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Svensson, E., Günther, T., Hoischen, A., Hervella, M., Munters, A. R., Ioana, M., . . . Jakobsson, M. (2021). Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe. Current Biology, 31(14), 2973-U21
Open this publication in new window or tab >>Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe
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2021 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 31, no 14, p. 2973-U21Article in journal (Refereed) Published
Abstract [en]

Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from “Peştera Muierii,” Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.

Place, publisher, year, edition, pages
Elsevier, 2021
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-453914 (URN)10.1016/j.cub.2021.04.045 (DOI)000680074300001 ()34010592 (PubMedID)
Funder
Swedish Research Council, 2017-05267EU, European Research Council, 833247Swedish National Infrastructure for Computing (SNIC)UPPMAXKnut and Alice Wallenberg Foundation
Note

De tre första författarna delar förstaförfattarskapet

Available from: 2021-10-04 Created: 2021-10-04 Last updated: 2024-06-11Bibliographically approved
Blank, M., Sjögren, K.-G., Knipper, C., Frei, K. M., Malmström, H., Fraser, M., . . . Storå, J. (2021). Mobility patterns in inland southwestern Sweden during the Neolithic and Early Bronze Age. Archaeological and Anthropological Sciences, 13(4), Article ID 64.
Open this publication in new window or tab >>Mobility patterns in inland southwestern Sweden during the Neolithic and Early Bronze Age
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2021 (English)In: Archaeological and Anthropological Sciences, ISSN 1866-9557, E-ISSN 1866-9565, Vol. 13, no 4, article id 64Article in journal (Refereed) Published
Abstract [en]

In this paper, we investigate population dynamics in the Scandinavian Neolithic and Early Bronze Age in southwestern Sweden. Human mobility patterns in Falbygden were studied by applying strontium isotope analysis combined with archaeological and bioarchaeological data, including mtDNA and sex assessment on a large dataset encompassing 141 individuals from 21 megalithic graves. In combination with other archaeological and anthropological records, we investigated the temporal and spatial scale of individual movement, mobility patterns of specific categories of people and possible social drivers behind them. Our results of strontium and biomolecular analyses suggest that mobility increased in the Late Neolithic and Early Bronze Age compared to the earlier parts of the Neolithic. The data indicate individuals moving both into and away from Falbygden. Mobility patterns and contact networks also shift over time.

Place, publisher, year, edition, pages
Springer, 2021
Keywords
Mobility, Southwestern Sweden, Megalithic graves, Strontium isotopes, Mitochondrial aDNA, Neolithic, Early Bronze Age
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-441857 (URN)10.1007/s12520-021-01294-4 (DOI)000630357600001 ()
Funder
Swedish Research Council, VR 2013-1905Riksbankens Jubileumsfond, M13-0904:1Knut and Alice Wallenberg FoundationUniversity of Gothenburg
Available from: 2021-05-12 Created: 2021-05-12 Last updated: 2024-06-10Bibliographically approved
Li, J., Zarzar, T. G., White, J. D., Indencleef, K., Hoskens, H., Matthews, H., . . . Claes, P. (2020). Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images. Scientific Reports, 10(1), Article ID 11850.
Open this publication in new window or tab >>Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images
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2020 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 11850Article in journal (Refereed) Published
Abstract [en]

Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.

National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-419786 (URN)10.1038/s41598-020-68259-w (DOI)000550057200163 ()32678112 (PubMedID)
Funder
Swedish Research Council, 2017-05267
Available from: 2020-09-17 Created: 2020-09-17 Last updated: 2022-09-15Bibliographically approved
Coutinho, A., Günther, T., Munters, A. R., Svensson, E. M., Götherström, A., Storå, J., . . . Jakobsson, M. (2020). The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders. American Journal of Physical Anthropology, 172(4), 638-649
Open this publication in new window or tab >>The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
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2020 (English)In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 172, no 4, p. 638-649Article in journal (Refereed) Published
Abstract [en]

Objectives

In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub‐Neolithic hunter‐gatherer Pitted Ware culture. By investigating the genetic make‐up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture‐influenced burials), we could determine the impact of migration and the impact of cultural influences.

Methods

We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene‐pools.

Results

The genomic data show that all individuals belonged to one genetic population—a population associated with the Pitted Ware culture—irrespective of the burial style.

Conclusion

We conclude that the Pitted Ware culture communities were not impacted by gene‐flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.

Keywords
admixture, ancient DNA, migration, Stone Age
National Category
Evolutionary Biology
Research subject
Biology with Specialisation in Human Evolution and Genetics
Identifiers
urn:nbn:se:uu:diva-397180 (URN)10.1002/ajpa.24079 (DOI)000537595500001 ()32497286 (PubMedID)
Funder
Swedish Research Council, 2017-02503Knut and Alice Wallenberg FoundationRiksbankens Jubileumsfond, M13-0904:1Swedish Research Council, 2013-1905Swedish Research Council, 2017-05267
Note

Title in thesis list of papers: The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture

De två sista författarna delar sistaförfattarskapet

Available from: 2019-11-17 Created: 2019-11-17 Last updated: 2021-04-07Bibliographically approved
Lombard, M., Malmström, H., Schlebusch, C., Svensson, E., Günther, T., Munters, A. R., . . . Jakobsson, M. (2019). Genetic data and radiocarbon dating question Plovers Lake as a Middle Stone Age hominin-bearing site. Journal of Human Evolution, 131, 203-209
Open this publication in new window or tab >>Genetic data and radiocarbon dating question Plovers Lake as a Middle Stone Age hominin-bearing site
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2019 (English)In: Journal of Human Evolution, ISSN 0047-2484, E-ISSN 1095-8606, Vol. 131, p. 203-209Article in journal (Refereed) Published
Abstract [en]

We have sampled five out of the eleven previously identified human specimens and some faunal remains from the Plovers Lake site in the Cradle of Humankind, South Africa, for ancient DNA. We were successful in obtaining positive results for three of the human individuals and three 'buffalo' teeth. Based on ages obtained for flowstone and one bovid tooth, the site was interpreted previously as a hominin-bearing Middle Stone Age site of more than 60 000 years old. Our work, however, revealed that not all the material accumulated during the Pleistocene. Instead, the sampled humans and bovids most likely represent a Bantu-speaking Iron Age population (mtDNA haplogroup L3d) and their Nguni cattle. Newly obtained radiocarbon dates confirmed that these remains are probably no older than the last 500 years bp. This study demonstrates the usefulness of inter-disciplinary investigation into the human past, and the depositional and stratigraphic complexities that researchers in the Cradle of Humankind need to contend with before interpreting their assemblages.

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
Plovers lake, Ancient DNA, Hominin-bearing site, South Africa, Middle Stone Age, C14 dating
National Category
Archaeology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-390338 (URN)10.1016/j.jhevol.2019.03.014 (DOI)000472706300014 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 642-2013-8019Swedish Research Council, 621-2014-5211Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyWenner-Gren Foundations
Available from: 2019-08-09 Created: 2019-08-09 Last updated: 2019-08-09Bibliographically approved
Sanchez-Quinto, F., Malmström, H., Fraser, M., Girdland-Flink, L., Svensson, E., Simões, L. G., . . . Jakobsson, M. (2019). Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society. Proceedings of the National Academy of Sciences of the United States of America, 116(19), 9469-9474
Open this publication in new window or tab >>Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society
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2019 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 19, p. 9469-9474Article in journal (Refereed) Published
Abstract [en]

Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic facade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.

Keywords
paleogenomics, population genomics, migration, megalithic tombs
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-384070 (URN)10.1073/pnas.1818037116 (DOI)000467226400047 ()30988179 (PubMedID)
Funder
Riksbankens JubileumsfondKnut and Alice Wallenberg Foundation
Note

De 3 första författarna delar förstaförfattarskapet.

Available from: 2019-05-28 Created: 2019-05-28 Last updated: 2019-05-28Bibliographically approved
Malmström, H., Günther, T., Svensson, E. M., Juras, A., Fraser, M., Munters, A. R., . . . Jakobsson, M. (2019). The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon. Proceedings of the Royal Society of London. Biological Sciences, 286(1912), Article ID 20191528.
Open this publication in new window or tab >>The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon
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2019 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1912, article id 20191528Article in journal (Refereed) Published
Abstract [en]

The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24x coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.

Keywords
ancient DNA, Battle Axe Culture, Corded Ware Culture, demography, European Neolithic, migration
National Category
Archaeology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-396732 (URN)10.1098/rspb.2019.1528 (DOI)000490551300007 ()31594508 (PubMedID)
Funder
Swedish Research Council, 2017-02503Swedish Research Council, 2017-05267Swedish Research Council, 2013-1905Riksbankens Jubileumsfond, M13-0904:1Knut and Alice Wallenberg FoundationBerit Wallenberg Foundation, BWS2011.0090
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2019-11-26 Created: 2019-11-26 Last updated: 2019-11-26Bibliographically approved
Valdiosera, C., Günther, T., Carlos Vera-Rodriguez, J., Urena, I., Iriarte, E., Rodriguez-Varela, R., . . . Jakobsson, M. (2018). Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia. Proceedings of the National Academy of Sciences of the United States of America, 115(13), 3428-3433
Open this publication in new window or tab >>Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 13, p. 3428-3433Article in journal (Refereed) Published
Abstract [en]

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500-3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2018
Keywords
archaeogenomics, Iberia, migrations, diversity, palaeodiet
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-351706 (URN)10.1073/pnas.1717762115 (DOI)000428382400066 ()29531053 (PubMedID)
Funder
Swedish Research CouncilAustralian Research Council, FT0992258]
Available from: 2018-05-31 Created: 2018-05-31 Last updated: 2018-05-31Bibliographically approved
Günther, T., Malmström, H., Svensson, E., Omrak, A., Sanchez-Quinto, F., Kilinc, G. M., . . . Jakobsson, M. (2018). Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. PLoS biology, 16(1), Article ID e2003703.
Open this publication in new window or tab >>Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
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2018 (English)In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 16, no 1, article id e2003703Article in journal (Refereed) Published
Abstract [en]

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). 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. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, 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 potential 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.

National Category
Biological Sciences Archaeology
Identifiers
urn:nbn:se:uu:diva-346367 (URN)10.1371/journal.pbio.2003703 (DOI)000423830300009 ()29315301 (PubMedID)
Funder
EU, European Research CouncilWenner-Gren FoundationsKnut and Alice Wallenberg FoundationRiksbankens JubileumsfondSwedish Research Council, 421-2013-730; 2013-1905Swedish Research Council Formas, 2011-1138
Available from: 2018-03-26 Created: 2018-03-26 Last updated: 2021-10-25Bibliographically approved
Omrak, A., Günther, T., Valdiosera, C., Svensson, E. M., Malmström, H., Kiesewetter, H., . . . Götherström, A. (2016). Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool. Current Biology, 26(2), 270-275
Open this publication in new window or tab >>Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool
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2016 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 26, no 2, p. 270-275Article in journal (Refereed) Published
Abstract [en]

Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.

Place, publisher, year, edition, pages
Elsevier, 2016
National Category
Evolutionary Biology Archaeology
Identifiers
urn:nbn:se:uu:diva-278008 (URN)10.1016/j.cub.2015.12.019 (DOI)000368972300032 ()26748850 (PubMedID)
Funder
Swedish Research Council, 2013-1905Wenner-Gren FoundationsEU, European Research Council, 311413Swedish National Infrastructure for Computing (SNIC), b2013236Swedish National Infrastructure for Computing (SNIC), b2013240Riksbankens Jubileumsfond, M13-0904:1UPPMAX
Available from: 2016-02-23 Created: 2016-02-23 Last updated: 2024-06-11Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-4349-849x

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