Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation

PLoS Computational Biology

Volumn 9, Issue 5, 2013, Pages

  Li, Haipeng ^a,b   Wiehe, Thomas ^b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES;

ADAPTIVE EVOLUTION; ANALYTICAL PROPERTIES; COARSE-GRAINED; DATA SET; MICROSATELLITE MARKERS; MICROSATELLITES; SELECTIVE SWEEP; SIMPLE TESTS; TREE IMBALANCE; TREE TOPOLOGY;

STATISTICAL TESTS;

ARTICLE; CASE STUDY; GENETIC RECOMBINATION; KAPPA STATISTICS; MATHEMATICAL MODEL; MICROSATELLITE MARKER; NONHUMAN; PHYLOGENETIC TREE; PLASMODIUM FALCIPARUM; RELIABILITY; SELECTIVE SWEEP;

PLASMODIUM FALCIPARUM;

EID: 84878490064     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003060     Document Type: Article

References (44)

1. Kingman JFC, (1982) The coalescent. Stochastic Processes and their Applications 13: 235-248.
2. Hudson RR (1990) Gene genealogies and the coalescent process. In: Oxford Surveys in Evolutionary Biology, volume 7. Oxford University Press. pp. 1-44.
3. Wakeley J (2009) Coalescent theory - an introduction. Greenwood Village, Colorado: Roberts&Company.
4. Ewens W, (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3: 87-112.
5. Tajima F, (1989) The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
6. Fay J, Wu C, (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
7. Fu Y, (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
8. Ferretti L, Perez-Enciso M, Ramos-Onsins S, (2010) Optimal neutrality tests based on the frequency spectrum. Genetics 186: 353-365.
9. Griffiths RC, Marjoram P, (1996) Ancestral inference from samples of DNA sequences with recombination. J Comput Biol 3: 479-502.
10. Hudson R, Kaplan N, (1988) The coalescent process in models with selection and recombination. Genetics 120: 831-840.
11. Kaplan NL, Hudson RR, Langley CH, (1989) The "hitchhiking effect" revisited. Genetics 123: 887-899.
12. McVean G, Cardin N, (2005) Approximating the coalescent with recombination. Philos Trans R Soc Lond B Biol Sci 360: 1387-1393.
13. Wiuf C, Hein J, (1999) Recombination as a point process along sequences. Theor Popul Biol 55: 248-259.
14. Eriksson A, Mahjani B, Mehlig B, (2009) Sequential markov coalescent algorithms for population models with demographic structure. Theor Popul Biol 76: 84-91.
15. Ferretti L, Disanto F, Wiehe T, (2013) The effect of single recombination events on coalescent tree height and shape. PLoS ONE 8 (4):: e60123.
16. Li H, (2011) A new test for detecting recent positive selection that is free from the confounding impacts of demography. Mol Biol Evol 28: 365-375.
17. Walsh J, Lynch M (2013) Evolution and Selection of Quantitative Traits. Sinauer Associates. Available: http://nitro.biosci.arizona.edu/zbook/NewVolume-2/pdf.
18. Wedderburn JHM, (1922) The functional equation g(x2) = 2 x + [g(x)]2. The Annals of Mathematics 24: 121-140.
19. Tajima F, (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
20. Hudson R, Kaplan N, (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
21. Zivkovic D, Wiehe T, (2008) Second-order moments of segregating sites under variable population size. Genetics 180: 341-357.
22. Reich D, Cargill M, Bolk S, Ireland J, Sabeti P, et al. (2001) Linkage disequilibrium in the human genome. Nature 411: 199-204.
23. Barton N, (2000) Genetic hitchhiking. Philos Trans R Soc Lond B Biol Sci 355: 1553-1562.
24. Sokal RR, Sneath PHA (1963) Principles of Numerical Taxonomy. New York: W. H. Freeman and Co.
25. Schug MD, Mackay TFC, Aquadro CF, (1997) Low mutation rates of microsatellite loci in Drosophila melanogaster. Nature Genetics 15: 99-102.
26. Fernando Vazquez J, Perez T, Albornoz J, Dominguez A, (2000) Estimation of microsatellite mutation rates in Drosophila melanogaster. Genet Res 76: 323-326.
27. Ellegren H, (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5: 435-445.
28. Wiehe T, Nolte V, Zivkovic D, Schlötterer C, (2007) Identification of selective sweeps using a dynamically adjusted number of linked microsatellites. Genetics 175: 207-218.
29. Nair S, Nash D, Sudimack D, Jaidee A, Barends M, et al. (2007) Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites. Mol Biol Evol 24: 562-573.
30. Griffiths RC, (1984) Asymptotic line-of-descent distributions. J Math Biol 21: 67-75.
31. Berestycki N (2009) Recent progress in coalescent theory. Ensaios matemáticos. Sociedade Brasileira De Matemática.
32. Colless DH, (1982) Review: [untitled]. Systematic Zoology 31: 100-104.
33. Kirkpatrick M, Slatkin M, (1993) Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47: 1171-1181.
34. Blum MGB, Franois O, Janson S, (2006) The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance. The Annals of Applied Probability 16: 2195-2214.
35. Schlötterer C, (2002) A microsatellite based multi-locus screen for the identification of local selective sweeps. Genetics 160: 753-763.
36. Cornuet J, Luikart G, (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
37. Schlötterer C, Kauer M, Dieringer D, (2004) Allele excess at neutrally evolving microsatellites and the implications for tests of neutrality. Proc R Soc Lond B 271: 869-874.
38. Neher R, Hallatschek O, (2013) Genealogies of rapidly adapting populations. Proc Natl Acad Sci U S A 110: 437-442.
39. Stolle E, Wilfert L, Schmid-Hempel R, Schmid-Hempel P, Kube M, et al. (2011) A second generation genetic map of the bumblebee bombus terrestris (linnaeus, 1758) reveals slow genome and chromosome evolution in the apidae. BMC Genomics 12: 48.
40. Behrens D, Huang Q, Gessner C, Rosenkranz P, Frey E, et al. (2011) Three QTL in the honey bee apis mellifera l. suppress reproduction of the parasitic mite varroa destructor. Ecol Evol 1: 451-458.
41. Kim Y, Stephan W, (2002) Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
42. Li H, Stephan W, (2006) Inferring the demographic history and rate of adaptive substitution in drosophila. PLoS Genet 2: e166.
43. Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
44. Feller W (1968) An Introduction to Probability Theory and Its Applications, volume 1. Wiley.