Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny

2013/08/01 by Paolo Francalacci, Laura Morelli, Andrea Angius +36 · 18 citations
Biochemistry, Genetics and Molecular Biology · Arts and Humanities · #Forensic and Genetic Research #Genetic diversity and population structure #Forensic Anthropology and Bioarchaeology Studies #Haplogroup #Phylogenetic tree #Evolutionary biology #Population #Biology #Mitochondrial DNA #Haplotype #DNA sequencing #Y chromosome #Genetics #Ancient DNA #Gene #Demography #Genotype

paper · doi:10.1126/science.1237947

openalex publication_date 2013/08/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Abstract

Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe, along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal the presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180,000 to 200,000 years ago, which is consistent with previous mitochondrial DNA-based estimates.

Citations

• A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
• Y chromosome sequence variation and the history of human populations
• Mitochondrial genome variation and the origin of modern humans
• The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia
• Peopling of three Mediterranean Islands (Corsica, Sardinia, and Sicily) inferred by Y‐chromosome biallelic variability
• An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree
• New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
• A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa
• An integrated map of genetic variation from 1,092 human genomes
• Phylogeography of Y-Chromosome Haplogroup I Reveals Distinct Domains of Prehistoric Gene Flow in Europe
• The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective

Cited by

• Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences
• Generation of high-resolution a priori Y-chromosome phylogenies using “next-generation” sequencing data
• Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families
• Complete mitochondrial sequences from Mesolithic Sardinia
• Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD
• Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences
• Regional Differences in the Accumulation of SNPs on the Male-Specific Portion of the Human Y Chromosome Replicate Autosomal Patterns: Implications for Genetic Dating
• Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge
• Detecting past male-mediated expansions using the Y chromosome
• A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean
• Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia)
• Massive migration from the steppe is a source for Indo-European languages in Europe
• Population genomics of Bronze Age Eurasia
• Refining the Y chromosome phylogeny with southern African sequences
• The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades
• Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements
• Haplogroup A (Y-DNA) [wikipedia]
• Haplogroup T-M184 [wikipedia]

Related

• Y-Chromosome Based Evidence for Pre-Neolithic Origin of the Genetically Homogeneous but Diverse Sardinian Population: Inference for Association Scans
• Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia
• Complete mitochondrial sequences from Mesolithic Sardinia
• Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe
• Large-scale recent expansion of European patrilineages shown by population resequencing