Introduction to Computational Biology; an Evolutionary Approach: Genes in Populations: Backward in Time

Introduction to Computational Biology; An Evolutionary Approach: Genes in Populations: Backward in Time

Bernhard Haubold & Thomas Wiehe

ICB c 2006 Birkhäuser Verlag Genealogy of Individuals

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ICB r c 2006 Birkhäuser Verlag The Coalescent

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ICB c 2006 Birkhäuser Verlag Coalescent Trees

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ICB c 2006 Birkhäuser Verlag Coalescent vs. Phylogeny

Feature Phylogeny Coalescent Level of comparison Inter-species gene history Intra-species gene history Purpose Reconstruct the true Simulate sets of potential species history gene histories Observation of interest Tree topology Frequency spectrum and distribution of segregating sites Data source Comparative data Model parameters Multiplicity Single Many

ICB c 2006 Birkhäuser Verlag Genealogy & Polymorphisms

genealogical history MRCA of a sample

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ICB c 2006 Birkhäuser Verlag TMRCA

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ICB c 2006 Birkhäuser Verlag Topology & Frequency Spectrum

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ICB c 2006 Birkhäuser Verlag Coalescent and SNPs

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ICB c 2006 Birkhäuser Verlag SNPs § Recombination

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ICB c 2006 Birkhäuser Verlag Coalescent with Recombination

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ICB c 2006 Birkhäuser Verlag Selective Sweep

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ICB c 2006 Birkhäuser Verlag Recombination & Selection

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ICB c 2006 Birkhäuser Verlag Recombination & Genetic Diversity in D. melanogaster

9 É È locus ÅÇÆ 10 reference

X-linked loci Yellow,Achaete 0.429 0.0008 [3] Pgd 1.466 0.0030 [3] Z,Tko 2.114 0.0044 [1] Per 4.952 0.0014 [3] White 13.30 0.0090 [13] Notch 11.54 0.0050 [14] Vermilion 5.619 0.0010 [4] Forked 4.330 0.0020 [9] Zw 4.619 0.0007 [6] Su(F) 0.476 0.0000 [9]

autosomal loci Gpdh 5.714 0.0078 [15] Adh 4.621 0.0060 [10] Ddc 1.314 0.0050 [4] Amy 3.107 0.0080 [11] Pu 5.129 0.0040 [15] Est6 4.314 0.0050 [7] MtnA 0.593 0.0010 [8] Hsp70A 0.493 0.0020 [12] Ry 3.364 0.0030 [2] CiD 0.000 0.0000 [5]

ICB c 2006 Birkhäuser Verlag PSfrag

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ICB c 2006 Birkhäuser Verlag References

M. Aguadé, N. Miyashita, and C. H. Langley. Restriction map variation at the zeste–tko region in natural populations of Drosophila melanogaster. Molecular Biology and Evolution, 6:123–130, 1989. C. F. Aquadro, K. M. Lado, and W. A. Noon. The rosy region of Drosophila melanogaster and Drosophila simulans. I. Contrasting levels of naturally occuring DNA restriction map variation and divergence. Genetics, 119:875–888, 1988. D.J. Begun and C. F. Aquadro. Molecular population genetics of the distal portion of the X chromosome in Drosophila: Evidence for genetic hitchhiking of the yellow–achaete region. Genetics, 129:1147–1158, 1991. D.J. Begun and C. F. Aquadro. Levels of naturally occuring DNA polymorphism are correlated with recombination rates in Drosophila melanogaster. Nature, 356:519–520, 1992. A. J. Berry, J. W. Ajioka, and M. Kreitman. Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics, 129:1111–1117, 1991. W. F. Eanes, J. W. Ajioka, J. Hey, and C. Wesley. Restriction map variation associated with the G6pd polymorphism in natural populations of Drosophila melanogaster. Molecular Biology and Evolution, 6:384–397, 1989. A. Y. Game and J. G. Oakeshott. The association between restriction site polymorphism and enzyme activity variation for Esterase6 in Drosophila melanogaster. Genetics, 126:1021–1031, 1990. B. W. Lange, C. H. Langley, and W. Stephan. Molecular evolution of Drosophila metallothionein genes. Genetics, 126:921–932, 1990. C. H. Langley. The molecular population genetics of Drosophila. In N. Takahata and J. F. Crow, editors, Population Biology of Genes and Molecules, pages 75–91. National Academy of Sciences, Baifukan, Japan, 1990. C. H. Langley, E. A. Montgomery, and W. F. Quattlebaum. Restriction map variation in the Adh region of Drosophila. Proceedings of the National Academy of Sciences, USA, 79:5631–5635, 1982. C. H. Langley, A. E. Shrimpton, T. Yamazaki, N. Miyashita, Y. Matsuo, and C. F. Aquadro. Naturally occuring variation in the restriction map of the Amy region of Drosophila melanogaster. Genetics, 119:619–629, 1988. A. J. Leigh-Brown. Variation of the 87A heat shock locus in Drosophila melanogaster. Proceedings of the National Academy of Sciences, USA, 80:5350–5354, 1983. N. Miyashita and C. H. Langley. Molecular and phenotypic variation of the white locus region in Drosophila melanogaster. Genetics, 120:199–212, 1988. S. W. Schaeffer, C. F. Aquadro, and C. H. Langley. Restriction map variation in the Notch region of Drosophila melanogaster. Molecular Biology and Evolution, 5:30–40, 1988. T. S. Takano, S. Kusakabe, and T. Mukai. The genetic structure of natural populations of Drosophila melanogaster. XXII. Comparative study of DNA polymorphisms in northern and southern natural populations. Genetics, 129:753–761, 1991.

ICB c 2006 Birkhäuser Verlag