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Bisso-Machado R, Fagundes NJR. Uniparental genetic markers in Native Americans: A summary of all available data from ancient and contemporary populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:445-458. [PMID: 34184252 DOI: 10.1002/ajpa.24357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/26/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The aim of this study was to create a comprehensive summary of available mtDNA and Y-chromosome data for Native Americans from North, Central, and South America, including both modern and ancient DNA. To illustrate the usefulness of this dataset we present a broad picture of the genetic variation for both markers across the Americas. METHODS We searched PubMed, ResearchGate, Google Scholar for studies about mtDNA or Y-chromosome variation in Native American populations, including geographic, linguistic, ecological (ecoregion), archeological and chronological information. We used AMOVA to estimate the genetic structure associated with language and ecoregion grouping and Mantel tests to evaluate the correlation between genetic and geographic distances. RESULTS Genetic data were obtained from 321 primary sources, including 22,569 individuals from 298 contemporary populations, and 3628 individuals from 202 archeological populations. MtDNA lineages of probable non-Amerindian origin were rare, in contrast with Y-chromosome lineages. Mantel tests showed a statistically significant correlation for the whole continent considering mtDNA but not the Y-chromosome. Genetic structure between groups was always stronger for mtDNA than for the Y-chromosome. CONCLUSIONS This study summarizes decades of research conducted in Native American populations for both mtDNA and the Y-chromosome. Continental or sub-continental patterns of variation reveal that most of the genetic variation occurs within populations rather than among linguistic or ecoregional groups, and that isolation by distance is barely detectable in most population sets. The genetic structure among groups was always larger for mtDNA than for the Y-chromosome, suggesting between-sex differences in gene flow.
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Affiliation(s)
- Rafael Bisso-Machado
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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2
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Maixner F, Thorell K, Granehäll L, Linz B, Moodley Y, Rattei T, Engstrand L, Zink A. Helicobacter pylori in ancient human remains. World J Gastroenterol 2019; 25:6289-6298. [PMID: 31754290 PMCID: PMC6861846 DOI: 10.3748/wjg.v25.i42.6289] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/13/2019] [Accepted: 11/01/2019] [Indexed: 02/06/2023] Open
Abstract
The bacterium Helicobacter pylori (H. pylori) infects the stomachs of approximately 50% of all humans. With its universal occurrence, high infectivity and virulence properties it is considered as one of the most severe global burdens of modern humankind. It has accompanied humans for many thousands of years, and due to its high genetic variability and vertical transmission, its population genetics reflects the history of human migrations. However, especially complex demographic events such as the colonisation of Europe cannot be resolved with population genetic analysis of modern H. pylori strains alone. This is best exemplified with the reconstruction of the 5300-year-old H. pylori genome of the Iceman, a European Copper Age mummy. Our analysis provided precious insights into the ancestry and evolution of the pathogen and underlined the high complexity of ancient European population history. In this review we will provide an overview on the molecular analysis of H. pylori in mummified human remains that were done so far and we will outline methodological advancements in the field of ancient DNA research that support the reconstruction and authentication of ancient H. pylori genome sequences.
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Affiliation(s)
- Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano 39100, Italy
| | - Kaisa Thorell
- Department of Infectious Diseases, University of Gothenburg, Göteborg SE405 30, Sweden
| | - Lena Granehäll
- Institute for Mummy Studies, EURAC Research, Bolzano 39100, Italy
| | - Bodo Linz
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, United States
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou 0950, South Africa
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna 1090, Austria
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Bolzano 39100, Italy
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3
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Sources of Materials for Paleomicrobiology. Microbiol Spectr 2017; 4. [PMID: 27726809 DOI: 10.1128/microbiolspec.poh-0016-2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Paleomicrobiology establishes the diagnosis of ancient infectious diseases by studying ancient pathogens. This recent science also analyzes the evolution of these pathogens, virulence, and their adaptation to their habitat and their vectors. The DNA persists a long time after the death of an organism despite the chemical and enzymatic degradation. The possibility of sequencing bacterial, viral, parasitic and archaeal DNA molecules persists over time.Various sources are used for these studies: frozen tissue and particularly human tissue are a exceptional source for the analysis because at very low temperatures, all biological activity is suspended. The coprolites are a source of choice for studying the human microbiome. Other sources, the ancient bones are the most abundant, however, they may contain only small amounts of DNA due to natural leaching. When the use of the tooth is possible, is a particularly interesting source because of its highly mineralized structure, which gives greater persistence than bone. The calcified tartar deposited on teeth is a source of interest for the study of oral microbiome.All these sources are subject to precautions (gloves and masks hat) at the time of sampling to avoid cross contamination and also be listed in the most precise way because they are precious and rare.
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4
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Bösl E. [aDNA Research From a Historical Perspective]. NTM 2017; 25:99-142. [PMID: 28389681 DOI: 10.1007/s00048-017-0168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
aDNA studies are a cooperative field of research with a broad range of applications including evolutionary biology, genetics, anthropology and archaeology. Scientists are using ancient molecules as source material for historical questions. Colleagues from the humanities are observing this with both interest and concern because aDNA research is affecting academic identities and both concepts of history and historiography. aDNA research developed in a way that can be described as a Hype Cycle (Chackie Fenn). Technological triggers such as Sanger Sequencing and the Polymerase Chain Reaction kicked off a multitude of experiments with ancient DNA during the 1980s and 1990s. Geneticists, microbiologists, anthropologists and many more euphorically joined a "molecule hunt". aDNA was promoted as a time machine. Media attention was enormous. As experiments and implementations began to fail and contamination was discovered to be a tremendous problem, media interest waned and many labs lost their interest. Some turned their disillusionment into systematic research into methodology and painstakingly established lab routines. The authenticity problem was first addressed by control oriented measures but later approached from a more cognitive theoretical perspective as the pitfalls and limits of aDNA became clearer. By the end of the 2000s the field reached its current plateau of productivity. Cross-disciplinary debates, conflicts and collaborations are increasing critical reflection among all participants. Historians should consider joining the field in a kind of critical friendship to both make the most of its possibilities and give an input from a constructivist perspective.
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Affiliation(s)
- Elsbeth Bösl
- Professur für Wirtschafts-, Sozial- und Technikgeschichte, Historisches Seminar, Universität der Bundeswehr München, Werner-Heisenberg-Weg 39, 85577, Neubiberg, Deutschland.
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5
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Elucidating the evolution of hominid dentition in the age of phenomics, modularity, and quantitative genetics. Ann Anat 2016; 203:3-11. [DOI: 10.1016/j.aanat.2015.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 12/11/2022]
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Ozdemir-Kaynak E, Yesil-Celiktas O. Microwave-assisted digestion combined with silica-based spin column for DNA isolation from human bones. Anal Biochem 2015; 486:44-50. [PMID: 26142220 DOI: 10.1016/j.ab.2015.06.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/25/2015] [Accepted: 06/28/2015] [Indexed: 12/25/2022]
Abstract
A protocol for the extraction of DNA from ancient skeletal material was developed. Bone specimen samples (powder or slice), buffer, pretreatment, and extraction methodologies were compared to investigate the best conditions yielding the highest concentration of DNA. The degree of extract contamination by polymerase chain reaction (PCR) inhibitors was compared as well. Pretreatment was carried out using agitation in an incubator shaker and microwave digestion. Subsequently, DNA from bones was isolated by the classical organic phenol-chloroform extraction and silica-based spin columns. Decalcification buffer for total demineralization was required as well as lysis buffer for cell lysis to obtain DNA, whereas microwave-assisted digestion proved to be very rapid, with an incubation time of 2min instead of 24h at an incubator shaker without using lysis buffer. The correction of isolated DNA was detected using real-time PCR with melt curve analysis, which was 82.8±0.2°C for highly repetitive α-satellite gene region specific for human chromosome 17 (locus D17Z1). Consequently, microwave-based DNA digestion followed by silica column yielded a high-purity DNA with a concentration of 19.40ng/μl and proved to be a superior alternative to the phenol-chloroform method, presenting an environmentally friendly and efficient technique for DNA extraction.
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Affiliation(s)
- Elif Ozdemir-Kaynak
- Department of Bioengineering, Faculty of Engineering, Canakkale Onsekiz Mart University, 17020 Canakkale, Turkey; Novel Fluidic Technologies and Applications Group, Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova-Izmir, Turkey
| | - Ozlem Yesil-Celiktas
- Novel Fluidic Technologies and Applications Group, Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova-Izmir, Turkey.
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Teasdale MD, van Doorn NL, Fiddyment S, Webb CC, O'Connor T, Hofreiter M, Collins MJ, Bradley DG. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130379. [PMID: 25487331 PMCID: PMC4275887 DOI: 10.1098/rstb.2013.0379] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.
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Affiliation(s)
- M D Teasdale
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | | | - S Fiddyment
- BioArCh, University of York, York YO10 5DD, UK
| | - C C Webb
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - T O'Connor
- BioArCh, University of York, York YO10 5DD, UK
| | - M Hofreiter
- BioArCh, University of York, York YO10 5DD, UK Institute for Biochemistry and Biology, Faculty of Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam 14476, Germany
| | - M J Collins
- BioArCh, University of York, York YO10 5DD, UK
| | - D G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
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8
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MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population. PLoS One 2015; 10:e0127182. [PMID: 25950581 PMCID: PMC4423966 DOI: 10.1371/journal.pone.0127182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The craniometric specificity of the indigenous West Siberian human populations cannot be completely explained by the genetic interactions of the western and eastern Eurasian groups recorded in the archaeology of the area from the beginning of the 2nd millennium BC. Anthropologists have proposed another probable explanation: contribution to the genetic structure of West Siberian indigenous populations by ancient human groups, which separated from western and eastern Eurasian populations before the final formation of their phenotypic and genetic features and evolved independently in the region over a long period of time. This hypothesis remains untested. From the genetic point of view, it could be confirmed by the presence in the gene pool of indigenous populations of autochthonous components that evolved in the region over long time periods. The detection of such components, particularly in the mtDNA gene pool, is crucial for further clarification of early regional genetic history. RESULTS AND CONCLUSION We present the results of analysis of mtDNA samples (n = 10) belonging to the A10 haplogroup, from Bronze Age populations of West Siberian forest-steppe (V-I millennium BC), that were identified in a screening study of a large diachronic sample (n = 96). A10 lineages, which are very rare in modern Eurasian populations, were found in all the Bronze Age groups under study. Data on the A10 lineages' phylogeny and phylogeography in ancient West Siberian and modern Eurasian populations suggest that A10 haplogroup underwent a long-term evolution in West Siberia or arose there autochthonously; thus, the presence of A10 lineages indicates the possible contribution of early autochthonous human groups to the genetic specificity of modern populations, in addition to contributions of later interactions of western and eastern Eurasian populations.
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Anagnostou P, Capocasa M, Milia N, Sanna E, Battaggia C, Luzi D, Destro Bisol G. When data sharing gets close to 100%: what human paleogenetics can teach the open science movement. PLoS One 2015; 10:e0121409. [PMID: 25799293 PMCID: PMC4370607 DOI: 10.1371/journal.pone.0121409] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 02/02/2015] [Indexed: 12/31/2022] Open
Abstract
This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals' editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers' awareness of the importance of openness and transparency for scientific progress may complement stakeholders' policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges.
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Affiliation(s)
- Paolo Anagnostou
- Dipartimento di Biologia Ambientale, “Sapienza” Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Marco Capocasa
- Istituto Italiano di Antropologia, Rome, Italy
- Dipartimento Biologia e Biotecnologie “Charles Darwin”, “Sapienza” Università di Roma, Rome, Italy
| | - Nicola Milia
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Emanuele Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Cinzia Battaggia
- Dipartimento di Biologia Ambientale, “Sapienza” Università di Roma, Rome, Italy
| | - Daniela Luzi
- Istituto di Ricerche sulla Popolazione e le Politiche Sociali, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Giovanni Destro Bisol
- Dipartimento di Biologia Ambientale, “Sapienza” Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
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10
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Nigra BT, Faull KF, Barnard H. Analytical Chemistry in Archaeological Research. Anal Chem 2014; 87:3-18. [DOI: 10.1021/ac5029616] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin T. Nigra
- Cotsen
Institute of Archaeology, University of California, Los Angeles, A331 Fowler
Museum, 308 Charles Young Drive North, Box 951510, Los Angeles, California 90095-1510, United States
| | - Kym F. Faull
- Department
of Psychiatry and Biobehavioral Sciences and Pasarow Mass Spectrometry
Laboratory, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Hans Barnard
- Cotsen
Institute of Archaeology, University of California, Los Angeles, A331 Fowler
Museum, 308 Charles Young Drive North, Box 951510, Los Angeles, California 90095-1510, United States
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11
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Maixner F, Thomma A, Cipollini G, Widder S, Rattei T, Zink A. Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman. PLoS One 2014; 9:e99994. [PMID: 24941044 PMCID: PMC4062476 DOI: 10.1371/journal.pone.0099994] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 05/20/2014] [Indexed: 12/29/2022] Open
Abstract
Ancient hominoid genome studies can be regarded by definition as metagenomic analyses since they represent a mixture of both hominoid and microbial sequences in an environment. Here, we report the molecular detection of the oral spirochete Treponema denticola in ancient human tissue biopsies of the Iceman, a 5,300-year-old Copper Age natural ice mummy. Initially, the metagenomic data of the Iceman’s genomic survey was screened for bacterial ribosomal RNA (rRNA) specific reads. Through ranking the reads by abundance a relatively high number of rRNA reads most similar to T. denticola was detected. Mapping of the metagenome sequences against the T. denticola genome revealed additional reads most similar to this opportunistic pathogen. The DNA damage pattern of specifically mapped reads suggests an ancient origin of these sequences. The haematogenous spread of bacteria of the oral microbiome often reported in the recent literature could already explain the presence of metagenomic reads specific for T. denticola in the Iceman’s bone biopsy. We extended, however, our survey to an Iceman gingival tissue sample and a mouth swab sample and could thereby detect T. denticola and Porphyrimonas gingivalis, another important member of the human commensal oral microflora. Taken together, this study clearly underlines the opportunity to detect disease-associated microorganisms when applying metagenomics- enabled approaches on datasets of ancient human remains.
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Affiliation(s)
- Frank Maixner
- Institute for Mummies and the Iceman, EURAC Research, Bolzano, Italy
| | - Anton Thomma
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Stefanie Widder
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Albert Zink
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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12
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Veeramah KR, Hammer MF. The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 2014; 15:149-62. [PMID: 24492235 DOI: 10.1038/nrg3625] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Examining patterns of molecular genetic variation in both modern-day and ancient humans has proved to be a powerful approach to learn about our origins. Rapid advances in DNA sequencing technology have allowed us to characterize increasing amounts of genomic information. Although this clearly provides unprecedented power for inference, it also introduces more complexity into the way we use and interpret such data. Here, we review ongoing debates that have been influenced by improvements in our ability to sequence DNA and discuss some of the analytical challenges that need to be overcome in order to fully exploit the rich historical information that is contained in the entirety of the human genome.
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Affiliation(s)
- Krishna R Veeramah
- 1] Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA. [2] Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA
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Fortes GG, Speller CF, Hofreiter M, King TE. Phenotypes from ancient DNA: approaches, insights and prospects. Bioessays 2013; 35:690-5. [PMID: 23703035 DOI: 10.1002/bies.201300036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome-wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes.
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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: 5.6] [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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Georges L, Seidenberg V, Hummel S, Fehren-Schmitz L. Molecular characterization of ABO blood group frequencies in pre-Columbian Peruvian highlanders. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:242-9. [DOI: 10.1002/ajpa.22115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/15/2012] [Indexed: 12/28/2022]
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16
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Huynen L, Millar CD, Lambert DM. Resurrecting ancient animal genomes: the extinct moa and more. Bioessays 2012; 34:661-9. [PMID: 22674514 DOI: 10.1002/bies.201200040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.
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Affiliation(s)
- Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
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