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Living fossils unearthed by blasting human chromosomes with Neanderthal mtDNA. DIGITAL CHINESE MEDICINE 2022. [DOI: 10.1016/j.dcmed.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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2
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Sarno S, Cilli E, Serventi P, De Fanti S, Corona A, Fontani F, Traversari M, Ferri G, Fariselli AC, Luiselli D. Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia). Ann Hum Biol 2021; 48:247-259. [PMID: 34459340 DOI: 10.1080/03014460.2021.1937699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Phoenician and Punic expansions have been protagonists of intense trade networks and settlements in the Mediterranean Sea. AIMS The maternal genetic variability of ancient Punic samples from the Sardinian necropolis of Tharros was analysed, with the aim to explore genetic interactions and signatures of past population events. SUBJECTS AND METHODS The mtDNA HVS-I and coding region SNPs were analysed in 14 Punic samples and 74 modern individuals from Cabras and Belvì (for which the HVS-II region was also analysed). The results were compared with 5,590 modern Euro-Mediterranean sequences and 127 ancient samples. RESULTS While contemporary groups fall within the genetic variability of other modern Sardinians, our Punic samples reveal proximity to present-day North-African and Iberian populations. Furthermore, Cabras and Belvì cluster mainly with pre-Phoenician groups, while samples from Tharros project with other Punic Sardinian individuals. CONCLUSION This study provides the first preliminary insights into the population dynamics of the Punic site of Tharros. While the number of currently available samples does not allow definitive investigation of the connection with indigenous Sardinian groups, our results seem to confirm internal migratory phenomena in the central-western Mediterranean and female participation in the Punic mobility.
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Affiliation(s)
- Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Patrizia Serventi
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, Bologna, Italy
| | - Andrea Corona
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Dipartimento di Scienze del Sistema Nervoso e del Comportamento, Università di Pavia, Pavia, Italy
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Mirko Traversari
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Gianmarco Ferri
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. Inferring archaic introgression from hominin genetic data. Evol Anthropol 2021; 30:199-220. [PMID: 33951239 PMCID: PMC8360192 DOI: 10.1002/evan.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/03/2020] [Accepted: 03/29/2021] [Indexed: 01/05/2023]
Abstract
Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA
| | - Laura T Buck
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, University of California, Davis, California, USA.,UC Davis Genome Center, University of California, Davis, California, USA
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4
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Kontopoulos I, Penkman K, Mullin VE, Winkelbach L, Unterländer M, Scheu A, Kreutzer S, Hansen HB, Margaryan A, Teasdale MD, Gehlen B, Street M, Lynnerup N, Liritzis I, Sampson A, Papageorgopoulou C, Allentoft ME, Burger J, Bradley DG, Collins MJ. Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PLoS One 2020; 15:e0235146. [PMID: 32584871 PMCID: PMC7316274 DOI: 10.1371/journal.pone.0235146] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals’ size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.
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Affiliation(s)
- Ioannis Kontopoulos
- Department of Archaeology, BioArCh, University of York, York, United Kingdom
- * E-mail:
| | - Kirsty Penkman
- Department of Chemistry, BioArCh, University of York, York, United Kingdom
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martina Unterländer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
- German Federal Criminal Police Office, Wiesbaden, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Henrik B. Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Birgit Gehlen
- Collaborative Research Centre, project D4, Cologne University, Cologne, Germany
| | - Martin Street
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM Leibniz Research Institute for Archaeology, Neuwied, Germany
| | - Niels Lynnerup
- Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ioannis Liritzis
- Laboratory of Archaeometry, Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
- Center on Yellow River Civilization of Henan Province, Key Research Institute of Yellow River Civilization and Sustainable Development and Collaborative Innovation, Henan University, Kaifeng, China
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
| | - Morten E. Allentoft
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Matthew J. Collins
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- Centre for Evogenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Serventi P, Panicucci C, Bodega R, De Fanti S, Sarno S, Fondevila Alvarez M, Brisighelli F, Trombetta B, Anagnostou P, Ferri G, Vazzana A, Delpino C, Gruppioni G, Luiselli D, Cilli E. Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC). Ann Hum Biol 2018; 45:34-43. [PMID: 29216758 DOI: 10.1080/03014460.2017.1414876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis. SUBJECTS AND METHODS In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers. RESULTS The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here. CONCLUSIONS This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials.
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Affiliation(s)
- Patrizia Serventi
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy.,b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Panicucci
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Roberta Bodega
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Sara De Fanti
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Manuel Fondevila Alvarez
- c Instituto de Ciencias Forenses 'Luis Concheiro' , University of Santiago de Compostela, Santiago de Compostela , Galicia , Spain
| | - Francesca Brisighelli
- d Sezione di Medicina Legale-Istituto di Sanità Pubblica , Università Cattolica del Sacro Cuore , Roma , Italy
| | - Beniamino Trombetta
- e Department of Biology and Biotechnology 'Charles Darwin' , Sapienza University , Rome , Italy
| | - Paolo Anagnostou
- f Department of Environmental Biology , University of Rome 'La Sapienza' , Rome , Italy.,g ISItA, Istituto Italiano di Antropologia , Rome , Italy
| | - Gianmarco Ferri
- h Department of Diagnostic and Clinical Medicine and Public Health , University of Modena and Reggio Emilia , Modena , Italy
| | - Antonino Vazzana
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Delpino
- i Superintendence of Archaeological Heritage of Marche Region , Ancona , Italy
| | - Giorgio Gruppioni
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Elisabetta Cilli
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
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De Fanti S, Vianello D, Giuliani C, Quagliariello A, Cherubini A, Sevini F, Iaquilano N, Franceschi C, Sazzini M, Luiselli D. Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:843-850. [PMID: 27822964 DOI: 10.1080/24701394.2016.1197218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.
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Affiliation(s)
- Sara De Fanti
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Dario Vianello
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Cristina Giuliani
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Andrea Quagliariello
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Anna Cherubini
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Federica Sevini
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Nicoletta Iaquilano
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Claudio Franceschi
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Marco Sazzini
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Donata Luiselli
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
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7
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Meng X, Pei H, Lan C. The mitochondrial tRNA(Gln) T4353C mutation may not be associated with essential hypertension in Han Chinese population. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:3311-2. [PMID: 25693701 DOI: 10.3109/19401736.2015.1018199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We reported here the possible role of a mitochondrial tRNA mutation: T4353C in clinical expression of essential hypertension in Chinese population. The human mammalian mitochondrial tRNA database was used to analyze the conservation index of this mutation between different species. Moreover, phylogenetic analysis showed that the T4353C mutation belonged to human mitochondrial haplogroup HV, a West Eurasian haplogroup found throughout Western Asia and Eastern European but was infrequent in China. In addition, structural prediction of the T4353C mutation indicated that this transition did not alter the secondary structure of tRNA(Gln). Together, our data indicated that the T4353C mutation occurred infrequent and may not be associated with essential hypertension in Han Chinese population.
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Affiliation(s)
- Xing Meng
- a Department of Emergency , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Hui Pei
- a Department of Emergency , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Chao Lan
- a Department of Emergency , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
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Bouwman A, Rühli F. Archaeogenetics in evolutionary medicine. J Mol Med (Berl) 2016; 94:971-7. [PMID: 27289479 DOI: 10.1007/s00109-016-1438-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/22/2016] [Accepted: 06/03/2016] [Indexed: 12/24/2022]
Abstract
Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.
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López S, van Dorp L, Hellenthal G. Human Dispersal Out of Africa: A Lasting Debate. Evol Bioinform Online 2016; 11:57-68. [PMID: 27127403 PMCID: PMC4844272 DOI: 10.4137/ebo.s33489] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023] Open
Abstract
Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings.
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Affiliation(s)
- Saioa López
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London, UK
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De Fanti S, Barbieri C, Sarno S, Sevini F, Vianello D, Tamm E, Metspalu E, van Oven M, Hübner A, Sazzini M, Franceschi C, Pettener D, Luiselli D. Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia. PLoS One 2015; 10:e0144391. [PMID: 26640946 PMCID: PMC4671665 DOI: 10.1371/journal.pone.0144391] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 11/17/2015] [Indexed: 02/08/2023] Open
Abstract
Genetic signatures from the Paleolithic inhabitants of Eurasia can be traced from the early divergent mitochondrial DNA lineages still present in contemporary human populations. Previous studies already suggested a pre-Neolithic diffusion of mitochondrial haplogroup HV*(xH,V) lineages, a relatively rare class of mtDNA types that includes parallel branches mainly distributed across Europe and West Asia with a certain degree of structure. Up till now, variation within haplogroup HV was addressed mainly by analyzing sequence data from the mtDNA control region, except for specific sub-branches, such as HV4 or the widely distributed haplogroups H and V. In this study, we present a revised HV topology based on full mtDNA genome data, and we include a comprehensive dataset consisting of 316 complete mtDNA sequences including 60 new samples from the Italian peninsula, a previously underrepresented geographic area. We highlight points of instability in the particular topology of this haplogroup, reconstructed with BEAST-generated trees and networks. We also confirm a major lineage expansion that probably followed the Late Glacial Maximum and preceded Neolithic population movements. We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent.
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Affiliation(s)
- Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Chiara Barbieri
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- * E-mail: (CB); (DL)
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federica Sevini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy
| | - Dario Vianello
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy
| | - Erika Tamm
- Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Mannis van Oven
- Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marco Sazzini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy
- IRCCS, Institute of Neurological Sciences of Bologna, Ospedale Bellaria, Bologna, Italy
- CNR, Institute of Organic Synthesis and Photoreactivity (ISOF), Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- * E-mail: (CB); (DL)
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11
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Rivollat M, Mendisco F, Pemonge MH, Safi A, Saint-Marc D, Brémond A, Couture-Veschambre C, Rottier S, Deguilloux MF. When the waves of European Neolithization met: first paleogenetic evidence from early farmers in the southern Paris Basin. PLoS One 2015; 10:e0125521. [PMID: 25928633 PMCID: PMC4415815 DOI: 10.1371/journal.pone.0125521] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/14/2015] [Indexed: 11/19/2022] Open
Abstract
An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.
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Affiliation(s)
- Maïté Rivollat
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Fanny Mendisco
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Audrey Safi
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Didier Saint-Marc
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Antoine Brémond
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Christine Couture-Veschambre
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Stéphane Rottier
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-France Deguilloux
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
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12
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Hagelberg E, Hofreiter M, Keyser C. Introduction. Ancient DNA: the first three decades. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130371. [PMID: 25487324 PMCID: PMC4275880 DOI: 10.1098/rstb.2013.0371] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Erika Hagelberg
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Christine Keyser
- Institut de Médecine Légale, Laboratoire AMIS, Université de Strasbourg, CNRS UMR 5288, Strasbourg, France
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Marciniak S, Klunk J, Devault A, Enk J, Poinar HN. Ancient human genomics: the methodology behind reconstructing evolutionary pathways. J Hum Evol 2015; 79:21-34. [PMID: 25601038 DOI: 10.1016/j.jhevol.2014.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 09/09/2014] [Accepted: 11/07/2014] [Indexed: 11/15/2022]
Abstract
High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility.
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Affiliation(s)
- Stephanie Marciniak
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada.
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Alison Devault
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; MYcroarray, Ann Arbor, MI, USA
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; MYcroarray, Ann Arbor, MI, USA
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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14
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution. Balkan J Med Genet 2014; 17:5-14. [PMID: 25741209 PMCID: PMC4347471 DOI: 10.2478/bjmg-2014-0019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data.
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Brandt G, Szécsényi-Nagy A, Roth C, Alt KW, Haak W. Human paleogenetics of Europe--the known knowns and the known unknowns. J Hum Evol 2014; 79:73-92. [PMID: 25467114 DOI: 10.1016/j.jhevol.2014.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/25/2014] [Accepted: 06/19/2014] [Indexed: 12/01/2022]
Abstract
The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Anna Szécsényi-Nagy
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany; Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1014 Budapest, Hungary
| | - Christina Roth
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Kurt Werner Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Richard-Wagner-Straße 9, D-06114 Halle, Germany; Institute for Prehistory and Archaeological Science, Basel University, Petersplatz 1, 4003 Basel, Switzerland; Danube Private University, Faculty of Medicine and Dentistry, Doktor-Karl-Dorrek-Straße 23, 3500 Krems an der Donau, Austria
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia.
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Antonioli F, Lo Presti V, Morticelli MG, Bonfiglio L, Mannino MA, Palombo MR, Sannino G, Ferranti L, Furlani S, Lambeck K, Canese S, Catalano R, Chiocci FL, Mangano G, Scicchitano G, Tonielli R. Timing of the emergence of the Europe–Sicily bridge (40–17 cal ka BP) and its implications for the spread of modern humans. ACTA ACUST UNITED AC 2014. [DOI: 10.1144/sp411.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractThe submerged sill in the Strait of Messina, which is located today at a minimum depth of 81 m below sea level (bsl), represents the only land connection between Sicily and mainland Italy (and thus Europe) during the last lowstand when the sea level locally stood at about 126 m bsl. Today, the sea crossing to Sicily, although it is less than 4 km at the narrowest point, faces hazardous sea conditions, made famous by the myth of Scylla and Charybdis. Through a multidisciplinary research project, we document the timing and mode of emergence of this land connection during the last 40 kyr. The integrated analysis takes into consideration morphobathymetric and lithological data, and relative sea-level change (both isostatic and tectonic), resulting in the hypothesis that a continental land bridge lasted for at least 500 years between 21.5 and 20 cal ka BP. The emergence may have occurred over an even longer time span if one allows for seafloor erosion by marine currents that have lowered the seabed since the Last Glacial Maximum (LGM). Modelling of palaeotidal velocities shows that sea crossings when sea level was lower than present would have faced even stronger and more hazardous sea currents than today, supporting the hypothesis that earliest human entry into Sicily most probably took place on foot during the period when the sill emerged as dry land. This hypothesis is compared with an analysis of Pleistocene vertebrate faunas in Sicily and mainland Italy, including a new radiocarbon date on bone collagen of an Equus hydruntinus specimen from Grotta di San Teodoro (23–21 cal ka BP), the dispersal abilities of the various animal species involved, particularly their swimming abilities, and the Palaeolithic archaeological record, all of which support the hypothesis of a relatively late land-based colonization of Sicily by Homo sapiens.
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Affiliation(s)
| | - Valeria Lo Presti
- Earth and Marine Science Deptartment, Palermo University, Palermo, Italy
| | | | - Laura Bonfiglio
- Fauna Museum, Department of Veterinary Science, Messina University, Messina, Italy
| | - Marcello A. Mannino
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Luigi Ferranti
- DiSTAR, Earth Science, Environmental and Resources Department, University of Naples, Naples, Italy
| | - Stefano Furlani
- Mathematics and Geoscience Deptartment, University of Trieste, Trieste, Italy
| | - Kurt Lambeck
- Australian National University, Canberra, ACT, Australia
- Ecole Normale Supérieure, Paris, France
| | - Simonepietro Canese
- ISPRA Italian National Institute for Environmental Protection and Research, Rome, Italy
| | - Raimondo Catalano
- Earth and Marine Science Deptartment, Palermo University, Palermo, Italy
| | | | - Gabriella Mangano
- Fauna Museum, Department of Veterinary Science, Messina University, Messina, Italy
| | - Giovanni Scicchitano
- Studio Geologi Associati T.S.T., Catania, Italy
- Earth and Marine Science Department, Catania University, Catania, Italy
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19
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An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy. PLoS One 2014; 9:e96074. [PMID: 24788788 PMCID: PMC4005757 DOI: 10.1371/journal.pone.0096074] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/03/2014] [Indexed: 11/19/2022] Open
Abstract
Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.
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20
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Genes, Fossils, and Culture. An Overview of the Evidence for Neandertal–Modern Human Interaction and Admixture. ACTA ACUST UNITED AC 2014. [DOI: 10.1017/s0079497x00000761] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This paper re-examines current arguments concerning the evidence for Neandertal-modern human interaction and admixture. While most researchers now agree that the ancestry of all present day humans can be traced back to African late Middle Pleistocene populations, at a time when the remainder of Eurasia was inhabited by ‘archaic humans’, most notably the Neandertals, issues that remain to be resolved are the tempo and mode of early modern human dispersal and interaction with archaic humans.This paper focuses on what happened at the time of contact in Europe, and assesses the level of admixture that may have occurred, as well as the extent to which such level may have varied in both time and space. It explains how the available mtDNA evidence does not preclude admixture at the time of contact, and is in fact consistent, depending on a number of parameters, with a possibly substantial Neandertal contribution to the initial modern human population of Europe. It is argued that the absence of Neandertal mtDNA lineages among present Europeans is likely, on dating evidence, to be simply a particular case of generalised loss of Pleistocene mtDNA lineages. Although the full range of interaction types (mutual avoidance, hostile confrontation, full integration) is conceivable, there is plenty of archaeological evidence to suggest that admixture must have been the general rule, and that the paleontological evidence for the generalised presence of archaic traits among Europe's earliest moderns implies the transmission of genes, and indicates that mixed groups should have been reproductively viable. In this context, it would seem that the most parsimonious explanation for the disappearance of the Neandertal mtDNA lineage is genetic swamping.
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Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Möller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nicklisch N, Pickrell JK, Sirocko F, Reich D, Cooper A, Alt KW. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science 2013; 342:257-61. [PMID: 24115443 DOI: 10.1126/science.1241844] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany.
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22
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Lacan M, Keyser C, Crubézy E, Ludes B. Ancestry of modern Europeans: contributions of ancient DNA. Cell Mol Life Sci 2013; 70:2473-87. [PMID: 23052219 PMCID: PMC11113793 DOI: 10.1007/s00018-012-1180-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 09/21/2012] [Accepted: 09/24/2012] [Indexed: 12/25/2022]
Abstract
Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period.
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Affiliation(s)
- Marie Lacan
- Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde,Toulouse cedex 3, France.
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Condemi S, Mounier A, Giunti P, Lari M, Caramelli D, Longo L. Possible interbreeding in late Italian Neanderthals? New data from the Mezzena jaw (Monti Lessini, Verona, Italy). PLoS One 2013; 8:e59781. [PMID: 23544098 PMCID: PMC3609795 DOI: 10.1371/journal.pone.0059781] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/18/2013] [Indexed: 01/08/2023] Open
Abstract
In this article we examine the mandible of Riparo Mezzena a Middle Paleolithic rockshelter in the Monti Lessini (NE Italy, Verona) found in 1957 in association with Charentian Mousterian lithic assemblages. Mitochondrial DNA analysis performed on this jaw and on other cranial fragments found at the same stratigraphic level has led to the identification of the only genetically typed Neanderthal of the Italian peninsula and has confirmed through direct dating that it belongs to a late Neanderthal. Our aim here is to re-evaluate the taxonomic affinities of the Mezzena mandible in a wide comparative framework using both comparative morphology and geometric morphometrics. The comparative sample includes mid-Pleistocene fossils, Neanderthals and anatomically modern humans. This study of the Mezzena jaw shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, La Ferrassie, Saint-Césaire). In our view, this change in morphology among late Neanderthals supports the hypothesis of anatomical change of late Neanderthals and the hypothesis of a certain degree of interbreeding with AMHs that, as the dating shows, was already present in the European territory. Our observations on the chin of the Mezzena mandible lead us to support a non abrupt phylogenetic transition for this period in Europe.
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Affiliation(s)
- Silvana Condemi
- UMR 7268 CNRS/Aix-Marseille Université/EFS ADES - Anthropologie bioculturelle, Droit, Ethique et Santé Faculté de Médecine - Secteur Nord Aix-Marseille Université, Marseille, France
- * E-mail: (SC); (LL)
| | - Aurélien Mounier
- UMR 7268 CNRS/Aix-Marseille Université/EFS ADES - Anthropologie bioculturelle, Droit, Ethique et Santé Faculté de Médecine - Secteur Nord Aix-Marseille Université, Marseille, France
- The Leverhulme Centre for Human Evolutionary Studies Biological, Anthropology Division, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Giunti
- Istituto Italiano di Preistoria e Protostoria, Firenze, Italy
| | - Martina Lari
- Università di Firenze, Dipartimento di Biologia Evoluzionistica, Laboratorio di Antropologia,Unità di Antropologia Molecolare/Paleogenetica, Firenze, Italy
| | - David Caramelli
- Università di Firenze, Dipartimento di Biologia Evoluzionistica, Laboratorio di Antropologia,Unità di Antropologia Molecolare/Paleogenetica, Firenze, Italy
| | - Laura Longo
- Musei Civici Fiorentini, Firenze, Italy
- * E-mail: (SC); (LL)
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Pilli E, Modi A, Serpico C, Achilli A, Lancioni H, Lippi B, Bertoldi F, Gelichi S, Lari M, Caramelli D. Monitoring DNA contamination in handled vs. directly excavated ancient human skeletal remains. PLoS One 2013; 8:e52524. [PMID: 23372650 PMCID: PMC3556025 DOI: 10.1371/journal.pone.0052524] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/15/2012] [Indexed: 11/18/2022] Open
Abstract
Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14(th) century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as "virgin samples" (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called "lab samples"(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from "lab samples" are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the "virgin samples" set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between "lab" and "virgin" samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.
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Affiliation(s)
- Elena Pilli
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Alessandra Modi
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Ciro Serpico
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Barbara Lippi
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
| | - Francesca Bertoldi
- Dipartimento di Studi Umanistici, Università Ca' Foscari Venezia, Venezia, Italy
| | - Sauro Gelichi
- Dipartimento di Studi Umanistici, Università Ca' Foscari Venezia, Venezia, Italy
| | - Martina Lari
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
- * E-mail:
| | - David Caramelli
- Dipartimento di Biologia Evoluzionistica Laboratori di Antropologia, Università di Firenze, Firenze, Italy
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Origin and diet of the prehistoric hunter-gatherers on the mediterranean island of Favignana (Ègadi Islands, Sicily). PLoS One 2012; 7:e49802. [PMID: 23209602 PMCID: PMC3509116 DOI: 10.1371/journal.pone.0049802] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/16/2012] [Indexed: 11/19/2022] Open
Abstract
Hunter-gatherers living in Europe during the transition from the late Pleistocene to the Holocene intensified food acquisition by broadening the range of resources exploited to include marine taxa. However, little is known on the nature of this dietary change in the Mediterranean Basin. A key area to investigate this issue is the archipelago of the Ègadi Islands, most of which were connected to Sicily until the early Holocene. The site of Grotta d’Oriente, on the present-day island of Favignana, was occupied by hunter-gatherers when Postglacial environmental changes were taking place (14,000-7,500 cal BP). Here we present the results of AMS radiocarbon dating, palaeogenetic and isotopic analyses undertaken on skeletal remains of the humans buried at Grotta d’Oriente. Analyses of the mitochondrial hypervariable first region of individual Oriente B, which belongs to the HV-1 haplogroup, suggest for the first time on genetic grounds that humans living in Sicily during the early Holocene could have originated from groups that migrated from the Italian Peninsula around the Last Glacial Maximum. Carbon and nitrogen isotope analyses show that the Upper Palaeolithic and Mesolithic hunter-gatherers of Favignana consumed almost exclusively protein from terrestrial game and that there was only a slight increase in marine food consumption from the late Pleistocene to the early Holocene. This dietary change was similar in scale to that at sites on mainland Sicily and in the rest of the Mediterranean, suggesting that the hunter-gatherers of Grotta d’Oriente did not modify their subsistence strategies specifically to adapt to the progressive isolation of Favignana. The limited development of technologies for intensively exploiting marine resources was probably a consequence both of Mediterranean oligotrophy and of the small effective population size of these increasingly isolated human groups, which made innovation less likely and prevented transmission of fitness-enhancing adaptations.
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Disotell TR. Archaic human genomics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149 Suppl 55:24-39. [PMID: 23124308 DOI: 10.1002/ajpa.22159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/18/2022]
Abstract
For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history.
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Affiliation(s)
- Todd R Disotell
- Center for Study of Human Origins, Department of Anthropology, New York University, New York, NY 10003, USA.
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Pinhasi R, Thomas MG, Hofreiter M, Currat M, Burger J. The genetic history of Europeans. Trends Genet 2012; 28:496-505. [PMID: 22889475 DOI: 10.1016/j.tig.2012.06.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 06/16/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
Abstract
The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.
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Affiliation(s)
- Ron Pinhasi
- Department of Archaeology, University College Cork, Cork, Ireland.
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Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
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Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
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30
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O'Rourke D, Enk J. Genetics, Geography, and Human Variation. Hum Biol 2012. [DOI: 10.1002/9781118108062.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Perego UA, Achilli A, Ekins JE, Milani L, Lari M, Pilli E, Brown A, Price EP, Wolken SR, Matthews M, Allen CA, Pearson TR, Angerhofer N, Caramelli D, Kupferschmid T, Keim PS, Woodward SR. The Mountain Meadows Massacre and "poisoned springs": scientific testing of the more recent, anthrax theory. Int J Legal Med 2012; 127:77-83. [PMID: 22395921 PMCID: PMC3538018 DOI: 10.1007/s00414-012-0681-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/14/2012] [Indexed: 10/29/2022]
Abstract
It has been recorded that one of the possible causes that eventually escalated into the 1857 manslaughter at Mountain Meadows in Southern Utah was the poisoning of an open spring by the Fancher-Baker party as they crossed the Utah territory on their way from Arkansas to California. Historical accounts report that a number of cattle died, followed by human casualties from those that came in contact with the dead animals. Even after the Arkansas party departed, animals continued to perish and people were still afflicted by some unknown plague. Proctor Hancock Robison, a local 14-year-old boy, died shortly after skinning one of the "poisoned" cows. A careful review of the historical records, along with the more recent scientific literature, seems to exclude the likelihood of actual poisoning in favor of a more recent theory that would point to the bacterium Bacillus anthracis as the possible cause of human and animal deaths. In order to test this hypothesis, Proctor's remains were exhumed, identified through mitochondrial DNA analysis, and tested for the presence of anthrax spores. Although preliminary testing of remains and soil was negative, description of the clinical conditions that affected Proctor and other individuals does not completely rule out the hypothesis of death by anthrax.
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Affiliation(s)
- Ugo A Perego
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA.
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Gamba C, Fernández E, Tirado M, Deguilloux MF, Pemonge MH, Utrilla P, Edo M, Molist M, Rasteiro R, Chikhi L, Arroyo-Pardo E. Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers. Mol Ecol 2011; 21:45-56. [PMID: 22117930 DOI: 10.1111/j.1365-294x.2011.05361.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations-N* and X1-are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (F(ST) ∼0.13, P<10(-5)), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.
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Affiliation(s)
- C Gamba
- Laboratorio de Genética Forense y Genética de Poblaciones, Facultad de Medicina, Pabellón 7, 4ª Planta, Universidad Complutense de Madrid, Avenida Complutense s/n, 28040 Madrid, Spain.
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Ghirotto S, Tassi F, Benazzo A, Barbujani G. No evidence of Neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:242-52. [DOI: 10.1002/ajpa.21569] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 05/10/2011] [Indexed: 11/06/2022]
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Winters M, Barta JL, Monroe C, Kemp BM. To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples. PLoS One 2011; 6:e21247. [PMID: 21738625 PMCID: PMC3124491 DOI: 10.1371/journal.pone.0021247] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/24/2011] [Indexed: 01/06/2023] Open
Abstract
The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones.To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous.
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Affiliation(s)
- Misa Winters
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jodi Lynn Barta
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
| | - Cara Monroe
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, University of California-Santa Barbara, Santa Barbara, California, United States of America
| | - Brian M. Kemp
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America
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Deguilloux MF, Ricaud S, Leahy R, Pemonge MH. Analysis of ancient human DNA and primer contamination: one step backward one step forward. Forensic Sci Int 2011; 210:102-9. [PMID: 21367547 DOI: 10.1016/j.forsciint.2011.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 12/14/2010] [Accepted: 02/06/2011] [Indexed: 11/25/2022]
Abstract
The analysis of DNA from archaeological human remains is plagued by a unique set of methodological problems concerning contamination with modern exogenous DNA. Through an original approach, we propose complementary methods to identify all potential sources of contamination and complete guidelines for the validation of ancient human sequences. The study presented was conducted on non-European human samples (Polynesian and Amerindian) which were collected with all precautions during excavation. This permitted us to distinguish without ambiguity authentic and contaminant sequences. The samples' origins and histories were perfectly known, allowing us to trace all potential contamination sources and to determine the efficiency of precautions followed during all steps of the study. The data obtained confirm that precautions taken during sampling effectively prevent contamination. However, we demonstrate that human contamination can also be introduced during genetic analyses even if all precautions are strictly followed. Indeed, numerous human contaminations were detected in template-PCR products and negative controls, resulting in a striking diversity of contaminant mitochondrial DNA sequences. We argue that this contamination partly derives from the primers. To our knowledge, no previous experiment has been performed to investigate primers as a possible source of human contamination despite the fact that this specific type of contamination poses a real problem in terms of validating ancient human DNA studies. Finally, we confirm that the detection of contaminants in negative controls is clearly related to the number of PCR cycles used. This study enhances our understanding of contamination processes and confirms that, in reality, an absolutely contamination-free situation cannot be obtained. As a consequence, we propose improvements to the guidelines usually followed in the field in order to take the highly probable contamination of PCR reagents, including primers, into account.
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Affiliation(s)
- Marie-France Deguilloux
- Université Bordeaux 1, UMR 5199 PACEA, Laboratoire d'Anthropologie des Populations du Passé, Avenue des Facultés, 33405 Talence Cedex,
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Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CSI, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A. Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PLoS Biol 2010; 8:e1000536. [PMID: 21085689 PMCID: PMC2976717 DOI: 10.1371/journal.pbio.1000536] [Citation(s) in RCA: 214] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 09/27/2010] [Indexed: 01/29/2023] Open
Abstract
The first farmers from Central Europe reveal a genetic affinity to modern-day populations from the Near East and Anatolia, which suggests a significant demographic input from this area during the early Neolithic. In Europe, the Neolithic transition (8,000–4,000 b.c.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 b.c.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated b.c.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated b.c.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic. The transition from a hunter–gatherer existence to a sedentary farming-based lifestyle has had key consequences for human groups around the world and has profoundly shaped human societies. Originating in the Near East around 11,000 y ago, an agricultural lifestyle subsequently spread across Europe during the New Stone Age (Neolithic). Whether it was mediated by incoming farmers or driven by the transmission of innovative ideas and techniques remains a subject of continuing debate in archaeology, anthropology, and human population genetics. Ancient DNA from the earliest farmers can provide a direct view of the genetic diversity of these populations in the earliest Neolithic. Here, we compare Neolithic haplogroups and their diversity to a large database of extant European and Eurasian populations. We identified Neolithic haplotypes that left clear traces in modern populations, and the data suggest a route for the migrating farmers that extends from the Near East and Anatolia into Central Europe. When compared to indigenous hunter–gatherer populations, the unique and characteristic genetic signature of the early farmers suggests a significant demographic input from the Near East during the onset of farming in Europe.
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Affiliation(s)
- Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, Australia.
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Lestrel P, Ohtsuki F, Wolfe C. Cranial vault shape in fossil hominids: Fourier descriptors in norma lateralis. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2010; 61:287-313. [DOI: 10.1016/j.jchb.2010.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 07/13/2010] [Indexed: 10/19/2022]
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Brotherton P, Sanchez JJ, Cooper A, Endicott P. Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX. Nucleic Acids Res 2009; 38:e7. [PMID: 19864251 PMCID: PMC2811011 DOI: 10.1093/nar/gkp897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples.
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Affiliation(s)
- Paul Brotherton
- Australian Centre for Ancient DNA, Darling Building, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia
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Is Homo sapiens polytypic? Human taxonomic diversity and its implications. Med Hypotheses 2009; 74:195-201. [PMID: 19695787 DOI: 10.1016/j.mehy.2009.07.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 07/22/2009] [Indexed: 11/23/2022]
Abstract
The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.
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Novelletto A. Y chromosome variation in Europe: Continental and local processes in the formation of the extant gene pool. Ann Hum Biol 2009; 34:139-72. [PMID: 17558587 DOI: 10.1080/03014460701206843] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.
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Endicott P, Sanchez JJ, Pichler I, Brotherton P, Brooks J, Egarter-Vigl E, Cooper A, Pramstaller P. Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman. BMC Genet 2009; 10:29. [PMID: 19545382 PMCID: PMC2717998 DOI: 10.1186/1471-2156-10-29] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 06/19/2009] [Indexed: 12/01/2022] Open
Abstract
Background Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman. Results The multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups. Conclusion The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results.
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Collins MJ, Penkman KEH, Rohland N, Shapiro B, Dobberstein RC, Ritz-Timme S, Hofreiter M. Is amino acid racemization a useful tool for screening for ancient DNA in bone? Proc Biol Sci 2009; 276:2971-7. [PMID: 19493899 PMCID: PMC2817214 DOI: 10.1098/rspb.2009.0563] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Many rare and valuable ancient specimens now carry the scars of ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02–0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for ancient DNA from bone.
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Affiliation(s)
- Matthew J Collins
- BioArCh, Departments of Biology, Archaeology and Chemistry, University of York, York, UK.
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Fabre V, Condemi S, Degioanni A. Genetic evidence of geographical groups among Neanderthals. PLoS One 2009; 4:e5151. [PMID: 19367332 PMCID: PMC2664900 DOI: 10.1371/journal.pone.0005151] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 03/12/2009] [Indexed: 11/18/2022] Open
Abstract
The Neanderthals are a well-distinguished Middle Pleistocene population which inhabited a vast geographical area extending from Europe to western Asia and the Middle East. Since the 1950s paleoanthropological studies have suggested variability in this group. Different sub-groups have been identified in western Europe, in southern Europe and in the Middle East. On the other hand, since 1997, research has been published in paleogenetics, carried out on 15 mtDNA sequences from 12 Neanderthals. In this paper we used a new methodology derived from different bioinformatic models based on data from genetics, demography and paleoanthropology. The adequacy of each model was measured by comparisons between simulated results (obtained by BayesianSSC software) and those estimated from nucleotide sequences (obtained by DNAsp4 software). The conclusions of this study are consistent with existing paleoanthropological research and show that Neanderthals can be divided into at least three groups: one in western Europe, a second in the Southern area and a third in western Asia. Moreover, it seems from our results that the size of the Neanderthal population was not constant and that some migration occurred among the demes.
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Affiliation(s)
- Virginie Fabre
- Laboratoire d'Anthropologie Bio-culturelle, UMR6578 Université de la Méditerranée -CNRS-EFS, Marseille, France
| | - Silvana Condemi
- Laboratoire d'Anthropologie Bio-culturelle, UMR6578 Université de la Méditerranée -CNRS-EFS, Marseille, France
| | - Anna Degioanni
- Laboratoire d'Anthropologie Bio-culturelle, UMR6578 Université de la Méditerranée -CNRS-EFS, Marseille, France
- * E-mail:
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Holt BM, Formicola V. Hunters of the Ice Age: The biology of Upper Paleolithic people. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; Suppl 47:70-99. [PMID: 19003886 DOI: 10.1002/ajpa.20950] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Upper Paleolithic represents both the phase during which anatomically modern humans appeared and the climax of hunter-gatherer cultures. Demographic expansion into new areas that took place during this period and the diffusion of burial practices resulted in an unprecedented number of well-preserved human remains. This skeletal record, dovetailed with archeological, environmental, and chronological contexts, allows testing of hypotheses regarding biological processes at the population level. In this article, we review key studies about the biology of Upper Paleolithic populations based primarily on European samples, but integrating information from other areas of the Old World whenever possible. Data about cranial morphology, skeletal robusticity, stature, body proportions, health status, diet, physical activity, and genetics are evaluated in Late Pleistocene climatic and cultural contexts. Various lines of evidence delineate the Last Glacial Maximum (LGM) as a critical phase in the biological and cultural evolution of Upper Paleolithic populations. The LGM, a long phase of climatic deterioration culminating around 20,000 BP, had a profound impact on the environment, lifestyle, and behavior of human groups. Some of these effects are recorded in aspects of skeletal biology of these populations. Groups living before and after the LGM, Early Upper Paleolithic (EUP) and Late Upper Paleolithic (LUP), respectively, differ significantly in craniofacial dimensions, stature, robusticity, and body proportions. While paleopathological and stable isotope data suggest good health status throughout the Upper Paleolithic, some stress indicators point to a slight decline in quality of life in LUP populations. The intriguing and unexpected incidence of individuals affected by congenital disorders probably indicates selective burial practices for these abnormal individuals. While some of the changes observed can be explained through models of biocultural or environmental adaptation (e.g., decreased lower limb robusticity following decreased mobility; changes in body proportions along with climatic change), others are more difficult to explain. For instance, craniodental and upper limb robusticity show complex evolutionary patterns that do not always correspond to expectations. In addition, the marked decline in stature and the mosaic nature of change in body proportions still await clarifications. These issues, as well as systematic analysis of specific pathologies and possible relationships between genetic lineages, population movements and cultural complexes, should be among the goals of future research.
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Affiliation(s)
- Brigitte M Holt
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003, USA.
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Abstract
A recent report in BMC Biology indicates that modern humans first arrived in southern East Asia 60,000 years ago and settled the rest of East Asia from there. This early date and migration route has significant implications for our understanding of the origins of present-day human populations.
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Affiliation(s)
- Roscoe Stanyon
- University of Florence, Department of Evolutionary Biology, Italy.
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Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, Soares P, Luciani S, Marota I, De Bellis G, Richards MB, Rollo F. Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr Biol 2008; 18:1687-93. [PMID: 18976917 DOI: 10.1016/j.cub.2008.09.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 08/22/2008] [Accepted: 09/03/2008] [Indexed: 11/29/2022]
Abstract
The Tyrolean Iceman was a witness to the Neolithic-Copper Age transition in Central Europe 5350-5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations. This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.
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Affiliation(s)
- Luca Ermini
- Laboratorio di Archeo-Antropologia Molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, 62032 Camerino, Italy
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Comparing models on the genealogical relationships among Neandertal, Cro-Magnoid and modern Europeans by serial coalescent simulations. Heredity (Edinb) 2008; 102:218-25. [DOI: 10.1038/hdy.2008.103] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Marini F, Carbonell Sala S, Falchetti A, Caramelli D, Brandi ML. The genetic ascertainment of multiple endocrine neoplasia type 1 syndrome by ancient DNA analysis. J Endocrinol Invest 2008; 31:905-9. [PMID: 19092297 DOI: 10.1007/bf03346440] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Multiple endocrine neoplasia type 1 (MEN1) is a rare autosomal dominant inherited endocrine cancer syndrome characterised by parathyroid, pancreas, and anterior pituitary tumors. The disease responsible gene, MEN1, was identified in 1997 and localizes to chromosome 11q13 in a minimal 600 kb interval between PYGM and D11S449 loci. About 10-20% of MEN1 patients do not have any mutation in the coding region and/or in the exon-intron junctions of the MEN1 gene. In this case, familial haplotype analysis of the 11q13 region, in at least two generations of affected members, is the only possible genetic ascertainment of the disease. We performed a microsatellite haplotype analysis at 11q13 region in 8 living and 1 deceased member of a MEN1 Italian family without any detected germline mutation of the MEN1 gene. The application of forensic techniques for ancient DNA analysis made it possible to identify the familial disease-associated haplotype and demonstrated that MEN1 disease haplotype family history can be reconstructed even when one or more family members are deceased. Identification of MEN1 disease haplotype is helpful in the clinical management of patients and relatives in families without any mutation of the MEN1 gene. Genetic screening allows the identification of individuals who are at risk before the development of clinical symptoms, limiting invasive annual cancer surveillance only to genetically positive individuals and making it possible to avoid further clinical screenings in non-carriers.
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Affiliation(s)
- F Marini
- Regional Center for Hereditary Endocrine Tumours, Department of Internal Medicine, University of Florence, Florence, Italy
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Separating "us" from "them": Neanderthal and modern human behavior. Proc Natl Acad Sci U S A 2008; 105:14241-2. [PMID: 18809932 DOI: 10.1073/pnas.0807931105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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