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Schurr TG, Shengelia R, Shamoon-Pour M, Chitanava D, Laliashvili S, Laliashvili I, Kibret R, Kume-Kangkolo Y, Akhvlediani I, Bitadze L, Mathieson I, Yardumian A. Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). Genome Biol Evol 2023; 15:evad198. [PMID: 37935112 PMCID: PMC10665041 DOI: 10.1093/gbe/evad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/09/2023] Open
Abstract
To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramaz Shengelia
- Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | - Michel Shamoon-Pour
- First-year Research Immersion, Binghamton University, Binghamton, New York, USA
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Redate Kibret
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| | - Yanu Kume-Kangkolo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aram Yardumian
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
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2
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Jayasekera LP, Ranasinghe R, Senathilake KS, Kotelawala JT, de Silva K, Abeygunasekara PH, Goonesinghe R, Tennekoon KH. Mitochondrial genome in sporadic breast cancer: A case control study and a proteomic analysis in a Sinhalese cohort from Sri Lanka. PLoS One 2023; 18:e0281620. [PMID: 36758048 PMCID: PMC9910733 DOI: 10.1371/journal.pone.0281620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Breast cancer is the commonest malignancy in women and the majority occurs sporadically with no hereditary predisposition. However, sporadic breast cancer has been studied less intensively than the hereditary form and to date hardly any predictive biomarkers exist for the former. Furthermore, although mitochondrial DNA variants have been reported to be associated with breast cancer, findings have been inconsistent across populations. Thus we carried out a case control study on sporadic breast cancer patients and healthy controls of Sinhalese ethnicity (N = 60 matched pairs) in order to characterize coding region variants associated with the disease and to identify any potential biomarkers. Mitochondrial genome was fully sequenced in 30 pairs and selected regions were sequenced in the remaining 30 pairs. Several in-silico tools were used to assess functional significance of the variants observed. A number of variants were identified among the patients and the controls. Missense variants identified were either polymorphisms or rare variants. Their prevalence did not significantly differ between patients and the healthy controls (matched for age, body mass index and menopausal status). MT-CYB, MT-ATP6 and MT-ND2 genes showed a higher mutation rate. A higher proportion of pre-menopausal patients carried missense and pathogenic variants. Unique combinations of missense variants were seen within genes and these occurred mostly in MT-ATP6 and MT-CYB genes. Such unique combinations that occurred exclusively among the patients were common in obese patients. Mitochondrial DNA variants may have a role in breast carcinogenesis in obesity and pre-menopause. Molecular dynamic simulations suggested the mutants, G78S in MT-CO3 gene and T146A in MT-ATP6 gene are likely to be more stable than their wild type counterparts.
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Affiliation(s)
- Lakshika P. Jayasekera
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Ruwandi Ranasinghe
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Kanishka S. Senathilake
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Joanne T. Kotelawala
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | | | | | | | - Kamani H. Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
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3
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Kristjansson D, Bohlin J, Nguyen TT, Jugessur A, Schurr TG. Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography. BMC Genomics 2022; 23:354. [PMID: 35525961 PMCID: PMC9080151 DOI: 10.1186/s12864-022-08572-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/20/2022] [Indexed: 12/28/2022] Open
Abstract
Background We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe. Methods Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering. The haplogroup statuses of the individual sequences were assessed using Haplogrep2. Results A total of 23 hierBAPS groups were identified, all of which corresponded to subclades defined in Phylotree, v.17. The hierBAPS groups projected onto the ML phylogeny accurately clustered all haplotypes belonging to a specific haplogroup in accordance with Haplogrep2. By incorporating the geographic source of each sequence and subclade age estimates into this framework, inferences about the diversification of U5 mtDNAs were made. Haplogroup U5 has been present in northern Europe since the Mesolithic, and spread in both eastern and western directions, undergoing significant diversification within Scandinavia. A review of historical and archeological evidence attests to some of the population interactions contributing to this pattern. Conclusions The hierBAPS algorithm accurately grouped mitogenome sequences into subclades in a phylogenetically robust manner. This analysis provided new insights into the phylogeographic structure of haplogroup U5 diversity in northern Europe, revealing a detailed perspective on the diversity of subclades in this region and their distribution in Scandinavian populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08572-y.
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Affiliation(s)
- Dana Kristjansson
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Jon Bohlin
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Truc Trung Nguyen
- IT Systems Bergen, Norwegian Institute of Public Health, Bergen, Norway
| | - Astanand Jugessur
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
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4
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Heraclides A, Fernández-Domínguez E. Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods. Int J Mol Sci 2022; 23:4651. [PMID: 35563041 PMCID: PMC9104972 DOI: 10.3390/ijms23094651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023] Open
Abstract
Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA. All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms. Here, we report findings from a thorough evaluation of two alternative tools (ANGSD and schmutzi) aimed at overcoming these issues and constructing high-quality ancient mitogenomes. Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were reconstructed using different quality filters, with their accuracy measured and compared. Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated. Complete mitogenomes were successfully reconstructed for all ancient samples, and for the majority of them, filtering substantially improved mtDNA consensus calling and haplogroup prediction. Overall, the schmutzi pipeline, which estimates and takes into consideration exogenous contamination, appeared to have the edge over the much faster and user-friendly alternative method (ANGSD) in moderate to high coverage samples (>1,000,000 reads). ANGSD, however, through its read termini trimming filter, showed better capabilities in calling the consensus sequence from low-quality samples. Among all the predictors of overall sample quality examined, the strongest correlation was found for the available number of sequence reads and bases. In the process, we report a previously unassigned haplogroup (U3b) for an Early Chalcolithic individual from Southern Anatolia/Northern Levant.
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Affiliation(s)
- Alexandros Heraclides
- Department of Health Sciences, European University Cyprus, Diogenis Str. 6, Nicosia 2404, Cyprus
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5
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Rio J, Quilodrán CS, Currat M. Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations. Commun Biol 2021; 4:1163. [PMID: 34621003 PMCID: PMC8497574 DOI: 10.1038/s42003-021-02670-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The Bronze Age is a complex period of social, cultural and economic changes. Recent paleogenomic studies have documented a large and rapid genetic change in early Bronze Age populations from Central Europe. However, the detailed demographic and genetic processes involved in this change are still debated. Here we have used spatially explicit simulations of genomic components to better characterize the demographic and migratory conditions that may have led to this change. We investigated various scenarios representing the expansion of pastoralists from the Pontic steppe, potentially linked to the Yamnaya cultural complex, and their interactions with local populations in Central Europe, considering various eco-evolutionary factors, such as population admixture, competition and long-distance dispersal. Our results do not support direct competition but rather the cohabitation of pastoralists and farmers in Central Europe, with limited gene flow between populations. They also suggest occasional long-distance migrations accompanying the expansion of pastoralists and a demographic decline in both populations following their initial contact. These results link recent archaeological and paleogenomic observations and move further the debate of genomic changes during the early Bronze Age.
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Affiliation(s)
- Jérémy Rio
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Claudio S Quilodrán
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Mathias Currat
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
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6
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Scorrano G, Yediay FE, Pinotti T, Feizabadifarahani M, Kristiansen K. The genetic and cultural impact of the Steppe migration into Europe. Ann Hum Biol 2021; 48:223-233. [PMID: 34459341 DOI: 10.1080/03014460.2021.1942984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND During the early 3rd millennium BCE migration from Pontic Steppe, mainly related to Yamnaya culture, has affected European populations both culturally and genetically, however, it has long been debated to what extent this migration was male-driven, and how this replacement process took place which eliminated partially/largely Neolithic male lines over time. AIM This paper aims to evaluate the influence of the Steppe migration on European Bronze Age populations by calculating both male and female genetic contributions of the Steppe-related ancestry to the European Bronze Age populations. With this approach, we will be able to clarify the hypotheses on whether it was male-biased migration or not. SUBJECTS AND METHODS To evaluate the genetic impact and the proportion of the Steppe-related ancestry to the European Bronze Age populations, we performed PCA and qpAdm analyses by using published genome-wide data. In addition, we quantified male and female genetic contribution into Europe by using the analysis of uniparental markers and the X-chromosome. RESULTS The Steppe migration had a considerable impact on the genetic makeup of the Bronze Age European populations. The data suggest that the Steppe-related ancestry arriving into Central Europe was male-driven, dominantly in the Corded Ware culture populations and lesser in the Bell Beaker populations. In fact, there is no evidence that this migration had a significant input on the mitochondrial genetic pool of all European Bronze Age populations. CONCLUSIONS Our analyses suggest that the Steppe-related ancestry had genetic impact on mainly Central-Eastern Europe. Moreover, this migration was male-driven for most of the Central European populations belonging to the Corded Ware groups, and to a lesser extent for the Bell Beaker groups.
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Affiliation(s)
- Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fulya Eylem Yediay
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomaz Pinotti
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratório de Biodiversidade e Evolução Molecular (LBEM), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
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7
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Juras A, Ehler E, Chyleński M, Pospieszny Ł, Spinek AE, Malmström H, Krzewińska M, Szostek K, Pasterkiewicz W, Florek M, Wilk S, Mnich B, Kruk J, Szmyt M, Kozieł S, Götherström A, Jakobsson M, Dabert M. Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:223-236. [PMID: 34308549 DOI: 10.1002/ajpa.24372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK.,Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
| | - Anna Elżbieta Spinek
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Kraków, Poland.,The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland
| | - Barbara Mnich
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.,Archaeological Museum, Poznań, Poland
| | - Sławomir Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
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8
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Juras A, Makarowicz P, Chyleński M, Ehler E, Malmström H, Krzewińska M, Pospieszny Ł, Górski J, Taras H, Szczepanek A, Polańska M, Włodarczak P, Szyca A, Lasota-Kuś A, Wójcik I, Jakobsson M, Dabert M. Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:176-188. [PMID: 32297323 DOI: 10.1002/ajpa.24057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/13/2020] [Accepted: 03/21/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes. MATERIALS AND METHODS We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples. RESULTS Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study. DISCUSSION Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | | | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Edvard Ehler
- Department of Biology and Environmental Studies, Charles University, Faculty of Education, Praha 1, Czech Republic
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Łukasz Pospieszny
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Kraków, Poland
- Archaeological Museum in Cracow, Kraków, Poland
| | - Halina Taras
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | - Marta Polańska
- Department of Material and Spiritual Culture, Lublin Museum, Lublin, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | - Agnieszka Szyca
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Anna Lasota-Kuś
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | | | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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9
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Linderholm A, Kılınç GM, Szczepanek A, Włodarczak P, Jarosz P, Belka Z, Dopieralska J, Werens K, Górski J, Mazurek M, Hozer M, Rybicka M, Ostrowski M, Bagińska J, Koman W, Rodríguez-Varela R, Storå J, Götherström A, Krzewińska M. Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland. Sci Rep 2020; 10:6885. [PMID: 32303690 PMCID: PMC7165176 DOI: 10.1038/s41598-020-63138-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/24/2020] [Indexed: 11/09/2022] Open
Abstract
During the Final Eneolithic the Corded Ware Complex (CWC) emerges, chiefly identified by its specific burial rites. This complex spanned most of central Europe and exhibits demographic and cultural associations to the Yamnaya culture. To study the genetic structure and kin relations in CWC communities, we sequenced the genomes of 19 individuals located in the heartland of the CWC complex region, south-eastern Poland. Whole genome sequence and strontium isotope data allowed us to investigate genetic ancestry, admixture, kinship and mobility. The analysis showed a unique pattern, not detected in other parts of Poland; maternally the individuals are linked to earlier Neolithic lineages, whereas on the paternal side a Steppe ancestry is clearly visible. We identified three cases of kinship. Of these two were between individuals buried in double graves. Interestingly, we identified kinship between a local and a non-local individual thus discovering a novel, previously unknown burial custom.
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Affiliation(s)
- Anna Linderholm
- The BiG lab (Bioarchaeology and Genomics Laboratory), Department of Anthropology, Texas A&M University, College Station, USA.
| | - Gülşah Merve Kılınç
- Centre for Palaeogenetics, 10691, Stockholm, Sweden.,Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Cracow, Poland.,Department of Anatomy, Jagiellonian University, Medical College, Cracow, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Cracow, Poland
| | - Paweł Jarosz
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Cracow, Poland
| | - Zdzislaw Belka
- Isotope Laboratory, Adam Mickiewicz University, Poznań, Poland
| | | | - Karolina Werens
- School of Archaeology 34-36 Beaumont Street, Oxford, OX1 2PG, United Kingdom
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Cracow, Poland
| | | | | | | | | | | | - Wiesław Koman
- Provincial Office for the Protection of Cultural Heritage, Zamość, Poland
| | | | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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10
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Malmström H, Günther T, Svensson EM, Juras A, Fraser M, Munters AR, Pospieszny Ł, Tõrv M, Lindström J, Götherström A, Storå J, Jakobsson M. The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon. Proc Biol Sci 2019; 286:20191528. [PMID: 31594508 PMCID: PMC6790770 DOI: 10.1098/rspb.2019.1528] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
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 0.26–3.24× 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.
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Affiliation(s)
- Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, 2006 Auckland Park, South Africa
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Magdalena Fraser
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.,Department of Archaeology and Ancient History, Uppsala University-Campus Gotland, 621 67 Visby, Sweden
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, UK.,Institute of Archaeology and Ethnology, Centre for Studies into Late Antiquity and Early Medieval Times, Polish Academy of Sciences, 61-612 Poznań, Poland
| | - Mari Tõrv
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, 50090 Tartu, Estonia
| | - Jonathan Lindström
- Graduate School of Contract Archaeology, Department of Archaeology, Linneaus University, 391 82 Kalmar, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology, and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, 2006 Auckland Park, South Africa
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11
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Malyarchuk BA. Sources of the mitochondrial gene pool of Russians by the results of analysis of modern and paleogenomic data. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Paleogenomic studies of recent years have shown that the Bronze Age migrations of populations of the PontoCaspian steppes from the east to the west of Europe had a great influence on the formation of the genetic makeup of modern Europeans. The results of studies of the variability of mitochondrial genomes in the modern Russian populations of Eastern Europe also made it possible to identify an increase in the effective population size during the Bronze Age, which, apparently, could be related to the migration processes of this time. This paper presents the results of analysis of data on the variability of entire mitochondrial genomes in the modern Russian populations in comparison with the distribution of mtDNA haplogroups in the ancient populations of Europe and the Caucasus of the Neolithic and Bronze Age. It was shown that the formation of the modern appearance of the Russian mitochondrial gene pool began approximately 4 thousand years B.C. due to the influx of mtDNA haplotypes characteristic of the population of Central and Western Europe to the east of Europe. It is assumed that the migrations of the ancient populations of the Ponto-Caspian steppes in the western direction led to the formation of mixed populations in Central Europe, bearing mitochondrial haplogroups H, J, T, K, W characteristic of Western and Central Europeans. Further expansion of these populations to the east of Europe and further to Asia explains the emergence of new features of the mitochondrial gene pool in Eastern Europeans. The results of a phylogeographic analysis are also presented, showing that the features of the geographical distribution of the subgroups of the mitochondrial haplogroup R1a in Europe are a reflection of the “Caucasian” component that appeared in the gene pools of various groups of Europeans during the migration of the Bronze Age. The results of phylogeographic analysis of mitochondrial haplogroups U2e2a1d, U4d2, N1a1a1a1, H2b, and H8b1 testify to the migrations of ancient Eastern Europeans to Asia – the south of Siberia and the Indian subcontinent.
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12
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Silva M, Justeau P, Rodrigues S, Oteo-Garcia G, Dulias K, Foody G, Fichera A, Yau B, Rito T, Wilson JF, Gandini F, Edwards CJ, Pala M, Soares PA, Richards MB. Untangling Neolithic and Bronze Age mitochondrial lineages in South Asia. Ann Hum Biol 2019; 46:140-144. [PMID: 31267777 DOI: 10.1080/03014460.2019.1623319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focuses on the phylogeographic patterns of mitochondrial haplogroups H2 and H13 in the Indian Subcontinent and incorporates evidence from recently released ancient genomes from Central and South Asia. It found signals of Neolithic arrivals from Iran and later movements in the Bronze Age from Central Asia that derived ultimately from the Steppe. This study shows how a detailed mtDNA phylogeographic approach, combining both modern and ancient variation, can provide evidence of population movements, even in a scenario of strong male bias such as in the case of the Bronze Age Steppe dispersals.
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Affiliation(s)
- M Silva
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - P Justeau
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - S Rodrigues
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - G Oteo-Garcia
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - K Dulias
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - G Foody
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - A Fichera
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - B Yau
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - T Rito
- b School of Medicine , Life and Health Sciences Research Institute (ICVS), University of Minho , Braga , Portugal.,c ICVS/3B's , PT Government Associate Laboratory , Guimarães , Portugal
| | - J F Wilson
- d Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Teviot Place , Edinburgh , UK.,e MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine , University of Edinburgh, Western General Hospital , Edinburgh , UK
| | - F Gandini
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - C J Edwards
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - M Pala
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - P A Soares
- f CBMA (Centre of Molecular and Environmental Biology), Department of Biology , University of Minho , Braga , Portugal.,g Institute of Science and Innovation for Bio-Sustainability (IB-S) , University of Minho , Braga , Portugal
| | - M B Richards
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
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13
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Chyleński M, Ehler E, Somel M, Yaka R, Krzewińska M, Dabert M, Juras A, Marciniak A. Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities. Genes (Basel) 2019; 10:genes10030207. [PMID: 30862131 PMCID: PMC6471721 DOI: 10.3390/genes10030207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 11/23/2022] Open
Abstract
Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site’s occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.
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Affiliation(s)
- Maciej Chyleński
- Institute of Archaeology, Faculty of Historical Studies, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland.
| | - Edvard Ehler
- Department of Biology and Environmental Studies, Faculty of Education, Charles University, Magdalény Rettigové 4, 116 39 Prague, Czech Republic.
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden.
| | - Mirosława Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznań, Poland.
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland.
| | - Arkadiusz Marciniak
- Institute of Archaeology, Faculty of Historical Studies, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland.
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14
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Robson HK, Skipitytė R, Piličiauskienė G, Lucquin A, Heron C, Craig OE, Piličiauskas G. Diet, cuisine and consumption practices of the first farmers in the southeastern Baltic. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2019; 11:4011-4024. [PMID: 31565086 PMCID: PMC6743674 DOI: 10.1007/s12520-019-00804-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/30/2019] [Indexed: 06/10/2023]
Abstract
With the arrival of the Early Neolithic Globular Amphora and Corded Ware cultures into the southeastern Baltic, ca. 2900/2800-2400 cal BC, a new type of economy was introduced, animal husbandry. However, the degree to which this transformed the subsistence economy is unknown. Here, we conducted organic residue analyses of 64 ceramic vessels to identify their contents. The vessels were sampled from 10 Lithuanian archaeological sites dating across the Subneolithic-Neolithic transition to the Early Bronze Age (ca. 2900/2800-1300 cal BC). Our results demonstrate that regardless of location or vessel type, many ceramics were used to process aquatic resources. Against our expectations, this association continued even after marked economic change concurrent with the migration of pastoralists from central and southeastern Europe, as evidenced by recent ancient DNA analysis of human remains. Moreover, we observed dairy fats in pottery from all cultures of the Early Neolithic (i.e. Rzucewo, Globular Amphora and Corded Ware) but unlike other regions of Europe, it seems that these were incorporated into indigenous culinary practices. Furthermore, some vessels were used to process plant foods, and others may have been used for the production and/or storage of birch bark tar. However, evidence for domesticated plant processing, for example millet, was absent. We show that organic residue analysis of pottery provides a different picture of past consumption patterns compared to the stable isotope analysis of human remains from isolated burials where a clear dietary shift is evident.
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Affiliation(s)
- Harry K. Robson
- BioArCh, Department of Archaeology, University of York, Heslington, York, YO10 5DD, UK
| | - Raminta Skipitytė
- Center for Physical Sciences and Technology, Saulėtekio Ave. 3, Vilnius 10257, Lithuania
- Lithuanian Institute of History, Kražių st. 5, Vilnius 01108, Lithuania
| | - Giedrė Piličiauskienė
- Faculty of History, Vilnius University, Universiteto st. 7, Vilnius 01513, Lithuania
| | - Alexandre Lucquin
- BioArCh, Department of Archaeology, University of York, Heslington, York, YO10 5DD, UK
| | - Carl Heron
- Department of Scientific Research, The British Museum, Great Russell Street, London, WC1B 3DG, UK
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, Heslington, York, YO10 5DD, UK
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