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. 2003 Aug;164(4):1677–1682. doi: 10.1093/genetics/164.4.1677

On the use of star-shaped genealogies in inference of coalescence times.

Noah A Rosenberg 1, Aaron E Hirsh 1
PMCID: PMC1462671  PMID: 12930771

Abstract

Genealogies from rapidly growing populations have approximate "star" shapes. We study the degree to which this approximation holds in the context of estimating the time to the most recent common ancestor (T(MRCA)) of a set of lineages. In an exponential growth scenario, we find that unless the product of population size (N) and growth rate (r) is at least approximately 10(5), the "pairwise comparison estimator" of T(MRCA) that derives from the star genealogy assumption has bias of 10-50%. Thus, the estimator is appropriate only for large populations that have grown very rapidly. The "tree-length estimator" of T(MRCA) is more biased than the pairwise comparison estimator, having low bias only for extremely large values of Nr.

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Selected References

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  1. Donnelly P., Tavaré S. Coalescents and genealogical structure under neutrality. Annu Rev Genet. 1995;29:401–421. doi: 10.1146/annurev.ge.29.120195.002153. [DOI] [PubMed] [Google Scholar]
  2. Karn Robert C., Orth Annie, Bonhomme François, Boursot Pierre. The complex history of a gene proposed to participate in a sexual isolation mechanism in house mice. Mol Biol Evol. 2002 Apr;19(4):462–471. doi: 10.1093/oxfordjournals.molbev.a004102. [DOI] [PubMed] [Google Scholar]
  3. Liu J. S., Sabatti C., Teng J., Keats B. J., Risch N. Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 2001 Oct;11(10):1716–1724. doi: 10.1101/gr.194801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Pritchard J. K., Seielstad M. T., Perez-Lezaun A., Feldman M. W. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol. 1999 Dec;16(12):1791–1798. doi: 10.1093/oxfordjournals.molbev.a026091. [DOI] [PubMed] [Google Scholar]
  5. Rannala B., Bertorelle G. Using linked markers to infer the age of a mutation. Hum Mutat. 2001 Aug;18(2):87–100. doi: 10.1002/humu.1158. [DOI] [PubMed] [Google Scholar]
  6. Risch N., de Leon D., Ozelius L., Kramer P., Almasy L., Singer B., Fahn S., Breakefield X., Bressman S. Genetic analysis of idiopathic torsion dystonia in Ashkenazi Jews and their recent descent from a small founder population. Nat Genet. 1995 Feb;9(2):152–159. doi: 10.1038/ng0295-152. [DOI] [PubMed] [Google Scholar]
  7. Rosenberg Noah A., Nordborg Magnus. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet. 2002 May;3(5):380–390. doi: 10.1038/nrg795. [DOI] [PubMed] [Google Scholar]
  8. Schierup M. H., Hein J. Consequences of recombination on traditional phylogenetic analysis. Genetics. 2000 Oct;156(2):879–891. doi: 10.1093/genetics/156.2.879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Slatkin M. Gene genealogies within mutant allelic classes. Genetics. 1996 May;143(1):579–587. doi: 10.1093/genetics/143.1.579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Slatkin M., Hudson R. R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 1991 Oct;129(2):555–562. doi: 10.1093/genetics/129.2.555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Slatkin M., Rannala B. Estimating allele age. Annu Rev Genomics Hum Genet. 2000;1:225–249. doi: 10.1146/annurev.genom.1.1.225. [DOI] [PubMed] [Google Scholar]
  12. Stumpf M. P., Goldstein D. B. Genealogical and evolutionary inference with the human Y chromosome. Science. 2001 Mar 2;291(5509):1738–1742. doi: 10.1126/science.291.5509.1738. [DOI] [PubMed] [Google Scholar]
  13. Tang Hua, Siegmund David O., Shen Peidong, Oefner Peter J., Feldman Marcus W. Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition. Genetics. 2002 May;161(1):447–459. doi: 10.1093/genetics/161.1.447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Tavaré S., Balding D. J., Griffiths R. C., Donnelly P. Inferring coalescence times from DNA sequence data. Genetics. 1997 Feb;145(2):505–518. doi: 10.1093/genetics/145.2.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Thomas M. G., Skorecki K., Ben-Ami H., Parfitt T., Bradman N., Goldstein D. B. Origins of Old Testament priests. Nature. 1998 Jul 9;394(6689):138–140. doi: 10.1038/28083. [DOI] [PubMed] [Google Scholar]
  16. Thomson R., Pritchard J. K., Shen P., Oefner P. J., Feldman M. W. Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7360–7365. doi: 10.1073/pnas.97.13.7360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Uyenoyama M. K. Genealogical structure among alleles regulating self-incompatibility in natural populations of flowering plants. Genetics. 1997 Nov;147(3):1389–1400. doi: 10.1093/genetics/147.3.1389. [DOI] [PMC free article] [PubMed] [Google Scholar]

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