ArticleGenome research2014
An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Introducing the Y-chromosomal Ancestral-like Reference Sequence-Improving the Capture of Human Evolutionary Information.Molecular biology and evolution · 2025Article
- Resolving the source of branch length variation in the Y chromosome phylogeny.Genome biology · 2025Article
- Editorial: Role of Y Chromosome in Molecular Anthropology, Forensics, and Genetic Genealogy.Frontiers in genetics · 2022Article
- New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion.Human molecular genetics · 2021Article
- CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics.PLoS genetics · 2021Article
- Origin and diffusion of human Y chromosome haplogroup J1-M267.Scientific reports · 2021Article
- Y Haplogroup Diversity of the Dominican Republic: Reconstructing the Effect of the European Colonization and the Trans-Atlantic Slave Trades.Genome biology and evolution · 2020Article
- Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.Genome biology and evolution · 2020Article
- A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa.Genetics · 2019Article
- The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola.European journal of human genetics : EJHG · 2019Article
- Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas.BMC biology · 2019Article
- Quantitative Trait Nucleotides Impacting the Technological Performances of IndustrialFrontiers in genetics · 2019Article
- Article
- Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago.BMC evolutionary biology · 2018Article
- Genetic Diversity on the Sex Chromosomes.Genome biology and evolution · 2018Review
- The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages.Genome biology · 2018Article
- 150,000-year palaeoclimate record from northern Ethiopia supports early, multiple dispersals of modern humans from Africa.Scientific reports · 2018Article
- Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81).Scientific reports · 2017Article
- The Y chromosome: a blueprint for men's health?European journal of human genetics : EJHG · 2017Review
- Human Y-chromosome variation in the genome-sequencing era.Nature reviews. Genetics · 2017Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence diversity and the ages of the deepest nodes of the MSY phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next-generation sequencing, including 18 deep-rooting ones, and identified 2386 SNPs, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome-wide de novo events, suggesting that in the MSY, a large proportion of newly arisen alleles has survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: (1) Patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; (2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; and (3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e., a period of our evolution that had been previously considered to be poorly accessible with paternally inherited markers.
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