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( . + - 5 /¥0 2$3¥4 6 , 1 @ ; = : > < 9 ? 8 7 A B E M F K H C I L D G J T X U$V O S Q$R P Y N W b ^ ] ` e d Z a c \ _ [ p h j n q i m k¥l o f¥g Present 11 3 5 9 12 4 8 6 7 10 1 2 ICB r c 2006 Birkhäuser Verlag The Coalescent Past MRCA T2 x CA T3 w CA T4 t u v Present s 4 8 2 1 ICB c 2006 Birkhäuser Verlag Coalescent Trees n y 2: z z z ~ ~ ~ | }~ | }~ | }~ { { { z z z n y 10: z z z ~ ~ ~ | }~ | }~ | }~ { { { z z z n y 50: z z z ~ ~ ~ | }~ | }~ | }~ { { { z z z 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 of two genes present day sequence comparison PSfrag replacements Seq 1 Seq 2 ICB c 2006 Birkhäuser Verlag TMRCA 10 2 ) ¡ ) 1 of ¡ of (units 1 alue v 0.5 (units PSfrag replacements ariance V Expected 0 0.2 10 100 1000 sample size ( ) ICB c 2006 Birkhäuser Verlag Topology & Frequency Spectrum MRCA MRCA ¢ ¢¤£ £ ¢¥ ¥ ¢ PSfrag replacements ¢¤¦ ¢¤¦ ICB c 2006 Birkhäuser Verlag Coalescent and SNPs 6 6 6 4 4 4 count 2 2 2 0 1 2 3 4 5 0 1 2 3 4 5 0 1 2 3 4 5 6 number of pairwise differences 1.0 1.0 1.0 0.6 0.6 0.6 0.3 0.3 0.3 proportion 1 2 3 1 2 3 1 2 3 number ICB c 2006 Birkhäuser Verlag SNPs § Recombination no recombination 0.04 with recombination 0.03 0.02 0.01 0 0 20 40 60 80 segregating sites ICB c 2006 Birkhäuser Verlag Coalescent with Recombination past º»­¼·½¿¾ À Á µ ¶ sampled chromosomes: «­¬®°¯²±´³ segment a segment b chromosome not contained in sample: º»²¼·½¾  Á « ¬®·¯²±´³ ¸ ¶ ¨©¨©¨©¨©¨©¨©¨©¨©¨©¨ ª©ª©ª©ª©ª©ª©ª©ª©ª©ª recombination x «­¹ PSfrag replacements present ICB c 2006 Birkhäuser Verlag Selective Sweep fB 0 0.5 1.0 past al neutr à al neutr present ICB c 2006 Birkhäuser Verlag Recombination & Selection 1.0 R a4 fB a3 0.5 MRCA a2 a1 0.0 Ä past present 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 Quantifying Selectionreplacements 0.012 autosomal X−linked 0.008 Ê 0.004 0 0 4e−09 8e−09 1.2e−08 Ë ICB c 2006 Birkhäuser Verlag References M. 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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.