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Whelan EC, Nwala AC, Osgood C, Olariu S. Selective mutation accumulation: a computational model of the paternal age effect. Bioinformatics 2016; 32:3790-3797. [PMID: 27531106 DOI: 10.1093/bioinformatics/btw528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 07/12/2016] [Accepted: 08/09/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION As the mean age of parenthood grows, the effect of parental age on genetic disease and child health becomes ever more important. A number of autosomal dominant disorders show a dramatic paternal age effect due to selfish mutations: substitutions that grant spermatogonial stem cells (SSCs) a selective advantage in the testes of the father, but have a deleterious effect in offspring. In this paper we present a computational technique to model the SSC niche in order to examine the phenomenon and draw conclusions across different genes and disorders. RESULTS We used a Markov chain to model the probabilities of mutation and positive selection with cell divisions. The model was fitted to available data on disease incidence and also mutation assays of sperm donors. Strength of selective advantage is presented for a range of disorders including Apert's syndrome and achondroplasia. Incidence of the diseases was predicted closely for most disorders and was heavily influenced by the site-specific mutation rate and the number of mutable alleles. The model also successfully predicted a stronger selective advantage for more strongly activating gain-of-function mutations within the same gene. Both positive selection and the rate of copy-error mutations are important in adequately explaining the paternal age effect. AVAILABILITY AND IMPLEMENTATION C ++/R source codes and documentation including compilation instructions are available under GNU license at https://github.com/anwala/NicheSimulation CONTACT: ewhel001@odu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Eoin C Whelan
- Department of Biology, Old Dominion University, Norfolk, VA, USA
| | - Alexander C Nwala
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
| | | | - Stephan Olariu
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA
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Balanovsky OP, Zaporozhchenko VV. Chromosome as a chronicler: Genetic dating, historical events, and DNA-genealogic temptation. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416070048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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53
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Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GRS, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, Bustamante CD, Tyler-Smith C. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet 2016; 48:593-9. [PMID: 27111036 PMCID: PMC4884158 DOI: 10.1038/ng.3559] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 04/01/2016] [Indexed: 12/21/2022]
Abstract
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
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Affiliation(s)
- G David Poznik
- Program in Biomedical Informatics, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fernando L Mendez
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Thomas F Willems
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- New York Genome Center, New York, New York, USA
| | - Andrea Massaia
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shane A McCarthy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Seva Kashin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ruby Banerjee
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Maria Cerezo
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Haojing Shao
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Melissa Gymrek
- New York Genome Center, New York, New York, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ankit Malhotra
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Sandra Louzada
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rob Desalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Graham R S Ritchie
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | - Erik Garrison
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anthony Marcketta
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David Mittelman
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Chengsheng Zhang
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Gonçalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Peter A Underhill
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Lachlan Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yaniv Erlich
- New York Genome Center, New York, New York, USA
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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Willems T, Gymrek M, Poznik G, Tyler-Smith C, Erlich Y, Erlich Y. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet 2016; 98:919-933. [PMID: 27126583 DOI: 10.1016/j.ajhg.2016.04.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/01/2016] [Indexed: 01/23/2023] Open
Abstract
Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2-6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes.
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Affiliation(s)
| | | | | | | | | | - Yaniv Erlich
- New York Genome Center, New York, NY 10013, USA; Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139, USA; Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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55
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Barbieri C, Hübner A, Macholdt E, Ni S, Lippold S, Schröder R, Mpoloka SW, Purps J, Roewer L, Stoneking M, Pakendorf B. Refining the Y chromosome phylogeny with southern African sequences. Hum Genet 2016; 135:541-553. [PMID: 27043341 PMCID: PMC4835522 DOI: 10.1007/s00439-016-1651-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/18/2016] [Indexed: 12/04/2022]
Abstract
The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species.
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Affiliation(s)
- Chiara Barbieri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Shengyu Ni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | | | - Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Brigitte Pakendorf
- Dynamique du Langage, UMR5596, CNRS & Université Lyon 2, 69363, Lyon Cedex 07, France.
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56
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Resque R, Gusmão L, Geppert M, Roewer L, Palha T, Alvarez L, Ribeiro-dos-Santos Â, Santos S. Male Lineages in Brazil: Intercontinental Admixture and Stratification of the European Background. PLoS One 2016; 11:e0152573. [PMID: 27046235 PMCID: PMC4821637 DOI: 10.1371/journal.pone.0152573] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 03/16/2016] [Indexed: 12/27/2022] Open
Abstract
The non-recombining nature of the Y chromosome and the well-established phylogeny of Y-specific Single Nucleotide Polymorphisms (Y-SNPs) make them useful for defining haplogroups with high geographical specificity; therefore, they are more apt than the Y-STRs to detect population stratification in admixed populations from diverse continental origins. Different Y-SNP typing strategies have been described to address issues of population history and movements within geographic territories of interest. In this study, we investigated a set of 41 Y-SNPs in 1217 unrelated males from the five Brazilian geopolitical regions, aiming to disclose the genetic structure of male lineages in the country. A population comparison based on pairwise FST genetic distances did not reveal statistically significant differences in haplogroup frequency distributions among populations from the different regions. The genetic differences observed among regions were, however, consistent with the colonization history of the country. The sample from the Northern region presented the highest Native American ancestry (8.4%), whereas the more pronounced African contribution could be observed in the Northeastern population (15.1%). The Central-Western and Southern samples showed the higher European contributions (95.7% and 93.6%, respectively). The Southeastern region presented significant European (86.1%) and African (12.0%) contributions. The subtyping of the most frequent European lineage in Brazil (R1b1a-M269) allowed differences in the genetic European background of the five Brazilian regions to be investigated for the first time.
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Affiliation(s)
- Rafael Resque
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Laboratório de Toxicologia e Química Farmacêutica, Departamento de Ciências da Saúde e Biológicas, Universidade Federal do Amapá, Macapá, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.,IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria Geppert
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Teresinha Palha
- Laboratório de Genética Forense, Instituto de Criminalística, Centro de Perícias Científicas Renato Chaves, Belém, Pará, Brasil
| | - Luis Alvarez
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Brazil
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57
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Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, Tyler-Smith C, Jobling MA. Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal. Genome Res 2016; 26:427-39. [PMID: 26883546 PMCID: PMC4817767 DOI: 10.1101/gr.198754.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 12/30/2022]
Abstract
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale–multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8–15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Mariano Rocchi
- Department of Biology, University of Bari, 70124 Bari, Italy
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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58
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Voskarides K, Mazières S, Hadjipanagi D, Di Cristofaro J, Ignatiou A, Stefanou C, King RJ, Underhill PA, Chiaroni J, Deltas C. Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements. INVESTIGATIVE GENETICS 2016; 7:1. [PMID: 26870315 PMCID: PMC4750176 DOI: 10.1186/s13323-016-0032-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/02/2016] [Indexed: 12/15/2022]
Abstract
Background The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization. Results Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography. Conclusions Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks. Electronic supplementary material The online version of this article (doi:10.1186/s13323-016-0032-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantinos Voskarides
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Stéphane Mazières
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Despina Hadjipanagi
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | | | - Anastasia Ignatiou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Charalambos Stefanou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Roy J King
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA USA
| | - Peter A Underhill
- Department of Genetics, Stanford University, Stanford, California 94305 USA
| | - Jacques Chiaroni
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
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59
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Prokop JW, Deschepper CF. Chromosome Y genetic variants: impact in animal models and on human disease. Physiol Genomics 2015; 47:525-37. [PMID: 26286457 DOI: 10.1152/physiolgenomics.00074.2015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Chromosome Y (chrY) variation has been associated with many complex diseases ranging from cancer to cardiovascular disorders. Functional roles of chrY genes outside of testes are suggested by the fact that they are broadly expressed in many other tissues and correspond to regulators of basic cellular functions (such as transcription, translation, and protein stability). However, the unique genetic properties of chrY (including the lack of meiotic crossover and the presence of numerous highly repetitive sequences) have made the identification of causal variants very difficult. Despite the prior lack of reliable sequences and/or data on genetic polymorphisms, earlier studies with animal chrY consomic strains have made it possible to narrow down the phenotypic contributions of chrY. Some of the evidence so far indicates that chrY gene variants associate with regulatory changes in the expression of other autosomal genes, in part via epigenetic effects. In humans, a limited number of studies have shown associations between chrY haplotypes and disease traits. However, recent sequencing efforts have made it possible to greatly increase the identification of genetic variants on chrY, which promises that future association of chrY with disease traits will be further refined. Continuing studies (both in humans and in animal models) will be critical to help explain the many sex-biased disease states in human that are contributed to not only by the classical sex steroid hormones, but also by chrY genetics.
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Affiliation(s)
- J W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; and
| | - C F Deschepper
- Institut de recherches cliniques de Montréal (IRCM) and Université de Montréal, Montreal, Quebec, Canada
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60
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Trombetta B, D'Atanasio E, Massaia A, Myres NM, Scozzari R, Cruciani F, Novelletto A. Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating. PLoS One 2015; 10:e0134646. [PMID: 26226630 PMCID: PMC4520482 DOI: 10.1371/journal.pone.0134646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/10/2015] [Indexed: 12/21/2022] Open
Abstract
Factors affecting the rate and pattern of the mutational process are being identified for human autosomes, but the same relationships for the male specific portion of the Y chromosome (MSY) are not established. We considered 3,390 mutations occurring in 19 sequence bins identified by sequencing 1.5 Mb of the MSY from each of 104 present-day chromosomes. The occurrence of mutations was not proportional to the amount of sequenced bases in each bin, with a 2-fold variation. The regression of the number of mutations per unit sequence against a number of indicators of the genomic features of each bin, revealed the same fundamental patterns as in the autosomes. By considering the sequences of the same region from two precisely dated ancient specimens, we obtained a calibrated region-specific substitution rate of 0.716 × 10-9/site/year. Despite its lack of recombination and other peculiar features, the MSY then resembles the autosomes in displaying a marked regional heterogeneity of the mutation rate. An immediate implication is that a given figure for the substitution rate only makes sense if bound to a specific DNA region. By strictly applying this principle we obtained an unbiased estimate of the antiquity of lineages relevant to the genetic history of the human Y chromosome. In particular, the two deepest nodes of the tree highlight the survival, in Central-Western Africa, of lineages whose coalescence (291 ky, 95% C.I. 253-343) predates the emergence of anatomically modern features in the fossil record.
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Affiliation(s)
- Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Eugenia D'Atanasio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Massaia
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | | | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Andrea Novelletto
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
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Large-scale recent expansion of European patrilineages shown by population resequencing. Nat Commun 2015; 6:7152. [PMID: 25988751 PMCID: PMC4441248 DOI: 10.1038/ncomms8152] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 04/13/2015] [Indexed: 12/12/2022] Open
Abstract
The proportion of Europeans descending from Neolithic farmers ∼ 10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ∼ 2.1-4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.
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Population-scale sequencing in Iceland. Nat Rev Genet 2015. [DOI: 10.1038/nrg3946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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