A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

@article{Grossman2010ACO,
  title={A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection},
  author={Sharon R. Grossman and Ilya Shlyakhter and Elinor K. Karlsson and Elizabeth H Byrne and Shannon Morales and Gabriel Frieden and Elizabeth Hostetter and Elaine Angelino and Manuel Garber and Or Zuk and Eric S. Lander and Stephen F. Schaffner and Pardis C Sabeti},
  journal={Science},
  year={2010},
  volume={327},
  pages={883 - 886}
}
Pinpointing Genetic Selection The human genome contains hundreds of regions with evidence of recent positive natural selection, yet, for all but a handful of cases, the underlying advantageous mutation remains unknown. Current methods to detect the signal of selection often results in the identification of a broad genomic region containing many candidate regions that vary among individuals. By combining existing statistical methods, Grossman et al. (p. 883, published online 7 January) developed… 

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References

SHOWING 1-10 OF 49 REFERENCES

A Map of Recent Positive Selection in the Human Genome

TLDR
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.

Genome-wide detection and characterization of positive selection in human populations

TLDR
‘Long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population are developed.

Constructing genomic maps of positive selection in humans: where do we go from here?

TLDR
The recent history of the burgeoning field of human population genomics is chronicle, genome-wide scans for positive selection in humans are critically assessed, important gaps in knowledge are identified, and both short- and long-term strategies for traversing the path from the low-resolution, incomplete, and error-prone maps of selection today to the ultimate goal of a detailed molecular, mechanistic, phenotypic, and population genetics characterization of adaptive alleles are discussed.

Positive Natural Selection in the Human Lineage

Positive natural selection is the force that drives the increase in prevalence of advantageous traits, and it has played a central role in our development as a species. Until recently, the study of

How reliable are empirical genomic scans for selective sweeps?

TLDR
This work considered a coalescent model of directional selection in a sensible demographic setting, allowing for selection on standing variation as well as on a new mutation, and concluded that, insofar as attributes of the beneficial mutation affect the power to detect targets of selection, genomic scans will yield an unrepresentative subset of loci that contribute to adaptations.

Localizing Recent Adaptive Evolution in the Human Genome

TLDR
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.

Calibrating a coalescent simulation of human genome sequence variation.

TLDR
The first calibrated population genetic model is presented and it is shown that, while still arbitrary, it successfully generates simulated data that closely resemble empirical data in allele frequency, linkage disequilibrium, and population differentiation.

A second generation human haplotype map of over 3.1 million SNPs

TLDR
The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.

Molecular genetics of human pigmentation diversity.

  • R. Sturm
  • Biology
    Human molecular genetics
  • 2009
TLDR
From a culmination of genetic and functional studies, it is apparent that a number of genes impacting melanosome biogenesis or the melanin biosynthetic pathway are candidates to explain the diversity seen in human pigmentation.

ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE

TLDR
The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973).