Biological Evolution

• The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes
  • "Many of these factors, and especially adaptation and speciation, are key components of the evolutionary phenomenon of adaptive radiation, that is, the rapid evolution of an array of species through adaptive diversification into a variety of ecological niches."
  • "Key feature of adaptive radiation is that new species emerge rapidly from a common ancestor as a consequence of their adaptation to distinct ecological niches, resulting in a correlation between adaptive phenotypes and the environment."
• Rosser, N., Seixas, F., Queste, L.M., Cama, B., Mori-Pezo, R., Kryvokhyzha, D., Nelson, M., Waite-Hudson, R., Goringe, M., Costa, M. and Elias, M., 2024. Hybrid speciation driven by multilocus introgression of ecological traits. Nature, pp.1-7.
  • "Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species." ... "The question of how new species originate and adapt to environments is fundamental to evolutionary biology. Hybridization might have a key role in establishing barriers to gene flow by creating new allelic combinations."
  • "How populations transition to new fitness peaks remains an unanswered question, but adaptive introgression provides a possible route."
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Heliconius Genome Consortium, 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487(7405), pp.94-98.
  • "Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species."
  • "We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation."
• 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.
• 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.
• Gavrilets, S. and Losos, J.B., 2009. Adaptive radiation: Contrasting theory with data. Science, 323(5915), pp.732-737.
• 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.
• 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."
• 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.
• 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.
• 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.
• Metzgar, D. and Wills, C., 2000. Evidence for the adaptive evolution of mutation rates. Cell, 101(6), pp.581-584.
• 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.
• Hanski, I., 1998. Metapopulation dynamics. Nature, 396(6706), pp.41-49.
• 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.
• Smith, J.M. and Szathmary, E., 1997. The major transitions in evolution. OUP Oxford.
• https://content.time.com/time/subscriber/article/0,33009,983789-1,00.html
• Szathmáry, E. and Smith, J.M., 1995. The major evolutionary transitions. Nature, 374(6519), pp.227-232.
• Hinton, G.E. and Nowlan, S.J., 1987. How learning can guide evolution. Complex Systems, 1(3), pp.495-502.
• 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.
• 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.
• 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.
• Schrödinger, E., 1944. What is life? The physical aspect of the living cell and mind. Cambridge: Cambridge University Press.
• 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.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., 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.