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Recent human effective population size estimated from linkage disequilibrium
Albert Tenesa1, Pau Navarro, Ben J Hayes
1Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh, UK.
Genome Research
|March 14, 2007
Summary
This study provides the first genome-wide estimates of human effective population size (N(e)) using linkage disequilibrium (LD) data. Results suggest lower N(e) than previously thought, reflecting ancient population bottlenecks.
Area of Science:
- Population Genetics
- Human Evolutionary Studies
Background:
- Effective population size (N(e)) is crucial for understanding genetic variation, drift, and linkage disequilibrium (LD).
- Previous estimates of human N(e) often relied on heterozygosity, potentially overlooking historical population dynamics.
Purpose of the Study:
- To generate the first genome-wide estimates of human effective population size using linkage disequilibrium (LD) data.
- To investigate human population history, including expansion and bottlenecks, through fine-scale recombination and LD analysis.
Main Methods:
- Estimated chromosome-specific effective population size for autosomes and the X chromosome using LD between single nucleotide polymorphism (SNP) pairs <100 kb apart.
- Accounted for recombination rate variation by correlating coalescent-based estimates with LD in independent HapMap Phase I samples (YRI, JPT, HCB, CEU).
Main Results:
- Effective population size estimates (adjusted for ascertainment bias) were ~3100 for CEU, JPT, and HCB, and ~7500 for YRI.
- LD decay patterns indicated recent human population growth.
- N(e) estimates derived from LD were lower than those from heterozygosity, suggesting significant past population bottlenecks.
Conclusions:
- The findings support the out-of-Africa theory and highlight the impact of ancient population bottlenecks on current genetic diversity.
- LD-based N(e) estimates provide a more nuanced view of human population history, potentially capturing effects of bottlenecks from 10,000 to 200,000 years ago.
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