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Feldmann MJ, Pincot DDA, Cole GS, Knapp SJ. Genetic gains underpinning a little-known strawberry Green Revolution. Nat Commun 2024; 15:2468. [PMID: 38504104 PMCID: PMC10951273 DOI: 10.1038/s41467-024-46421-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
The annual production of strawberry has increased by one million tonnes in the US and 8.4 million tonnes worldwide since 1960. Here we show that the US expansion was driven by genetic gains from Green Revolution breeding and production advances that increased yields by 2,755%. Using a California population with a century-long breeding history and phenotypes of hybrids observed in coastal California environments, we estimate that breeding has increased fruit yields by 2,974-6,636%, counts by 1,454-3,940%, weights by 228-504%, and firmness by 239-769%. Using genomic prediction approaches, we pinpoint the origin of the Green Revolution to the early 1950s and uncover significant increases in additive genetic variation caused by transgressive segregation and phenotypic diversification. Lastly, we show that the most consequential Green Revolution breeding breakthrough was the introduction of photoperiod-insensitive, PERPETUAL FLOWERING hybrids in the 1970s that doubled yields and drove the dramatic expansion of strawberry production in California.
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Affiliation(s)
- Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.
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2
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Kristjansson D, Schurr TG, Bohlin J, Jugessur A. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:298-315. [PMID: 36790764 PMCID: PMC10100211 DOI: 10.1002/ajpa.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach. METHODS Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates. RESULTS Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers. CONCLUSIONS Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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3
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Hou X, Zhang X, Li X, Huang T, Li W, Zhang H, Huang H, Wen Y. Genomic insights into the genetic structure and population history of Mongolians in Liaoning Province. Front Genet 2022; 13:947758. [PMID: 36313460 PMCID: PMC9596793 DOI: 10.3389/fgene.2022.947758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
The Mongolian population exceeds six million and is the largest population among the Mongolic speakers in China. However, the genetic structure and admixture history of the Mongolians are still unclear due to the limited number of samples and lower coverage of single-nucleotide polymorphism (SNP). In this study, we genotyped genome-wide data of over 700,000 SNPs in 38 Mongolian individuals from Fuxin in Liaoning Province to explore the genetic structure and population history based on typical and advanced population genetic analysis methods [principal component analysis (PCA), admixture, FST, f3-statistics, f4-statistics, qpAdm/qpWave, qpGraph, ALDER, and TreeMix]. We found that Fuxin Mongolians had a close genetic relationship with Han people, northern Mongolians, other Mongolic speakers, and Tungusic speakers in East Asia. Also, we found that Neolithic millet farmers in the Yellow River Basin and West Liao River Basin and Neolithic hunter–gatherers in the Mongolian Plateau and Amur River Basin were the dominant ancestral sources, and there were additional gene flows related to Eurasian Steppe pastoralists and Neolithic Iranian farmers in the gene pool of Fuxin Mongolians. These results shed light on dynamic demographic history, complex population admixture, and multiple sources of genetic diversity in Fuxin Mongolians.
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4
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Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample. Int J Mol Sci 2022; 23:ijms23126725. [PMID: 35743173 PMCID: PMC9223851 DOI: 10.3390/ijms23126725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
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5
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First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy). Genes (Basel) 2021; 12:genes12050636. [PMID: 33922908 PMCID: PMC8146030 DOI: 10.3390/genes12050636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/02/2021] [Accepted: 04/20/2021] [Indexed: 11/17/2022] Open
Abstract
The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies.
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Dashti M, Alsaleh H, Eaaswarkhanth M, John SE, Nizam R, Melhem M, Hebbar P, Sharma P, Al-Mulla F, Thanaraj TA. Delineation of Mitochondrial DNA Variants From Exome Sequencing Data and Association of Haplogroups With Obesity in Kuwait. Front Genet 2021; 12:626260. [PMID: 33659027 PMCID: PMC7920096 DOI: 10.3389/fgene.2021.626260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/13/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND/OBJECTIVES Whole-exome sequencing is a valuable tool to determine genetic variations that are associated with rare and common health conditions. A limited number of studies demonstrated that mitochondrial DNA can be captured using whole-exome sequencing. Previous studies have suggested that mitochondrial DNA variants and haplogroup lineages are associated with obesity. Therefore, we investigated the role of mitochondrial variants and haplogroups contributing to the risk of obesity in Arabs in Kuwait using exome sequencing data. SUBJECTS/METHODS Indirect mitochondrial genomes were extracted from exome sequencing data from 288 unrelated native Arab individuals from Kuwait. The cohort was divided into obese [body mass index (BMI) ≥ 30 kg/m2] and non-obese (BMI < 30 kg/m2) groups. Mitochondrial variants were identified, and haplogroups were classified and compared with other sequencing technologies. Statistical analysis was performed to determine associations and identify mitochondrial variants and haplogroups affecting obesity. RESULTS Haplogroup R showed a protective effect on obesity [odds ratio (OR) = 0.311; P = 0.006], whereas haplogroup L individuals were at high risk of obesity (OR = 2.285; P = 0.046). Significant differences in mitochondrial variants between the obese and non-obese groups were mainly haplogroup-defining mutations and were involved in processes in energy generation. The majority of mitochondrial variants and haplogroups extracted from exome were in agreement with technical replica from Sanger and whole-genome sequencing. CONCLUSIONS This is the first to utilize whole-exome data to extract entire mitochondrial haplogroups to study its association with obesity in an Arab population.
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Affiliation(s)
- Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Hussain Alsaleh
- Kuwait Identification DNA Laboratory, General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | | | - Sumi Elsa John
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Rasheeba Nizam
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Motasem Melhem
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Prashantha Hebbar
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Prem Sharma
- Department Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
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Magnusson M, Eisfeldt J, Nilsson D, Rosenbaum A, Wirta V, Lindstrand A, Wedell A, Stranneheim H. Loqusdb: added value of an observations database of local genomic variation. BMC Bioinformatics 2020; 21:273. [PMID: 32611382 PMCID: PMC7329469 DOI: 10.1186/s12859-020-03609-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/17/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Exome and genome sequencing is becoming the method of choice for rare disease diagnostics. One of the key challenges remaining is distinguishing the disease causing variants from the benign background variation. After analysis and annotation of the sequencing data there are typically thousands of candidate variants requiring further investigation. One of the most effective and least biased ways to reduce this number is to assess the rarity of a variant in any population. Currently, there are a number of reliable sources of information for major population frequencies when considering single nucleotide variants (SNVs) and small insertion and deletions (INDELs), with gnomAD as the most prominent public resource available. However, local variation or frequencies in sub-populations may be underrepresented in these public resources. In contrast, for structural variation (SV), the background frequency in the general population is more or less unknown mostly due to challenges in calling SVs in a consistent way. Keeping track of local variation is one way to overcome these problems and significantly reduce the number of potential disease causing variants retained for manual inspection, both for SNVs and SVs. RESULTS Here, we present loqusdb, a tool to solve the challenge of keeping track of any type of variant observations from genome sequencing data. Loqusdb was designed to handle a large flow of samples and unlike other solutions, samples can be added continuously to the database without rebuilding it, facilitating improvements and additions. We assessed the added value of a local observations database using 98 samples annotated with information from a background of 888 unrelated individuals. CONCLUSIONS We show both how powerful SV analysis can be when filtering for population frequencies and how the number of apparently rare SNVs/INDELs can be reduced by adding local population information even after annotating the data with other large frequency databases, such as gnomAD. In conclusion, we show that a local frequency database is an attractive, and a necessary addition to the publicly available databases that facilitate the analysis of exome and genome data in a clinical setting.
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Affiliation(s)
- Måns Magnusson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm, Sweden. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. .,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
| | - Jesper Eisfeldt
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Adam Rosenbaum
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
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8
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Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I, Mathieson I, Ekoru K, DeGorter MK, Nsubuga RN, Finan C, Wheeler E, Chen L, Cooper DN, Schiffels S, Chen Y, Ritchie GRS, Pollard MO, Fortune MD, Mentzer AJ, Garrison E, Bergström A, Hatzikotoulas K, Adeyemo A, Doumatey A, Elding H, Wain LV, Ehret G, Auer PL, Kooperberg CL, Reiner AP, Franceschini N, Maher D, Montgomery SB, Kadie C, Widmer C, Xue Y, Seeley J, Asiki G, Kamali A, Young EH, Pomilla C, Soranzo N, Zeggini E, Pirie F, Morris AP, Heckerman D, Tyler-Smith C, Motala AA, Rotimi C, Kaleebu P, Barroso I, Sandhu MS. Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa. Cell 2020; 179:984-1002.e36. [PMID: 31675503 DOI: 10.1016/j.cell.2019.10.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/03/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region.
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Affiliation(s)
- Deepti Gurdasani
- William Harvey Research Institute, Queen Mary's University of London, London, UK
| | | | - Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation (CGRI)/National Biotechnology Development Agency CGRI/NABDA, Abuja, Nigeria
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | | | | | | | - Marc Haber
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ioanna Tachmazidou
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage Hertfordshire SG1 2NY, UK
| | - Iain Mathieson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth Ekoru
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca N Nsubuga
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Chris Finan
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Li Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Yuan Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Alex J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Konstantinos Hatzikotoulas
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Georg Ehret
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Charles L Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Dermot Maher
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Stephen B Montgomery
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Janet Seeley
- London School of Hygiene and Tropical Medicine, London, UK; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Gershim Asiki
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Elizabeth H Young
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Cristina Pomilla
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew P Morris
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Biostatistics, University of Liverpool, Liverpool, UK
| | | | | | - Ayesha A Motala
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa.
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA.
| | - Pontiano Kaleebu
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda.
| | - Inês Barroso
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
| | - Manj S Sandhu
- Department of Medicine, University of Cambridge, Cambridge, UK.
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9
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Wagner C, De Gezelle J, Komarnytsky S. Celtic Provenance in Traditional Herbal Medicine of Medieval Wales and Classical Antiquity. Front Pharmacol 2020; 11:105. [PMID: 32184721 PMCID: PMC7058801 DOI: 10.3389/fphar.2020.00105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/28/2020] [Indexed: 11/13/2022] Open
Abstract
The Celtic linguistic community dominated large spans of Central and Western Europe between 800 BC and 500 AD, but knowledge of their traditional medicine is very limited. Multiple progressive plant gains in Neolithic settlements along the Danube and up the Rhine valleys suggested that taxon diversity of gathered plants peaked at the Balkans and was subsequently reduced as crop and gathered plants packages were adopted and dispersed throughout Neolithic Europe. This process coincided with the Bronze Age migration of the R1b proto-Celtic tribes, and their herbal traditions were occasionally recorded in the classic Greco-Roman texts on herbal medicines. The provenance of Celtic (Gallic) healing methods and magical formulas as recorded by Pliny, Scribonius Largus, and Marcellus Empiricus can still be found in the first part of the medieval Welsh (Cymry) herbal manuscript Meddygon Myddfai (recipes 1–188). Although the majority of Myddfai I recipes were based on the Mediterranean herbal tradition of Dioscorides and Macer Floridus, they preserved the unique herbal preparation signatures distinct from continental and Anglo-Saxon counterparts in increased use of whey and ashes as vehicles for formulation of herbal remedies. Six plants could be hypothetically attributed to the Celtic (Welsh) herbal tradition including foxglove (Digitalis purpurea L.), corn bellflower (Legousia speculum-veneris L.), self-heal (Prunella vulgaris L.), sharp dock (Rumex conglomeratus Murray), water pimpernel (Samolus valerandi L.), and river startip (Scapania undulata L.) This review provides initial evidence for traces of Celtic framework in the Welsh herbal tradition and warrants further investigations of bioactivity and clinical applications of the described plant leads.
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Affiliation(s)
- Charles Wagner
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, United States.,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Jillian De Gezelle
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Slavko Komarnytsky
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, United States.,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States.,Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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10
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Jones JR, Marín-Arroyo AB, Straus LG, Richards MP. Adaptability, resilience and environmental buffering in European Refugia during the Late Pleistocene: Insights from La Riera Cave (Asturias, Cantabria, Spain). Sci Rep 2020; 10:1217. [PMID: 31988327 PMCID: PMC6985176 DOI: 10.1038/s41598-020-57715-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/31/2019] [Indexed: 11/26/2022] Open
Abstract
The Upper Palaeolithic in Europe was a time of extensive climatic changes that impacted on the survival and distribution of human populations. During the Late Glacial Maximum (LGM), southern European peninsulas were refugia for flora, fauna, and human groups. One of these refugia, the Cantabrian region (northern Atlantic Spain), was intensively occupied throughout the Upper Palaeolithic. Characterising how climatic events were expressed in local environments is crucial to understand human and animal survival. La Riera Cave (Asturias) has a rich geo-cultural sequence dating between 20.5kyr BP to 6.5kyr BP and represents an ideal location in which to explore this. Stable isotope analysis of red deer and ibex is used alongside other environmental and climatic proxies to reconstruct Late Upper Palaeolithic conditions. Results show that during the LGM, ibex adapted their niche to survive, and became a major prey species for humans. The diverse environmental opportunities offered in the high-relief and coastal environs of La Riera may help to explain the high human population levels in the Cantabrian Region throughout the Late Upper Palaeolithic. Despite fluctuating conditions, herbivores and humans had the flexibility and resilience to adapt, demonstrating the importance of southern European refugia for the survival of different species.
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Affiliation(s)
- Jennifer R Jones
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, (Universidad de Cantabria, Santander, Gobierno de Cantabria), Santander, 39005, Spain.
| | - Ana B Marín-Arroyo
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, (Universidad de Cantabria, Santander, Gobierno de Cantabria), Santander, 39005, Spain
| | - Lawrence G Straus
- Department of Anthropology, MSC01 1040, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Michael P Richards
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
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11
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Skonieczna K, Jawień A, Marszałek A, Grzybowski T. Mitogenome germline mutations and colorectal cancer risk in Polish population. Arch Med Sci 2020; 16:366-373. [PMID: 32190148 PMCID: PMC7069428 DOI: 10.5114/aoms.2018.80893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION To date, several nuclear DNA variants have been shown to be associated with increased risk of developing colorectal cancer. Despite the fact that mitochondria play an important role in carcinogenesis, little is known about inherited mitochondrial DNA mutations that could be involved in this disease. Thus, potential associations between inherited mutations in the entire mitochondrial genomes and colorectal cancer were analysed in this study. MATERIAL AND METHODS Two hundred mitogenome sequences determined for colorectal cancer patients and healthy individuals from Poland were used to investigate the association between mtDNA alleles or haplogroups and colorectal cancer. Additional mtDNA control region haplotypes determined for 1353 individuals from the general Polish population were used for comparison of haplogroup and certain allele frequencies between case and control groups. RESULTS The non-R clades together with their diagnostic T alleles at positions 12705 and 16223 were observed with higher frequencies in healthy individuals than in colorectal cancer patients. Nevertheless, the differences of the R macrohaplogroup (as well as 12705 or 16223 alleles) frequencies between cases and controls were statistically insignificant after Bonferroni correction. Most of the non-R clades were of Asian and African origin, but none of them were prevalent in the control group. Moreover, neither mtDNA alleles nor haplogroups were associated with clinicopathological parameters of colorectal cancer patients. CONCLUSIONS Contrary to some previous reports, the findings of this study do not support the hypothesis that mitochondrial DNA variants contribute to inherited predisposition to colorectal cancer.
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Affiliation(s)
- Katarzyna Skonieczna
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Arkadiusz Jawień
- Department of Vascular Surgery and Angiology, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Andrzej Marszałek
- Department of Pathology, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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12
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Environmental factors modulated ancient mitochondrial DNA variability and the prevalence of rheumatic diseases in the Basque Country. Sci Rep 2019; 9:20380. [PMID: 31892727 PMCID: PMC6938509 DOI: 10.1038/s41598-019-56921-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/17/2019] [Indexed: 11/09/2022] Open
Abstract
Among the factors that would explain the distribution of mitochondrial lineages in Europe, climate and diseases may have played an important role. A possible explanation lies in the nature of the mitochondrion, in which the energy generation process produces reactive oxygen species that may influence the development of different diseases. The present study is focused on the medieval necropolis of San Miguel de Ereñozar (13th-16th centuries, Basque Country), whose inhabitants presented a high prevalence of rheumatic diseases and lived during the Little Ice Age (LIA). Our results indicate a close relationship between rheumatic diseases and mitochondrial haplogroup H, and specifically between spondyloarthropathies and sub-haplogroup H2. One possible explanation may be the climate change that took place in the LIA that favoured those haplogroups that were more energy-efficient, such as haplogroup H, to endure lower temperatures and food shortage. However, it had a biological trade-off: the increased risk of developing rheumatic diseases.
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13
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Silva M, Justeau P, Rodrigues S, Oteo-Garcia G, Dulias K, Foody G, Fichera A, Yau B, Rito T, Wilson JF, Gandini F, Edwards CJ, Pala M, Soares PA, Richards MB. Untangling Neolithic and Bronze Age mitochondrial lineages in South Asia. Ann Hum Biol 2019; 46:140-144. [PMID: 31267777 DOI: 10.1080/03014460.2019.1623319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focuses on the phylogeographic patterns of mitochondrial haplogroups H2 and H13 in the Indian Subcontinent and incorporates evidence from recently released ancient genomes from Central and South Asia. It found signals of Neolithic arrivals from Iran and later movements in the Bronze Age from Central Asia that derived ultimately from the Steppe. This study shows how a detailed mtDNA phylogeographic approach, combining both modern and ancient variation, can provide evidence of population movements, even in a scenario of strong male bias such as in the case of the Bronze Age Steppe dispersals.
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Affiliation(s)
- M Silva
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - P Justeau
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - S Rodrigues
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - G Oteo-Garcia
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - K Dulias
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - G Foody
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - A Fichera
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - B Yau
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - T Rito
- b School of Medicine , Life and Health Sciences Research Institute (ICVS), University of Minho , Braga , Portugal.,c ICVS/3B's , PT Government Associate Laboratory , Guimarães , Portugal
| | - J F Wilson
- d Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Teviot Place , Edinburgh , UK.,e MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine , University of Edinburgh, Western General Hospital , Edinburgh , UK
| | - F Gandini
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - C J Edwards
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - M Pala
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
| | - P A Soares
- f CBMA (Centre of Molecular and Environmental Biology), Department of Biology , University of Minho , Braga , Portugal.,g Institute of Science and Innovation for Bio-Sustainability (IB-S) , University of Minho , Braga , Portugal
| | - M B Richards
- a Department of Biological and Geographical Sciences, School of Applied Sciences , University of Huddersfield , Queensgate , UK
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14
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Hernández CL, Dugoujon JM, Sánchez-Martínez LJ, Cuesta P, Novelletto A, Calderón R. Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world. Ann Hum Biol 2019; 46:63-76. [PMID: 30822152 DOI: 10.1080/03014460.2019.1587507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. AIM To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. SUBJECT AND METHODS Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. RESULTS Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. CONCLUSION The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
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Affiliation(s)
- Candela L Hernández
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Jean-Michel Dugoujon
- b CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS) , Université Paul Sabatier Toulouse III , Toulouse , France
| | - Luis J Sánchez-Martínez
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Pedro Cuesta
- c Centro de Proceso de Datos , Universidad Complutense , Madrid , Spain
| | | | - Rosario Calderón
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
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15
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Varano S, Gaspari L, De Angelis F, Scano G, Contini I, Martínez-Labarga C, Rickards O. Mitochondrial characterisation of two Spanish populations from the Vera and Bejar valleys (Central Spain). Ann Hum Biol 2019; 45:531-539. [DOI: 10.1080/03014460.2018.1559355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sara Varano
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Luca Gaspari
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Giuseppina Scano
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Irene Contini
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Cristina Martínez-Labarga
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Olga Rickards
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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16
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Bybjerg-Grauholm J, Hagen CM, Gonçalves VF, Bækvad-Hansen M, Hansen CS, Hedley PL, Kanters JK, Nielsen J, Theisen M, Mors O, Kennedy J, Als TD, Demur AB, Nordentoft M, Børglum A, Mortensen PB, Werge TM, Hougaard DM, Christiansen M. Complex spatio-temporal distribution and genomic ancestry of mitochondrial DNA haplogroups in 24,216 Danes. PLoS One 2018; 13:e0208829. [PMID: 30543675 PMCID: PMC6292624 DOI: 10.1371/journal.pone.0208829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroups (hgs) are evolutionarily conserved sets of mtDNA SNP-haplotypes with characteristic geographical distribution. Associations of hgs with disease and physiological characteristics have been reported, but have frequently not been reproducible. Using 418 mtDNA SNPs on the PsychChip (Illumina), we assessed the spatio-temporal distribution of mtDNA hgs in Denmark from DNA isolated from 24,642 geographically un-biased dried blood spots (DBS), collected from 1981 to 2005 through the Danish National Neonatal Screening program. ADMIXTURE was used to establish the genomic ancestry of all samples using a reference of 100K+ autosomal SNPs in 2,248 individuals from nine populations. Median-joining analysis determined that the hgs were highly variable, despite being typically Northern European in origin, suggesting multiple founder events. Furthermore, considerable heterogeneity and variation in nuclear genomic ancestry was observed. Thus, individuals with hg H exhibited 95%, and U hgs 38.2% - 92.5%, Danish ancestry. Significant clines between geographical regions and rural and metropolitan populations were found. Over 25 years, macro-hg L increased from 0.2% to 1.2% (p = 1.1*E-10), and M from 1% to 2.4% (p = 3.7*E-8). Hg U increased among the R macro-hg from 14.1% to 16.5% (p = 1.9*E-3). Genomic ancestry, geographical skewedness, and sub-hg distribution suggested that the L, M and U increases are due to immigration. The complex spatio-temporal dynamics and genomic ancestry of mtDNA in the Danish population reflect repeated migratory events and, in later years, net immigration. Such complexity may explain the often contradictory and population-specific reports of mito-genomic association with disease.
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Affiliation(s)
| | - Christian M. Hagen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Christine S. Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Paula L. Hedley
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jimmi Nielsen
- Aalborg Psychiatric Hospital. Aalborg University Hospital, Aalborg, Denmark
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Mors
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - James Kennedy
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Thomas D. Als
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Alfonso B. Demur
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | | | - Anders Børglum
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Preben B. Mortensen
- Center for Register Research, Institute of Economics, Aarhus University, Århus, Denmark
| | - Thomas M. Werge
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | - David M. Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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17
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Langgut D, Almogi-Labin A, Bar-Matthews M, Pickarski N, Weinstein-Evron M. Evidence for a humid interval at ∼56–44 ka in the Levant and its potential link to modern humans dispersal out of Africa. J Hum Evol 2018; 124:75-90. [DOI: 10.1016/j.jhevol.2018.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
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18
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De Angelis F, Scorrano G, Martínez-Labarga C, Scano G, Macciardi F, Rickards O. Mitochondrial variability in the Mediterranean area: a complex stage for human migrations. Ann Hum Biol 2018; 45:5-19. [PMID: 29382277 DOI: 10.1080/03014460.2017.1416172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations. OBJECTIVE This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time. METHODS Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories. RESULTS The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations. CONCLUSION Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.
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Affiliation(s)
- Flavio De Angelis
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Gabriele Scorrano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Cristina Martínez-Labarga
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Giuseppina Scano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Fabio Macciardi
- b Laboratory of Molecular Psychiatry, Department of Psychiatry and Human Behavior , University of California , Irvine , CA , USA
| | - Olga Rickards
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
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19
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Strobbe D, Caporali L, Iommarini L, Maresca A, Montopoli M, Martinuzzi A, Achilli A, Olivieri A, Torroni A, Carelli V, Ghelli A. Haplogroup J mitogenomes are the most sensitive to the pesticide rotenone: Relevance for human diseases. Neurobiol Dis 2018; 114:129-139. [PMID: 29486301 DOI: 10.1016/j.nbd.2018.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/30/2018] [Accepted: 02/21/2018] [Indexed: 12/21/2022] Open
Abstract
There is growing evidence that the sequence variation of mitochondrial DNA (mtDNA), which clusters in population- and/or geographic-specific haplogroups, may result in functional effects that, in turn, become relevant in disease predisposition or protection, interaction with environmental factors and ultimately in modulating longevity. To unravel functional differences between mtDNA haplogroups we here employed transmitochondrial cytoplasmic hybrid cells (cybrids) grown in galactose medium, a culture condition that forces oxidative phosphorylation, and in the presence of rotenone, the classic inhibitor of respiratory Complex I. Under this experimental paradigm we assessed functional parameters such as cell viability and respiration, ATP synthesis, reactive oxygen species production and mtDNA copy number. Our analyses show that haplogroup J1, which is common in western Eurasian populations, is the most sensitive to rotenone, whereas K1 mitogenomes orchestrate the best compensation, possibly because of the haplogroup-specific missense variants impinging on Complex I function. Remarkably, haplogroups J1 and K1 fit the genetic associations previously established with Leber's hereditary optic neuropathy (LHON) for J1, as a penetrance enhancer, and with Parkinson's disease (PD) for K1, as a protective background. Our findings provide functional evidences supporting previous well-established genetic associations of specific haplogroups with two neurodegenerative pathologies, LHON and PD. Our experimental paradigm is instrumental to highlighting the subtle functional differences characterizing mtDNA haplogroups, which will be increasingly needed to dissect the role of mtDNA genetic variation in health, disease and longevity.
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Affiliation(s)
- Daniela Strobbe
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine-University of Padua, Italy
| | | | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | | | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine-University of Padua, Italy
| | - Andrea Martinuzzi
- IRCCS "E. Medea" Scientific Institute Conegliano-Pieve di Soligo Research Center, Pieve di Soligo, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Valerio Carelli
- IRCCS Institute of Neurological Sciences of Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.
| | - Anna Ghelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy.
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20
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A mosaic genetic structure of the human population living in the South Baltic region during the Iron Age. Sci Rep 2018; 8:2455. [PMID: 29410482 PMCID: PMC5802798 DOI: 10.1038/s41598-018-20705-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 11/24/2022] Open
Abstract
Despite the increase in our knowledge about the factors that shaped the genetic structure of the human population in Europe, the demographic processes that occurred during and after the Early Bronze Age (EBA) in Central-East Europe remain unclear. To fill the gap, we isolated and sequenced DNAs of 60 individuals from Kowalewko, a bi-ritual cemetery of the Iron Age (IA) Wielbark culture, located between the Oder and Vistula rivers (Kow-OVIA population). The collected data revealed high genetic diversity of Kow-OVIA, suggesting that it was not a small isolated population. Analyses of mtDNA haplogroup frequencies and genetic distances performed for Kow-OVIA and other ancient European populations showed that Kow-OVIA was most closely linked to the Jutland Iron Age (JIA) population. However, the relationship of both populations to the preceding Late Neolithic (LN) and EBA populations were different. We found that this phenomenon is most likely the consequence of the distinct genetic history observed for Kow-OVIA women and men. Females were related to the Early-Middle Neolithic farmers, whereas males were related to JIA and LN Bell Beakers. In general, our findings disclose the mechanisms that could underlie the formation of the local genetic substructures in the South Baltic region during the IA.
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21
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Pereira JB, Costa MD, Vieira D, Pala M, Bamford L, Harich N, Cherni L, Alshamali F, Hatina J, Rychkov S, Stefanescu G, King T, Torroni A, Soares P, Pereira L, Richards MB. Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. Proc Biol Sci 2018; 284:rspb.2016.1976. [PMID: 28330913 DOI: 10.1098/rspb.2016.1976] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/14/2017] [Indexed: 11/12/2022] Open
Abstract
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.
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Affiliation(s)
- Joana B Pereira
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Marta D Costa
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniel Vieira
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Lisa Bamford
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nourdin Harich
- Laboratoire d'Anthropogenetique, Department de Biologie, Universite Chouaib Doukkali, El Jadida 24000, Morocco
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia.,Tunis and High Institute of Biotechnology, University of Monastir, 5000 Monastir, Tunisia
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Jiři Hatina
- Medical Faculty in Pilsen, Institute of Biology, Charles University, Pilsen, Czech Republic
| | | | | | - Turi King
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Università di Pavia, Pavia, Italy
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Luísa Pereira
- Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Martin B Richards
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK .,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
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22
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Elkamel S, Boussetta S, Khodjet-El-Khil H, Benammar Elgaaied A, Cherni L. Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations. Am J Hum Biol 2018; 30:e23100. [PMID: 29359455 DOI: 10.1002/ajhb.23100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/06/2017] [Accepted: 12/29/2017] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. MATERIALS AND METHODS A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). RESULTS Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. CONCLUSIONS The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE.
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Affiliation(s)
- Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Amel Benammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
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23
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Šebest L, Baldovič M, Frtús A, Bognár C, Kyselicová K, Kádasi Ľ, Beňuš R. Detection of mitochondrial haplogroups in a small avar-slavic population from the eigth-ninth century AD. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:536-553. [PMID: 29345305 DOI: 10.1002/ajpa.23380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 10/31/2017] [Accepted: 12/09/2017] [Indexed: 11/08/2022]
Abstract
OBJECTIVES In the sixth century AD, Avars came to Central Europe from middle Eurasian steppes and founded a strong Empire called the Avar Khagante (568-799/803 AD) in the Pannonian basin. During the existence of this empire, they undertook many military and pugnacious campaigns. In the seventh century, they conquered the northern territory inhabited by Slavs, who were further recruited in Avar military and were commissioned with obtaining food supplies. During almost 200 years of Avar domination, a significant influence by the Avar culture (especially on the burial rite) and assimilation with indigenous population (occurrence of "East Asian"cranial features) could be noticed in this mixed area, which is supported by achaeological and anthropologcal research. Therefore we expected higher incidence of east Eurasian haplogroups (introduced by Avars) than the frequencies detected in present-day central European populations. MATERIALS AND METHODS Mitochondrial DNA from 62 human skeletal remains excavated from the Avar-Slavic burial site Cífer-Pác (Slovakia) dated to the eighth and ninth century was analyzed by the sequencing of hypervariable region I and selected parts of coding region. Obtained haplotypes were compared with other present-day and historical populations and genetic distances were calculated using standard statistical method. RESULTS AND DISCUSSION In total, the detection of mitochondrial haplogroups was possible in 46 individuals. Our results prooved a higher frequency of east Eurasian haplogroups in our analyzed population (6.52%) than in present-day central European populations. However, it is almost three times lower than the frequency of east Eurasian haplogroups detected in other medieval Avar populations. The statistical analysis showed a greater similarity and the lowest genetic distances between the Avar-Slavic burial site Cifer-Pac and medieval European populations than the South Siberian, East and Central Asian populations. CONCLUSION Our results indicate that the transfer of Avar genetic variation through their mtDNA was rather weak in the analyzed mixed population.
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Affiliation(s)
- Lukáš Šebest
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Marian Baldovič
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Adam Frtús
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Csaba Bognár
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Klaudia Kyselicová
- Faculty of Medicine, Institute of Physiology, Comenius University, Sasinkova 2, Bratislava 813 72, Slovak Republic.,Department of Anthropology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
| | - Ľudevít Kádasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic.,Biomedical Research Center Slovak Academy of Sciences, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovak Republic
| | - Radoslav Beňuš
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Mlynska Dolina, Ilkovicova 6, Bratislava 842 15, Slovak Republic
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24
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Ancient mitogenomes of Phoenicians from Sardinia and Lebanon: A story of settlement, integration, and female mobility. PLoS One 2018; 13:e0190169. [PMID: 29320542 PMCID: PMC5761892 DOI: 10.1371/journal.pone.0190169] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 12/08/2017] [Indexed: 11/19/2022] Open
Abstract
The Phoenicians emerged in the Northern Levant around 1800 BCE and by the 9th century BCE had spread their culture across the Mediterranean Basin, establishing trading posts, and settlements in various European Mediterranean and North African locations. Despite their widespread influence, what is known of the Phoenicians comes from what was written about them by the Greeks and Egyptians. In this study, we investigate the extent of Phoenician integration with the Sardinian communities they settled. We present 14 new ancient mitogenome sequences from pre-Phoenician (~1800 BCE) and Phoenician (~700–400 BCE) samples from Lebanon (n = 4) and Sardinia (n = 10) and compare these with 87 new complete mitogenomes from modern Lebanese and 21 recently published pre-Phoenician ancient mitogenomes from Sardinia to investigate the population dynamics of the Phoenician (Punic) site of Monte Sirai, in southern Sardinia. Our results indicate evidence of continuity of some lineages from pre-Phoenician populations suggesting integration of indigenous Sardinians in the Monte Sirai Phoenician community. We also find evidence of the arrival of new, unique mitochondrial lineages, indicating the movement of women from sites in the Near East or North Africa to Sardinia, but also possibly from non-Mediterranean populations and the likely movement of women from Europe to Phoenician sites in Lebanon. Combined, this evidence suggests female mobility and genetic diversity in Phoenician communities, reflecting the inclusive and multicultural nature of Phoenician society.
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25
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The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age. Sci Rep 2017; 7:15644. [PMID: 29142317 PMCID: PMC5688114 DOI: 10.1038/s41598-017-15480-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focus on the maternal genetic makeup of the Neolithic (~ 5500–3000 BCE), Chalcolithic (~ 3000–2200 BCE) and Early Bronze Age (~ 2200–1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.
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26
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Harris EE. Demic and cultural diffusion in prehistoric Europe in the age of ancient genomes. Evol Anthropol 2017; 26:228-241. [PMID: 29027332 DOI: 10.1002/evan.21545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 11/10/2022]
Abstract
Ancient genomes can help us detect prehistoric migrations, population contractions, and admixture among populations. Knowing the dynamics of demography is invaluable for understanding culture change in prehistory, particularly the roles played by demic and cultural diffusion in transformations of material cultures. Prehistoric Europe is a region where ancient genome analyses can help illuminate the interplay between demography and culture change. In Europe, there is more archeological evidence, in terms of detailed studies, radiometric dates, and explanatory hypotheses that can be evaluated, than in any other region of the world. Here I show some important ways that ancient genomes have given us insights into population movements in European prehistory. I also propose that studies might be increasingly focused on specific questions of culture change, for example in evaluating the makers of "transitional" industries as well as the origins of the Gravettian and spread of the Magdalenian. I also discuss genomic evidence supporting the large role that demic expansion has played in the Neolithization of Europe and the formation of the European population during the Bronze Age.
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Affiliation(s)
- Eugene E Harris
- Department of Biological Sciences and Geology, Queensborough Community College, City University of New York, Medical Arts Building, M-213, 222-05, 56th Avenue Bayside, NY, 1136411364.,Affiliated Researcher, Center for the Study of Human Origins, New York University
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27
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Olivieri A, Sidore C, Achilli A, Angius A, Posth C, Furtwängler A, Brandini S, Capodiferro MR, Gandini F, Zoledziewska M, Pitzalis M, Maschio A, Busonero F, Lai L, Skeates R, Gradoli MG, Beckett J, Marongiu M, Mazzarello V, Marongiu P, Rubino S, Rito T, Macaulay V, Semino O, Pala M, Abecasis GR, Schlessinger D, Conde-Sousa E, Soares P, Richards MB, Cucca F, Torroni A. Mitogenome Diversity in Sardinians: A Genetic Window onto an Island's Past. Mol Biol Evol 2017; 34:1230-1239. [PMID: 28177087 PMCID: PMC5400395 DOI: 10.1093/molbev/msx082] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sardinians are "outliers" in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most likely arose in situ. For each Sardinian-specific haplogroup (SSH), we also identified the upstream node in the phylogeny, from which non-Sardinian mitogenomes radiate. This provided minimum and maximum time estimates for the presence of each SSH on the island. In agreement with demographic evidence, almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. For some rare SSHs, however, we could not dismiss the possibility that they might have been on the island prior to the Neolithic, a scenario that would be in agreement with archeological evidence of a Mesolithic occupation of Sardinia.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.,Center for Advanced Studies, Research and Development in Sardinia (CRS4), AGCT Program, Parco Scientifico e Tecnologico della Sardegna, Pula, Italy
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | | | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy.,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, Queensgate, United Kingdom
| | | | | | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, United Kingdom
| | | | | | - Michele Marongiu
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy
| | | | - Patrizia Marongiu
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Salvatore Rubino
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences & ICVS/3B's-PT Government Associate Laboratory, University of Minho, Braga, Portugal
| | - Vincent Macaulay
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, Queensgate, United Kingdom
| | - Gonçalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging US National Institutes of Health, Baltimore, Maryland, MD
| | - Eduardo Conde-Sousa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, Queensgate, United Kingdom
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
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28
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Kulichová I, Fernandes V, Deme A, Nováčková J, Stenzl V, Novelletto A, Pereira L, Černý V. Internal diversification of non-Sub-Saharan haplogroups in Sahelian populations and the spread of pastoralism beyond the Sahara. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:424-434. [DOI: 10.1002/ajpa.23285] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Iva Kulichová
- Department of Anthropology and Human Genetics, Faculty of Science; Charles University in Prague; Czech Republic
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto; Porto Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto Portugal
| | - Alioune Deme
- Département d'Histoire, Faculté des Lettres et Sciences humaines; Université Cheikh Anta Diop de Dakar; Senegal
| | - Jana Nováčková
- Archaeogenetics Laboratory; Institute of Archaeology of the Academy of Sciences of the Czech Republic; Czech Republic
| | - Vlastimil Stenzl
- Department of Forensic Genetics; Institute of Criminalistics; Prague Czech Republic
| | | | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto; Porto Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto Portugal
- Faculdade de Medicina da Universidade do Porto; Porto Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory; Institute of Archaeology of the Academy of Sciences of the Czech Republic; Czech Republic
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29
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González-Fortes G, Jones ER, Lightfoot E, Bonsall C, Lazar C, Grandal-d'Anglade A, Garralda MD, Drak L, Siska V, Simalcsik A, Boroneanţ A, Vidal Romaní JR, Vaqueiro Rodríguez M, Arias P, Pinhasi R, Manica A, Hofreiter M. Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin. Curr Biol 2017; 27:1801-1810.e10. [PMID: 28552360 PMCID: PMC5483232 DOI: 10.1016/j.cub.2017.05.023] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/21/2017] [Accepted: 05/04/2017] [Indexed: 11/18/2022]
Abstract
The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.1× to 4.1× coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.7× and 5.3×) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stable-isotope analysis of this sample suggests a mixed terrestrial/aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization.
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Affiliation(s)
- Gloria González-Fortes
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara 44100, Italy; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam OT Golm, Germany.
| | - Eppie R Jones
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Emma Lightfoot
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Catalin Lazar
- National History Museum of Romania, Bucharest 030026, Romania
| | | | - María Dolores Garralda
- Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid 28040, Spain
| | - Labib Drak
- Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid 28040, Spain
| | - Veronika Siska
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Angela Simalcsik
- "Olga Necrasov" Centre for Anthropological Research of the Romanian Academy, Iaşi Branch, Theodor Codrescu Strada 2, 700481 Iaşi, Romania
| | - Adina Boroneanţ
- "Vasile Pârvan" Institute of Archaeology, Romanian Academy, Henri Coandă Strada 11, Bucharest 010667, Romania
| | | | | | - Pablo Arias
- International Institute of Prehistorical Research, University of Cantabria-Government of Cantabria-Bank of Santander, Santander 39005, Spain
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland; Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam OT Golm, Germany.
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30
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Origin and spread of human mitochondrial DNA haplogroup U7. Sci Rep 2017; 7:46044. [PMID: 28387361 PMCID: PMC5384202 DOI: 10.1038/srep46044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/07/2017] [Indexed: 01/17/2023] Open
Abstract
Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.
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31
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Palencia-Madrid L, Cardoso S, Keyser C, López-Quintana JC, Guenaga-Lizasu A, de Pancorbo MM. Ancient mitochondrial lineages support the prehistoric maternal root of Basques in Northern Iberian Peninsula. Eur J Hum Genet 2017; 25:631-636. [PMID: 28272540 DOI: 10.1038/ejhg.2017.24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/23/2017] [Accepted: 02/01/2017] [Indexed: 11/09/2022] Open
Abstract
The Basque population inhabits the Franco-Cantabrian region in southwest Europe where Palaeolithic human groups took refuge during the Last Glacial Maximum. Basques have been an isolated population, largely considered as one of the most ancient European populations and it is possible that they maintained some pre-Neolithic genetic characteristics. This work shows the results of mitochondrial DNA analysis of seven ancient human remains from the Cave of Santimamiñe in the Basque Country dated from Mesolithic to the Late Roman period. In addition, we compared these data with those obtained from a modern sample of Basque population, 158 individuals that nowadays inhabits next to the cave. The results support the hypothesis that Iberians might have been less affected by the Neolithic mitochondrial lineages carried from the Near East than populations of Central Europe and revealed the unexpected presence of prehistoric maternal lineages such as U5a2a and U3a in the Basque region. Comparison between ancient and current population samples upholds the hypothesis of continuity of the maternal lineages in the area of the Franco-Cantabrian region.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Sergio Cardoso
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Christine Keyser
- Laboratoire AMIS, CNRS, UMR 5288, Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | | | | | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
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32
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Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain. Forensic Sci Int Genet 2017; 27:142-148. [DOI: 10.1016/j.fsigen.2016.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 12/22/2016] [Accepted: 12/29/2016] [Indexed: 11/20/2022]
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A cryptic mitochondrial DNA link between North European and West African dogs. J Genet Genomics 2016; 44:163-170. [PMID: 28302420 DOI: 10.1016/j.jgg.2016.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/17/2016] [Accepted: 10/21/2016] [Indexed: 01/25/2023]
Abstract
Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA (mtDNA) D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups (matrilines; clades): A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1 (but not the entire haplogroup D) coalescing around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.
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Gautier M, Moazami-Goudarzi K, Levéziel H, Parinello H, Grohs C, Rialle S, Kowalczyk R, Flori L. Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences. Mol Biol Evol 2016; 33:2801-2814. [PMID: 27436010 PMCID: PMC5062319 DOI: 10.1093/molbev/msw144] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7 × 106 to 850,000 years before present (YBP) through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (∼150,000 YBP), between the wisent and (European) taurine cattle lineages. Although the wisent and bovine population sizes experienced a similar sharp decline since the Last Glacial Maximum, we find that the wisent demography remained more fluctuating during the Pleistocene. This is in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors. We finally detect 423 genes under positive selection between the wisent and bovine lineages, which shed a new light on the genome response to different living conditions (temperature, available food resource, and pathogen exposure) and on the key gene functions altered by the domestication process.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Supagro, Montferrier-sur-Lez, France IBC, Institut de Biologie Computationnelle, Montpellier, France
| | | | | | - Hugues Parinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Laurence Flori
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France INTERTRYP, CIRAD, IRD, Montpellier, France
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35
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Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 2016; 538:238-242. [PMID: 27654910 PMCID: PMC5164938 DOI: 10.1038/nature19792] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 08/24/2016] [Indexed: 12/20/2022]
Abstract
High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
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Affiliation(s)
- Luca Pagani
- Estonian Biocentre, Tartu, Estonia
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniel John Lawson
- Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Evelyn Jagoda
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Mörseburg
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Anders Eriksson
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Florian Clemente
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- Institut de Biologie Computationnelle, Université Montpellier 2, Montpellier, France
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, Estonia
- Department of Psychology, University of Auckland, Auckland, 1142, New Zealand
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Jeffrey D. Wall
- Institute for Human Genetics, University of California, San Francisco, California 94143, USA
| | - Alexia Cardona
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- MRC Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Box 285, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Melissa A. Wilson Sayres
- School of Life Sciences, Tempe, AZ, 85287 USA
- Center for Evolution and Medicine, The Biodesign Institute, Tempe, AZ, 85287 USA
| | - Sarah Kaewert
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte Inchley
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Christiana L. Scheib
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | | | - Monika Karmin
- Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Guy S. Jacobs
- Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Institute for Complex Systems Simulation, University of Southampton, Southampton SO17 1BJ, UK
| | - Tiago Antao
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Florin Mircea Iliescu
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Alena Kushniarevich
- Estonian Biocentre, Tartu, Estonia
- Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Bayazit Yunusbayev
- Estonian Biocentre, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | | | | | - Lehti Saag
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - George Andriadze
- Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Georgia
| | - Craig Muller
- Center for GeoGenetics, University of Copenhagen, Denmark
| | - Michael C. Westaway
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - David M. Lambert
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - Grigor Zoraqi
- Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania
| | | | - Dilbar Dalimova
- Institute of Bioorganic Chemistry Academy of Science, Republic of Uzbekistan
| | | | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka-1000, Bangladesh
| | - Joseph Lachance
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sarah Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek, Kyrgyz Republic
| | - Larisa D. Damba
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, Russia
- Anthony Nolan, London, United Kingdom
| | | | - Olga Utevska
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - François-Xavier Ricaut
- Evolutionary Medicine group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Nicolas Brucato
- Evolutionary Medicine group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Thierry Letellier
- Evolutionary Medicine group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Murray P. Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nikolay A. Barashkov
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia
| | - Vedrana Skaro
- Genos, DNA laboratory, Zagreb, Croatia
- University of Osijek, Medical School, Osijek, Croatia
| | | | - Dragan Primorac
- University of Osijek, Medical School, Osijek, Croatia
- St. Catherine Speciality Hospital, Zabok, Croatia
- Eberly College of Science, The Pennsylvania State University, University Park, PA, USA
- University of Split, Medical School, Split, Croatia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, Estonia
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK
| | - Christina A. Eichstaedt
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- Thoraxclinic at the University Hospital Heidelberg, Heidelberg, Germany
| | - Daria V. Lichman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | | | - Alexandra Karunas
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Sergei Litvinov
- Estonian Biocentre, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Natalya Ekomasova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Damir Marjanović
- Department of Genetics and Bioengineering. Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina
- Institute for Anthropological Researches, Zagreb, Croatia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | | | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
| | - Andres Metspalu
- Department of Zoology, University of Cambridge, Cambridge, UK
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Mikhail Voevoda
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Sardana A. Fedorova
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia
| | - Ludmila P. Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Pascale Gerbault
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Matthew Leavesley
- Department of Archaeology, University of Papua New Guinea, University PO Box 320, NCD, Papua New Guinea
- College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns QLD 4870, Australia
| | | | - Michael Petraglia
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07743 Jena, Germany
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elza K. Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Ene Metspalu
- Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mark G. Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley 94720, CA, USA
| | - Richard Villems
- Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, 6 Kohtu Street, Tallinn 10130, Estonia
| | | | - Toomas Kivisild
- Estonian Biocentre, Tartu, Estonia
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
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Parker GJ, Leppert T, Anex DS, Hilmer JK, Matsunami N, Baird L, Stevens J, Parsawar K, Durbin-Johnson BP, Rocke DM, Nelson C, Fairbanks DJ, Wilson AS, Rice RH, Woodward SR, Bothner B, Hart BR, Leppert M. Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome. PLoS One 2016; 11:e0160653. [PMID: 27603779 PMCID: PMC5014411 DOI: 10.1371/journal.pone.0160653] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 07/21/2016] [Indexed: 12/28/2022] Open
Abstract
Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects' DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European-American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.
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Affiliation(s)
- Glendon J. Parker
- Department of Biology, Utah Valley University, Orem, Utah, United States of America
- Protein-Based Identification Technologies L.L.C., Orem, Utah, United States of America
- * E-mail: parker64@llnl;
| | - Tami Leppert
- Protein-Based Identification Technologies L.L.C., Orem, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Deon S. Anex
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Jonathan K. Hilmer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Nori Matsunami
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lisa Baird
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jeffery Stevens
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Krishna Parsawar
- Mass Spectrometry and Proteomics Core Facility, University of Utah, Salt Lake City, Utah, United States of America
| | - Blythe P. Durbin-Johnson
- Department of Public Health Sciences, University of California, Davis, California, United States of America
| | - David M. Rocke
- Department of Public Health Sciences, University of California, Davis, California, United States of America
| | - Chad Nelson
- Mass Spectrometry and Proteomics Core Facility, University of Utah, Salt Lake City, Utah, United States of America
| | - Daniel J. Fairbanks
- Department of Biology, Utah Valley University, Orem, Utah, United States of America
| | - Andrew S. Wilson
- School of Archaeological Sciences, University of Bradford, Bradford, United Kingdom
| | - Robert H. Rice
- Department of Environmental Toxicology, University of California, Davis, California, United States of America
| | - Scott R. Woodward
- Sorenson Molecular Genealogical Foundation, Salt Lake City, Utah, United States of America
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Bradley R. Hart
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
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37
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Abstract
The latest in a series of transformative studies of DNA from prehistoric Europeans focuses on mitochondrial DNA, bringing fresh surprises and filling in important details of the early stages of a European ancestry stretching back more than 40,000 years.
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38
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Bankoff RJ, Perry GH. Hunter-gatherer genomics: evolutionary insights and ethical considerations. Curr Opin Genet Dev 2016; 41:1-7. [PMID: 27400119 DOI: 10.1016/j.gde.2016.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 10/21/2022]
Abstract
Hunting and gathering societies currently comprise only a small proportion of all human populations. However, the geographic and environmental diversity of modern hunter-gatherer groups, their inherent dependence on ecological resources, and their connection to patterns of behavior and subsistence that represent the vast majority of human history provide opportunities for scientific research to deliver major insights into the evolutionary history of our species. We review recent evolutionary genomic studies of hunter-gatherers, focusing especially on those that identify and functionally characterize phenotypic adaptations to local environments. We also call attention to specific ethical issues that scientists conducting hunter-gatherer genomics research ought to consider, including potential social and economic tensions between traditionally mobile hunter-gatherers and the land ownership-based nation-states by which they are governed, and the implications of genomic-based evidence of long-term evolutionary associations with particular habitats.
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Affiliation(s)
- Richard J Bankoff
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Intercollege Program in Bioethics, Pennsylvania State University, University Park, PA 16802, USA.
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Nesheva DV, Karachanak-Yankova S, Lari M, Yordanov Y, Galabov A, Caramelli D, Toncheva D. Mitochondrial DNA Suggests a Western Eurasian Origin for Ancient (Proto-) Bulgarians. Hum Biol 2016; 87:19-28. [PMID: 26416319 DOI: 10.13110/humanbiology.87.1.0019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ancient (proto-) Bulgarians have long been thought of as a Turkic population. However, evidence found in the past three decades shows that this is not the case. Until now, this evidence has not included ancient mitochondrial DNA (mtDNA) analysis. To fill this void, we collected human remains from the 8th to the 10th century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in northeastern Bulgaria, and Tuhovishte (Satovcha region) in southwestern Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified into mtDNA haplogroups found in present-day European and western Eurasian populations. Our results suggest a western Eurasian matrilineal origin for proto-Bulgarians, as well as a genetic similarity between proto- and modern Bulgarians. Our future work will provide additional data that will further clarify proto-Bulgarian origins, thereby adding new clues to the current understanding of European genetic evolution.
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Affiliation(s)
- D V Nesheva
- 1 Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | | | - M Lari
- 2 Department of Biology, Laboratory of Anthropology, Molecular Anthropology/Paleogenetics Unit, University of Florence, Florence, Italy
| | - Y Yordanov
- 3 Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - A Galabov
- 4 Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - D Caramelli
- 2 Department of Biology, Laboratory of Anthropology, Molecular Anthropology/Paleogenetics Unit, University of Florence, Florence, Italy
| | - D Toncheva
- 1 Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
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Csákyová V, Szécsényi-Nagy A, Csősz A, Nagy M, Fusek G, Langó P, Bauer M, Mende BG, Makovický P, Bauerová M. Maternal Genetic Composition of a Medieval Population from a Hungarian-Slavic Contact Zone in Central Europe. PLoS One 2016; 11:e0151206. [PMID: 26963389 PMCID: PMC4786151 DOI: 10.1371/journal.pone.0151206] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
The genetic composition of the medieval populations of Central Europe has been poorly investigated to date. In particular, the region of modern-day Slovakia is a blank spot in archaeogenetic research. This paper reports the study of mitochondrial DNA (mtDNA) in ancient samples from the 9th–12th centuries originating from the cemeteries discovered in Nitra-Šindolka and Čakajovce, located in western Slovakia (Central Europe). This geographical region is interesting to study because its medieval multi-ethnic population lived in the so-called contact zone of the territory of the Great Moravian and later Hungarian state formations. We described 16 different mtDNA haplotypes in 19 individuals, which belong to the most widespread European mtDNA haplogroups: H, J, T, U and R0. Using comparative statistical and population genetic analyses, we showed the differentiation of the European gene pool in the medieval period. We also demonstrated the heterogeneous genetic characteristics of the investigated population and its affinity to the populations of modern Europe.
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Affiliation(s)
- Veronika Csákyová
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nitra, Slovakia
- * E-mail:
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Aranka Csősz
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Melinda Nagy
- Department of Biology, Faculty of Education, J. Selye University in Komárno, Komárno, Slovakia
| | - Gabriel Fusek
- Institute of Archaeology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Péter Langó
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Miroslav Bauer
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nitra, Slovakia
- Research Institute for Animal Production, NAFC, Nitra, Slovakia
| | - Balázs Gusztáv Mende
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Pavol Makovický
- Department of Biology, Faculty of Education, J. Selye University in Komárno, Komárno, Slovakia
| | - Mária Bauerová
- Department of Botany and Genetics, Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nitra, Slovakia
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Zehender G, Frati ER, Martinelli M, Bianchi S, Amendola A, Ebranati E, Ciccozzi M, Galli M, Lai A, Tanzi E. Dating the origin and dispersal of Human Papillomavirus type 16 on the basis of ancestral human migrations. INFECTION GENETICS AND EVOLUTION 2016; 39:258-264. [PMID: 26827632 DOI: 10.1016/j.meegid.2016.01.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 01/22/2016] [Accepted: 01/26/2016] [Indexed: 01/04/2023]
Abstract
A major limitation when reconstructing the origin and evolution of HPV-16 is the lack of reliable substitution rate estimates for the viral genes. On the basis of the hypothesis of human HPV-16 co-divergence, we estimated a mean evolutionary rate of 1.47×10(-7) (95% HPD=0.64-2.47×10(-7)) subs/site/year for the viral LCR region. The results of a Bayesian phylogeographical analysis suggest that the currently circulating HPV-16 most probably originated in Africa about 110 thousand years ago (Kya), before giving rise to four known geographical lineages: the Asian/European lineage, which most probably originated in Asia a mean 38 Kya, and the Asian/American and two African lineages, which probably respectively originated about 33 and 27 Kya. These data closely reflect current hypotheses concerning modern human expansion based on studies of mitochondrial DNA phylogeny. The correlation between ancient human migration and the present HPV phylogeny may be explained by the co-existence of modes of transmission other than sexual transmission.
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Affiliation(s)
- Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy.
| | - Elena Rosanna Frati
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Marianna Martinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Silvia Bianchi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Antonella Amendola
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Erika Ebranati
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Campus Bio-Medico University, Rome, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Elisabetta Tanzi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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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: 19] [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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Straus LG. The Human Occupation of Southwestern Europe during the Last Glacial Maximum. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2015. [DOI: 10.3998/jar.0521004.0071.401] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Parolo S, Lisa A, Gentilini D, Di Blasio AM, Barlera S, Nicolis EB, Boncoraglio GB, Parati EA, Bione S. Characterization of the biological processes shaping the genetic structure of the Italian population. BMC Genet 2015; 16:132. [PMID: 26553317 PMCID: PMC4640365 DOI: 10.1186/s12863-015-0293-x] [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: 09/02/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background The genetic structure of human populations is the outcome of the combined action of different processes such as demographic dynamics and natural selection. Several efforts toward the characterization of population genetic architectures and the identification of adaptation signatures were recently made. In this study, we provide a genome-wide depiction of the Italian population structure and the analysis of the major determinants of the current existing genetic variation. Results We defined and characterized 210 genomic loci associated with the first Principal Component calculated on the Italian genotypic data and correlated to the North–south genetic gradient. Using a gene-enrichment approach we identified the immune function as primarily involved in the Italian population differentiation and we described a locus on chromosome 13 showing combined evidence of North–south diversification in allele frequencies and signs of recent positive selection. In this region our bioinformatics analysis pinpointed an uncharacterized long intergenic non-coding (lincRNA), whose expression appeared specific for immune-related tissues suggesting its relevance for the immune function. Conclusions Our study, combining population genetic analyses with biological insights provides a description of the Italian genetic structure that in future could contribute to the evaluation of complex diseases risk in the population context. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0293-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Parolo
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Antonella Lisa
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Davide Gentilini
- Molecular Biology Laboratory, Istituto Auxologico Italiano, Milan, Italy.
| | | | - Simona Barlera
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Enrico B Nicolis
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Giorgio B Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Eugenio A Parati
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Silvia Bione
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
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Chaplin G, Jablonski NG. The human environment and the vitamin D compromise: Scotland as a case study in human biocultural adaptation and disease susceptibility. Hum Biol 2015; 85:529-52. [PMID: 25019187 DOI: 10.3378/027.085.0402] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2013] [Indexed: 11/05/2022]
Abstract
Year-round human habitation of environments with highly seasonal regimes of ultraviolet B radiation (UVB) depended on adaptive complexes of biological and cultural traits to ensure adequacy of vitamin D. Perturbations of such adaptive complexes resulting from changes in the physical environment, human behavior and culture, or both have had unexpected and untoward consequences for health. Scotland is an excellent case study of the changing nature of human biocultural adaptation to low-UVB environments. Occupation of Scotland after the last Pleistocene glaciation event about 14,000 YBP was made possible by maximally depigmented skin, which facilitated cutaneous biosynthesis of vitamin D3, and by a diet that emphasized foods rich in vitamin D. Changes in human subsistence and diet began with the introduction of agriculture and grazing about 5,000 YBP and accelerated greatly in the last 200 years through industrialization and urbanization. The resulting changes in domiciles, patterns of daily activity and behavior, and diet have led to reduced exposure to UVB and reduced consumption of vitamin D-rich foods. This has perturbed the "vitamin D compromise," an adaptive complex established in Scotland during the Mesolithic and Neolithic. We describe the UVB environment of Scotland from remotely sensed data and combine these data with information from the archaeological record to describe the vitamin D compromise in Scotland. Changes in human exposure to UVB and vitamin D consumption, which occurred as the result of urbanization and the dietary shift away from the consumption of oily fish, are traced. Vitamin D deficiency contributes to increased disease prevalence in Scotland, including that of the autoimmune disease multiple sclerosis, a debilitating neurodegenerative disease caused by demyelination of the central nervous system. These conditions have created an "imperfect storm" of poor health that should command the attention of public health experts and policy makers.
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Affiliation(s)
- George Chaplin
- Department of Anthropology, The Pennsylvania State University, University Park, PA and Stellenbosch Institute of Advanced Study, Stellenbosch 7600, South Africa
| | - Nina G Jablonski
- Department of Anthropology, The Pennsylvania State University, University Park, PA and Stellenbosch Institute of Advanced Study, Stellenbosch 7600, South Africa
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Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, Oliveira M, Melhaoui M, Baali A, Pereira L, Calderón R. Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm. PLoS One 2015; 10:e0139784. [PMID: 26509580 PMCID: PMC4624789 DOI: 10.1371/journal.pone.0139784] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/17/2015] [Indexed: 11/18/2022] Open
Abstract
Determining the timing, identity and direction of migrations in the Mediterranean Basin, the role of "migratory routes" in and among regions of Africa, Europe and Asia, and the effects of sex-specific behaviors of population movements have important implications for our understanding of the present human genetic diversity. A crucial component of the Mediterranean world is its westernmost region. Clear features of transcontinental ancient contacts between North African and Iberian populations surrounding the maritime region of Gibraltar Strait have been identified from archeological data. The attempt to discern origin and dates of migration between close geographically related regions has been a challenge in the field of uniparental-based population genetics. Mitochondrial DNA (mtDNA) studies have been focused on surveying the H1, H3 and V lineages when trying to ascertain north-south migrations, and U6 and L in the opposite direction, assuming that those lineages are good proxies for the ancestry of each side of the Mediterranean. To this end, in the present work we have screened entire mtDNA sequences belonging to U6, M1 and L haplogroups in Andalusians--from Huelva and Granada provinces--and Moroccan Berbers. We present here pioneer data and interpretations on the role of NW Africa and the Iberian Peninsula regarding the time of origin, number of founders and expansion directions of these specific markers. The estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene. Still, founder analysis highlights that the high sharing of lineages between North Africa and Iberia results from a complex process continued through time, impairing simplistic interpretations. In particular, our work supports the existence of an ancient, frequently denied, bridge connecting the Maghreb and Andalusia.
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Affiliation(s)
- Candela L. Hernández
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal
| | - Jean M. Dugoujon
- CNRS UMR 5288 Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, 31073 Toulouse, France
| | - Andrea Novelletto
- Dipartimento di Biologia, Università Tor Vergata di Rome, Rome, Italy
| | | | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Marisa Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | | | - Abdellatif Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - Luisa Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
- * E-mail:
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Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L. Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Hum Mutat 2015; 36:1100-11. [DOI: 10.1002/humu.22849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Department of Biology; CBMA (Centre of Molecular and Environmental Biology); University of Minho; Braga 4704-553 Portugal
| | - Rui Camacho
- INESC TEC; Porto 4200-465 Portugal
- Departamento de Engenharia Informática; Faculdade de Engenharia da Universidade do Porto; Porto 4200-465 Portugal
| | - Andreia Brandão
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS); Porto 4050-313 Portugal
| | - Marta D. Costa
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - David C. Samuels
- Vanderbilt Genetics Institute; Department of Molecular Physiology and Biophysics; Vanderbilt University Medical Center; Nashville Tennessee 37232-0700
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Faculdade de Medicina da Universidade do Porto; Porto 4200-319 Portugal
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Triki-Fendri S, Sánchez-Diz P, Rey-González D, Alfadhli S, Ayadi I, Ben Marzoug R, Carracedo Á, Rebai A. Genetic structure of the Kuwaiti population revealed by paternal lineages. Am J Hum Biol 2015; 28:203-12. [PMID: 26293354 DOI: 10.1002/ajhb.22773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/18/2015] [Accepted: 07/25/2015] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE We analyzed the Y-chromosome haplogroup diversity in the Kuwaiti population to gain a more complete overview of its genetic landscape. METHOD A sample of 117 males from the Kuwaiti population was studied through the analysis of 22 Y-SNPs. The results were then interpreted in conjunction with those of other populations from the Middle East, South Asia, North and East Africa, and East Europe. RESULTS The analyzed markers allowed the discrimination of 19 different haplogroups with a diversity of 0.7713. J-M304 was the most frequent haplogroup in the Kuwaiti population (55.5%) followed by E-M96 (18%). They revealed a genetic homogeneity between the Kuwaiti population and those of the Middle East (FST = 6.1%, P-value < 0.0001), although a significant correlation between genetic and geographic distances was found (r = 0.41, P-value = 0.009). Moreover, the nonsignificant pairwise FST genetic distances between the Kuwait population on the one hand and the Arabs of Iran and those of Sudan on the other, corroborate the hypothesis of bidirectional gene flow between Arabia and both Iran and Sudan. CONCLUSION Overall, we have revealed that the Kuwaiti population has experienced significant gene flow from neighboring populations like Saudi Arabia, Iran, and East Africa. Therefore, we have confirmed that the population of Kuwait is genetically coextensive with those of the Middle East.
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Affiliation(s)
- Soumaya Triki-Fendri
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Paula Sánchez-Diz
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Danel Rey-González
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain
| | - Suad Alfadhli
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Kuwait University, Kuwait
| | - Imen Ayadi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Riadh Ben Marzoug
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Science, University of Santiago De Compostela, Santiago De Compostela, Galicia, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, BP1177 Route Sidi Mansour Km 6, Sfax, Tunisia
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49
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60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Sci Rep 2015. [PMID: 26211407 PMCID: PMC4515592 DOI: 10.1038/srep12526] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70–50 ka into Eastern or Southern Africa, (2) postglacial movements (15–10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.
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Paraskevis D, Angelis K, Magiorkinis G, Kostaki E, Ho SYW, Hatzakis A. Dating the origin of hepatitis B virus reveals higher substitution rate and adaptation on the branch leading to F/H genotypes. Mol Phylogenet Evol 2015. [PMID: 26220838 DOI: 10.1016/j.ympev.2015.07.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The evolution of hepatitis B virus (HBV), particularly its origins and evolutionary timescale, has been the subject of debate. Three major scenarios have been proposed, variously placing the origin of HBV in humans and great apes from some million years to only a few thousand years ago (ka). To compare these scenarios, we analyzed 105 full-length HBV genome sequences from all major genotypes sampled globally. We found a high correlation between the demographic histories of HBV and humans, as well as coincidence in the times of origin of specific subgenotypes with human migrations giving rise to their host indigenous populations. Together with phylogenetic evidence, this suggests that HBV has co-expanded with modern humans. Based on the co-expansion, we conducted a Bayesian dating analysis to estimate a precise evolutionary timescale for HBV. Five calibrations were used at the origins of F/H genotypes, D4, C3 and B6 from respective indigenous populations in the Pacific and Arctic and A5 from Haiti. The estimated time for the origin of HBV was 34.1ka (95% highest posterior density interval 27.6-41.3ka), coinciding with the dispersal of modern non-African humans. Our study, the first to use full-length HBV sequences, places a precise timescale on the HBV epidemic and also shows that the "branching paradox" of the more divergent genotypes F/H from Amerindians is due to an accelerated substitution rate, probably driven by positive selection. This may explain previously observed differences in the natural history of HBV between genotypes F1 and A2, B1, and D.
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Affiliation(s)
- Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece.
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece; Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece; Department of Zoology, University of Oxford, United Kingdom
| | - Evangelia Kostaki
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece
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