Biological Evolution

2024

• Backman, T., et al., 2024. A phage tail–like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria. Science, 384(6701), p.eado0713. [ metapopulation ]
• Sommer-Trembo, C., et al., 2024. The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes. Science, 384(6694), pp.470-475.
• Rosser, N., et al., 2024. Hybrid speciation driven by multilocus introgression of ecological traits. Nature, pp.1-7.
• Gitschlag, B.L., Pereira, C.V., Held, J.P., McCandlish, D.M. and Patel, M.R., 2024. Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans. Nature Communications, 15(1), p.8237.
• Melissa, M.J. and Desai, M.M., 2024. A dynamical limit to evolutionary adaptation. Proceedings of the National Academy of Sciences, 121(4), p.e2312845121.

2023

• Klein, R.G., 2023. Profile of Svante Pääbo: 2022 Nobel laureate in physiology or medicine. Proceedings of the National Academy of Sciences, 120(1), p.e2217025119.
• Su, Q., McAvoy, A. and Plotkin, J.B., 2023. Strategy evolution on dynamic networks. Nature Computational Science, 3(9), pp.763-776. [ Evolution of Cooperation ]
• Tkadlec, J., Kaveh, K., Chatterjee, K. and Nowak, M.A., 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society Interface, 20(208), p.20230355.
• Haight, J.D., et al., 2023. Urbanization, climate and species traits shape mammal communities from local to continental scales. Nature Ecology & Evolution, 7(10), pp.1654-1666. [ multi-scale biodiversity ]
• Rolland, J., et al., 2023. Conceptual and empirical bridges between micro- and macroevolution. Nature Ecology & Evolution, 7(8), pp.1181-1193.
• Yagoobi, S., Sharma, N. and Traulsen, A., 2023. Categorizing update mechanisms for graph-structured metapopulations. Journal of the Royal Society Interface, 20(200), p.20220769.
• Cooney, D.B., Levin, S.A., Mori, Y. and Plotkin, J.B., 2023. Evolutionary dynamics within and among competing groups. Proceedings of the National Academy of Sciences, 120(20), p.e2216186120.
• Wilson, D.S., Madhavan, G., Gelfand, M.J., Hayes, S.C., Atkins, P.W. and Colwell, R.R., 2023. Multilevel cultural evolution: From new theory to practical applications. Proceedings of the National Academy of Sciences, 120(16), p.e2218222120.
• Davison, D.R. and Michod, R.E., 2023. Steps to individuality in biology and culture. Philosophical Transactions of the Royal Society B, 378(1872), p.20210407.
• Tu, C., D’Odorico, P., Li, Z. and Suweis, S., 2023. The emergence of cooperation from shared goals in the governance of common-pool resources. Nature Sustainability, 6(2), pp.139-147.
• L. Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R. and Godinho, R., 2023. North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nature Ecology & Evolution, 7(8), pp.1267-1286.
• Cooney, D.B., Rossine, F.W., Morris, D.H. and Levin, S.A., 2022. A PDE model for protocell evolution and the origin of chromosomes via multilevel selection. Bulletin of Mathematical Biology, 84(10), p.109.
• Herron, M.D., Conlin, P.L. and Ratcliff, W.C. eds., 2022. The evolution of multicellularity. CRC Press.
• Hench, K., Helmkampf, M., McMillan, W.O. and Puebla, O., 2022. Rapid radiation in a highly diverse marine environment. Proceedings of the National Academy of Sciences, 119(4), p.e2020457119.
  • "Adaptive radiation is driven by ecological opportunity, whereby newly accessible niches provide potential for diversification."
  • "Genomic analysis suggests that color pattern diversity is generated by different combinations of alleles at a few genes with large effect."
  • "The historically high effective population size of hamlets provides a rich genomic substrate from which hybridization can rapidly assemble new phenotypic variation. This attribute is emerging as the common denominator to a variety of radiations on land and in the sea."
• Stephan, T., Burgess, S.M., Cheng, H., Danko, C.G., Gill, C.A., Jarvis, E.D., Koepfli, K.P., Koltes, J.E., Lyons, E., Ronald, P. and Ryder, O.A., 2022. Darwinian genomics and diversity in the tree of life. Proceedings of the National Academy of Sciences, 119(4), p.e2115644119.
• Vanchurin, V., Wolf, Y.I., Katsnelson, M.I. and Koonin, E.V., 2022. Toward a theory of evolution as multilevel learning. Proceedings of the National Academy of Sciences, 119(6), p.e2120037119.
  • Persi, E., Wolf, Y.I., Karamycheva, S., Makarova, K.S. and Koonin, E.V., 2023. Compensatory relationship between low-complexity regions and gene paralogy in the evolution of prokaryotes. Proceedings of the National Academy of Sciences, 120(16), p.e2300154120.
    • "Compensatory relationships between short-term and longer-term mechanisms are likely to represent a universal feature of the evolutionary process in all kinds of biological contexts."
  • Vanchurin, V., Wolf, Y.I., Koonin, E.V. and Katsnelson, M.I., 2022. Thermodynamics of evolution and the origin of life. Proceedings of the National Academy of Sciences, 119(6), p.e2120042119.
  • Persi, E., Wolf, Y.I., Horn, D., Ruppin, E., Demichelis, F., Gatenby, R.A., Gillies, R.J. and Koonin, E.V., 2021. Mutation–selection balance and compensatory mechanisms in tumour evolution. Nature Reviews Genetics, 22(4), pp.251-262.
  • Frank, S.A., 2012. Natural selection. V. How to read the fundamental equations of evolutionary change in terms of information theory. Journal of Evolutionary Biology, 25(12), pp.2377-2396.
• Ronco, F., Matschiner, M., Böhne, A., Boila, A., Büscher, H.H., El Taher, A., Indermaur, A., Malinsky, M., Ricci, V., Kahmen, A. and Jentoft, S., 2021. Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature, 589(7840), pp.76-81.

2020

• Urban, M.C., Strauss, S.Y., Pelletier, F., Palkovacs, E.P., Leibold, M.A., Hendry, A.P., De Meester, L., Carlson, S.M., Angert, A.L. and Giery, S.T., 2020. Evolutionary origins for ecological patterns in space. Proceedings of the National Academy of Sciences, 117(30), pp.17482-17490.
• Zheng, J., Guo, N. and Wagner, A., 2020. Selection enhances protein evolvability by increasing mutational robustness and foldability. Science, 370(6521), p.eabb5962.
• McGee, M.D., Borstein, S.R., Meier, J.I., Marques, D.A., Mwaiko, S., Taabu, A., Kishe, M.A., O’Meara, B., Bruggmann, R., Excoffier, L. and Seehausen, O., 2020. The ecological and genomic basis of explosive adaptive radiation. Nature, 586(7827), pp.75-79.
• Yu, L., Boström, C., Franzenburg, S., Bayer, T., Dagan, T. and Reusch, T.B., 2020. Somatic genetic drift and multilevel selection in a clonal seagrass. Nature Ecology & Evolution, 4(7), pp.952-962.
• Nande, A., Ferdowsian, A., Lubin, E., Yoeli, E. and Nowak, M., 2020. DyPy: A python library for simulating matrix-form games. arXiv preprint arXiv:2007.13815.
• Segar, S.T., Fayle, T.M., Srivastava, D.S., Lewinsohn, T.M., Lewis, O.T., Novotny, V., Kitching, R.L. and Maunsell, S.C., 2020. The role of evolution in shaping ecological networks. Trends in Ecology & Evolution, 35(5), pp.454-466.

2010s

2019

• Leibold, M.A., Urban, M.C., De Meester, L., Klausmeier, C.A. and Vanoverbeke, J., 2019. Regional neutrality evolves through local adaptive niche evolution. Proceedings of the National Academy of Sciences, 116(7), pp.2612-2617.
• Birch, J., 2019. Are kin and group selection rivals or friends?. Current Biology, 29(11), pp.R433-R438.
• Van Vliet, S. and Doebeli, M., 2019. The role of multilevel selection in host microbiome evolution. Proceedings of the National Academy of Sciences, 116(41), pp.20591-20597.
• Czégel, D., Giaffar, H., Zachar, I., Tenenbaum, J.B. and Szathmáry, E., 2019. Evolutionary implementation of Bayesian computations. BioRxiv, p.685842.
• Czégel, D., Zachar, I. and Szathmáry, E., 2019. Multilevel selection as Bayesian inference, major transitions in individuality as structure learning. Royal Society Open Science, 6(8), p.190202.
• Edelman, N.B., Frandsen, P.B., Miyagi, M., Clavijo, B., Davey, J., Dikow, R.B., García-Accinelli, G., Van Belleghem, S.M., Patterson, N., Neafsey, D.E. and Challis, R., 2019. Genomic architecture and introgression shape a butterfly radiation. Science, 366(6465), pp.594-599.
• Wolf, Y.I., Katsnelson, M.I. and Koonin, E.V., 2018. Physical foundations of biological complexity. Proceedings of the National Academy of Sciences, 115(37), pp.E8678-E8687.
• Lamichhaney, S., Han, F., Webster, M.T., Andersson, L., Grant, B.R. and Grant, P.R., 2018. Rapid hybrid speciation in Darwin’s finches. Science, 359(6372), pp.224-228.

2017

• Allen, B., Lippner, G., Chen, Y.T., Fotouhi, B., Momeni, N., Yau, S.T. and Nowak, M.A., 2017. Evolutionary dynamics on any population structure. Nature, 544(7649), pp.227-230.

2015

• Szathmáry, E., 2015. Toward major evolutionary transitions theory 2.0. Proceedings of the National Academy of Sciences, 112(33), pp.10104-10111.
• West, S.A., Fisher, R.M., Gardner, A. and Kiers, E.T., 2015. Major evolutionary transitions in individuality. Proceedings of the National Academy of Sciences, 112(33), pp.10112-10119.
• Markvoort, A.J., Sinai, S. and Nowak, M.A., 2014. Computer simulations of cellular group selection reveal mechanism for sustaining cooperation. Journal of Theoretical Biology, 357, pp.123-133.
• Goodnight, C., 2013. On multilevel selection and kin selection: Contextual analysis meets direct fitness. Evolution, 67(6), pp.1539-1548.
• Heliconius Genome Consortium, 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487(7405), pp.94-98.
• Woods, R.J., Barrick, J.E., Cooper, T.F., Shrestha, U., Kauth, M.R. and Lenski, R.E., 2011. Second-order selection for evolvability in a large Escherichia coli population. Science, 331(6023), pp.1433-1436.
• Sachs, J.L., Skophammer, R.G. and Regus, J.U., 2011. Evolutionary transitions in bacterial symbiosis. Proceedings of the National Academy of Sciences, 108, pp.10800-10807.

2010

• Lynch, M., 2010. Evolution of the mutation rate. Trends in Genetics, 26(8), pp.345-352.
• Vasas, V., Szathmáry, E. and Santos, M., 2010. Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life. Proceedings of the National Academy of Sciences, 107(4), pp.1470-1475.
• Nowak, M.A., Tarnita, C.E. and Wilson, E.O., 2010. The evolution of eusociality. Nature, 466(7310), pp.1057-1062.
• Wade, M.J., Wilson, D.S., Goodnight, C., Taylor, D., Bar-Yam, Y., de Aguiar, M.A., Stacey, B., Werfel, J., Hoelzer, G.A., Brodie III, E.D. and Fields, P., 2010. Multilevel and kin selection in a connected world. Nature, 463(7283), pp.E8-E9.

2000s

2009

• Reznick, D.N. and Ricklefs, R.E., 2009. Darwin's bridge between microevolution and macroevolution. Nature, 457(7231), pp.837-842.
• Gavrilets, S. and Losos, J.B., 2009. Adaptive radiation: Contrasting theory with data. Science, 323(5915), pp.732-737.

2008

• Khila, A. and Abouheif, E., 2008. Reproductive constraint is a developmental mechanism that maintains social harmony in advanced ant societies. Proceedings of the National Academy of Sciences, 105(46), pp.17884-17889.
• Lehmann, L., Keller, L., West, S. and Roze, D., 2007. Group selection and kin selection: Two concepts but one process. Proceedings of the National Academy of Sciences, 104(16), pp.6736-6739.
• Lynch, M., 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proceedings of the National Academy of Sciences, 104(suppl_1), pp.8597-8604.
• Mallet, J., 2007. Hybrid speciation. Nature, 446(7133), pp.279-283.
  • "Today, armed with new and abundant molecular marker data, biologists increasingly find new examples where hybridization seems to facilitate speciation and adaptive radiation in animals, as well as plants."
  • "Hybrid speciation is only possible if reproductive isolation is weak; if hybrids are intermediate, hybrid species will be even more weakly isolated."
  • "Most speciation involves natural selection; natural selection requires genetic variation; genetic variation is enhanced by hybridization; and hybridization and introgression between species is a regular occurrence, especially in rapidly radiating groups."
• Wilson, D.S. and Wilson, E.O., 2007. Rethinking the theoretical foundation of sociobiology. Quarterly Review of Biology, 82(4), pp.327-348.
• West, S.A., Griffin, A.S. and Gardner, A., 2007. Social semantics: Altruism, cooperation, mutualism, strong reciprocity and group selection. Journal of Evolutionary Biology, 20(2), pp.415-432.

2006

• Michod, R.E., 2006. The group covariance effect and fitness trade-offs during evolutionary transitions in individuality. Proceedings of the National Academy of Sciences, 103(24), pp.9113-9117.
• Okasha, S., 2006. Evolution and the levels of selection. Clarendon Press.
• Okasha, S., 2005. Multilevel selection and the major transitions in evolution. Philosophy of Science, 72(5), pp.1013-1025.

2004

• Chow, S.S., Wilke, C.O., Ofria, C., Lenski, R.E. and Adami, C., 2004. Adaptive radiation from resource competition in digital organisms. Science, 305(5680), pp.84-86.
• Werfel, J. and Bar-Yam, Y., 2004. The evolution of reproductive restraint through social communication. Proceedings of the National Academy of Sciences, 101(30), pp.11019-11024. [ metapopulation + group selection ]
• Leibold, M.A., et al., 2004. The metacommunity concept: A framework for multi‐scale community ecology. Ecology Letters, 7(7), pp.601-613. [ metacommunity ]

2003

• Lynch, M. and Conery, J.S., 2003. The origins of genome complexity. Science, 302(5649), pp.1401-1404.
• Rieseberg, L.H., Raymond, O., Rosenthal, D.M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J.L., Schwarzbach, A.E., Donovan, L.A. and Lexer, C., 2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science, 301(5637), pp.1211-1216.
• Partridge, L. and Barton, N.H., 2000. Evolving evolvability. Nature, 407(6803), pp.457-458.
• Swenson, W., Wilson, D.S. and Elias, R., 2000. Artificial ecosystem selection. Proceedings of the National Academy of Sciences, 97(16), pp.9110-9114.
• Metzgar, D. and Wills, C., 2000. Evidence for the adaptive evolution of mutation rates. Cell, 101(6), pp.581-584.

1990s

• Arjan G, J., Visser, M.D., Zeyl, C.W., Gerrish, P.J., Blanchard, J.L. and Lenski, R.E., 1999. Diminishing returns from mutation supply rate in asexual populations. Science, 283(5400), pp.404-406.
• Dickinson, W.J. and Seger, J., 1999. Cause and effect in evolution. Nature, 399(6731), pp.30-30.
• Gonzalez, A., Lawton, J.H., Gilbert, F.S., Blackburn, T.M. and Evans-Freke, I., 1998. Metapopulation dynamics, abundance, and distribution in a microecosystem. Science, 281(5385), pp.2045-2047.
• Hanski, I., 1998. Metapopulation dynamics. Nature, 396(6706), pp.41-49.
  • https://www.nature.com/articles/534180a
  • Saccheri, I., Kuussaari, M., Kankare, M., Vikman, P., Fortelius, W. and Hanski, I., 1998. Inbreeding and extinction in a butterfly metapopulation. Nature, 392(6675), pp.491-494.
  • Hanski, I. and Gyllenberg, M., 1997. Uniting two general patterns in the distribution of species. Science, 275(5298), pp.397-400.
• Rosenberg, S.M., Thulin, C. and Harris, R.S., 1998. Transient and heritable mutators in adaptive evolution in the lab and in nature. Genetics, 148(4), pp.1559-1566.
• Wilson, D.S., 1997. Human groups as units of selection. Science, 276(5320), pp.1816-1817.
• Smith, J.M. and Szathmary, E., 1997. The major transitions in evolution. Oxford University Press.
  • Szathmáry, E. and Smith, J.M., 1995. The major evolutionary transitions. Nature, 374(6519), pp.227-232.
• Wilson, D.S. and Sober, E., 1994. Reintroducing group selection to the human behavioral sciences. Behavioral and Brain Sciences, 17(4), pp.585-608.

1980s

• Hinton, G.E. and Nowlan, S.J., 1987. How learning can guide evolution. Complex Systems, 1(3), pp.495-502.
• Gould, S.J., 1982. Darwinism and the expansion of evolutionary theory. Science, 216(4544), pp.380-387.

1970s

• Wilson, D.S., 1976. Evolution on the level of communities. Science, 192(4246), pp.1358-1360.
• Stanley, S.M., 1975. A theory of evolution above the species level. Proceedings of the National Academy of Sciences, 72(2), pp.646-650.

1960s

• Levins, R., 1969. Some demographic and genetic consequences of environmental heterogeneity for biological control. Bulletin of the ESA, 15(3), pp.237-240.
• Sagan, L., 1967. On the origin of mitosing cells. Journal of Theoretical Biology, 14(3), pp.225-IN6.
• Smith, J.M., 1964. Group selection and kin selection. Nature, 201(4924), pp.1145-1147.
• Wynne-Edwards, V.C., 1963. Intergroup selection in the evolution of social systems. Nature, 200(4907), pp.623-626.
  • Wynne-Edwards, V.C., 1962. Animal dispersion in relation to social behaviour. Oliver and Boyd.
• Mayr, E., 1961. Cause and effect in biology: Kinds of causes, predictability, and teleology are viewed by a practicing biologist. Science, 134(3489), pp.1501-1506.
• Hamilton, W.D., 1964. The genetical evolution of social behaviour. II. Journal of Theoretical Biology, 7(1), pp.17-52.

1940s

• Schrödinger, E., 1944. What is life? The physical aspect of the living cell and mind. Cambridge University Press.
• Huxley, J., 1942. Evolution: The modern synthesis.

1930s

• Wright, S., 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. In Proceedings of Sixth International Congress of Genetics (Vol. 1, pp. 356-366).
  • https://www.nasonline.org/wp-content/uploads/2024/06/wright-sewall.pdf
  • https://www.nature.com/articles/332492a0
  • https://www.nasonline.org/member-directory/deceased-members/48919.html
  • https://royalsocietypublishing.org/doi/10.1098/rsbm.1990.0044
  • https://www.annualreviews.org/doi/10.1146/annurev.ge.23.120189.000245
  • https://www.nytimes.com/1988/03/04/obituaries/sewall-wright-98-who-formed-mathematical-basis-for-evolution.html
  • Wright, S., 1986. Evolution: Selected papers. University of Chicago Press.
  • Wright, S., 1984. Evolution and the genetics of populations, volume 4: Variability within and among natural populations. University of Chicago Press.
  • Wright, S., 1982. Character change, speciation, and the higher taxa. Evolution, pp.427-443.
  • Wright, S., 1945. Tempo and mode in evolution: A critical review. Ecology, 26(4), pp.415-419.
  • Wright, S., 1940. Breeding structure of populations in relation to speciation. American Naturalist, 74(752), pp.232-248.
  • Wright, S., 1931. Evolution in Mendelian populations. Genetics, 16(2), p.97.

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