Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species

@article{Gao2015FootprintsOA,
  title={Footprints of ancient-balanced polymorphisms in genetic variation data from closely related species},
  author={Ziyue Gao and Molly Przeworski and Guy Sella},
  journal={Evolution; International Journal of Organic Evolution},
  year={2015},
  volume={69},
  pages={431 - 446}
}
When long‐lasting, balancing selection can lead to “trans‐species” polymorphisms that are shared by two or more species identical by descent. In such cases, the gene genealogy at the selected site clusters by allele instead of by species, and nearby neutral sites also have unusual genealogies because of linkage. While this scenario is expected to leave discernible footprints in genetic variation data, the specific patterns remain poorly characterized. Motivated by recent findings in primates… 

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References

SHOWING 1-10 OF 63 REFERENCES

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

TLDR
Findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets.

Selection, Recombination and Demographic History in Drosophila miranda

TLDR
It is found that noncoding DNA generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in nonc coding DNA is significantly skewed toward rare variants relative to synonymous Sites, and that long introns evolve significantly slower than short introns or synonymous sites.

Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives.

TLDR
There is a good correspondence between the genomic regions associated with reproductive isolation and the regions that show little or no evidence of gene flow, and a model in which D. pseudoobscura and D. persimilis have exchanged genes at some loci is supported.

MHC polymorphism pre-dating speciation

TLDR
Evidence is presented for an alternative explanation of the origin of MHC polymorphism: a large part of the M HC polymorphism pre-dates speciation and is passed on from species to species.

The prospects for polymorphisms shared between species

TLDR
The maintenance of many MHC polymorphisms via overdominant and frequency-dependent selection is discussed and the variance of allele frequencies is suggested to be one way to distinguish between these two selection models.

Great ape genetic diversity and population history

TLDR
This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.

The Probability and Chromosomal Extent of trans-specific Polymorphism

TLDR
The main finding is that the trans-specific region surrounding a single-locus balanced polymorphism is expected to be quite short, probably too short to be readily detectable and should not be taken as evidence against balancing selection.

Molecular evolution near a two-locus balanced polymorphism.

TLDR
It is found that variation at neutral sites is increased across a much larger genomic region relative to the single-locus models: the entire region lying between the two loci in balanced combination is affected to some degree.

Genomic Variation in Natural Populations of Drosophila melanogaster

TLDR
This report of independent genome sequences of two natural populations of Drosophila melanogaster provides unique insight into forces shaping genomic polymorphism and divergence, suggesting many targets of directional selection are shared between these species.

Scan of Human Genome Reveals No New Loci Under Ancient Balancing Selection

TLDR
It is proposed that because it is rarely stable, long-term balancing selection is an evolutionary oddity, and when a balanced polymorphism is ancient in origin, the requirements for detection by means of SNP data alone will rarely be met.
...