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Journal articles on the topic 'Adaptive or fitness landscapes'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Srivastava, Malvika, and Joshua L. Payne. "On the incongruence of genotype-phenotype and fitness landscapes." PLOS Computational Biology 18, no. 9 (2022): e1010524. http://dx.doi.org/10.1371/journal.pcbi.1010524.

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The mapping from genotype to phenotype to fitness typically involves multiple nonlinearities that can transform the effects of mutations. For example, mutations may contribute additively to a phenotype, but their effects on fitness may combine non-additively because selection favors a low or intermediate value of that phenotype. This can cause incongruence between the topographical properties of a fitness landscape and its underlying genotype-phenotype landscape. Yet, genotype-phenotype landscapes are often used as a proxy for fitness landscapes to study the dynamics and predictability of evol

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Zheng, Liming, and Shiqi Luo. "Adaptive Differential Evolution Algorithm Based on Fitness Landscape Characteristic." Mathematics 10, no. 9 (2022): 1511. http://dx.doi.org/10.3390/math10091511.

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Differential evolution (DE) is a simple, effective, and robust algorithm, which has demonstrated excellent performance in dealing with global optimization problems. However, different search strategies are designed for different fitness landscape conditions to find the optimal solution, and there is not a single strategy that can be suitable for all fitness landscapes. As a result, developing a strategy to adaptively steer population evolution based on fitness landscape is critical. Motivated by this fact, in this paper, a novel adaptive DE based on fitness landscape (FL-ADE) is proposed, whic

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Trujillo, Leonardo, Paul Banse, and Guillaume Beslon. "Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes." PLOS Computational Biology 18, no. 10 (2022): e1010647. http://dx.doi.org/10.1371/journal.pcbi.1010647.

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Molecular evolution is often conceptualised as adaptive walks on rugged fitness landscapes, driven by mutations and constrained by incremental fitness selection. It is well known that epistasis shapes the ruggedness of the landscape’s surface, outlining their topography (with high-fitness peaks separated by valleys of lower fitness genotypes). However, within the strong selection weak mutation (SSWM) limit, once an adaptive walk reaches a local peak, natural selection restricts passage through downstream paths and hampers any possibility of reaching higher fitness values. Here, in addition to

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Reia, Sandro M., and Paulo R. A. Campos. "Analysis of statistical correlations between properties of adaptive walks in fitness landscapes." Royal Society Open Science 7, no. 1 (2020): 192118. http://dx.doi.org/10.1098/rsos.192118.

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The fitness landscape metaphor has been central in our way of thinking about adaptation. In this scenario, adaptive walks are idealized dynamics that mimic the uphill movement of an evolving population towards a fitness peak of the landscape. Recent works in experimental evolution have demonstrated that the constraints imposed by epistasis are responsible for reducing the number of accessible mutational pathways towards fitness peaks. Here, we exhaustively analyse the statistical properties of adaptive walks for two empirical fitness landscapes and theoretical NK landscapes. Some general concl

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Li, Ye, and Claus O. Wilke. "Digital Evolution in Time-Dependent Fitness Landscapes." Artificial Life 10, no. 2 (2004): 123–34. http://dx.doi.org/10.1162/106454604773563559.

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We study the response of populations of digital organisms that adapt to a time-varying (periodic) fitness landscape of two oscillating peaks. We corroborate in general predictions from quasi-species theory in dynamic landscapes, such as adaptation to the average fitness landscape at small periods (high frequency) and quasistatic adaptation at large periods (low frequency). We also observe adaptive phase shifts (time lags between a change in the fitness landscape and an adaptive change in the population) that indicate a low-pass filter effect, in agreement with existing theory. Finally, we witn

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Bajić, Djordje, Jean C. C. Vila, Zachary D. Blount, and Alvaro Sánchez. "On the deformability of an empirical fitness landscape by microbial evolution." Proceedings of the National Academy of Sciences 115, no. 44 (2018): 11286–91. http://dx.doi.org/10.1073/pnas.1808485115.

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A fitness landscape is a map between the genotype and its reproductive success in a given environment. The topography of fitness landscapes largely governs adaptive dynamics, constraining evolutionary trajectories and the predictability of evolution. Theory suggests that this topography can be deformed by mutations that produce substantial changes to the environment. Despite its importance, the deformability of fitness landscapes has not been systematically studied beyond abstract models, and little is known about its reach and consequences in empirical systems. Here we have systematically cha

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Bertram, Jason, and Joanna Masel. "Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes." Genetics 214, no. 4 (2020): 1047–57. http://dx.doi.org/10.1534/genetics.120.302815.

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The “fitness” landscapes of genetic sequences are characterized by high dimensionality and “ruggedness” due to sign epistasis. Ascending from low to high fitness on such landscapes can be difficult because adaptive trajectories get stuck at low-fitness local peaks. Compounding matters, recent theoretical arguments have proposed that extremely long, winding adaptive paths may be required to reach even local peaks: a “maze-like” landscape topography. The extent to which peaks and mazes shape the mode and tempo of evolution is poorly understood, due to empirical limitations and the abstractness o

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Cervera, Héctor, Jasna Lalić, and Santiago F. Elena. "Effect of Host Species on Topography of the Fitness Landscape for a Plant RNA Virus." Journal of Virology 90, no. 22 (2016): 10160–69. http://dx.doi.org/10.1128/jvi.01243-16.

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ABSTRACTAdaptive fitness landscapes are a fundamental concept in evolutionary biology that relate the genotypes of individuals to their fitness. In the end, the evolutionary fate of evolving populations depends on the topography of the landscape, that is, the numbers of accessible mutational pathways and possible fitness peaks (i.e., adaptive solutions). For a long time, fitness landscapes were only theoretical constructions due to a lack of precise information on the mapping between genotypes and phenotypes. In recent years, however, efforts have been devoted to characterizing the properties

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Beck, Richard J., and Noemi Andor. "Abstract PR018: Adaptive local fitness landscapes for aneuploid karyotypes." Cancer Research 84, no. 3_Supplement_2 (2024): PR018. http://dx.doi.org/10.1158/1538-7445.canevol23-pr018.

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Abstract Aneuploidy, which occurs in most solid tumors, dramatically alters the expression of many genes which in turn has broad phenotypic effects. Recent evidence suggests that specific aneuploid karyotypes confer a selective advantage. However, various questions remain unanswered regarding the magnitude of these selective advantages, as well as the repeatability and predictability of karyotype evolution. We developed ALFA-K (Adaptive Local Fitness landscapes for Aneuploid Karotypes) – the first approach to infer karyotype fitness landscapes in a context-dependent manner. Based on the dynami

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Wilke, Claus O., and Thomas Martinetz. "Adaptive walks on time-dependent fitness landscapes." Physical Review E 60, no. 2 (1999): 2154–59. http://dx.doi.org/10.1103/physreve.60.2154.

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11

Hadany, L., and T. Beker. "Fitness-associated recombination on rugged adaptive landscapes." Journal of Evolutionary Biology 16, no. 5 (2003): 862–70. http://dx.doi.org/10.1046/j.1420-9101.2003.00586.x.

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12

Hendry, Andrew P., Peter R. Grant, B. Rosemary Grant, Hugh A. Ford, Mark J. Brewer, and Jeffrey Podos. "Possible human impacts on adaptive radiation: beak size bimodality in Darwin's finches." Proceedings of the Royal Society B: Biological Sciences 273, no. 1596 (2006): 1887–94. http://dx.doi.org/10.1098/rspb.2006.3534.

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Adaptive radiation is facilitated by a rugged adaptive landscape, where fitness peaks correspond to trait values that enhance the use of distinct resources. Different species are thought to occupy the different peaks, with hybrids falling into low-fitness valleys between them. We hypothesize that human activities can smooth adaptive landscapes, increase hybrid fitness and hamper evolutionary diversification. We investigated this possibility by analysing beak size data for 1755 Geospiza fortis measured between 1964 and 2005 on the island of Santa Cruz, Galápagos. Some populations of this specie

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Latrille, Thibault, Julien Joseph, Diego A. Hartasánchez, and Nicolas Salamin. "Estimating the proportion of beneficial mutations that are not adaptive in mammals." PLOS Genetics 20, no. 12 (2024): e1011536. https://doi.org/10.1371/journal.pgen.1011536.

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Mutations can be beneficial by bringing innovation to their bearer, allowing them to adapt to environmental change. These mutations are typically unpredictable since they respond to an unforeseen change in the environment. However, mutations can also be beneficial because they are simply restoring a state of higher fitness that was lost due to genetic drift in a stable environment. In contrast to adaptive mutations, these beneficial non-adaptive mutations can be predicted if the underlying fitness landscape is stable and known. The contribution of such non-adaptive mutations to molecular evolu

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Cervera, Héctor, Jasna Lalić, and Santiago F. Elena. "Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations." Proceedings of the Royal Society B: Biological Sciences 283, no. 1836 (2016): 20160984. http://dx.doi.org/10.1098/rspb.2016.0984.

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Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an

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15

Wilson, David Sloan, and Alexandra Wells. "Radical Epistasis and the Genotype-Phenotype Relationship." Artificial Life 2, no. 1 (1994): 117–28. http://dx.doi.org/10.1162/artl.1994.2.1.117.

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Models of evolution often assume that the offspring of two genotypes, which are genetically intermediate by definition, are also phenotypically intermediate. The continuity between genotype and phenotype interferes with the process of evolution on multipeaked adaptive landscapes because the progeny of genotypes that lie on separate adaptive peaks fall into valleys of low fitness. This problem can be solved by epistasis, which disrupts the continuity between genotype and phenotype. In a five-locus sexual haploid model with maximum epistasis, natural selection in multipeak landscapes evolves a s

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Niklas, Karl J. "Effects of hypothetical developmental barriers and abrupt environmental changes on adaptive walks in a computer-generated domain for early vascular land plants." Paleobiology 23, no. 1 (1997): 63–76. http://dx.doi.org/10.1017/s009483730001664x.

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Computer-generated searches through hypothetical fitness landscapes for progressively more fit variants were used to assess the effects of developmental barriers (mimicked by barring specific types of morphological transformations) and abruptly shifting environmental conditions (mimicked by sudden shifts in how fitness was defined) on the number and accessibility of optimal phenotypes. Relative fitness was defined in terms of maximizing light interception, mechanical stability, or reproductive success, or minimizing surface area, or optimizing the performance of various combinations of these t

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Laughlin, Daniel C., and Julie Messier. "Fitness of multidimensional phenotypes in dynamic adaptive landscapes." Trends in Ecology & Evolution 30, no. 8 (2015): 487–96. http://dx.doi.org/10.1016/j.tree.2015.06.003.

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18

Pfaender, Jobst, Renny K. Hadiaty, Ulrich K. Schliewen, and Fabian Herder. "Rugged adaptive landscapes shape a complex, sympatric radiation." Proceedings of the Royal Society B: Biological Sciences 283, no. 1822 (2016): 20152342. http://dx.doi.org/10.1098/rspb.2015.2342.

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Strong disruptive ecological selection can initiate speciation, even in the absence of physical isolation of diverging populations. Species evolving under disruptive ecological selection are expected to be ecologically distinct but, at least initially, genetically weakly differentiated. Strong selection and the associated fitness advantages of narrowly adapted individuals, coupled with assortative mating, are predicted to overcome the homogenizing effects of gene flow. Theoretical plausibility is, however, contrasted by limited evidence for the existence of rugged adaptive landscapes in nature

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19

Heckmann, David. "Modelling metabolic evolution on phenotypic fitness landscapes: a case study on C4 photosynthesis." Biochemical Society Transactions 43, no. 6 (2015): 1172–76. http://dx.doi.org/10.1042/bst20150148.

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How did the complex metabolic systems we observe today evolve through adaptive evolution? The fitness landscape is the theoretical framework to answer this question. Since experimental data on natural fitness landscapes is scarce, computational models are a valuable tool to predict landscape topologies and evolutionary trajectories. Careful assumptions about the genetic and phenotypic features of the system under study can simplify the design of such models significantly. The analysis of C4 photosynthesis evolution provides an example for accurate predictions based on the phenotypic fitness la

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20

Arias, Mónica, Yann le Poul, Mathieu Chouteau, et al. "Crossing fitness valleys: empirical estimation of a fitness landscape associated with polymorphic mimicry." Proceedings of the Royal Society B: Biological Sciences 283, no. 1829 (2016): 20160391. http://dx.doi.org/10.1098/rspb.2016.0391.

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Characterizing fitness landscapes associated with polymorphic adaptive traits enables investigation of mechanisms allowing transitions between fitness peaks. Here, we explore how natural selection can promote genetic mechanisms preventing heterozygous phenotypes from falling into non-adaptive valleys. Polymorphic mimicry is an ideal system to investigate such fitness landscapes, because the direction of selection acting on complex mimetic colour patterns can be predicted by the local mimetic community composition. Using more than 5000 artificial butterflies displaying colour patterns exhibited

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de Lima Filho, J. A., F. G. B. Moreira, P. R. A. Campos, and Viviane M. de Oliveira. "Adaptive walks on correlated fitness landscapes with heterogeneous connectivities." Journal of Statistical Mechanics: Theory and Experiment 2012, no. 02 (2012): P02014. http://dx.doi.org/10.1088/1742-5468/2012/02/p02014.

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22

Campos, Paulo R. A., Christoph Adami, and Claus O. Wilke. "Optimal adaptive performance and delocalization in NK fitness landscapes." Physica A: Statistical Mechanics and its Applications 304, no. 3-4 (2002): 495–506. http://dx.doi.org/10.1016/s0378-4371(01)00572-6.

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23

Rubin, Ilan N., Yaroslav Ispolatov, and Michael Doebeli. "Adaptive diversification and niche packing on rugged fitness landscapes." Journal of Theoretical Biology 562 (April 2023): 111421. http://dx.doi.org/10.1016/j.jtbi.2023.111421.

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24

Østman, Bjørn, Arend Hintze, and Christoph Adami. "Impact of epistasis and pleiotropy on evolutionary adaptation." Proceedings of the Royal Society B: Biological Sciences 279, no. 1727 (2011): 247–56. http://dx.doi.org/10.1098/rspb.2011.0870.

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Evolutionary adaptation is often likened to climbing a hill or peak. While this process is simple for fitness landscapes where mutations are independent, the interaction between mutations (epistasis) as well as mutations at loci that affect more than one trait (pleiotropy) are crucial in complex and realistic fitness landscapes. We investigate the impact of epistasis and pleiotropy on adaptive evolution by studying the evolution of a population of asexual haploid organisms (haplotypes) in a model of N interacting loci, where each locus interacts with K other loci. We use a quantitative measure

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25

Geard, Nicholas, and Janet Wiles. "LinMap: Visualizing Complexity Gradients in Evolutionary Landscapes." Artificial Life 14, no. 3 (2008): 277–97. http://dx.doi.org/10.1162/artl.2008.14.3.14304.

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This article describes an interactive visualization tool, LinMap, for exploring the structure of complexity gradients in evolutionary landscapes. LinMap is a computationally efficient and intuitive tool for visualizing and exploring multidimensional parameter spaces. An artificial cell lineage model is presented that allows complexity to be quantified according to several different developmental and phenotypic metrics. LinMap is applied to the evolutionary landscapes generated by this model to demonstrate that different definitions of complexity produce different gradients across the same land

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Niklas, Karl J. "Adaptive walks through fitness landscapes for early vascular land plants." American Journal of Botany 84, no. 1 (1997): 16–25. http://dx.doi.org/10.2307/2445878.

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27

DeWitt, Thomas J., and Jin Yoshimura. "The fitness threshold model: Random environmental change alters adaptive landscapes." Evolutionary Ecology 12, no. 5 (1998): 615–26. http://dx.doi.org/10.1023/a:1006564911480.

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Rendel, Mark D. "Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes." Theoretical Population Biology 79, no. 1-2 (2011): 12–18. http://dx.doi.org/10.1016/j.tpb.2010.10.001.

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Rozen, Daniel E., Michelle G. J. L. Habets, Andreas Handel, and J. Arjan G. M. de Visser. "Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes." PLoS ONE 3, no. 3 (2008): e1715. http://dx.doi.org/10.1371/journal.pone.0001715.

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30

Burch, Christina L., та Lin Chao. "Evolution by Small Steps and Rugged Landscapes in the RNA Virus ϕ6". Genetics 151, № 3 (1999): 921–27. http://dx.doi.org/10.1093/genetics/151.3.921.

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Abstract Fisher’s geometric model of adaptive evolution argues that adaptive evolution should generally result from the substitution of many mutations of small effect because advantageous mutations of small effect should be more common than those of large effect. However, evidence for both evolution by small steps and for Fisher’s model has been mixed. Here we report supporting results from a new experimental test of the model. We subjected the bacteriophage ϕ6 to intensified genetic drift in small populations and caused viral fitness to decline through the accumulation of a deleterious mutati

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Ravi Kumar, Vrinda, Gaurav Agavekar, and Deepa Agashe. "Fitness landscapes reveal context-dependent benefits of oviposition behavior." Evolution 77, no. 2 (2022): 550–61. http://dx.doi.org/10.1093/evolut/qpac035.

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Abstract Resource choice behavior has enormous fitness consequences and can drive niche expansion. However, individual behavioral choices are often mediated by context, determined by past experience. Do such context-dependent behaviors reflect maladaptive variation or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behavior reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviors (i.e., combinations of fe

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Erwin, Douglas H. "The topology of evolutionary novelty and innovation in macroevolution." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1735 (2017): 20160422. http://dx.doi.org/10.1098/rstb.2016.0422.

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Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932. George Gaylord Simpson modified this to an adaptive, phenotypic landscape in 1944 and since then evolutionary spaces have played an important role in evolutionary theory through fitness and adaptive landscapes, phenotypic and functional trait spaces, morphospaces and related concepts. Although the topology of such spaces is highly variable, from locally Euclidean to pre-topological, evolutionary change has often been interpreted as a search through a pre-existing space of possibilities, with novelty arisin

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Taylor, Mark A., Amity M. Wilczek, Judith L. Roe, et al. "Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana." Proceedings of the National Academy of Sciences 116, no. 36 (2019): 17890–99. http://dx.doi.org/10.1073/pnas.1902731116.

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Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based

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Hayden, Eric J., and Andreas Wagner. "Environmental change exposes beneficial epistatic interactions in a catalytic RNA." Proceedings of the Royal Society B: Biological Sciences 279, no. 1742 (2012): 3418–25. http://dx.doi.org/10.1098/rspb.2012.0956.

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Natural selection drives populations of individuals towards local peaks in a fitness landscape. These peaks are created by the interactions between individual mutations. Fitness landscapes may change as an environment changes. In a previous contribution, we discovered a variant of the Azoarcus group I ribozyme that represents a local peak in the RNA fitness landscape. The genotype at this peak is distinguished from the wild-type by four point mutations. We here report ribozyme fitness data derived from constructing all possible combinations of these point mutations. We find that these mutation

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Campos, P. R. A., C. Adami, and C. O. Wilke. "Erratum to “Optimal adaptive performance and delocalization in NK fitness landscapes”." Physica A: Statistical Mechanics and its Applications 318, no. 3-4 (2003): 637. http://dx.doi.org/10.1016/s0378-4371(02)01554-6.

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Jordan, Lyndon A., and Michael J. Ryan. "The sensory ecology of adaptive landscapes." Biology Letters 11, no. 5 (2015): 20141054. http://dx.doi.org/10.1098/rsbl.2014.1054.

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In complex environments, behavioural plasticity depends on the ability of an animal to integrate numerous sensory stimuli. The multidimensionality of factors interacting to shape plastic behaviour means it is difficult for both organisms and researchers to predict what constitutes an adaptive response to a given set of conditions. Although researchers may be able to map the fitness pay-offs of different behavioural strategies in changing environments, there is no guarantee that the study species will be able to perceive these pay-offs. We thus risk a disconnect between our own predictions abou

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Otwinowski, Jakub, Colin H. LaMont, and Armita Nourmohammad. "Information-Geometric Optimization with Natural Selection." Entropy 22, no. 9 (2020): 967. http://dx.doi.org/10.3390/e22090967.

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Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between classical population genetics of quantitative traits and evolutionary optimization, and formulate a new evolutionary algorithm. Optimization of a continuous objective function is analogous to searching for high fitness phenotypes on a fitness landscape. We describe how natural selection moves a population along the non-Euclidean gradient that is induced by the population on the fitness landscape (the natural gradient). We s

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Nowak, Stefan, and Joachim Krug. "Analysis of adaptive walks on NK fitness landscapes with different interaction schemes." Journal of Statistical Mechanics: Theory and Experiment 2015, no. 6 (2015): P06014. http://dx.doi.org/10.1088/1742-5468/2015/06/p06014.

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Camus, M. Florencia, Kevin Fowler, Matthew W. D. Piper, and Max Reuter. "Sex and genotype effects on nutrient-dependent fitness landscapes in Drosophila melanogaster." Proceedings of the Royal Society B: Biological Sciences 284, no. 1869 (2017): 20172237. http://dx.doi.org/10.1098/rspb.2017.2237.

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The sexes perform different reproductive roles and have evolved sometimes strikingly different phenotypes. One focal point of adaptive divergence occurs in the context of diet and metabolism, and males and females of a range of species have been shown to require different nutrients to maximize their fitness. Biochemical analyses in Drosophila melanogaster have confirmed that dimorphism in dietary requirements is associated with molecular sex differences in metabolite titres. In addition, they also showed significant within-sex genetic variation in the metabolome. To date however, it is unknown

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Kauffman, Stuart A. "Cambrian explosion and Permian quiescence: implications of rugged fitness landscapes." Paleontological Society Special Publications 6 (1992): 160. http://dx.doi.org/10.1017/s2475262200007206.

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The Cambrian explosion witnessed the formation of a large number of the higher taxa extant today. The higher taxa are said to have “filled in” from the top down, with species that found phyla giving rise to daughter species which found classes, then orders, and so on. During the Permian extinction, in contrast, 96% of all species go extinct. During the rebound, a large number of new families are created, a few new orders are created, but no new phyla are created. The higher taxa are said to have “filled in” from the bottom up. The profound asymmetry between the Cambrian and Permian has been a

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Kumai, William. "Adaptive Walks and Fitness Peak Climbing: Language Learning as Inducing Adaptive Change in L2 Systems." Nagoya JALT Journal 1, no. 1 (2020): 29–42. http://dx.doi.org/10.37546/jaltchap.nagoya1.1-2.

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This paper adopts the perspective of students, groups, and entire classes as being complex adaptive systems, or CAS. Two important concepts from complexity theory, adaptive walks and fitness landscapes, can be used to create optimal language learning conditions for producing changes in students’ L2 systems. Every configuration of L2 traits a student might have can be assigned a fitness value, that is, an L2 competence level. The set of all such values creates an abstract landscape, the fitness landscape. By changing traits, the position on the landscape changes, meaning a student can take a jo

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Gomez-Uribe, Carlos A., Japheth Gado, and Meiirbek Islamov. "Designing diverse and high-performance proteins with a large language model in the loop." PLOS Computational Biology 21, no. 6 (2025): e1013119. https://doi.org/10.1371/journal.pcbi.1013119.

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We present a protein engineering approach to directed evolution with machine learning that integrates a new semi-supervised neural network fitness prediction model, Seq2Fitness, and an innovative optimization algorithm, biphasic annealing for diverse and adaptive sequence sampling (BADASS) to design sequences. Seq2Fitness leverages protein language models to predict fitness landscapes, combining evolutionary data with experimental labels, while BADASS efficiently explores these landscapes by dynamically adjusting temperature and mutation energies to prevent premature convergence and to generat

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Capblancq, Thibaut, Matthew C. Fitzpatrick, Rachael A. Bay, Moises Exposito-Alonso, and Stephen R. Keller. "Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes." Annual Review of Ecology, Evolution, and Systematics 51, no. 1 (2020): 245–69. http://dx.doi.org/10.1146/annurev-ecolsys-020720-042553.

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Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to l

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Agarwala, Atish, and Daniel S. Fisher. "Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics." Theoretical Population Biology 130 (December 2019): 13–49. http://dx.doi.org/10.1016/j.tpb.2019.09.011.

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Reiss, John O. "Relative Fitness, Teleology, and the Adaptive Landscape." Evolutionary Biology 34, no. 1-2 (2007): 4–27. http://dx.doi.org/10.1007/s11692-007-9000-9.

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Leushkin, Evgeny V., Georgii A. Bazykin, and Alexey S. Kondrashov. "Insertions and deletions trigger adaptive walks in Drosophila proteins." Proceedings of the Royal Society B: Biological Sciences 279, no. 1740 (2012): 3075–82. http://dx.doi.org/10.1098/rspb.2011.2571.

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Maps that relate all possible genotypes or phenotypes to fitness—fitness landscapes—are central to the evolution of life, but remain poorly known. An insertion or a deletion (indel) of one or several amino acids constitutes a substantial leap of a protein within the space of amino acid sequences, and it is unlikely that after such a leap the new sequence corresponds precisely to a fitness peak. Thus, one can expect an indel in the protein-coding sequence that gets fixed in a population to be followed by some number of adaptive amino acid substitutions, which move the new sequence towards a nea

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Leprêtre, Florian, Cyril Fonlupt, Sébastien Verel, et al. "Fitness landscapes analysis and adaptive algorithms design for traffic lights optimization on SIALAC benchmark." Applied Soft Computing 85 (December 2019): 105869. http://dx.doi.org/10.1016/j.asoc.2019.105869.

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Hartman, Stefan. "Towards adaptive tourism areas: using fitness landscapes for managing and futureproofing tourism area development." Journal of Tourism Futures 4, no. 2 (2018): 152–62. http://dx.doi.org/10.1108/jtf-03-2018-0009.

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Gorton, Amanda J., David A. Moeller, and Peter Tiffin. "Little plant, big city: a test of adaptation to urban environments in common ragweed ( Ambrosia artemisiifolia )." Proceedings of the Royal Society B: Biological Sciences 285, no. 1881 (2018): 20180968. http://dx.doi.org/10.1098/rspb.2018.0968.

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A full understanding of how cities shape adaptation requires characterizing genetically-based phenotypic and fitness differences between urban and rural populations under field conditions. We used a reciprocal transplant experiment with the native plant common ragweed, ( Ambrosia artemisiifolia ), and found that urban and rural populations have diverged in flowering time, a trait that strongly affects fitness. Although urban populations flowered earlier than rural populations, plants growing in urban field sites flowered later than plants in rural field sites. This counter-gradient variation i

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Park, Su-Chan, Johannes Neidhart, and Joachim Krug. "Greedy adaptive walks on a correlated fitness landscape." Journal of Theoretical Biology 397 (May 2016): 89–102. http://dx.doi.org/10.1016/j.jtbi.2016.02.035.

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