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Ausmees, K., Sanchez-Quinto, F., Jakobsson, M. & Nettelblad, C. (2019). An empirical evaluation of genotype imputation of ancient DNA.
Open this publication in new window or tab >>An empirical evaluation of genotype imputation of ancient DNA
2019 (English)Report (Other academic)
Series
Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2019-008
National Category
Computational Mathematics Genetics
Identifiers
urn:nbn:se:uu:diva-396336 (URN)
Projects
eSSENCE
Available from: 2019-11-04 Created: 2019-11-04 Last updated: 2019-11-11Bibliographically approved
Shebanits, K., Günther, T., Johansson, A. C. V., Maqbool, K., Feuk, L., Jakobsson, M. & Larhammar, D. (2019). Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.. BMC Biotechnology, 19, Article ID 31.
Open this publication in new window or tab >>Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.
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2019 (English)In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 19, article id 31Article in journal (Refereed) Published
Abstract [en]

Background: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.

Results: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split.

Conclusions: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation.

National Category
Cell Biology Genetics
Identifiers
urn:nbn:se:uu:diva-356569 (URN)10.1186/s12896-019-0523-9 (DOI)000470281900001 ()31164119 (PubMedID)
Funder
Swedish Research CouncilThe Swedish Brain Foundation
Available from: 2018-08-01 Created: 2018-08-01 Last updated: 2019-06-25Bibliographically approved
Vicente, M., Jakobsson, M., Ebbesen, P. & Schlebusch, C. (2019). Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations. Molecular biology and evolution, 36(9), 1849-1861
Open this publication in new window or tab >>Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations
2019 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 9, p. 1849-1861Article in journal (Refereed) Published
Abstract [en]

Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as "Khoe-San" populations and have a long history in southern Africa. Their ancestors were largely isolated up until similar to 2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx'a-language family (double dagger Hoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.

Keywords
Khoe-San, southern Africa, population structure, isolation-by-distance, adaptive gene-flow
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-397127 (URN)10.1093/molbev/msz089 (DOI)000493043800001 ()31288264 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2014-5211Swedish Research Council, 6422013-8019EU, European Research Council, 759933Göran Gustafsson Foundation for Research in Natural Sciences and Medicine
Available from: 2019-11-29 Created: 2019-11-29 Last updated: 2019-11-29Bibliographically 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
Tournebize, R., Poncet, V., Jakobsson, M., Vigouroux, Y. & Manel, S. (2019). McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes. Molecular Ecology Resources, 19(1), 283-295
Open this publication in new window or tab >>McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes
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2019 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 19, no 1, p. 283-295Article in journal (Refereed) Published
Abstract [en]

Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here, we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic models that include selection. McSwan demonstrated high power (high sensitivity and specificity) in capturing hard selective sweep events without requiring haplotype phasing. It performed slightly better than SweeD when the recent effective population size was low and the genomic region was small. We then applied our method to a European (CEU) and an African (LWK) human re-sequencing data set. Most hard sweeps were detected in the CEU population (96%). Moreover, hard sweeps in the African population were estimated to have occurred further back in time (mode: 43,625 years BP) compared to those of Europeans (mode: 24,850 years BP). Most of the estimated ages of hard sweeps in Europeans were associated with the Last Glacial Maximum and were enriched in immunity-associated genes.

Keywords
age of selection, coalescent process, high-performance computing, human, selective sweep, site frequency spectrum
National Category
Ecology
Identifiers
urn:nbn:se:uu:diva-377712 (URN)10.1111/1755-0998.12957 (DOI)000457579800022 ()30358170 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationForte, Swedish Research Council for Health, Working Life and Welfare
Available from: 2019-03-08 Created: 2019-03-08 Last updated: 2019-03-08Bibliographically 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
Price, N., Hedenstierna-Jonson, C., Zachrisson, T., Kjellström, A., Storå, J., Krzewińska, M., . . . Götherström, A. (2019). Viking warrior women?: Reassessing Birka chamber grave Bj.581. Antiquity, 93(367), 181-198
Open this publication in new window or tab >>Viking warrior women?: Reassessing Birka chamber grave Bj.581
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2019 (English)In: Antiquity, ISSN 0003-598X, E-ISSN 1745-1744, Vol. 93, no 367, p. 181-198Article in journal (Refereed) Published
Abstract [en]

The warrior woman has long been part of the Viking image, with a pedigree that extends from the Valkyries of Old Norse prose and poetry to modern media entertainment. Until recently, however, actual Viking Age evidence for such individuals has been sparse. This article addresses research showing that the individual buried at Birka in an 'archetypal' high-status warrior grave-always assumed to be male since its excavation in 1878-is, in fact, biologically female. Publication, in 2017, of the genomic data led to unprecedented public debate about this individual. Here, the authors address in detail the interpretation of the burial, discussing source-critical issues and parallels.

Keywords
Sweden, Birka, Viking Age, female warriors, aDNA
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-378730 (URN)10.15184/aqy.2018.258 (DOI)000459044500019 ()
Funder
Riksbankens Jubileumsfond, M13-0904: 1Swedish Research Council, 2013-1905Swedish Research Council, 2015-00466
Available from: 2019-03-08 Created: 2019-03-08 Last updated: 2019-03-08Bibliographically approved
Krzewinska, M., Kilinc, G. M., Juras, A., Koptekin, D., Chylenski, M., Nikitin, A. G., . . . Gotherstrom, A. (2018). Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads. Science Advances, 4(10), Article ID eaat4457.
Open this publication in new window or tab >>Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads
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2018 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 4, no 10, article id eaat4457Article in journal (Refereed) Published
Abstract [en]

For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

Place, publisher, year, edition, pages
AMER ASSOC ADVANCEMENT SCIENCE, 2018
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-369757 (URN)10.1126/sciadv.aat4457 (DOI)000449221200019 ()30417088 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationRiksbankens Jubileumsfond, P16-0553:1
Available from: 2018-12-17 Created: 2018-12-17 Last updated: 2018-12-17Bibliographically approved
Lombard, M., Jakobsson, M. & Schlebusch, C. (2018). Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history. South African Journal of Science, 114(1-2), Article ID a0253.
Open this publication in new window or tab >>Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history
2018 (English)In: South African Journal of Science, ISSN 0038-2353, E-ISSN 1996-7489, Vol. 114, no 1-2, article id a0253Article in journal, Editorial material (Other academic) Published
Keywords
human genome, hunter-gatherer, Homo sapiens, population split-time estimations
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-350207 (URN)10.17159/sajs.2018/a0253 (DOI)000423551800002 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 642-2013-8019; 621-2014-5211Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of Technology
Available from: 2018-05-08 Created: 2018-05-08 Last updated: 2018-05-08Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7840-7853

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