The Coalescent of Bacterial Populations

Bacterial Population Genetics in Infectious Disease

Volumn , Issue , 2010, Pages 1-18

  Schierup, Mikkel H ^a   Wiuf, Carsten ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Bacterial populations Wright Fisher reproduction model; Coalescent theory and sequence sample genealogy mean depth and sample size; Recombination and gene conversion coalescent based analysis

Indexed keywords

EID: 79955641747     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470600122.ch1     Document Type: Chapter

References (27)

1. Balding , D. J. , Bishop , M. , and Cannings , C. , eds. ( 2007 ) Handbook of Statistical Genetics , 3rd ed. Wiley , New York .
2. Charlesworth , B. ( 2009 ) Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation . Nat Rev Genet . Advanced online publication.
3. Charlesworth , J. and Eyre - Walker , A. ( 2006 ) The rate of adaptive evolution in enteric bacteria . Mol Biol Evol 23 , 1348-1356 .
4. Ewens , W. ( 2005 ) Mathematical Population Genetics , 2nd ed. Springer , New York .
5. Ewens , W. J. ( 1972 ) Sampling Theory Of Selectively Neutral Alleles . Theor Popul Biol 3 , 87-112 .
6. Falush , D. , Wirth , T. , Linz , B. et al. ( 2003 ) Traces of human migrations in Helicobacter pylori populations . Science 299 , 1582-1585 .
7. Fisher , R. ( 1930 ) The Genetical Theory of Natural Selection . Clarendon Press , Oxford .
8. Hein , J. , Schierup , M. H. , and Wiuf , C. ( 2005 ) Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory . Oxford University Press , Oxford .
9. Hudson , R. R. ( 1983a ) Properties of a neutral allele model with intragenic recombination . Theor Popul Biol 23 , 183-201 .
10. Hudson , R. R. ( 1983b ) Testing the constant - rate neutral allele model with protein - sequence data . Evolution 37 , 203-217 .
11. Hudson , R. R. ( 1994 ) Analytical results concerning linkage disequilibrium in models with genetic - transformation and conjugation . J Evol Biol 7 , 535-548 .
12. Kingman , J. F. C. ( 1980 ) Mathematics of Genetic Diversity . SIAM , Philadelphia, PA .
13. Kingman , J. F. C. ( 1982a ) The coalescent . Stoch Process Appl 13 , 235-248 .
14. Kingman , J. F. C. ( 1982b ) Exchangeability and the Evolution of Large Populations. Exchangeability in Probability and Statistics , pp. 97-112 . North - Holland , Amsterdam .
15. Kingman , J. F. C. ( 1982c ) On the genealogy of large populations . J Appl Probab 19 A, 27-43.
16. Li , J. Z. , Absher , D. M. , Tang , H. et al. ( 2008 ) Worldwide human relationships inferred from genome - wide patterns of variation . Science 319 , 1100-1104 .
17. Moodley , Y. , Linz , B. , Yamaoka , Y. et al. ( 2009 ) The peopling of the Pacifi c from a bacterial perspective . Science 323 , 527-530 .
18. Sniegowski , P. ( 2004 ) Evolution: Bacterial mutation in stationary phase . Curr Biol 14 , R245 - R246 .
19. Tajima , F. ( 1983 ) Evolutionary relationship of DNA sequences in fi nite populations . Genetics 105 , 437-460 .
20. Tajima , F. ( 1989 ) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism . Genetics 123 , 585-595 .
21. Venkatesan , M. , Westbrook , C. J. , Hauer , M. C. , and Rasgon , J. L. ( 2007 ) Evidence for a population expansion in the West Nile virus vector Culex tarsalis . Mol Biol Evol 24 , 1208-1218 .
22. Wakeley , J. ( 2008 ) Coalescent Theory: An Introduction . Roberts & Co. , Greenwood Village .
23. Watterson , G. ( 1974 ) The sampling theory of selectively neutral alleles . Adv Appl Probab 6 , 463-488.
24. Watterson , G. A. ( 1975 ) Number of segregating sites in genetic models without recombination . Theor Popul Biol 7 , 256-276 .
25. Wiuf , C. ( 2001 ) Recombination in human mitochondrial DNA? Genetics 159 , 749-756 .
26. Wiuf , C. and Hein , J. ( 2000 ) The coalescent with gene conversion . G enetics 155 , 451-462 .
27. Wright , S. ( 1931 ) Evolution in Mendelian populations . Genetics 16 , 97-159 .