New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

2008/04/02 by Tatiana M. Karafet, Fernando L. Méndez, Monica B. Meilerman +3 · 73 citations
Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · Mathematics · #Forensic and Genetic Research #Genetic diversity and population structure #Chromosomal and Genetic Variations #Haplogroup #Biology #Evolutionary biology #Genetics #Y chromosome #Clade #Chromosome #Phylogenetic tree #Tree (set theory) #Haplotype #Gene #Combinatorics #Allele #Mathematics

paper · pdf · doi:10.1101/gr.7172008

openalex publication_date 2008/04/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Citations

• A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
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• Sub-populations within the major European and African derived haplogroups R1b3 and E3a are differentiated by previously phylogenetically undefined Y-SNPs
• Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes
• Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific
• A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe
• MtDNA and Y‐chromosome Variation in Kurdish Groups
• Phylogeography of Y-Chromosome Haplogroup I Reveals Distinct Domains of Prehistoric Gene Flow in Europe
• Frequentist Estimation of Coalescence Times From Nucleotide Sequence Data Using a Tree-Based Partition
• Thomas Jefferson's Y chromosome belongs to a rare European lineage
• Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes
• 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
• Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes
• A Predominantly Indigenous Paternal Heritage for the Austronesian-Speaking Peoples of Insular Southeast Asia and Oceania
• Human Population Structure and Its Effects on Sampling Y Chromosome Sequence Variation
• Polynesian origins: Insights from the Y chromosome
• Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area
• Y‐chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y‐STR Polymorphisms
• Genetic Evidence for Unequal Effective Population Sizes of Human Females and Males
• Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations
• High-Resolution SNPs and Microsatellite Haplotypes Point to a Single, Recent Entry of Native American Y Chromosomes into the Americas
• Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes
• The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations
• The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective
• The Race for the 1000 Genome

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• Haplogroup A (Y-DNA) [wikipedia]
• Haplogroup B-M60 [wikipedia]
• Haplogroup C-M130 [wikipedia]
• Haplogroup D-M174 [wikipedia]
• Haplogroup E-M215 [wikipedia]
• Haplogroup E-M96 [wikipedia]
• Haplogroup E-V38 [wikipedia]
• Haplogroup F-M89 [wikipedia]
• Haplogroup J-M172 [wikipedia]
• Haplogroup J-M267 [wikipedia]
• Haplogroup J (Y-DNA) [wikipedia]
• Haplogroup L-M20 [wikipedia]
• Haplogroup M-P256 [wikipedia]
• Haplogroup N-M231 [wikipedia]
• Haplogroup O-M175 [wikipedia]
• Haplogroup R (Y-DNA) [wikipedia]

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