Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

@article{Li2008WorldwideHR,
  title={Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation},
  author={Jun Z. Li and Devin M Absher and Hua Tang and Audrey M. Southwick and Amanda M. Casto and Sohini Ramachandran and Howard M. Cann and Gregory S. Barsh and Marcus W. Feldman and Luigi Luca Cavalli-Sforza and Richard M. Myers},
  journal={Science},
  year={2008},
  volume={319},
  pages={1100 - 1104}
}
Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of… 
View on AAAS
bio.davidson.edu
1,871 Citations
Highly Influential Citations
241
Background Citations
627
Methods Citations
422
Results Citations
106

1,871 Citations

Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs

Two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature are identified.

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

Genes mirror geography within Europe

Despite low average levels of genetic differentiation among Europeans, there is a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans.

Global distribution of genomic diversity underscores rich complex history of continental human populations.

Patterns of variation across 443,434 single nucleotide polymorphisms genotyped in 3845 individuals from four continental regions are analyzed, suggesting both demographic history and recent ancestry events play an important role in patterning variation in large modern human populations.

Insights into human genetic variation and population history from 929 diverse genomes

The authors' study adds data about African, Oceanian, and Amerindian populations and indicates that diversity tends to result from differences at the single-nucleotide level rather than copy number variation.

Title : Genes mirror geography within Europe

Despite low average levels of genetic differentiation among Europeans, there is a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans.

African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping.

This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility.

Human genome diversity: frequently asked questions.

Human Relationships Inferred from Genetic Variation

Studying human genetic variation allows to some degree the reconstruction of human migration and adaptation history and provides data evidence for elucidating whether humans can be classified according to genetically homogeneous groups or not, with implications for medical and forensic studies.

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes.

It is found that single-site measures of evolutionary constraint derived from mammalian multiple sequence alignments are strongly predictive of reductions in modern-day genetic diversity across a range of annotation categories and across the allele frequency spectrum from rare to high frequency.
...

References

SHOWING 1-10 OF 41 REFERENCES

A haplotype map of the human genome

A public database of common variation in the human genome: more than one million single nucleotide polymorphisms for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted.

Genetic Structure of Human Populations

General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HAPMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.

High resolution of human evolutionary trees with polymorphic microsatellites

It is shown that polymorphic microsatellites (primarily CA repeats) allow trees of human individuals to be constructed that reflect their geographic origin with remarkable accuracy by the analysis of a large number of loci for each individual, in spite of the small variations in allele frequencies existing between populations.

Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers.

Variation at di-, tri-, and tetranucleotide repeat loci is distributed differently, although each class of markers exhibits a decrease of within-population genetic variation in the following order: sub-Saharan Africa, Eurasia, East Asia, Oceania, and America.

Localizing Recent Adaptive Evolution in the Human Genome

It is found that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep.

Robustness of the inference of human population structure: A comparison of X-chromosomal and autosomal microsatellites

Data on 20 X-chromosomal microsatellite polymorphisms from the HGDP-CEPH cell line panel are used to infer human population structure and differences between the X- chromosome and autosomal results can be explained without requiring major differences in demographic parameters between males and females.

The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations

A simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories is derived, which generates spectra for a large number of alternative histories on a multidimensional parameter grid.

Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.

It is found that heterozygosities in the globally distributed populations of the data set are best explained by an expansion originating in Africa and that no geographic origin outside of Africa accounts as well for the observed patterns of genetic diversity.

A Map of Recent Positive Selection in the Human Genome

A set of SNPs is developed that can be used to tag the strongest ∼250 signals of recent selection in each population, and it is found that by some measures the authors' strongest signals of selection are from the Yoruba population.