A calibrated human Y-chromosomal phylogeny based on resequencing

Area of Science:

• Human Genetics
• Population Genomics
• Paleogenetics

Background:

• The human Y chromosome carries genetic information crucial for tracing paternal lineage and understanding human evolutionary history.
• Previous studies have identified key Y-chromosome variants, but a comprehensive analysis with high-resolution data across diverse populations was lacking.

Purpose of the Study:

• To identify a substantial number of novel genetic variants within the male-specific Y chromosome sequence.
• To construct an accurate phylogenetic tree of human Y-chromosome haplogroups.
• To date key events in human male lineage evolution, including ancient expansions and migrations.

Main Methods:

• High-coverage sequencing of 36 diverse human Y chromosomes from multiple continents.
• Identification and analysis of single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and indels within the male-specific Y sequence.
• Phylogenetic tree construction and molecular dating using an established male mutation rate.

Main Results:

• Discovery of 6662 high-confidence Y-chromosome variants, significantly increasing the number of informative markers.
• Recapitulation of known Y-chromosome haplogroup structure and confirmation of expected divergence times for African and non-African lineages.
• Dating of a Paleolithic male lineage expansion to 41,000–52,000 years ago and the major European R1b lineage to 4,000–13,000 years ago.

Conclusions:

• The study provides a greatly expanded set of Y-chromosome markers for phylogenetic analysis.
• The findings offer novel insights into human evolutionary history, including ancient population dynamics and the origins of modern European Y chromosomes.
• The calibrated phylogenetic tree enhances our understanding of human paternal lineage dispersal and diversification.