Journal ArticleDOI
High mutation rates have driven extensive structural polymorphism among human Y chromosomes.
Sjoerd Repping,Sjoerd Repping,Sjoerd Repping,Saskia K.M. van Daalen,Laura G. Brown,Laura G. Brown,Cindy M. Korver,Julian Lange,Julian Lange,Janet D. Marszalek,Janet D. Marszalek,Tatyana Pyntikova,Tatyana Pyntikova,Fulco van der Veen,Helen Skaletsky,Helen Skaletsky,David C. Page,David C. Page,Steve Rozen,Steve Rozen +19 more
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TLDR
High mutation rates have driven extensive structural polymorphism among human Y chromosomes and limited variation in the copy number of Y-linked genes is found, which raises the possibility of selective constraints.Abstract:
Although much structural polymorphism in the human genome has been catalogued, the kinetics of underlying change remain largely unexplored. Because human Y chromosomes are clonally inherited, it has been possible to capture their detailed relationships in a robust, worldwide genealogical tree. Examination of structural variation across this tree opens avenues for investigating rates of underlying mutations. We selected one Y chromosome from each of 47 branches of this tree and searched for large-scale variation. Four chromosomal regions showed extensive variation resulting from numerous large-scale mutations. Within the tree encompassed by the studied chromosomes, the distal-Yq heterochromatin changed length > or = 12 times, the TSPY gene array changed length > or = 23 times, the 3.6-Mb IR3/IR3 region changed orientation > or = 12 times and the AZFc region was rearranged > or = 20 times. After determining the total time spanned by all branches of this tree (approximately 1.3 million years or 52,000 generations), we converted these mutation counts to lower bounds on rates: > or = 2.3 x 10(-4), > or = 4.4 x 10(-4), > or = 2.3 x 10(-4) and > or = 3.8 x 10(-4) large-scale mutations per father-to-son Y transmission, respectively. Thus, high mutation rates have driven extensive structural polymorphism among human Y chromosomes. At the same time, we found limited variation in the copy number of Y-linked genes, which raises the possibility of selective constraints.read more
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Journal ArticleDOI
Global variation in copy number in the human genome
Richard Redon,Shumpei Ishikawa,Karen R. Fitch,Lars Feuk,George H. Perry,T. Daniel Andrews,Heike Fiegler,Michael H. Shapero,Andrew R. Carson,Wenwei Chen,Eun Kyung Cho,Stephanie Dallaire,Jennifer L. Freeman,Juan R. González,Mònica Gratacòs,Jing Huang,Dimitrios Kalaitzopoulos,Daisuke Komura,Jeffrey R. MacDonald,Christian R. Marshall,Rui Mei,Lyndal Montgomery,Keunihiro Nishimura,Kohji Okamura,Fan Shen,Martin J. Somerville,Joelle Tchinda,Armand Valsesia,Cara Woodwark,Fengtang Yang,Junjun Zhang,Tatiana Zerjal,Jane Zhang,Lluís Armengol,Donald F. Conrad,Xavier Estivill,Chris Tyler-Smith,Nigel P. Carter,Hiroyuki Aburatani,Charles Lee,Keith W. Jones,Stephen W. Scherer,Matthew E. Hurles +42 more
TL;DR: A first-generation CNV map of the human genome is constructed through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia, underscoring the importance of CNV in genetic diversity and evolution and the utility of this resource for genetic disease studies.
Journal ArticleDOI
Copy number variation: New insights in genome diversity
Jennifer L. Freeman,George H. Perry,Lars Feuk,Richard Redon,Steven A. McCarroll,David Altshuler,Hiroyuki Aburatani,Keith W. Jones,Chris Tyler-Smith,Matthew E. Hurles,Nigel P. Carter,Stephen W. Scherer,Charles Lee +12 more
TL;DR: Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases.
Journal ArticleDOI
New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
Tatiana M. Karafet,Fernando L. Mendez,Monica B. Meilerman,Peter A. Underhill,Stephen L. Zegura,Michael F. Hammer +5 more
TL;DR: Major changes in the topology of the parsimony tree are described and names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002 are provided.
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In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning
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Journal ArticleDOI
Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations
TL;DR: This work compares and contrast uniparentally inherited loci for patterns of continuity and discreteness and discusses how their phylogenetic diversity and progression provide means to disentangle ancient colonization events by pioneering migrants from subsequent overlying migrations.
References
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Journal ArticleDOI
Fine-scale structural variation of the human genome.
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TL;DR: This work systematically compared the human genome reference sequence with a second genome to detect intermediate-sized structural variants >8 kb in length and validated 112 of the structural variants, including several that are of biomedical relevance.
Journal ArticleDOI
Y chromosome sequence variation and the history of human populations
Peter A. Underhill,Peidong Shen,A. A. Lin,Li Jin,Giuseppe Passarino,Wei-Hsien Yang,Kauffman E,Batsheva Bonne-Tamir,Jaume Bertranpetit,Paolo Francalacci,Muntaser E. Ibrahim,Trefor Jenkins,Kidd,S.Q. Mehdi,Mark Seielstad,R. S. Wells,Alberto Piazza,Ronald W. Davis,Marcus W. Feldman,Luigi Luca Cavalli-Sforza,Peter J. Oefner +20 more
TL;DR: Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of the authors' species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history.
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