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Haplogroup R Private SNPs, Notes and Papers - 2017

NOTE: Corrections/Additions made to this page are shown at the bottom of the main Haplogroup R page.

Frequently Mutating SNPs are SNPs that appear many times in many places either in one or more haplogroups. They are inconsistent and not useful for genealogical purposes.

NOTES:

References:

Adams et al, The Case of the Unreliable SNP: Recurrent Back-mutation of Y-chromosomal Marker P25 Through Gene Conversion. (abstract) Forensic Science International 159:14-20, 2006.
Adams et al, The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula, American Journal of Human Genetics, 83(6): 725-36, 2008.
Alonso et al, The Place of the Basques in the European Y-chromosome Diversity Landscape. (available by subscription) European Journal of Human Genetics, 13:1293-1302, 2005.
Balanovsky et al, Parallel Evolution of Genes and Languages in the Caucasus Region. Molecular Biology and Evolution, 13 May 2011.
Balaresque et al, A Predominantly Neolithic Origin for European Paternal Lineages. PLoS biology. 8(1):e1000285 2010.
Behar et al, Contrasting Patterns of Y Chromosome Variation in Ashkenazi Jewish and Host Non-Jewish European Populations. (pdf) Human Genetics 114:354-365, 2004.
Behar et al, Genome-Wide Structure of the Jewish People. Nature, 446:238-42, 2010.
Bosch et al, Paternal and Maternal Lineages in the Balkans Show a Homogeneous Landscape over Linguistis Barriers except for the Isolated Aromuns. Annals of Human Genetics, 70:459-87, (2006).
Capelli et al, Population Structure in the Mediterranean Basin: A Y Chromosome Perspective. (pdf) Annals of Human Genetics, 2005.
Cinnioglu et al, Excavating Y-chromosome Haplotype Strata in Anatolia. (pdf) Human Genetics, 114:127-148, 2004.
Cruciani et al, A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes. American Journal of Human Genetics, 70:1197-1214, 2002.
Cruciani et al, Human Y Chromosome Haplogroup R-V88: A Paternal Genetic Record of Early Mid Holocene Trans-Saharan Connections and the Spread of Chadic Languages. (abstract) (Epub ahead of print) European Journal of Human Genetics, January 6, 2010a.
Cruciani et al, Strong Intra- and Inter-continental Differentiation Revealed by Y chromosome SNPs M269, U106 and U152. Forensic Science International. Genetics,7-10, 2010b.
Deng et al, Evolution and Migration History of the Chinese Population Inferred from the Chinese Y-chromosome Evidence. (pdf) Journal of Human Genetics, 49:339-348, 2004.
Dulik et al, Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. (pdf) The American Journal of Human Genetics, doi: 10.1016/ajhg.2011.12.014, 2012.
Flores et al, Reduced Genetic Structure of the Iberian Peninsula Revealed by Y-chromosome Analysis: Implications for Population Demography. (pdf) European Journal of Human Genetics, 12:855-863, 2004.
Francalacci et al, Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. Science: Vol. 341 no. 6145, pp. 565-569, DOI: 10.1126/science.1237947, 2 August 2013.
Hallast et al, The Y-chromosome Tree Bursts into Leaf: 13,000 High-confidence SNPs Covering the Majority of Known Clades, Molecular Biology and Evolution, doi: 10.1093/molbev/msu327, 2014.
Herrera et al, Neolithic Patrilineal Signals Indicate that the Armenian Plateau was Repopulated by Agriculturalists. European Journal of Human Genetics, 10.1038/ejhg.2011.192, 2011.
Hinds et al, Whole-genome Patterns of Common DNA Variation in Three Human Populations. Science, 307:1072-1079, 2005.
Karafet et al, New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Abstract. Genome Research, published online April 2, 2008. Supplementary Material.
Karafet et al, Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes. (pdf) American Journal of Human Genetics, 69:615-628, 2001.
Karlsson et al, Y-chromosome Diversity in Sweden - A Long-time Perspective. (pdf) European Journal of Human Genetics, 14:963-970, 2006.
Karmin et al, A Recent Bottleneck of Y chromosome Diversity Coincides with a Global Change in Culture. Genome Research, doi: 10.1101/gr.186684.114, published online March 13, 2015.
Kayser et al. Reduced Y-Chromosome, but Not Mitochondrial DNA, Diversity in Human Populations from West New Guinea. American Journal of Human Genetics, 72:281-302, 2003.
Kivisild et al, The Genetic Heritage of the Earliest Settlers Persists in Both Indian Tribal and Caste Populations. (pdf) American Journal of Human Genetics, 72:313-332, 2003.
Malhi et al, Distribution of Y Chromosomes among Native North Americans: A Study of Athapaskan Population History American Journal of Physical Anthropology, 137:412-24, 2008.
McEvoy et al, Y-chromosomes and the Extent of Patrilineal Ancestry in Irish Surnames (abstract) Human Genetics 2006 Jan 12;:1-8 (Epub ahead of print).
Mohyuddin et al, Detection of Novel Y SNPs Provides Further Insights into Y Chromosomal Variation in Pakistan. Journal of Human Genetics, 2006.
Moore et al, A Y-chromosome Signature of Hegemony in Gaelic Ireland. American Journal of Human Genetics, 78(2):334-338, 2006.
Myres et al, A Major Y-chromosome Haplogroup R1b Holocene Era Founder Effect in Central and Western Europe. European Journal of Human Genetics: EJHG. (July):1-7, 2010.
Myres et al, (2007), Y-chromosome Short Tandem Repeat DYS458.2 Non-concensus Alleles Occur Independently in Both Binary Haplogroups J1-M267 and R1b3-M405. Croatian Medical Journal, 48, 2007.
Nasidze et al, MtDNA and Y-chromosome Variation in Kurdish Groups. (abstract) Annals of Human Genetics, 69:401-412, 2005.
Regueiro et al, Iran: Tricontinental Nexus for Y-Chromosome Driven Migration. (abstract) Human Heredity, Vol. 61, No 3, 132-143, 2006.
Repping et al, High Mutation Rates Have Driven Extensive Structural Polymorphism among Human Y Chromosomes. (pdf) National Genetics, 38: 463-467, 2006.
Rocca et al, Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach. (pdf) PLoS ONE 7(7): e41634. doi:10.1371/journal.pone.0041634, 2012.
Rootsi et al, Phylogenetic Applications of Whole Y-chromosome Sequences and the Near Eastern Origin of Ashkenazi Levites. Nature Communications 4, Article number: 2928, doi:10.1038/ncomms3928, 2013.
Rozen et al, Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection. American Journal of Human Genetics. 2009 December 11; 85(6): 923-928.
Semino et al, The Genetic Legacy of Paleolithic Homo Sapiens Sapiens in Extant Europeans. (pdf) Science, V290:1155-1159, 2000.
Semino et al, Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny. (pdf) American Journal of Human Genetics, 70:265-268, 2002.
Sengupta et al, Polarity and Temporality of High Resolution Y-chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. (available by subscription) American Journal of Human Genetics, 78:202-221, 2006.
Sharma et al, The Indian Origin of Paternal Haplogroup R1a1 Substantiates the Autochthonous Origin of Brahmins and the Caste SystemOrigin of Paternal Haplogroup R1a1. (abstract) Journal of Human Genetics, 54:47-55, 2009.
Shen et al, Reconstruction of Patrilineages and Matrilineages of Samaritans and other Israeli Populations from Y-Chromosome and Mitochondrial DNA Sequence Variation. (pdf) Human Mutation, 24:248-260, 2004.
Sims et al, Sub-Populations Within the Major European and African Derived Haplogroups R1b3 and E3a Are Differentiated by Previously Phylogenetically Undefined Y-SNPs. Human Mutation: Mutation in Brief #940, Online, 2007.
Su et al, Y-chromosome Evidence for a Northward Migration of Modern Humans into Eastern Asia during the Last Ice Age. (pdf) American Journal of Human Genetics, 65:1718-1724, 1999.
Underhill et al, Separating the Post-Glacial Coancestry of European and Asian Y Chromosomes within Haplogroup R1a. (abstract) European Journal of Human Genetics, 1-6, 2009.
Underhill et al, The Phylogenetic and Geographic Structure of Y-chromosome Haplogroup R1a. European Journal of Human Genetics, doi:10.1038/ejhg.2014.50, 2014.
Valone et al, Y SNP Typing of African-American and Caucasian Samples Using Allele-Specific Hybridization and Primer Extension. (pdf) Journal of Forensic Science, 49:4, July 2004.
Van Geystelen et al, In silico detection of phylogenetic informative Y-chromosomal single nucleotide polymorphisms from whole genome sequencing data. (abstract) ELECTROPHORESIS, doi: 10.1002/elps.201300459, 35:3102-10, Nov 2014.
Wells et al, The Eurasian Heartland: A Continental Perspective on Y-chromosome Diversity. PNAS, Vol. 98; 18:10244-10249, 2001.
Zhao et al, Presence of Three Different Paternal Lineages among North Indians: A Study of 560 Y Chromosomes. (abstract) Annals of Human Biology, 36(1):46-59, 2009.

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