## <u>Publications of the Program for Evolutionary Dynamics at Harvard University</u>

## 2003

I. Frank SA, Y Iwasa, MA Nowak (2003). Patterns of cell division and the risk of cancer. Genetics 163: 1527-1532.

2. Frank SA, MA Nowak (2003). Developmental predisposition to cancer. Nature 422: 494.

3. Hudson R R, Turelli M (2003). Stochasticity overrules the "three-times rule": Genetic drift, genetic draft, and coalescence times for nuclear loci versus mitochondria! DNA. Evolution 57: 182-190.

4. Iwasa Y, F Michor, MA Nowak (2003). Evolutionary dynamics of escape from biomedical intervention. Proc R Soc B 270: 2573-2578.

5. Jones AG, SJ Arnold, R Burger (2003). Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and genetic drift. Evolution 57: 1747- 1760.

6. Komarova NL, MA Nowak (2003). Language dynamics in finite populations. J theor Biol 221: 445457.

7. Komarova NL, MA Nowak (2003). Language, learning and evolution. In Language Evolution, eds. MH Christiansen, S Kirby. Oxford University Press, 317-337.

8. Komarova NL, A Sengupta, MA Nowak (2003). Mutation-selection networks of cancer initiation: Tumor suppressor genes and chromosomal instability. J theor Biol 223: 433-450.

9. Lorenz A, J Fuchs, R Burger, J Loidl (2003). Chromosome pairing does not contribute to nuclear architecture in vegetative yeast cells. Eulcaryotic Cell 2: 856-866.

10. Michor F, SA Frank, RM May, Y Iwasa, MA Nowak (2003). Somatic selection for and against cancer. I theor Biol 225: 377-382.

- II. Michor F, Y Iwasa, NL Komarova, MA Nowak (2003). Local regulation of homeostasis favors chromosomal instability. Curr Biol 13: 581-584.

12. Michor F, MA Nowak, SA Frank, Y Iwasa (2003). Stochastic elimination of cancer cells. Proc R Soc B 270: 2017-2024.

13. Mitchener G, MA Nowak (2003). Competitive exclusion and coexistence of universal grammars. B Math Biol 65: 67-93.

14. Nowak MA, F Michor, Y Iwasa (2003). The linear process of somatic evolution. P Nail Acad Sci USA 100: 14966-14969.

15. Rajagopalan H, MA Nowak, B Vogelstein, C Lengauer (2003). The significance of unstable chromosomes in colorectal cancer. Nat Rev Cancer 3: 695-701.

16. Sasaki A, MA Nowak (2003). Mutation landscapes. J theor Biol 224: 241-247.

17. Wei X, JM Decker, S Wang, H Hui, JC Kappes, W Xiaoyun, JF Salazar, MG Salazar, JM Kilby, MS Saag, NL Komarova, MA Nowak, BH Hahn, PD Kwong, GM Shaw (2003). Antibody neutralization and escape by HIV-1. Nature 422: 307-312.

18. Willensdorfer M, R Burger (2003). The two-locus model of Gaussian stabilizing selection. Theor Popul Biol 64: 101-117.

## 2004

19. Barton NH, M Turelli (2004). Effects of genetic drift on variance components under a general model of epistasis. Evolution 58: 2111-2132.

20. Boots M, PJ Hudson, A Sasaki (2004). Large shifts in pathogen virulence relate to host population structure. Science 303: 842-845.

21. Burger R, A Gimelfarb (2004). The effects of intraspecific competition and stabilizing selection on a polygenic trait. Genetics 167: 1425-1443.

## 2004 (cont.)

22. Burger R, C Krall (2004). Quantitative genetic models and changing environments. In Evolutionary Conservation Biology, cds. R Fcrricrc, U Dicckmann, D Couvet. Cambridge: Cambridge University Press, 171-186.

23. Doebeli M, C Haucrt, T Killingback (2004). The evolutionary origin of cooperators and defectors. Science 306: 859-862.

24. Frank SA (2004). Age-specific acceleration of cancer. Curr Biol 14: 242-246.

25. Frank SA, MA Nowak (2004). Problems of somatic mutation and cancer. Bioessays 26: 291- 299.

26. Frankham, R (2004). Evolutionary conservation genetics. In Evolutionary Genetics: Concepts and Case Studies, eds. CW Fox, JB Wolf. New York: Oxford University Press.

27. Frankham R, JD Ballou, DA Briscoe (2004). A Primer of Conservation Genetics. Cambridge: Cambridge University Press.

28. Frankham R, BW Brook (2004). The importance of time scale in conservation biology and ecology. Annalcs Zoologici Fennici 41: 459-463.

29. Frankham R, JG Kingslover (2004). Adaptation and extinction: The empirical view. In Evolutionary Conservation Biology, eds. R Ferriere, U Dieckmann, D Couvet. Cambridge: Cambridge University Press.

30. Ganapathy G, V Ramachandran, T Wamow (2004). On contract-and-refine-transformations between phylogenefic trees. In Proceedings of the Fifteenth ACM-SIAM Symposium on Discrete Algorithms (SODA), 893-902.

31. Iwasa Y, F Michor, MA Nowak (2004). Evolutionary dynamics ofinvasion and escape. J thcor Biol 226: 205-214.

32. Iwasa Y, F Michor, MA Nowak (2004). Some basic properties of immune selection. J theor Biol 229: 179-188.

33. Iwasa Y, F Michor, MA Nowak (2004). Stochastic tunnels in evolutionary dynamics. Genetics 166: 1571-1579.

34. Jones AG, SJ Arnold, R Bilrger (2004). Evolution and stability of the G-matrix on a landscape with a moving optimum. Evolution 58: 1639-1654.

35. Jones NA, X Wei, D Flower, M Wong, F Michor, M Saag, B Hahn, M Nowak, G Shaw (2004). Determinants ofhuman immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic Y lymphocyte response. J Exp Math 200: 1243-1256.

36. Matsen E, MA Nowak (2004). Win-stay, lose-shift in language learning from peers. P Natl Acad Sci USA 101: 18053-18057.

37. Michor F, Y Iwasa, MA Nowak (2004). Dynamics of cancer progression. Nat Rev Cancer 4: 197-205.

38. Michor F, Y Iwasa, H Rajagopalan, C Lengauer, MA Nowak (2004). Linear model of colon cancer initiation. Cell Cycle 3: 358-362.

39. Mitchener WG, MA Nowak (2004). Chaos and language. Proc R Soc B 271: 701-704.

40. Moret BME, L Nakhleh, T Wamow, CR Linder, A Tholse, A Padolina, J Sun, R Timme (2004). Phylogenetic networks: Modeling, reconstructibility, and accuracy. IEEE T Comput Biol Biocomp I: 13-23.

41. Moret BME, U Roshan, T Wamow, TL Williams (2004). Performance of supertree methods on various dataset decompositions. In Phylogenetic Supertrees, ed. ORP Bininda-Edmonds. Dordrecht, Netherlands: Kluwer Academic Publishers, 301-328.

42. Nakhleh L, T Wamow, CR Linder (2004). Reconstructing reticulate evolution in species — theory and practice. In Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), 337-346.

43. Nowak MA (2004). Prisoners of the dilemma. Nature 427: 491.

44. Nowak MA (2004) Theory is available light. Curr Biol 14: R406-R407.

45. Nowak MA, F Michor, Y Iwasa (2004). Evolutionary dynamics of tumor suppressor gene inactivation. P Natl Acad Sci USA 101: 10635-10638.

## 2004 (cont.)

46. Nowak MA, A Sasaki, C Taylor, D Fudenberg (2004). Emergence of cooperation and evolutionary stability in finite populations. Nature 428: 646-650.

47. Nowak MA, K Sigmund (2004). Evolutionary dynamics of biological games. Science 303: 793-799.

48. Nowak MA, K Sigmund (2004). Population dynamics in evolutionary ecology. In Life Sciences for the 21st Century, eds. E Kcinan, I Schechter, M Sela. Weinheim: Wiley-VCH Verlag GmbH & Co.

49. O'Grady JJ, MA Burgman, DA Keith, LL Master, SJ Andelman, BW Brook, GA Hammerson, T Regan, R Frankham (2004). Correlations among extinction risks assessed by different systcms of threatened species categorization. Consery Biol 18: 1624-1635.

50. O'Grady JJ, DH Reed, BW Brook, R Frankham (2004). What are the best correlates of predicted extinction risk? Biol Consery 118: 513-520.

51. Reed DH, JJ O'Grady, BW Brook, JD Ballou, R Frankham (2004). Large estimates of minimum viable population sizes. Consery Biol 18: 1179.

52. Roshan U, BME Moret, 'It Williams, T Warnow (2004). Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees. In Proc. IEEE Computer Society Bioinformatics Conference CSB 2004. Stanford: Stanford University Press.

53. Spielman D, BW Brook, It Frankham (2004). Does inbreeding and loss of genetic diversity decrease disease resistance? Consery Gen 5: 439-448.

54. Spielman D, BW Brook, R Frankham (2004). Most species are not driven to extinction before genetic factors impact them. P Natl Acad Sci USA 101: 15261-15264.

55. Taylor C, D Fudenberg, A Sasaki, MA Nowak (2004). Evolutionary game dynamics in finite populations. B Math Biol 66: 1621-1644.

56. Turelli M, NH Barton (2004). Polygenic variation maintained by balancing selection: Pleiotropy, sex-dependent allelic effects and G x E interactions. Genetics 166: 1053-1079.

57. Wang L, T Warnow (2004). Distance-based genome rearrangement phylogeny. In Mathematics of Evolution and Phylogeny, ed. O Gascucl. Ox ford: Oxford University Press.

58. Wamow T, SN Evans, D Range, L Nakhleh (2004). Stochastic models of language evolution and an application to the Indo-European family of languages. In Proceedings of the Conference on Phylogenetic Methods and the Prehistory of Languages. Cambridge: Cambridge University Press.

59. Whitlock MC, R Burger (2004). The good, the bad, and the ugly: Fixation of new mutations in small populations. In Evolutionary Conservation Biology, eds. R Ferriere, U Dieckmann, D Couvet. Cambridge: Cambridge University Press.

60. Wodarz D, N Komarova, Y Iwasa (2004). On the emergence of multifocal cancers. J Carcinogenesis 3: 13.

## 2005

61. Burger R (2005). A multilocus analysis of intraspecific competition and stabilizing selection on a quantitative trait. J Math Biol 50: 355-396.

62. Boeckx C, M Piattelli-Palmarini (2005). Language as a natural object, linguistics as a natural science. Linguist Rev 22: 351-370.

63. 63.Brown WM, L Cronk, K Grochow, A Jacobson, CK Liu, Z Popovik, R Travers (2005). Dance reveals symmetry especially in young men. Nature 438: T148-T150.

64. Claussen J, Traulsen A (2005). Nongaussian fluctuations arising from finite populations: Exact results for the evolutionary Moran process. Phys Rev E 71: 025101.

65. Docbeli M, C Hauert (2005). Models of cooperation based on the Prisoner's Dilemma and the Snowdrift game. Ecol Lett 8: 748-766.

## 2005 (cont.)

66. Feugier FG, A Mochizuki, Y Iwasa (2005). Self-organizing formation of vascular system of plant leaves: Co-orientation between auxin flux and pump proteins.) thcor Biol 236: 366- 375.

67. Gerhart J, C Lowe, M Kirschner (2005). Hcmichordatcs and the origin of chordates. Curr Opin Genet Dev 15: 461-467. Gilligan DM, DA Briscoe, R Frankham (2005). Comparative losses of quantitative and molecular genetic variation in finite populations ofDrosophila melanogaster. Genet Res 85: 47-55.

68. Gilligan DM, DA Briscoe, R Frankham (2005). Comparative losses ofquantitative and molecular genetic variation in finite populations ofDrosophila melanogaster. Genet Res 85: 47-55.

69. Hale J, EP Stabler (2005). Strict deterministic aspects of minimalist grammars. In Logical Aspects ofComputational Linguistics, ed. P Blachc et al. Springer LNCS-3492, 162-176.

70. Hauert C, G Szabo (2005). Game theory and physics. Am J Phys 73: 405-414.

71. ImhofLA (2005). Evolutionary game dynamics under stochastic influences. Jahresbericht der DMV 107: 197-213.

72. ImhofLA (2005). The long-run behavior of the stochastic replicator dynamics. Ann Appl Probab 15: 1019-1045.

73. ImhofLA, D Fudenberg, MA Nowak (2005). Evolutionary cycles of cooperation and defection. P Natl Acad Sci USA 102: 10797-10800.

74. ImhofLA, S Walcher (2005). Exclusion and persistence in deterministic and stochastic chemostat models. J Differ Equations 217: 26-53.

75. Iwasa Y, F Michor, NL Komarova, MA Nowak (2005). Population genetics of tumor suppressor genes.) theor Biol 233: 15-23.

76. Iwasa Y, F Michor, MA Nowak (2005). Virus evolution within patients increases pathogenicity.) theor Biol 232: 17-26.

77. Keenan EL, EP Stabler (2005). Linguistic invariants and language variation. In Logic, Methodology and Philosophy of Science, ed. P Hajck et al. London: Kings College Publications, 395-411.

78. Lee Y, T Collier, C Taylor, EP Stabler (2005). The role of population structure in language evolution. In Proceedings of the 10th International Symposium on Artificial Life and Robotics.

79. Lee Y, T Collier, EP Stabler, C Taylor (2005). Grammar structure and the dynamics of language evolution. In Proceedings of the 8th European Conference on Artificial Lifc.

80. Lieberman E, C Hauert, MA Nowak (2005). Evolutionary dynamics on graphs. Nature 433: 312-316.

81. Lieberman E, C Hauert, MA Nowak (2005). Evolutionary dynamics on graphs. Nature 433: 312-316.

82. Michor F (2005). Chromosomal instability and human cancer. Proc R Soc B 360: 631-635.

83. Michor F, TP Hughes, Y Iwasa, S Branford, NP Shah, CL Sawyers, MA Nowak (2005). Dynamics of chronic myeloid leukemia. Nature 435: 1267-1270.

84. Michor F, Y Iwasa, C Lengauer, MA Nowak (2005). Dynamics of colorectal cancer. Semin Cancer Biol 15: 484-493.

85. Michor F, Y Iwasa, C Lengauer, B Vogelstein, MA Nowak (2005). Can chromosomal instability initiate tumorigenesis? Semin Cancer Biol 15: 43-49.

86. Michor PW, D Mumford (2005). Vanishing geodesic distance on spaces of submanifolds and diffeomorphisms. Documenta Math 10: 217-245.

87. Moret BME, J Tang, T Wamow (2005). Reconstructing phylogenies from gene-content and gene-order data. In Mathematics of Evolution and Phylogeny, ed. 0 Gascuel. Oxford: Oxford University Press, 321-352.

## 2005 (cont.)

88. Nakamaru M, Y Iwasa (2005). The evolution of altruism by costly punishment in the lattice structured population: Score-dependent viability versus score-dependent fertility. Evol Ecol Rev 7: 853-870.

89. Nakhlch L, D Ringc, T Warnow (2005). Perfect phylogenctic networks: A new methodology for reconstructing the evolutionary history of natural languages. Language 81: 382-420.

90. Nowak MA, NL Komarova (2005). The evolution of altruism: From game theory to human language. In Spiritual Information, ed. CL Harper. Templeton Foundation Press, 308-314.

91. Nowak MA, K Sigmund (2005). Evolution of indirect reciprocity. Nature 427: 1291-1298.

92. Satake A, ON Bjornstad, Y Iwasa (2005). Invasibility of seed predators on synchronized and intermittent seed production of host plants. In Conceptual Ecology and Invasions Biology: Reciprocal Approaches to Nature, ed. MW Cadotte, SM McMahon, T Fukami. Kluwer, Netherlands: Kluwer Academic Press, 281-298.

93. Slade P, J Wakeley (2005). The structured ancestral selection graph and the many-demes limit. Genetics 169: 1117-1131.

94. Traulsen A, JC Claussen, C Hauert (2005). Coevolutionary dynamics: From finite to infinite populations. Phys Rev Lett 95: 238701.

95. Traulsen A, AM Sengupta, MA Nowak (2005). Stochastic evolutionary dynamics on two levels..1 thcor Biol 235: 393-401.

96. Trivers R (2005). Reciprocal altruism: 30 years later. In Cooperation in Primates and Springer-Verlag, Humans: 67-83. Mechanisms and Evolution, ed. CP van Schaik, PM Kappeler. Berlin:

97. Wakelcy J (2005). The limits of theoretical population genetics. Genetics 169: 1-7.

98. Wedekind C, R Muller (2005). Risk-induced hatching in salmonids. Ecology 86: 2525-2529.

99. Wedekind C, R Muller (2005). The hatchery. B Ecol Soc USA 86: 124-125.

100. Wedekind C, M Walker, TJ Little (2005). The course of malaria in mice: MHC effects, but no general MHC heterozygote advantage in single-strain infections. Genetics 170: 1427- 1430.

101. Willensdorfer M, MA Nowak (2005). Mutation in evolutionary games can increase average fitness at equilibrium. J thcor Biol 237: 355-362.

## 2006

102. Abbott LH, F Michor (2006). Mathematical models of targeted cancer therapy. Brit J Cancer 95: 1136-1141.

103. Antal T, PL Krapivsky (2006). Flows on graphs with random capacities. Phys Rev E 74: 051110.

104. Brandt H, C Haucrt, K Sigmund (2006). Punishing and abstaining for public goods. P Natl Acad Sci USA 103: 495497.

105. Burger R, KA Schneider (2006). Intraspecific competitive divergence and convergence under assortative mating. Am Nat 167: 190-205.

106. Burger R, KA Schneider, M Willensdorfer (2006). The conditions for speciation through intraspecific competition. Evolution 60: 2185-2206.

107. Burger R, M Willensdorfer, MA Nowak (2006). Why are phenotypic mutation rates much higher than genotypic mutation rates? Genetics 172: 197-206.

108. Boeckx C (2006). Linguistic Minimalism: Origins, Concepts, Methods, and Aims. Oxford/New York: Oxford University Press.

109. Burt A, R Trivers (2006). Genes in Conflict: The Biology of Selfish Genetic Elements. Cambridge, MA: Harvard University Press.

110. Dingli D, F Michor (2006). Successful therapy must eradicate cancer stem cells. Stem Cells 24: 2603-2610.

## 2006 (cont.)

- III. Dingli D, MA Nowak (2006). Infectious tumor cells. Nature 443: 35-36.

112. Dingli D, JM Pacheco (2006). Allometric scaling of the active hcmatopoictic stem cell pool across mammals. PLoS ONE I: e2.

113. Doebeli M, C Haucrt (2006). The limits of Hamilton's rule..1 Evol Biol 19: 1386-1388.

114. Eldon 8, J Wakeley (2006). Coalescent processes when the distribution of offspring numbcr among individuals is highly skewed. Genetics 172: 2621-2633.

115. Evans SN, D Ringe, T Warnow (2006). Inference of divergence times as a statistical inverse problem. In Phylogenetic Methods and the Prehistory of Languages, ed.. P Forster, C Renfrew. Series eds. C Scarre, DA Kemp. McDonald Institute for Archaeological Research/University of Cambridge, 119-129.

116. Foster KR (2006). The Phoenix effect. Nature 441: 291-292.

117. Fudenberg D, LA Imhof (2006). Imitation processes with small mutations. J Econ Theory 131: 251-262.

118. Fudenberg D, MA Nowak, C Taylor, LA Imhof (2006). Evolutionary game dynamics in finite populations with strong selection and weak mutation. Theor Popul Biol 70: 352-363.

119. Ghirlanda S, M Enquist, M Nakamaru (2006). Cultural evolution develops its own rules: The rise of conservatism and persuasion. Curr Anthro 47: 1027-1034.

120. Haig D (2006). Intragenomic politics. Cytogenet Genome Res 113: 68-74.

121. X-chromosome Haig D (2006). inactivation. Self-imposed Evolution silence: 60: Parental 440-447. antagonism and the evolution of

122. Hauert C (2006). Spatial effects in social dilemmas. J theor Biol 240: 627-636.

123. Haucrt C, M Holmes, M Doebeli (2006). Evolutionary games and population dynamics: Maintenance of cooperation in public goods games. Proc R Soc B 273: 2565-2570.

124. Hauert C, F Michor, MA Nowak, M Doebeli (2006). Synergy and discounting of cooperation in social dilemmas. I theor Biol 239: 195-202.

125. Imhof LA, MA Nowak (2006). Evolutionary game dynamics in a Wright-Fisher process. Math Biol 52: 667-681.

126. Iwasa Y, MA Nowak, F Michor (2006). Evolution of resistance during clonal expansion. Genetics 172: 2557-2566.

127. Matson FA, J Wakeley (2006). Convergence to the island-model coalescent process in populations with restricted migration. Genetics 172: 701-708.

128. Michor F, Y Iwasa, MA Nowak (2006). The age incidence of chronic myeloid leukemia can be explained by a one-mutation model. P Natl Acad Sci USA 103: 14931-14934.

129. Michor F, MA Nowak, Y Iwasa (2006). Evolution of resistance to cancer therapy. Curr Phann Design 12: 261-271.

130. Michor F, MA Nowak, Y Iwasa (2006). Stochastic dynamics of metastasis formation. J theor Biol 240: 521-530.

131. Michor PW, D Mumford (2006). Riemannian geometries on spaces of plane curves. .I Eur Math Soc 8: 1.48.

132. Nowak MA (2006). Evolutionary Dynamics. Cambridge, MA: Harvard University Press.

133. Nowak MA (2006). Five rules for the evolution of cooperation. Science 314: 1560-1563.

134. Nowak MA, F Michor, Y Iwasa (2006). Genetic instability and clonal expansion. J theor Biol 241: 26-32.

135. Ohtsuki H, C Hauert, E Lieberman, MA Nowak (2006). A simple rule for the evolution of cooperation on graphs and social networks. Nature 441: 502-505.

136. Ohtsuki H, Y Iwasa (2006). The leading eight: Social norms that can maintain cooperation by indirect reciprocity. J theor Biol 239: 435-444.

137. Ohtsuki H, MA Nowak (2006). Evolutionary games on cycles. Proc R Soc B 273: 2249- 2256.

138. Ohtsuki H, MA Nowak (2006). The replicator equation on graphs. J thcor Biol 243: 86-97.

## 2006 (cont.)

139. Pacheco 3M, A Traulsen, MA Nowak (2006). Active linking in evolutionary games. J theor Biol 243: 437-443.

140. Pacheco JM, A Traulsen, MA Nowak (2006). Coevolution of strategy and structure in complex networks with dynamical linking. Phys Rev Lett 97: 258103.

141. Pfeiffer T, MA Nowak (2006). Climate change: All in the game. Nature 441: 583-584.

142. Pfeiffer T, MA Nowak (2006). Digital cows grazing on digital grounds. Curr Biol 16: R946- R949.

143. Ralicke T, N Guncz, C Wedekind (2006). Early maternal investment in mice: No evidence for 'compatible-genes' sexual selection despite hybrid vigor. J Evol Biol 19: 922-928.

144. Santos FC, JM Pacheco, T Lenaens (2006). Cooperation prevails when individuals adjust their social ties. PLoS Comput Biol 2: e140.

145. Santos FC, JM Pacheco, T Lcnaerts (2006). Evolutionary dynamics of social dilemmas in structured heterogeneous populations. P Natl Acad Sci USA 103: 3490-3494.

146. Taylor C, Y Iwasa, MA Nowak (2006). A symmetry of fixation times in evolutionary dynamics. J theor Biol 243: 245-251.

147. Taylor C, MA Nowak (2006). Evolutionary game dynamics with non-uniform interaction rates. Theor Popul Biol 69: 243-252.

148. Traulsen A, JC Claussen, C Hauert (2006). Coevolutionary dynamics in large but finite populations. Phys Rev E 74: 011901.

149. Traulsen A, MA Nowak (2006). Evolution of cooperation by multilevel selection. P Natl Acad Sci USA 103: 10952-10955.

150. Traulsen A, MA Nowak, .1 Pacheco (2006). Stochastic dynamics of invasion and fixation. Phys Rev E 74: 011909.

151. Traulsen A, .IM Pacheco, L Imhof (2006). Stochasticity and evolutionary stability. Phys Rev E 74: 021905.

152. Trivers R, JT Manning, A Jacobson (2006). A longitudinal study of digit ratio (2D:4D) and other forger ratios in Jamaican children. Horm Bchav 49: 150-156.

153. Wamow T, SN Evans, D Ringe, L Nakhleh (2006). A stochastic model of language evolution that incorporates homoplasy and borrowing. In Phylogenctic Methods and the Prehistory of Languages, eds. P Forster, C Renfrew. Series eds. C Scarre, DA Kemp. McDonald Institute for Archaeological Research/University of Cambridge, 75-87.

## 2007

154. Antal T, I Bena, M Droz, K Martens, Z Racz (2007). Guiding-fields for phase-separation: Controlling liesegang patterns. Phys Rev E 76: 046203.

155. Antal T, KB Blagoev, SA Trugman, S Ratner (2007). Aging and immortality in a cell proliferation model. J theor Biol 248: 411-417.

156. Antal T, PL Krapivsky (2007). Molecular spiders with memory. Phys Rev E 76: 021121.

157. Mech-Theory Antal T, E: PL P08027. Krapivsky, K Mallick (2007). Molecular spiders in one dimension. J Stat

158. Antal T, PL Krapivsky, S Redner, M Mailman, B Chakraborty (2007). Dynamics of an idealized model of microtubule growth and catastrophe. Phys Rev E 76: 041907.

159. Beerenwinkel N, T Antal, D Dingli, A Traulsen, KW Kinzler, VE Velculescu, B Vogelstein, MA Nowak (2007). Genetic progression and the waiting time to cancer. PLoS Comput Biol 3: e225.

160. Brandt H, H Ohtsuki, Y Iwasa, K Sigmund (2007). A survey ofindirect reciprocity. In Mathematics for Ecology and Evolution, eds. Y Takeuchi, Y Iwasa, K Sato. Berlin: Springer, 21-50.

161. Burnham TC (2007). High-testosterone men reject low ultimatum game offers. Proc R Soc B 274: 2327-2330.

## 2007 (cont.)

162. Burnham TC, B Hare (2007). Engineering human cooperation. Hum Nat 18: 88-108.

163. Dingli D, F Michor, T Antal, .11.4 Pacheco (2007). The emergence of tumor mctastascs. Cancer Biol Ther 6: e1-e8.

164. Dingli D, JM Pacheco (2007). Ontogenic growth of the hacmatopoictic stem cell pool in humans. Proc R Soc B 274: 2497-2501.

165. Dingli D, JM Pacheco, A Dispenzieri, S Hayman, S Kumar, M Lacy, D Gastineau, M Gertz (2007). In vivo and in silico studies on single versus multiple transplants for multiple myeloma. Cancer Sci 98: 734-739.

166. Dingli D, A Traulsen, F Michor (2007). (A)Synunetric stem cell replication and cancer. PLoS Comput Biol 3: e53.

167. Dingli D, A Traulsen, JM Pacheco (2007). Stochastic dynamics of hematopoietic tumor stem cells. Cell Cycle 6: c1-c6.

168. Dingli D, A Traulsen, JM Pacheco (2007). Compartmental architecture and dynamics of hernatopoicsis. PLoS One 2: e345.

169. D'Orsogna MR, T Chou, T Antal (2007). Exact steady-state velocity of ratchets driven by random sequential absorption. J Phys A: Math Theor 40: 5575-5584.

170. Hauert C, A Traulsen, H Brandt, MA Nowak, K Sigmund (2007). Via freedom to coercion: The emergence of costly punishment. Science 316: 1905-1907.

171. ImhofLA, D Fudenberg, MA Nowak (2007). Tit-for-tat or win-stay, lose-shift? J theor Biol 247: 574-580.

172. Iwasa Y, F Michor, MA Nowak (2007). Directional evolution of virus within a host under immune selection. In Mathematics for Life Science and Medicine, cds. Y Takeuchi, Y Iwasa, K Sato. Springer: New York.

173. Lieberman E, JB Michel, J Jackson, T Tang, MA Nowak (2007). Quantifying the evolutionary dynamics oflanguage. Nature 449: 713-716.

174. Lopes J V, JM Pacheco, D Dingli (2007). Acquired hematopoietic stem-cell disorders and mammalian size. Blood 110: 4120-4122.

175. Masuda N, H Ohtsuki (2007). Tag-based indirect reciprocity by incomplete social information. Proc R Soc B 274: 689-695.

176. Nowak MA, S Roch (2007). Upstream reciprocity and the evolution ofgratitude. Proc R Soc B 274: 605-609.

177. Nowak MA, K Sigmund (2007). How populations cohere: Five rules for cooperation. In Theoretical Ecology: Principles and Applications, eds. RM May, A McLean. Oxford: Oxford University Press, 7-16.

178. Ohtsuki H. P Bordalo, MA Nowak (2007). The one third law ofevolutionary dynamics. J theor Biol 249: 289-295.

179. Ohisuki H, Y Iwasa (2007). Global analyses of evolutionary dynamics and exhaustive search for social norms that maintain cooperation by reputation. J theor Biol 244: 518-531.

180. Ohtsuki H, MA Nowak (2007). Direct reciprocity on graphs. 3 theor Biol 247: 462-470.

181. Ohtsuki H, J Pacheco, MA Nowak (2007). Evolutionary graph theory: Breaking the symmetry between interaction and replacement. J theor Biol 246: 681-694.

182. Ohtsuki H, J Pacheco, MA Nowak (2007). Breaking the symmetry between interaction and replacement in evolutionary dynamics on graphs. Phys Rev Lett 98: 108106.

183. Pfeiffer T, R Hoffman (2007). Temporal patterns of genes in scientific publications. P Natl Acad Sci USA 104: 12052-12056.

184. Pinker S (2007). Games people play. In The Stuff of Thought: Language as a Window Into Human Nature. New York: Viking Press.

185. Roehl T, C Roehl, HG Schuster, A Traulsen (2007). The impact of fraud on the mean-field dynamics of cooperative social systems. Phys Rev E 76: 026114.

186. Steiner UK, T Pfeiffer (2007). Optimizing time and resource allocation trade-offs for investment in morphological and behavioral defense. Am Nat 169: 118-129.

## 2007 (cont.)

187. Taylor C, J Chen, Y Iwasa (2007). Cooperation maintained by fitness adjustment. Evol Ecol Res 9: 1023-1041.

188. Taylor C, MA Nowak (2007). Transforming the dilemma. Evolution 61: 2281-2292.

189. Traulsen A, Y Iwasa, MA Nowak (2007). The fastest evolutionary trajectory. J theor Biol 249: 617-623.

190. Traulsen A, MA Nowak (2007). Chromodynamics of cooperation in finite populations. PLoS ONE 2: e270.

191. Traulsen A, MA Nowak, J Pacheco (2007). Stochastic payoff evaluation increases the temperature of selection. J theor Biol 244: 349-356.

192. Traulsen A, IM Pacheco, D Dingli (2007). On the origin of multiple mutant clones in paroxysmal nocturnal hemoglobinuria. Stem Cells 25: 3081-3084.

193. Traulsen A, JM Pacheco, MA Nowak (2007). Pairwise comparison and selection temperature in evolutionary game dynamics. J theor Biol 246: 522-529.

194. Uehara T, Y Iwasa, H Ohtsuki (2007). ESS distribution of display duration in animal contests to assess an opponent before fighting or fleeing. Evol Ecol Res 9: 395-408.

195. Wild G, A Traulsen (2007). The different limits of weak selection and the evolutionary dynamics of finite populations. J theor Biol 247: 382-390.

196. Wilknsdorfcr M, R Burger, MA Nowak (2007). Phenotypic mutation rates and the abundance of abnormal proteins in yeast. PLoS Comput Biol 3: e203.

197. Worden L, SA Levin (2007). Evolutionary escape from the prisoner's dilemma. .1 theor Biol 245:411-422.

## 2008

198. Apicella CL, A Dreber, B Campbell, PB Gray, M Hoffman, AC Little (2008). Testosterone and financial risk preferences. Evol Hum Behav 29: 384-390.

199. Bomze 1, C Pawlowitsch (2008). One-third rules with equality: Second-order evolutionary stability conditions in finite populations. J theor Biol 254: 616-620.

200. Dingli D, MA Nowak (2008). Evolutionary dynamics of cancer. Book review of Dynamics of Cancer: Incidence, Inheritance, and Evolution, SA Frank. Trends Ecol Evol 23: 254-255.

201. Dreber A, M Johannesson (2008). Gender differences in deception. Econ Lett 99: 197-199.

202. Dreber A, MA Nowak (2008). Gambling for global goods. P Natl Acad Sci USA 105: 2261- 2262.

203. Dreber A, DG Rand, D Fudenberg, MA Nowak (2008). Winners don't punish. Nature 452: 348-351.

204. Fu F, C Hauert, MA Nowak, L Wang (2008). Reputation-based partner choice promotes cooperation in social networks. Phys Rev E 78: 026117. appears in Vir J Bio Phys Res 16(5).

205. Goldstein R, J Almenbcrg, A Dreber, JW Emerson, A Herschkowitsch, J Katz (2008). Do more expensive wines taste better? Evidence from a large sample of blind tastings. J Wine Econ 3: 1-9.

206. Hauert C, A Traulsen, H Brandt, MA Nowak, K Sigmund (2008). Public goods with punishment and abstaining in finite and infinite populations. Biological Theory 3(2): 114-122.

207. Hauert C, JY Wakano, M Doebeli (2008). Ecological public goods games: Cooperation and bifurcation. Theor Popul Biol 73: 257-263.

208. Jones S, W Chen, G Parmigiani, F Diehl, N Beerenwinkel, T Antal, A Traulsen, MA Nowak, C Siegel, VE Velculescu, KW Kinzler, B Vogelstein, J Willis, SD Markowitz (2008). Comparative lesion sequencing provides insights into tumor evolution. P Natl Acad Sci USA 105: 4283-4288.

## 2008 (cont.)

209. Langer P, MA Nowak, C Hauert (2008). Spatial invasion of cooperation. J theor Biol 250: 634-641.

210. Michel 1B, P1 Yeh, R Chait, RC Moellering, R Kishony (2008). Drug interactions modulate the potential for evolution ofresistance. P Nad Acad Sci USA 105: 14918-14923.

211. Nowak MA (2008). Generosity: A winner's advice. Nature. 456: 579.

212. Nowak MA, H Ohtsuki (2008). Prevolutionary dynamics and the origin of evolution. P Nail Acad Sci USA 105: 14924-14927.

213. Ohtsuki H, MA Nowak (2008). Evolutionary stability on graphs. J theor Biol 251: 698-707.

214. Pacheco JM, A Traulsen, H Ohtsuki, MA Nowak (2008). Repeated games and direct reciprocity under active linking. J theor Biol 250: 723-731.

215. Peischl S, R Burger (2008). Evolution of dominance under frequency-dependent intraspecific competition. J thcor Biol 251: 210-226.

216. Pinker S, MA Nowak, JJ Lee (2008). The logic of indirect speech. P Nail Acad Sci USA 105: 833-838.

217. Schuster S, JU Kreft, A Schroeter, T Pfeiffer (2008). Use of game-theoretical methods in biochemistry and biophysics. J Biol Phys. 34: 1-17.

218. Schuster S, T Pfeiffer, DA Fell (2008). Is maximization of molar yield in metabolic networks a universal principle? J Theor Biol. 252: 497-504.

219. Traulsen A,N Shoresh, MA Nowak (2008). Analytical results for individual and group selection of any intensity. B Math Biol 70: 1410-1424.

220. Willensdorfer M (2008). Organism size promotes the evolution of specialized cells in multicellular digital organisms. J Evol Biol 21: 104-110.

## 2009

221. Almenberg J, K Kittlitz, T Pfciffer(2009). An experiment on prediction markets in science. PLoS ONE 4: e8500.

222. Antal T, H Ohtsuki, J Wakeley, PD Taylor, MA Nowak (2009). Evolution of cooperation by phenotypic similarity. P Natl Acad Sci USA 106: 8597-8600.

223. Antal T, MA Nowak, A Traulsen (2009). Strategy abundance in 2x2 games for arbitrary mutation rates. J theor Biol 257: 340-344.

224. Antal T, A Traulsen, H Ohtsuki, CE Tarnita, MA Nowak (2009). Mutation—selection equilibrium in games with multiple strategics. J theor Biol 258: 614-622.

225. Burger R (2009). Multilocus selection in subdivided populations I: Convergence properties for weak or strong migration. J Math Biol 58: 939-978.

226. Burger R (2009). Multilocus selection in subdivided populations II: Maintenance of polymorphism under weak or strong migration. J Math Biol 58: 979-997.

227. Burger R (2009). Polymorphism in the two-locus Levene model with nonepistatic directional selection. Theor Popul Biol 76: 214-228.

228. Dingli D, T Antal, A Traulsen, JM Pacheco (2009). Progenitor cell self-renewal and cyclic ncutropcnia. Cell proliferation 42: 330-338.

229. Dreber A, CL Apicella, DTA Eisenberg, JR Garcia, RS Zamore, JK Lum, B Campbell (2009). The 7R polymorphism in the dopamine receptor D4 gene (DRD4) is associated with financial risk taking in men. Evol Hum Behav 30: 85-92.

230. Fu F, L Wang, MA Nowak, C Hauert (2009). Evolutionary dynamics on graphs: Efficient method for weak selection. Phys Rev E 79: 046707.

231. Gokhale CS, Y Iwasa, MA Nowak, A Traulsen (2009). The pace ofevolution across fitness valleys. J theor Biol 259: 613-620.

232. Lieberman E, NL Bcrkum, L Williams, M Imakaev, T Ragoczy, A Telling, I Amit, BR Lajoic, PJ Sabo, MO Dorschner, R Sandstrom, B Bernstein, MA Bender, M Groudinc, A Gnirke, J Stamatoyannopoulos, LA Mimy, ES Lander, J Dekker (2009). Comprehensive

## 2009 (cont.)

Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326: 289-293.

233. Manapat M, H Ohtsuki, R Burger, MA Nowak (2009). Originator dynamics. J theor Biol 256: 586-595.

234. Nathanson CG, CE Tarnita, MA Nowak (2009). Calculating evolutionary dynamics in structured populations. PLoS Comput Biol 5: e1000615.

235. Novak M, T Pfeiffer, M Ackerman, S Bonhoeffer (2009). Bacterial growth properties at low optical densities. Antonie van Leeuwenhoek 96: 267-274.

236. Ohtsuki H, Y Iwasa, MA Nowak (2009). Indirect reciprocity provides only a narrow margin of efficiency for costly punishment. Nature 457: 79-82.

237. Ohtsuki H. MA Nowak (2009). Prelife catalysts and replicators. Proc R Soc B 276: 3783- 3790.

238. Pfeiffer T, R Hoffmann (2009). Large-scale assessment of the effect of popularity on the reliability of research. PLoS ONE 4: e5996.

239. Pfeiffer T, D Rand, A Dreber (2009). Decision-making in research tasks with sequential testing. PLoS ONE 4: e4607.

240. Rand DG, A Dreher, T Ellingsen, D Fudenberg, MA Nowak (2009). Positive interactions promote public cooperation. Science 325: 1272-1275.

241. Rand DG, A Dreher, T Ellingson, D Fudenberg, MA Nowak (2009). Weighing Reward and Punishment — Response. Science 326: 1632-1633.

242. Rand DG, MA Nowak (2009). Name and shame: How reputation could save the Earth. New Scientist 2734: 28-29.

243. Rand DG, H Ohtsuki, MA Nowak (2009). Direct reciprocity with costly punishment: Generous tit-for-tat prevails. .1 theor Biol 256: 45-57.

244. Rand DG, T Pfeiffer (2009). Systematic differences in impact across publication tracks at PNAS. PLoS ONE 4: e8092.

245. Rand DG, T Pfeiffer, A Dreber, RW Sheketoff, NC Wernerfelt, Y Boulder (2009). Dynamic remodeling of in-group bias during the 2008 presidential election. P Nati Acad Sci USA 106: 6187-6191.

246. Rune C, T Pfeiffer (2009). Evolution of reciprocal altruism by copying of observed behavior. Current Science 97: 1573-1578.

247. Tarnita CE, T Antal, MA Nowak (2009). Mutation-selection equilibrium in games with mixed strategies. J theor Biol 261: 50-57.

248. Tarnita CE, T Antal, H Ohtsuki, MA Nowak (2009). Evolutionary dynamics in set structured populations. P Natl Acad Sci USA 106: 8601-8604.

249. Tarnita CE, H Ohtsuki,T Antal, F Fu, MA Nowak (2009). Strategy selection in structured populations. J theor Biol 259: 570-581.

250. Taylor C, MA Nowak (2009). How to evolve cooperation. pages 41-56. In Games, Groups, and the Global Good, ed. S Levin. New York: Springer.

251. Traulsen A, C Hauert, H Brandt De Silva, MA Nowak, K Sigmund (2009). Exploration dynamics in evolutionary games. P Natl Acad Sci USA 106: 709-712.

252. Tu K, DG Cooper, HT Siegehnann (2009). Memory reconsolidation for natural language processing. Cogn Neurodyn 3: 365-372.

253. Wakano JY, MA Nowak, C Hauert (2009). Spatial dynamics of ecological public goods. P Natl Acad Sci USA 106: 7910-7914.

254. Woelfing B, A Traulsen, M Milinski, T Boehm (2009). Does intra-individual major histocompatibility complex diversity keep a golden mean? Phil Trans R Soc B 364: 117-128.

## 2010

## 2010 (cont.)

255. ImhofLA, MA Nowak (2010). Stochastic evolutionary dynamics ofdirect reciprocity. Proc R Soc B 277: 463-468.

256. Manapat ML, IA Chen, MA Nowak (2010). The basic reproductive ratio oflife. J theor Biol 263: 317-327.

257. Nowak MA, CE Tamita, T Antal (2010). Evolutionary dynamics in structured populations. Phil Trans R Soc B 365: 19-30.

258. Ojosnegros S, N Beerenwinkel, T Antal, MA Nowak, C Escarmis, E Domingo (2010).

	- Competition-colonization dynamics in an RNA virus. P Nail Acad Sci USA 107: 2108-2112.

259. Rajamani S, JK Ichida, T Antal, DA Treco, K Leu, MA Nowak, JW Szostak, IA Chen (2010). Offset of the error catastrophe in non-enzymatic nucleic acid replication. J Am Chem Soc (in press).

Compiled by Lydia Liu