Classical papers in evolutionary biology.
Daniel R. Matute
I. Sex
1. The origin of sex. Muller, H. J. (1964). The relation of recombination to mutational
advance. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis,
1(1), 2-9; Kondrashov, A. S. (1988). Deleterious mutations and the evolution of sexual
reproduction. Nature, 336(6198), 435-440; Hill, W. G., and A. Robertson. 1966. The
effect of linkage on limits to artificial selection. Genet. Res. 8:269-294. Charlesworth, B.,
& Charlesworth, D. (1997). Rapid fixation of deleterious alleles can be caused by Muller's
ratchet. Genetical research, 70(01), 63-73; Barton, N. H., & Charlesworth, B. (1998). Why
sex and recombination?. Science, 281(5385), 1986-1990.
2. Asexual populations. Muller HJ (1932). "Some genetic aspects of sex". American
Naturalist 66 (703): 118–138.; Chao, L. (1990). Fitness of RNA virus decreased by
Muller's ratchet; Desai. Chao, L., Tran, T., & Matthews, C. (1992). Muller's ratchet and
the advantage of sex in the RNA virus Φ6. Evolution, 289-299; Neher, R. A., & Shraiman,
B. I. (2012). Fluctuations of fitness distributions and the rate of Muller’s ratchet. Genetics,
191(4), 1283-1293; Goyal, S., Balick, D. J., Jerison, E. R., Neher, R. A., Shraiman, B. I.,
& Desai, M. M. (2012). Dynamic mutation–selection balance as an evolutionary attractor.
Genetics, 191(4), 1309-1319.
II. The neutral theory
3. On the fitness effects of mutations I. Kimura M. (1968). Evolutionary Rate at the
Molecular Level. Nature 217:624-6; King JL, Jukes TH. (1969). Non-Darwinian Evolution.
Science 164:788-97; Nei, M., Suzuki, Y., and M. Nozawa. (2010). The neutral theory of
molecular evolution in the genomic era. Ann Rev Genomics Hum Genet. 11:265-89;
Wagner A. (2008). "Neutralism and selectionism: a network-based reconciliation". Nature
Reviews Genetics 9 (12): 965–974. Gould, S. J., & Lewontin, R. C. (1979). The spandrels
of San Marco and the Panglossian paradigm: a critique of the adaptationist programme.
Proceedings of the Royal Society of London. Series B. Biological Sciences, 205(1161),
581-598.
4. On the fitness effects of mutations II. Langley CH, Fitch WM. 1974. An examination of the
constancy of the rate of molecular evolution. Journal J Mol Evol.;3(3):161-77. 1);
Zuckerkandl and Pauling. Evolutionary Divergence and Convergence in Proteins," in
Evolving Genes and Proteins, eds. V. Bryson and H. Vogel (New York: Academic Press,
1965). pp. 97-166. 2; Kimura, "Evolutionary Rate at the Molecular Level," Nature 217
(1968), 624-626; King and Jukes. 1969. "Non-Darwinian Evolution," Science 164: 788798. Ohta, 1973. Slightly Deleterious Mutant Substitutions in Evolution. Nature 246: 9698.
III. Molecular evolution and Population genetics
5. Molecular evolution. Kreitman, M. (1983). Nucleotide polymorphism at the alcohol
dehydrogenase locus of Drosophila melanogaster. Nature, 304(5925), 412-417.
McDonald, J. H., & Kreitman, M. (1991). Adaptive protein evolution at the Adh locus in
Drosophila. Nature, 351(6328), 652-654. Hudson, R. R., Kreitman, M., & Aguadé, M.
1987. A test of neutral molecular evolution based on nucleotide data. Genetics, 116(1),
153-159. Yang, Z. (1997). PAML: a program package for phylogenetic analysis by
maximum likelihood. Computer applications in the biosciences: CABIOS, 13(5), 555-556
6. Coalescent theory. Kingman, J. F. C. 1982. The coalescent. Stochastic processes and
their applications, 13(3), 235-248; Donnelly, P., & Tavaré, S. (1986). The ages of alleles
and a coalescent. Advances in Applied Probability, 1-19; Hudson, R. R. (1990). Gene
genealogies and the coalescent process. Oxford surveys in evolutionary biology, 7(1), 44
V. Adaptation
7. Natural selection: Darwin C (1859) On the Origin of Species by Means of Natural
Selection, or the Preservation of Favoured Races in the Struggle for Life John Murray,
London Chapters 3-5; Haldane, J.B.S. The cost of natural selection. (1957) Journal of
genetics: 55 pp 511-524. Price, G. R. (1970). Selection and covariance. Nature, 227,
520-21; Lande, R., & Arnold, S. J. (1983). The measurement of selection on correlated
characters. Evolution, 1210-1226; Clausen, J., Keck, D. D., & Hiesey, W. M. (1939). The
concept of species based on experiment. American Journal of Botany, 26(2), 103-106.
Kettlewell, H. B. D. (1955). Selection experiments on industrial melanism in the
Lepidoptera. Heredity, 9(3), 323-42.
8. Fisher’s geometric model: Fisher RA. 1930. The Genetical Theory of Natural Selection.
Clarendon Press, Oxford. Chapters 1 and 2; Orr and Coyne. 1992 The genetics of
adaptation: a reassessment. Am. Nat. 140: 725–742; Burch, C. L., & Chao, L. (1999).
Evolution by small steps and rugged landscapes in the RNA virus ϕ6. Genetics, 151(3),
921-927; Orr, H. A. (2005). The genetic theory of adaptation: a brief history. Nature
Reviews Genetics, 6(2), 119-127; Orr, H. A. (2006). The distribution of fitness effects
among beneficial mutations in Fisher's geometric model of adaptation. Journal of
theoretical biology, 238(2), 279-285.
VI. Adaptation (continued)
9. Longitudinal studies: Grant, P. R., & Grant, B. R. (2002). Unpredictable evolution in a 30year study of Darwin's finches. Science, 296(5568), 707-711. Elena, S. F., & Lenski, R.
E. (1997). Test of synergistic interactions among deleterious mutations in bacteria.
Nature, 390(6658), 395-398. Rambaut, A., Robertson, D. L., Pybus, O. G., Peeters, M., &
Holmes, E. C. (2001). Human immunodeficiency virus: phylogeny and the origin of HIV-1.
Nature, 410(6832), 1047-1048.
10. Shifting balance. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and
selection in evolution. Proceedings of the VI International Congress of Genetrics: 1. pp
356-366; Wright, S. (1982). The shifting balance theory and macroevolution. Annual
review of genetics, 16(1), 1-20; Wade, M. J., & Goodnight, C. J. (1991). Wright's shifting
balance theory: an experimental study. Science, 253(5023), 1015-1018; Coyne, J.A.,
N.H. Barton, and M. Turelli. (1997) A critique of Wright's shifting balance theory of
evolution. Evolution 51: 643-671.
11. Fitness landscapes. Dean, A. 1995. A Molecular Investigation of Genotype by
Environment Interactions. Genetics. 139:19-33; Gavrilets, S. 1997. "Evolution and
speciation on holey adaptive landscapes.". Trends in ecology & evolution 12 (8): 307–12;
Lehman, N. and Joyce, G. 1993. Evolution in Vitro: Analysis of a Lineage of Ribozymes
Current Biology 3: 723–34; Kouyos, R. D., Leventhal, G. E., Hinkley, T., Haddad, M.,
Whitcomb, J. M., Petropoulos, C. J., & Bonhoeffer, S. (2012). Exploring the complexity of
the HIV-1 fitness landscape. PLoS genetics, 8(3), e1002551; Martin, C. H., & Wainwright,
P. C. (2013). Multiple fitness peaks on the adaptive landscape drive adaptive radiation in
the wild. Science, 339(6116), 208-211
VII. Speciation and reproductive isolation
12. Reproductive isolation. Dobzhansky, T. (1935). A critique of the species concept in
biology. Philosophy of Science, 344-355; Simpson, G. G. (1951). The species concept.
Evolution, 5(4), 285-298; Muller, H. J. (1942). Isolating mechanisms, evolution and
temperature. In Biol. Symp (Vol. 6, No. 811, pp. 71-125); Coyne, J. A., & Orr, H. A.
(1989). Patterns of speciation in Drosophila. Evolution, 362-381; Haffer, J. (1969).
Speciation in Amazonian forest birds. Science, 165(3889), 131-137; Yukilevich, R.
(2012). Asymmetrical patterns of speciation uniquely support reinforcement in
Drosophila. Evolution, 66(5), 1430-1446; Straw, R. M. (1955). Hybridization, homogamy,
and sympatric speciation. Evolution, 441-444.
13. Speciation modes. White, M. J. D. (1968). Models of Speciation New concepts suggest
that the classical sympatric and allopatric models are not the only alternatives. Science,
159(3819), 1065-1070; Futuyma, D. J., & Mayer, G. C. (1980): Felsenstein, J. (1981).
Skepticism towards Santa Rosalia, or why are there so few kinds of animals?. Evolution,
124-138; Futuyma, D. J., & Mayer, G. C. (1980). Non-allopatric speciation in animals.
Systematic Biology, 29(3), 254-271; Chesser, R. T., & Zink, R. M. (1994). Modes of
speciation in birds: a test of Lynch's method. Evolution, 490-497; Bush, G. L. (1975).
Modes of animal speciation. Annual Review of Ecology and Systematics, 339-364;
MacArthur, R. H., & Wilson, E. O. (1963). An equilibrium theory of insular zoogeography.
Evolution, 373-387.
VIII. Hybrid zones
14. Hybrid zones. Barton, N. H. (1979). The dynamics of hybrid zones. Heredity, 43, 341359; Harrison, R. G. (1990). Hybrid zones: windows on evolutionary process. Oxford
surveys in evolutionary biology, 7, 69-128; Bigelow, R. S. (1965). Hybrid zones and
reproductive isolation. Evolution, 449-458; Remington, C. L. (1968). Suture-zones of
hybrid interaction between recently joined biotas. In Evolutionary biology (pp. 321-428).
Springer US; Short, L. L. (1969). Taxonomic aspects of avian hybridization. The Auk, 84105.
15. Reinforcement. D.J. Howard Reinforcement: origin, dynamics and fate of an evolutionary
hypothesis R.G. Harrison (Ed.), Hybrid Zones and the Evolutionary Process, Oxford
University Press, New York (1993), pp. 46–69; Liou, L. W., & Price, T. D. (1994).
Speciation by reinforcement of premating isolation. Evolution, 1451-1459; Dobzhansky,
T. (1940). Speciation as a stage in evolutionary divergence. American Naturalist, 312321; Noor, M. A. (1995). Speciation driven by natural selection in Drosophila. Nature,
375(6533), 674-675; Koopman, K. F. (1950). Natural selection for reproductive isolation
between Drosophila pseudoobscura and Drosophila persimilis. Evolution, 135-148;
Haldane, J. B. S. (1948). The theory of a cline. Journal of genetics, 48(3), 277-284.
IX. Sexual selection
16. Sexual selection. Zahavi, A. 1975. Mate selection - a selection of a handicap. J. Theor.
Biol. 53:205-214; Kirkpatrick, M., and Ryan, M.J. 1991. The evolution of mating
preferences and the paradox of the lek. Nature. 350:33-38; West-Eberhard, M. J. (1983).
Sexual selection, social competition, and speciation. Quarterly Review of Biology, 155183; Bateman AJ (1948) Intra-sexual selection in Drosophila. Heredity (Edinb) 2:349–
368; Gowaty, P. A., Kim, Y. K., & Anderson, W. W. (2012). No evidence of sexual
selection in a repetition of Bateman’s classic study of Drosophila melanogaster.
Proceedings of the National Academy of Sciences, 109(29), 11740-11745.
X. Hybridization
17. Hybridization. Anderson, E., & Stebbins Jr, G. L. (1954). Hybridization as an evolutionary
stimulus. Evolution, 378-388; Mallet, J. (2005). Hybridization as an invasion of the
genome. Trends in Ecology & Evolution, 20(5), 229-237; Seehausen, O. (2004).
Hybridization and adaptive radiation. Trends in ecology & evolution, 19(4), 198-207;
Rieseberg, L. H., Van Fossen, C., & Desrochers, A. M. (1995). Hybrid speciation
accompanied by genomic reorganization in wild sunflowers. Nature, 375(6529), 313-316.
18. The evolution of hybrid incompatibilities. Turelli, M., & Orr, H. A. (2000). Dominance,
epistasis and the genetics of postzygotic isolation. Genetics, 154(4), 1663-1679: Orr, H.
A., & Turelli, M. (2001). The evolution of postzygotic isolation: accumulating Dobzhansky‐
Muller incompatibilities. Evolution, 55(6), 1085-1094; Turelli, M., & Orr, H. A. (1995). The
dominance theory of Haldane's rule. Genetics, 140(1), 389-402; Turelli, M., & Begun, D.
J. (1997). Haldane's rule and X-chromosome size in Drosophila. Genetics, 147(4), 17991815; Orr, H. A., & Orr, L. H. (1996). Waiting for speciation: the effect of population
subdivision on the time to speciation. Evolution, 1742-1749; Orr, H. A. (1995). The
population genetics of speciation: the evolution of hybrid incompatibilities. Genetics,
139(4), 1805-1813.
XII. Genome evolution
19. Chromosomal rearrangements. Levene, H., & Dobzhansky, T. (1958). New evidence of
heterosis in naturally occurring inversion heterozygotes in Drosophila pseudoobscura.
Heredity, 12, 37-49; Carson, H. L. Chromosomal sequences and interisland colonizations
in Hawaiian Drosophila(1983) Genetics: 10: 465-482; Wilson, A. C., Sarich, V. M., &
Maxson, L. R. (1974). The importance of gene rearrangement in evolution: evidence from
studies on rates of chromosomal, protein, and anatomical evolution. Proceedings of the
National Academy of Sciences, 71(8), 3028-3030; Navarro, A., & Barton, N. H. (2003).
Chromosomal speciation and molecular divergence--accelerated evolution in rearranged
chromosomes. Science, 300(5617), 321-324.; Faria, R., & Navarro, A. (2010).
Chromosomal speciation revisited: rearranging theory with pieces of evidence. Trends in
Ecology & Evolution, 25(11), 660-669.
20. Genome size evolution. Sessions, S. K., & Larson, A. (1987). Developmental correlates
of genome size in plethodontid salamanders and their implications for genome evolution.
Evolution, 1239-1251; Lynch, M., and J. S. Conery. 2003. The origins of genome
complexity. Science 302: 1401-1404; Charlesworth, B., & Charlesworth, D. (2000). The
degeneration of Y chromosomes. Philosophical Transactions of the Royal Society of
London. Series B: Biological Sciences, 355(1403), 1563-1572; Petrov, D. A. (2001).
Evolution of genome size: new approaches to an old problem. Trends in Genetics, 17(1),
23-28; Eichler, E. E., & Sankoff, D. (2003). Structural dynamics of eukaryotic
chromosome evolution. Science, 301(5634), 793-797.
XIII. Cooperation and altruism
21. Trivers, R. L. (1971). The evolution of reciprocal altruism. Quarterly review of biology, 3557. Axelrod, R., & Hamilton, W. D. (1981). The evolution of
cooperation. Science,211(4489), 1390-1396. Smith, J. M. (1964). Group selection and kin
selection. Nature, 201, 1145-1147. Eberhard, M. J. W. (1975). The evolution of social
behavior by kin selection. Quarterly Review of Biology, 1-33. Wade, M. J. (1985). Soft
selection, hard selection, kin selection, and group selection. American naturalist, 61-73.
Wade, M. J. (1980). An experimental study of kin selection. Evolution, 844-855.
XIV. Phenotypic plasticity
22. Waddington, C. H. (1942). Canalization of development and the inheritance of acquired
characters. Nature, 150(3811), 563-565; Waddington, C. H. (1953). Genetic assimilation
of an acquired character. Evolution, 118-126; Via, S., Gomulkiewicz, R., De Jong, G.,
Scheiner, S. M., Schlichting, C. D., & Van Tienderen, P. H. (1995). Adaptive phenotypic
plasticity: consensus and controversy. Trends in Ecology & Evolution, 10(5), 212-217;
Via, S., & Lande, R. (1985). Genotype-environment interaction and the evolution of
phenotypic plasticity. Evolution, 505-522; Pigliucci, M. (2005). Evolution of phenotypic
plasticity: where are we going now?. Trends in Ecology & Evolution, 20(9), 481-486;
Price, T. D., Qvarnström, A., & Irwin, D. E. (2003). The role of phenotypic plasticity in
driving genetic evolution. Proceedings of the Royal Society of London. Series B:
Biological Sciences, 270(1523), 1433-1440.
XIV. Coevolution
23. Coevolution. Ehrlich, P.R. & Raven, P.H Butterflies and plants: a study in coevolution
(1964) Evolution: 18 pp 586-608. Holling, C. S. (1959). Some characteristics of simple
types of predation and parasitism. The Canadian Entomologist, 91(07), 385-398. Janzen,
D. H. (1980). When is it coevolution. Evolution, 34(3), 611-612. Stebbins, G. L. (1981).
Coevolution of grasses and herbivores. Annals of the Missouri Botanical Garden, 75-86;
Connell, J. H. (1980). Diversity and the coevolution of competitors, or the ghost of
competition past. Oikos, 131-138. Janzen, D. H. (1966). Coevolution of mutualism
between ants and acacias in Central America. Evolution, 249-275; Slatkin, M., & Smith, J.
M. (1979). Models of coevolution. Quarterly Review of Biology, 233-263.
24. Red Queen and conflict. . Van Valen. (1973). A new evolutionary law. Evolutionary
Theory 1: 1—30; van Valen, L. (1976). The red queen lives. Nature, 260, 575. Hallam, A.
(1976). The Red Queen dethroned. Nature, 259, 12-13. Chr, N. (1979). Where have all
the species gone? On the nature of extinction and the Red Queen hypothesis. Oikos,
196-227. Salthe, S. N. (1975). Some comments on Van Valen's law of extinction.
Paleobiology, 356-358. Smith, J. M., & Price, G. R. (1973). The Logic of Animal
Conflict. Nature, 246, 15. Chapman, T., Arnqvist, G., Bangham, J., & Rowe, L. (2003).
Sexual conflict. Trends in Ecology & Evolution, 18(1), 41-47
Multilevel selection
25. Species selection. Stanley, S. M. (1975). A theory of evolution above the species level.
Proceedings of the National Academy of sciences, 72(2), 646-650; Gould, N. E. S. J.
(2014). Punctuated equilibria: an alternative to phyletic gradualism. Essential Readings in
Evolutionary Biology, 239; Jablonski, D. (2008). Species selection: theory and data.
Annual Review of Ecology, Evolution, and Systematics, 39, 501-524; Rabosky, D. L., &
McCune, A. R. (2010). Reinventing species selection with molecular phylogenies. Trends
in ecology & evolution, 25(2), 68-74.
26. Below the individual level: Rispe, C., & Moran, N. A. (2000). Accumulation of deleterious
mutations in endosymbionts: Muller’s ratchet with two levels of selection. The American
Naturalist, 156(4), 425-441. Orgel, L. E., & Crick, F. H. (1980). Selfish DNA: the ultimate
parasite. Nature, 284, 604-607. Doolittle, W. F., & Sapienza, C. (1980). Selfish genes,
the phenotype paradigm and genome evolution. Nature, 284(5757), 601-3. Hickey 1982
Selfish DNA: sexually-transmitted parasite.
Conclusions
27. On the new for a new synthesis. Carroll, R. L. (2000). Towards a new evolutionary
synthesis. Trends in ecology & evolution, 15(1), 27-32. Mayr, E., & Provine, W. B. (Eds.).
(1998). The evolutionary synthesis: perspectives on the unification of biology. Harvard
University Press. Pigliucci, M. (2007). Do we need an extended evolutionary synthesis?.
Evolution, 61(12), 2743-2749. Koonin, E. V. (2009). The< i> Origin</i> at 150: is a new
evolutionary synthesis in sight?. Trends in genetics, 25(11), 473-475. Carroll, S. B.
(2008). Evo-devo and an expanding evolutionary synthesis: a genetic theory of
morphological evolution. Cell, 134(1), 25-36.