The Human Y Chromosome Haplogroup Tree: Nomenclature and Phylogeography of Its Major Divisions

▪ Abstract In this review we discuss the recent construction of a highly resolved tree of the nonrecombining portion of the Y chromosome (NRY), and the development of a cladistic nomenclatural system to name the resulting haplogroups. This phylogenetic gene tree comprises 18 major haplogroups that are defined by 48 binary polymorphisms. We also present results from a phylogeographic analysis of NRY haplogroups in a global sample of 2007 males, as well as from a regional study focusing on Siberia (n = 902). We use the following statistical techniques to explicate our presentation: analysis of molecular variance, multidimensional scaling, comparative measures of genetic diversity, and phylogeography-based frequency distributions. Our global results, based on the 18 major haplogroups, are similar to those from previous analyses employing additional markers and support the hypothesis of an African origin of human NRY diversity. Although Africa exhibits greater divergence among haplogroups, Asia contains the l...

[1]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.

[2]  A Sajantila,et al.  Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. , 2000, American journal of human genetics.

[3]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[4]  M. Hammer,et al.  High levels of Y-chromosome nucleotide diversity in the genus Pan , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[5]  P. de Knijff,et al.  Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees. , 1997, Human molecular genetics.

[6]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[7]  R. W. Davis,et al.  Population genetic implications from sequence variation in four Y chromosome genes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[8]  M. Hammer,et al.  Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. , 1998, Molecular biology and evolution.

[9]  P. Underhill,et al.  Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition. , 1994, Human molecular genetics.

[10]  J. Sulston,et al.  Sequence variation of the human Y chromosome , 1995, Nature.

[11]  M. Nei.  Molecular Evolutionary Genetics , 1987 .

[12]  R. W. Davis,et al.  Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. , 1997, Genome research.

[13]  M. Stoneking,et al.  Sex determination of ancient human skeletons using DNA. , 1996, American journal of physical anthropology.

[14]  M. Donoghue.  A Critique of the Biological Species Concept and Recommendations for a Phylogenetic Alternative , 1985 .

[15]  C. Tyler-Smith,et al.  The Y chromosome in forensic analysis and paternity testing , 1997, International Journal of Legal Medicine.

[16]  L. Jin,et al.  A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[17]  L L Cavalli-Sforza,et al.  The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations , 2001, Annals of human genetics.

[18]  S. Rozen,et al.  A physical map of the human Y chromosome , 2001, Nature.

[19]  M. Hammer,et al.  The role of the Y chromosome in human evolutionary studies , 1996 .

[20]  C. E. Bessey.  Evolution and Classification , 1893, Botanical Gazette.

[21]  M W Feldman,et al.  Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  K. Jegalian,et al.  Why the y is So Weird. , 2001 .

[23]  M A Jobling,et al.  In the name of the father: surnames and genetics. , 2001, Trends in genetics : TIG.

[24]  R. J. Mitchell,et al.  Recurrent duplication and deletion polymorphisms on the long arm of the Y chromosome in normal males. , 1996, Human molecular genetics.

[25]  L. Excoffier,et al.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. , 1992, Genetics.

[26]  P. Knijff.  Messages through Bottlenecks: On the Combined Use of Slow and Fast Evolving Polymorphic Markers on the Human Y Chromosome , 2000 .

[27]  M. Hammer,et al.  Y chromosomal DNA variation and the peopling of Japan. , 1995, American journal of human genetics.

[28]  M. Hammer,et al.  A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. , 1994, Molecular biology and evolution.

[29]  Li Jin,et al.  Y chromosome sequence variation and the history of human populations , 2000, Nature Genetics.

[30]  David L. Hull,et al.  Science as a Process: An Evolutionary Account of the Social and Conceptual Development of Science, David L. Hull. 1988. The University of Chicago Press, Chicago, IL. 608 pages. ISBN: 0-226-35060-4. $39.95 , 1989 .

[31]  E Mayr,et al.  Biological Classification: Toward a Synthesis of Opposing Methodologies , 1981, Science.

[32]  C. Tyler-Smith,et al.  PCR haplotypes for the human Y chromosome based on alphoid satellite DNA variants and heteroduplex analysis. , 1995, Gene.

[33]  Eric Minch,et al.  Genetic evidence for a higher female migration rate in humans , 1998, Nature Genetics.

[34]  A. Redd,et al.  A nomenclature system for the tree of human Y-chromosomal binary haplogroups. , 2002, Genome research.

[35]  D. Nickerson,et al.  Variation is the spice of life , 2001, Nature Genetics.

[36]  B. Charlesworth,et al.  Towards a complete sequence of the human Y chromosome , 2001, Genome Biology.

[37]  M. Hammer,et al.  Ancestral Asian source(s) of new world Y-chromosome founder haplotypes. , 1999, American journal of human genetics.

[38]  R. Griffiths,et al.  Inference from gene trees in a subdivided population. , 2000, Theoretical population biology.

[39]  J. Weissenbach,et al.  A human Y-linked DNA polymorphism and its potential for estimating genetic and evolutionary distance. , 1985, Science.

[40]  M. Hammer,et al.  Hierarchical patterns of global human Y-chromosome diversity. , 2001, Molecular biology and evolution.

[41]  Henry E. Kyburg,et al.  Science as Process. , 1993 .

[42]  G. Lucotte,et al.  p49f, A highly polymorphic probe, that detects Taq1 RFLPs on the human Y chromosome. , 1985, Nucleic acids research.

[43]  C. Jolly,et al.  A proper study for mankind: Analogies from the Papionin monkeys and their implications for human evolution. , 2001, American journal of physical anthropology.