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Psonis N, Vassou D, Nafplioti A, Tabakaki E, Pavlidis P, Stamatakis A, Poulakakis N. Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes. Forensic Sci Int Genet 2024; 71:103060. [PMID: 38796876 DOI: 10.1016/j.fsigen.2024.103060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/29/2024]
Abstract
In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond.
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Affiliation(s)
- Nikolaos Psonis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece.
| | - Despoina Vassou
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Argyro Nafplioti
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Eugenia Tabakaki
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece
| | - Alexandros Stamatakis
- Institute of Computer Science (ICS), Foundation for Research and Technology-Hellas (FORTH), Irakleio 70013, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Nikos Poulakakis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Irakleio 70013, Greece; Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio 70013, Greece
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2
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Aktürk Ş, Mapelli I, Güler MN, Gürün K, Katırcıoğlu B, Vural KB, Sağlıcan E, Çetin M, Yaka R, Sürer E, Atağ G, Çokoğlu SS, Sevkar A, Altınışık NE, Koptekin D, Somel M. Benchmarking kinship estimation tools for ancient genomes using pedigree simulations. Mol Ecol Resour 2024; 24:e13960. [PMID: 38676702 DOI: 10.1111/1755-0998.13960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024]
Abstract
There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.
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Affiliation(s)
- Şevval Aktürk
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Merve N Güler
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Büşra Katırcıoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Çetin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sevim Seda Çokoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Arda Sevkar
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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3
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Atağ G, Kaptan D, Yüncü E, Başak Vural K, Mereu P, Pirastru M, Barbato M, Leoni GG, Güler MN, Er T, Eker E, Yazıcı TD, Kılıç MS, Altınışık NE, Çelik EA, Morell Miranda P, Dehasque M, Floridia V, Götherström A, Bilgin CC, Togan İ, Günther T, Özer F, Hadjisterkotis E, Somel M. Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages. Genome Biol Evol 2024; 16:evae090. [PMID: 38670119 PMCID: PMC11109821 DOI: 10.1093/gbe/evae090] [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: 01/15/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.
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Affiliation(s)
- Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Paolo Mereu
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Monica Pirastru
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Mario Barbato
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | | | - Merve Nur Güler
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Tuğçe Er
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Elifnaz Eker
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Tunca Deniz Yazıcı
- Graduate School for Evolution, Ecology and Systematics, Ludwig Maximillian University of Munich, Munich, Germany
| | - Muhammed Sıddık Kılıç
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | | | - Ecem Ayşe Çelik
- Department of Settlement Archeology, Middle East Technical University, Ankara, Turkey
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Marianne Dehasque
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Viviana Floridia
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
| | - Cemal Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Eleftherios Hadjisterkotis
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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4
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Heraclides A, Aristodemou A, Georgiou AN, Antoniou M, Ilgner E, Davranoglou LR. Palaeogenomic insights into the origins of early settlers on the island of Cyprus. Sci Rep 2024; 14:9632. [PMID: 38671010 PMCID: PMC11053055 DOI: 10.1038/s41598-024-60161-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Archaeological evidence supports sporadic seafaring visits to the Eastern Mediterranean island of Cyprus by Epipaleolithic hunter-gatherers over 12,000 years ago, followed by permanent settlements during the early Neolithic. The geographical origins of these early seafarers have so far remained elusive. By systematically analysing all available genomes from the late Pleistocene to early Holocene Near East (c. 14,000-7000 cal BCE), we provide a comprehensive overview of the genetic landscape of the early Neolithic Fertile Crescent and Anatolia and infer the likely origins of three recently published genomes from Kissonerga-Mylouthkia (Cypriot Late Pre-Pottery Neolithic B, c. 7600-6800 cal BCE). These appear to derive roughly 80% of their ancestry from Aceramic Neolithic Central Anatolians residing in or near the Konya plain, and the remainder from a genetically basal Levantine population. Based on genome-wide weighted ancestry covariance analysis, we infer that this admixture event took place roughly between 14,000 and 10,000 BCE, coinciding with the transition from the Cypriot late Epipaleolithic to the Pre-Pottery Neolithic A (PPNA). Additionally, we identify strong genetic affinities between the examined Cypro-LPPNB individuals and later northwestern Anatolians and the earliest European Neolithic farmers. Our results inform archaeological evidence on prehistoric demographic processes in the Eastern Mediterranean, providing important insights into early seafaring, maritime connections, and insular settlement.
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Affiliation(s)
- Alexandros Heraclides
- School of Sciences, European University Cyprus, 6 Diogenis Str., 2404 Engomi, P.O. Box: 22006, 1516, Nicosia, Cyprus.
| | - Aris Aristodemou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Andrea N Georgiou
- School of Sciences, European University Cyprus, 6 Diogenis Str., 2404 Engomi, P.O. Box: 22006, 1516, Nicosia, Cyprus
| | - Marios Antoniou
- Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece
| | - Elisabeth Ilgner
- School of Archaeology/Merton College, University of Oxford, Oxford, UK
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5
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [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: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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6
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Gavashelishvili A, Chukhua M, Sakhltkhutsishvili K, Koptekin D, Somel M. The time and place of origin of South Caucasian languages: insights into past human societies, ecosystems and human population genetics. Sci Rep 2023; 13:21133. [PMID: 38036582 PMCID: PMC10689496 DOI: 10.1038/s41598-023-45500-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/20/2023] [Indexed: 12/02/2023] Open
Abstract
This study re-examines the linguistic phylogeny of the South Caucasian linguistic family (aka the Kartvelian linguistic family) and attempts to identify its Urheimat. We apply Bayesian phylogenetics to infer a dated phylogeny of the South Caucasian languages. We infer the Urheimat and the reasons for the split of the Kartvelian languages by taking into consideration (1) the past distribution ranges of wildlife elements whose names can be traced back to proto-Kartvelian roots, (2) the distribution ranges of past cultures and (3) the genetic variations of past and extant human populations. Our best-fit Bayesian phylogenetic model is in agreement with the widely accepted topology suggested by previous studies. However, in contrast to these studies, our model suggests earlier mean split dates, according to which the divergence between Svan and Karto-Zan occurred in the early Copper Age, while Georgian and Zan diverged in the early Iron Age. The split of Zan into Megrelian and Laz is widely attributed to the spread of Georgian and/or Georgian speakers in the seventh-eighth centuries CE. Our analyses place the Kartvelian Urheimat in an area that largely intersects the Colchis glacial refugium in the South Caucasus. The divergence of Kartvelian languages is strongly associated with differences in the rate of technological expansions in relation to landscape heterogeneity, as well as the emergence of state-run communities. Neolithic societies could not colonize dense forests, whereas Copper Age societies made limited progress in this regard, but not to the same degree of success achieved by Bronze and Iron Age societies. The paper also discusses the importance of glacial refugia in laying the foundation for linguistic families and where Indo-European languages might have originated.
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Affiliation(s)
- Alexander Gavashelishvili
- Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Cholokashvili Str. 5, 0162, Tbilisi, Georgia.
| | - Merab Chukhua
- Head of the Institute of Caucasiology, Faculty of Humanities, Ivane Javakhishvili Tbilisi State University, Ilia Chavchavadze Str. 1, 0162, Tbilisi, Georgia
| | - Kakhi Sakhltkhutsishvili
- Georgian DNA Project, Family Tree DNA, Ilia State University, Cholokashvili Str. 5, 0162, Tbilisi, Georgia
| | - Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
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7
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Williams MP, Flegontov P, Maier R, Huber CD. Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566841. [PMID: 38014190 PMCID: PMC10680674 DOI: 10.1101/2023.11.13.566841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and the f3-statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate and P-values of qpAdm models, and f3-statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-length f2-statistics, demonstrating the improved demographic inference that could be achieved with advancements in f-statistic estimations.
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Affiliation(s)
- Matthew P. Williams
- Pennsylvania State University, Department of Biology, University Park, PA 16802, USA
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian D. Huber
- Pennsylvania State University, Department of Biology, University Park, PA 16802, USA
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8
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Moots HM, Antonio M, Sawyer S, Spence JP, Oberreiter V, Weiß CL, Lucci M, Cherifi YMS, La Pastina F, Genchi F, Praxmeier E, Zagorc B, Cheronet O, Özdoğan KT, Demetz L, Amrani S, Candilio F, De Angelis D, Gasperetti G, Fernandes D, Gao Z, Fantar M, Coppa A, Pritchard JK, Pinhasi R. A genetic history of continuity and mobility in the Iron Age central Mediterranean. Nat Ecol Evol 2023; 7:1515-1524. [PMID: 37592021 DOI: 10.1038/s41559-023-02143-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/30/2023] [Indexed: 08/19/2023]
Abstract
The Iron Age was a dynamic period in central Mediterranean history, with the expansion of Greek and Phoenician colonies and the growth of Carthage into the dominant maritime power of the Mediterranean. These events were facilitated by the ease of long-distance travel following major advances in seafaring. We know from the archaeological record that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. Here, to investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from coastal cities around the central Mediterranean, in Tunisia, Sardinia and central Italy. We observe a meaningful contribution of autochthonous populations, as well as highly heterogeneous ancestry including many individuals with non-local ancestries from other parts of the Mediterranean region. These results highlight both the role of local populations and the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbours together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.
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Affiliation(s)
- Hannah M Moots
- Stanford Archaeology Center, Stanford University, Stanford, CA, USA
- Department of Anthropology, Stanford University, Stanford, CA, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Margaret Antonio
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | | | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Clemens L Weiß
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michaela Lucci
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Yahia Mehdi Seddik Cherifi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Cardiolo-Oncology Research Collaborative Group (CORCG), Faculty of Medicine, Benyoucef Benkhedda University, Algiers, Algeria
- Molecular Pathology, University Paul Sabatier Toulouse III, Toulouse, France
| | | | - Francesco Genchi
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Department of Oriental Studies, Sapienza University of Rome, Rome, Italy
| | - Elisa Praxmeier
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of History and Art History, Utrecht University, Utrecht, the Netherlands
| | - Lea Demetz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Selma Amrani
- LBEIG, Population Genetics and Conservation Unit, Department of Cellular and Molecular Biology-Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene, Algiers, Algeria
| | | | - Daniela De Angelis
- Museo Nazionale Etrusco di Tarquinia, Direzione Generale Musei Lazio, Rome, Italy
| | - Gabriella Gasperetti
- Soprintendenza Archeologia, belle arti e paesaggio per le province di Sassari e Nuoro, Sassari, Italy
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ziyue Gao
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Mounir Fantar
- Département des Monuments et des Sites Antiques-Institut National du Patrimoine INP, Tunis, Tunisia
| | - Alfredo Coppa
- Department of Biology, Stanford University, Stanford, CA, USA
- Dipartimento di Storia Antropologia Religioni Arte Spettacolo, Sapienza Università di Roma, Rome, Italy
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Genetics, Harvard Medical School, Cambridge, MA, USA.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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Aqil A, Gill S, Gokcumen O, Malhi RS, Reese EA, Smith JL, Heaton TT, Lindqvist C. A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. iScience 2023; 26:106581. [PMID: 37138779 PMCID: PMC10149335 DOI: 10.1016/j.isci.2023.106581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.
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Affiliation(s)
- Alber Aqil
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Ripan S. Malhi
- Department of Anthropology and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Jane L. Smith
- USDA-Forest Service, Tongass National Forest, Petersburg, AK 99833, USA
| | - Timothy T. Heaton
- Department of Earth Sciences, University of South Dakota, Vermillion, SD 57069, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
- Corresponding author
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