age, by Szécsényi-Nagy et al. (2017).

Abstract:

Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focused on the maternal genetic makeup of the Neolithic (~ 5500-3000 BCE), Chalcolithic (~ 3000-2200 BCE) and Early Bronze Age (~ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.

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Iberian mtDNA samples

Detailed conclusions of their work,

The present study, based on 213 new and 125 published mtDNA data of prehistoric Iberian individuals suggests a more complex mode of interaction between local hunter-gatherers and incoming early farmers during the Early and Middle Neolithic of the Iberian Peninsula, as compared to Central Europe. A characteristic of Iberian population dynamics is the proportion of autochthonous hunter-gatherer haplogroups, which increased in relation to the distance to the Mediterranean coast. In contrast, the early farmers in Central Europe showed comparatively little admixture of contemporaneous hunter-gatherer groups. Already during the first centuries of Neolithic transition in Iberia, we observe a mix of female DNA lineages of different origins. Earlier hunter-gatherer haplogroups were found together with a variety of new lineages, which ultimately derive from Near Eastern farming groups. On the other hand, some early Neolithic sites in northeast Iberia, especially the early group from the cave site of Els Trocs in the central Pyrenees, seem to exhibit affinities to Central European LBK communities. The diversity of female lineages in the Iberian communities continued even during the Chalcolithic, when populations became more homogeneous, indicating higher mobility and admixture across different geographic regions. Even though the sample size available for Early Bronze Age populations is still limited, especially with regards to El Argar groups, we observe no significant changes to the mitochondrial DNA pool until the end of our time transect (1500 BCE). The expansion of groups from the eastern steppe, which profoundly impacted Late Neolithic and EBA groups of Central and North Europe, cannot (yet) be seen in the contemporaneous population substrate of the Iberian Peninsula at the present level of genetic resolution. This highlights the distinct character of the Neolithic transition both in the Iberian Peninsula and elsewhere and emphasizes the need for further in depth archaeogenetic studies for reconstructing the close reciprocal relationship of genetic and cultural processes on the population level.

So it seems more and more likely that the North-West Indo-European invasion during the Copper Age (signaled by changes in Y-DNA lineages) was not, as in central Europe, accompanied by much mtDNA turnover. What that means – either a male-dominated invasion, or a longer internal evolution of invasive Y-DNA subclades – remains to bee seen, but I am still more inclined to see the former as the most likely interpretation, in spite of admixture results.

Related:

Featured images: from the article, licensed BY-NC-ND.

Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains

lepenski-vir-mesolithic-anatolia-neolithic

PhD Thesis Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains, by Zuzana Hofmanova (2017) at the University of Mainz.
Abstract:

Palaeogenomic data have illuminated several important periods of human past with surprising im- plications for our understanding of human evolution. One of the major changes in human prehistory was Neolithisation, the introduction of the farming lifestyle to human societies. Farming originated in the Fertile Crescent approximately 10,000 years BC and in Europe it was associated with a major population turnover. Ancient DNA from Anatolia, the presumed source area of the demic spread to Europe, and the Balkans, one of the first known contact zones between local hunter-gatherers and incoming farmers, was obtained from roughly contemporaneous human remains dated to ∼6 th millennium BC. This new unprecedented dataset comprised of 86 full mitogenomes, five whole genomes (7.1–3.7x coverage) and 20 high coverage (7.6–93.8x) genomic samples. The Aegean Neolithic pop- ulation, relatively homogeneous on both sides of the Aegean Sea, was positively proven to be a core zone for demic spread of farmers to Europe. The farmers were shown to migrate through the central Balkans and while the local sedentary hunter-gathers of Vlasac in the Danube Gorges seemed to be isolated from the farmers coming from the south, the individuals of the Aegean origin infiltrated the nearby hunter-gatherer community of Lepenski Vir. The intensity of infiltration increased over time and even though there was an impact of the Danubian hunter-gatherers on genetic variation of Neolithic central Europe, the Aegean ancestry dominated during the introduction of farming to the continent.

Taking only admixture analyses using Yamna samples:

This increased genetic affinity of Neolithic farmers to Danubians was observed for Neolithic Hungarians, LBK from central Europe and LBK Stuttgart sample. Some post-Neolithic samples also proved to share more drift with Danubians, again samples from Hungary (Bronze Age and Copper Age samples and also Yamnaya and samples with elevated Yamnaya ancestry (Early Bronze Age samples from Únětice, Bell Beaker samples, Late Neolithic Karlsdorf sample and Corded Ware samples).

(…)

The results of our ADMIXTURE analysis for the dataset including also Yamnaya samples are shown in Figure S1c. The cross-validation error was the lowest for K=2. Supervised and unsupervised analyses for K=3 are again highly concordant. Early Neolithic farmers again demonstrate almost no evidence of hunter-gatherer admixture, while it is observable in the Middle Neolithic farmers. However, much of the Late Neolithic hunter-gatherer ancestry from the previous analysis is replaced by Yamnaya ancestry. These results are consistent with the results of Haak et al. who demonstrated a resurgence of hunter-gatherer ancestry followed by the establishment of Eastern hunter-gatherer ancestry.

Again, admixture results show that something in the simplistic Yamna -> Corded Ware model is off. It is still interesting to review admixture results of European Mesolithic and Late Neolithic genomic data in relation to the so-called steppe or yamna ancestry or component (most likely an eastern steppe / forest zone ancestry probably also present in the earlier Corded Ware horizons) and its interpretation…

yamna-ancestry-europe
Image composed by me, from two different images of the PhD Thesis. To the left: Supervised run of ADMIXTURE. The clusters to be supervised were chosen to best fit the presumed ancestral populations (for HG Motala and for farmers Bar8 and Bar31 and for later Eastern migration Yamnaya). To the Right: Unsupervised run of ADMIXTURE for the Anatolian genomic dataset with Yamnaya samples for K=8.

Discovered via Généalogie génétique

Ancient DNA samples from Mesolithic Scandinavia show east-west genetic gradient

mesolithic-scandinavia

New pre-print article at BioRxiv, Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation, by Günther et al. (2017), from the Uppsala University (group led by Mattias Jakobsson).

Abstract (emphasis mine):

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans. Finally, we were able to compute a 3D facial reconstruction of a Mesolithic woman from her high-coverage genome, giving a glimpse into an individual’s physical appearance in the Mesolithic.

Interesting is the genetic similarity found with Baltic hunter-gatherers from Zvejnieki:

To investigate the postglacial colonization of Scandinavia, we explored four hypothetical migration routes (primarily based on natural geography) linked to WHGs and EHGs, respectively (Supplementary Information 11); a) a migration of WHGs from the south, b) a migration of EHGs from the east across the Baltic Sea, c) a migration of EHGs from the east and along the north-Atlantic coast, d) a migration of EHGs from the east and south of the Baltic Sea, and combinations of these four migration routes.
(…)
The SHGs from northern and western Scandinavia show a distinct and significantly stronger affinity to the EHGs compared to the central and eastern SHGs (Fig. 1). Conversely, the SHGs from eastern and central Scandinavia were genetically more similar to WHGs compared to the northern and western SHGs (Fig. 1). Using a model-based approach (15, 16), the EHG genetic component of northern and western SHGs was estimated to 55% on average (43-67%) and significantly different (Wilcoxon test, p=0.014) from the average 35% (22-44%) in eastern and south-central SHGs. This average is similar to eastern Baltic hunter-gatherers from Latvia (28) (average 33%, Fig. 1A, Supplementary Information 6). These patterns of genetic affinity within SHGs are in direct contrast to the expectation based on geographic proximity with EHGs and WHGs and do not correlate with age of the sample.
(…)
Combining these isotopic results with the patterns of genetic variation, we suggest an initial colonization from the south, likely by WHGs. A second migration of people who were related to the EHGs – that brought the new pressure blade technique to Scandinavia and that utilized the rich Atlantic coastal marine resources –entered from the northeast moving southwards along the ice-free Atlantic coast where they encountered WHG groups. The admixture between the two colonizing groups created the observed pattern of a substantial EHG component in the northern and the western SHGs, contrary to the higher levels of WHG genetic component in eastern and central SHGs (Fig. 1, Supplementary Information 11).

From the same article, three samples with reported Y-DNA, the three of haplogroup I2 (one more specifically I2a1b). Regarding mtDNA, four samples U5a1 (two of them U5a1d), two samples U4a1, one U4a2.

Featured image: potential migration routes, taken from the supplementary material.

Related:

My European Family: The First 54,000 years, by Karin Bojs

steppe-expansion-corded-ware

I have recently read the book My European Family: The First 54,000 years (2015), by Karin Bojs, a known Swedish scientific journalist, former science editor of the Dagens Nyheter.

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My European Family: The First 54,000 Years
It is written in a fresh, dynamic style, and contains general introductory knowledge to Genetics, Archaeology, and their relation to language, and is written in a time of great change (2015) for the disciplines involved.

The book is informed, it shows a balanced exercise between responsible science journalism and entertaining content, and it is at times nuanced, going beyond the limits of popular science books. It is not written for scholars, although you might learn – as I did – interesting details about researchers and institutions of the anthropological disciplines involved. It contains, for example, interviews with known academics, which she uses to share details about their personalities and careers, which give – in my opinion – a much needed context to some of their publications.

Since I am clearly biased against some of the findings and research papers which are nevertheless considered mainstream in the field (like the identification of haplogroup R1a with the Proto-Indo-European expansion, or the concept of steppe admixture), I asked my wife (who knew almost nothing about genetics, or Indo-European studies) to read it and write a summary, if she liked it. She did. So much, that I have convinced her to read The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World (2007), by David Anthony.

Here is her summary of the book, translated from Spanish:

The book is divided in three main parts: The Hunters, The Farmers, and The Indo-Europeans, and each has in turn chapters which introduce and break down information in an entertaining way, mixing them with recounts of her interactions and personal genealogical quest.

Part one, The Hunters, offers intriguing accounts about the direct role music had in the development of the first civilizations, the first mtDNA analyses of dogs (Savolainen), and the discovery of the author’s Saami roots. Explanations about the first DNA studies and their value for archaeological studies are clear and comprehensible for any non-specialized reader. Interviews help give a close view of investigations, like that of Frederic Plassard’s in Les Combarelles cave.

Part two, The Farmers, begins with her travel to Cyprus, and arouses the interest of the reader with her description of the circular houses, her notes on the Basque language, the new papers and theories related to DNA analyses, the theory of the decision of cats to live with humans, the first beers, and the houses built over graves. Karin Bojs analyses the subgroup H1g1 of her grandmother Hilda, and how it belonged to the first migratory wave into Central Europe. This interest in her grandmother’s origins lead her to a conference in Pilsen about the first farmers in Europe, where she knows firsthand of the results of studies by János Jakucs, and studies of nuclear DNA. Later on she interviews Guido Brandt and Joachim Burguer, with whom she talks about haplogroups U, H, and J.

The chapter on Ötzi and the South Tyrol Museum of Archaeology (Bolzano) introduces the reader to the first prehistoric individual whose DNA was analysed, belonging to haplogroup G2a4, but also revealing other information on the Iceman, such as his lactose intolerance.

Part three, dealing with the origin of Indo-Europeans, begins with the difficulties that researchers have in locating the origin of horse domestication (which probably happened in western Kazakhstan, in the Russian steppe between the rivers Volga and Don). She mentions studies by David Anthony and on the Yamna culture, and its likely role in the diffusion of Proto-Indo-European. In an interview with Mallory in Belfast, she recalls the potential interest of far-right extremists in genetic studies (and early links of the Journal of Indo-European Studies to certain ideology), as well as controversial statements of Gimbutas, and her potentially biased vision as a refugee from communist Europe. During the interview, Mallory had a copy of the latest genetic paper sent to Nature Magazine by Haak et al., not yet published, for review, but he didn’t share it.

Then haplogroups R1a and R1b are introduced as the most common in Europe. She visits the Halle State Museum of Prehistory (where the Nebra sky disk is exhibited), and later Krakow, where she interviews Slawomir Kadrow, dealing with the potential creation of the Corded Ware culture from a mix of Funnelbeaker and Globular Amphorae cultures. New studies of ancient DNA samples, published in the meantime, are showing that admixture analyses between Yamna and Corded Ware correlate in about 75%.

In the following chapters there is a broad review of all studies published to date, as well as individuals studied in different parts of Europe, stressing the importance of ships for the expansion of R1b lineages (Hjortspring boat).

The concluding chapter is dedicated to vikings, and is used to demystify them as aggressive warmongers, sketching their relevance as founders of the Russian state.

To sum up, it is a highly documented book, written in a clear style, and is capable of awakening the reader’s interest in genetic and anthropological research. The author enthusiastically looks for new publications and information from researchers, but is at the same time critic with them, showing often her own personal reactions to new discoveries, all of which offers a complex personal dynamic often shared by the reader, engaged with her first-person account the full length of the book.

Mayte Batalla (July 2017)

DISCLAIMER: The author sent me a copy of the book (a translation into Spanish), so there is a potential conflict of interest in this review. She didn’t ask for a review, though, and it was my wife who did it.

Collapse of the European ice sheet caused chaos in northern and eastern Europe until about 8000 BC

deglaciation-europe-east

A new paper with open access has appeared in Quaternary Science Reviews, authored by Patton et al.: Deglaciation of the Eurasian ice sheet complex, which offers a new model investigating the retreat of this ice sheet and its many impacts.

According to the comments of professor Alun Hubbard, the paper’s second author and a leading glaciologist:

To place it in context, this is almost 10 times the current rates of ice lost from Greenland and Antarctica today. What’s fascinating is that not all Eurasian ice retreat was from surface melting alone. Its northern and western sectors across the Barents Sea, Norway and Britain terminated directly into the sea. They underwent rapid collapse through calving of vast armadas of icebergs and undercutting of the ice margin by warm ocean currents.

Some speculate that at some points during the European deglaciation, this river system had a discharge twice that of the Amazon today. Based on our latest reconstruction of this system, we have calculated that its catchment area was similar to that of the Mississippi. It was certainly the largest river system to have ever drained the Eurasian continent.

One thing that we show pretty well in this study is that our simulation is relevant to a range of different research disciplines, not only glaciology. It can even be useful for archaeologists who look at human migration routes, and are interested to see how the European environment developed over the last 20,000 years.

Interesting is its effect on population movements in eastern Europe, including the steppe, the forest-steppe, and the Forest Zone, during the Younger Dryas period and thereafter.

Another, recent build-up article on this model also by Patton and cols. of december 2016, in the same journal, is The build-up, configuration, and dynamical sensitivity of the Eurasian ice-sheet complex to Late Weichselian climatic and oceanic forcing. A summary is found at the University of Tromso website.

Discovered via News at Phys.org.

Featured image: Younger Dryas period, from the article.