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The Roles of Mutation, Inbreeding, Crossbreeding and Selection in Evolution
... Natural selection drives populations towards higher fitness (i.e. reproductive success), but actual fitness landscapes (representing fitness versus genotype [1,2]) can possess several distinct local maxima or peaks. Such rugged fitness landscapes arise from epistasis, i.e. interactions between genetic variants [3][4][5][6], especially from reciprocal sign epistasis [4], where two mutations together yield a benefit while they are deleterious separately, giving rise to a fitness valley [7,8]. ...
... We assume that their environment is constant, and we neglect interactions between genotypes (individual types, characterized by the state of all genes) and frequency-dependent selection. Each genotype is mapped to a fitness through a fitness landscape [1,2], which is static under these hypotheses [6]. We consider various rugged fitness landscapes (see Results). ...
... Indeed, complex spatial structures with asymmetric updates or migrations impact the probabilities of fixation of mutations [64][65][66][67][68], which should affect early adaptation. Beyond the weak mutation regime, fitness valley crossing by tunnelling can aid adaptation [59,60], which may especially impact subdivided populations, as first discussed in Wright's shifting balance theory [1,69] and shown in a minimal model [70]. Another interesting direction regards the effect of environment-induced modifications of fitness landscapes on adaptation [15,71]. ...
Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases with population size, we find that the height of the first fitness peak encountered when starting from a random genotype displays various behaviours versus population size, even among small and simple rugged landscapes. We show that the accessibility of the different fitness peaks is key to determining whether this height overall increases or decreases with population size. Furthermore, there is often a finite population size that maximizes the height of the first fitness peak encountered when starting from a random genotype. This holds across various classes of model rugged landscapes with sparse peaks, and in some experimental and experimentally inspired ones. Thus, early adaptation in rugged fitness landscapes can be more efficient and predictable for relatively small population sizes than in the large-size limit.
This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
... The complex dynamics of evolving population can be captured by a Fokker-Planck equation on the evolutionary landscape 14 , an abstract space of all possible genetic variations and their corresponding biological properties within a given ecological context 15 . The number of relevant evolving genetic traits corresponds to the dimensionality of this space 16 , where every combination corresponds to an unique position. ...
... The landscape is typically represented as a multi-dimensional Euclidean space R D , where each point ⃗ x represents a unique combination of D scalar-strategy genetic traits 16 . When the maximum fitness R(⃗ x) (which represents the selection pressure) remains constant over time 15,18 , the population distribution density b(⃗ x, t) within this landscape evolves via the Fokker-Planck equation 14 : ...
We establish an analogy between the Fokker-Planck equation describing evolutionary landscape dynamics and the Schr\"odinger-Bloch equation which characterizes quantum mechanical particles, showing how a population with multiple genetic traits evolves analogously to a wavefunction under a multi-dimensional energy potential in imaginary time. Furthermore, we discover within this analogy that the stationary population distribution on the landscape corresponds exactly to the ground-state wavefunction. This mathematical equivalence grants entry to a wide range of analytical tools developed by the quantum mechanics community, such as the Rayleigh-Ritz variational method and the Rayleigh-Schr\"odinger perturbation theory, allowing us to not only make reasonable quantitative assessments but also explore fundamental biological inquiries. We demonstrate the effectiveness of these tools by estimating the population success on landscapes where precise answers are elusive, and unveiling the ecological consequences of stress-induced mutagenesis -- a prevalent evolutionary mechanism in pathogenic and neoplastic systems. We show that, even in a unchanging environment, a sharp mutational burst resulting from stress can always be advantageous, while a gradual increase only enhances population size when the number of relevant evolving traits is limited. Our interdisciplinary approach offers novel insights, opening up new avenues for deeper understanding and predictive capability regarding the complex dynamics of evolving populations.
... The foundation of our framework is the fitness landscape, first introduced in evolutionary biology (Wright, 1932), which is central to trait-based eco-evolutionary models (reviewed in Klausmeier et al., 2020). In this approach, a population's growth rate depends on the functional trait values that determine its phenotype in a particular environment. ...
... A positive intrinsic growth rate means a species can establish itself in a local environment (see review by Klausmeier et al., 2020). The functional dimensions along which intrinsic growth rates vary reflect how species traits affect local demography (Kandlikar et al., 2022;Laughlin et al., 2020;Wright (1) ...
Recent work has shown that evaluating functional trait distinctiveness, the average trait distance of a species to other species in a community offers promising insights into biodiversity dynamics and ecosystem functioning. However, the ecological mechanisms underlying the emergence and persistence of functionally distinct species are poorly understood. Here, we address the issue by considering a heterogeneous fitness landscape whereby functional dimensions encompass peaks representing trait combinations yielding positive population growth rates in a community. We identify four ecological cases contributing to the emergence and persistence of functionally distinct species. First, environmental heterogeneity or alternative phenotypic designs can drive positive population growth of functionally distinct species. Second, sink populations with negative population growth can deviate from local fitness peaks and be functionally distinct. Third, species found at the margin of the fitness landscape can persist but be functionally distinct. Fourth, biotic interactions (positive or negative) can dynamically alter the fitness landscape. We offer examples of these four cases and guidelines to distinguish between them. In addition to these deterministic processes, we explore how stochastic dispersal limitation can yield functional distinctiveness. Our framework offers a novel perspective on the relationship between fitness landscape heterogeneity and the functional composition of ecological assemblages.
... Adaptive landscapes map genotypes within a collection 48 or 'space' of genotypes onto fitness or some proxy thereof. They are also powerful 49 conceptual tools for studying long-term evolution (Wright 1932;Wu et al. 2016;Aguirre 50 et al. 2018;Ferretti et al. 2018;Bataillon et al. 2022). Because genotype spaces are 51 high-dimensional discrete spaces, they have geometrical properties different from those 52 of low-dimensional continuous spaces (Aguirre et al. 2018). ...
... Because the experimentally determined landscapes we consider (Wu et al. 2016;Lite 146 et al. 2020) are based on a small number of nucleotide sites, we assume that adaptive 147 evoluiton occurs in the weak mutation, strong selection regime (Gillespie 1983;Gillespie 148 1984). In this regime, only one mutation segregates at any point in time, and adaptive 149 evolution effectively becomes an adaptive walk in which a population steps from one 150 genotype to the next (Wright 1932;Maynard Smith 1970;Gillespie 1984) (fig. 1F). ...
Mistranslation - the erroneous incorporation of amino acids into nascent proteins - is a source of protein variation that is orders of magnitude more frequent than DNA mutation. Like other sources of nongenetic variation, it can affect adaptive evolution. We study the evolutionary consequences of mistranslation with experimental data on mistranslation rates applied to three empirical adaptive landscapes. We find that mistranslation generally flattens adaptive landscapes by reducing the fitness of high fitness genotypes and increasing that of low fitness genotypes, but it does not affect all genotypes equally. Most importantly, it increases genetic variation available to selection by rendering many neutral DNA mutations non-neutral. Mistranslation also renders some beneficial mutations deleterious and vice versa. It increases the probability of fixation of 3 to 8 percent of beneficial mutations. Even though mistranslation increases the incidence of epistasis, it also allows populations evolving on a rugged landscape to evolve modestly higher fitness. Our observations show that mistranslation is an important source of non-genetic variation that can affect adaptive evolution on fitness landscapes in multiple ways.
... The fitness landscape is a concept in theoretical biology introduced by Sewall Wright almost a hundred years ago (Wright 1932). Since then it has become one of the most fundamental and influential models in evolutionary biology and beyond (i.e., Adami 2012; Laue & Wright 2019;McCanlish 2011;McGhee 2006). ...
In traditional hunting and gathering societies, it is a common practice to fashion projectiles for
different purposes. The spectrum of the available morphologies for projectiles and their tips is dictated
by several kinds of constraints such as aerodynamic and mechanical properties, different
hunting strategies, the available game or the range of the shot. This article focuses on a particular
aspect of duality in primitive projectile technology interpreted with a fitness landscape model.
Using geometric morphometric analysis, the author argues that the duality in projectile morphology
and performance characteristics observed in the studied projectile weapon systems is the
result of technological and physical constraints placed upon primitive projectile technology. For
a more comprehensive explanation of this phenomenon, an optimality model explaining the development
of flexible projectile weapon systems is proposed.
... For example, biases in the available genetic variation in a population might arise from a higher likelihood of certain mutation types (Payne et al. 2019), from structural properties of specific DNA sequences (Xie et al. 2019), from different rates of mutations across different regions of the genome (Hodgkinson and Eyre-Walker 2011) or the presence of mutator or antimutator mechanisms (Wielgoss et al. 2012). Although such molecular biases exist, mutations have nevertheless been traditionally regarded as random relative to their fitness effects (Wright 1932;Lenski and Mittler 1993). Recently, however, Monroe et al. (2022) reported a mutational bias in Arabidopsis thaliana that not only reflects molecular propensities of mutagenesis but also the importance of the biological functions of genes. ...
The notion that mutations are random relative to their fitness effects is central to the Neo-Darwinian view of evolution. However, a recent interpretation of the patterns of mutation accumulation in the genome of Arabidopsis thaliana has challenged this notion, arguing for the presence of a targeted DNA repair mechanism that causes a non-random association of mutation rates and fitness effects. Specifically, this mechanism was suggested to cause a reduction in the rates of mutations on essential genes, thus lowering the rates of deleterious mutations. Central to this argument were attempts to rule out selection at the population level. Here, we offer an alternative and parsimonious interpretation of the patterns of mutation accumulation previously attributed to mutation bias, showing how they can instead or additionally be caused by developmental selection, i.e., selection occurring at the cellular level during the development of a multicellular organism. Thus, the depletion of deleterious mutations in A. thaliana may indeed be the result of a selective process, rather than a bias in mutation. More broadly, our work highlights the importance of considering development in the interpretation of population genetic analyses of multicellular organisms, and it emphasizes that efforts to identify mechanisms involved in mutational biases should explicitly account for developmental selection.
... Evolution is often thought of as an optimization process, in which natural selection pushes populations inevitably uphill, towards a local optimum in the fitness landscape (Wright, 1932). However, much recent work has shown that in many populations, numerous linked mutations often arise and segregate simultaneously (Barroso-Batista et al., 2014;De Visser et al., 1999;Kao and Sherlock, 2008;Lang et al., 2013;Miralles et al., 1999;Nourmohammad et al., 2019;Strelkowa and Lässig, 2012). ...
Natural selection makes evolutionary adaptation possible even if the overwhelming majority of new mutations are deleterious. However, in rapidly evolving populations where numerous linked mutations occur and segregate simultaneously, clonal interference and genetic hitchhiking can limit the efficiency of selection, allowing deleterious mutations to accumulate over time. This can in principle overwhelm the fitness increases provided by beneficial mutations, leading to an overall fitness decline. Here, we analyze the conditions under which evolution will tend to drive populations to higher versus lower fitness. Our analysis focuses on quantifying the boundary between these two regimes, as a function of parameters such as population size, mutation rates, and selection pressures. This boundary represents a state in which adaptation is precisely balanced by Muller's ratchet, and we show that it can be characterized by rapid molecular evolution without any net fitness change. Finally, we consider the implications of global fitness-mediated epistasis, and find that under some circumstances this can drive populations towards the boundary state, which can thus represent a long-term evolutionary attractor.
... FLA is a powerful tool for analyzing the relationship between the space of decision variables and the values of fitness functions, which was first employed by Sewell Wright [27]. Stadler developed the formal representation of the fitness landscape [28]. ...
... It is possible to represent the complexity of a problem by mapping the entire set of possible solutions to that problem into an evaluation space (also called a fitness landscape) which indicates the quality of each solution (Wright 1932;Levinthal 1997). Indeed, the extent to which the contribution of each solution element depends on the other elements is often described as the problem's complexity, such that the simplest problems are those in which each solution element can be optimized independently (Siggelkow & Levinthal 2003;Levinthal & March 1981). ...
... In the philosophy of biology, hypersurface representations have received considerable attention (Fusco et al., 2014), traceable to Wright's (1932) and Waddington's (1939;1940;1957) iconic 'landscape'-style representations. For Waddington, the threedimensional landscape emerged out of an attempt to conceptualize an explanatory framework that could ontologically house numerous organizational structures and functions of biological development. ...
By broadening disciplinary perspectives to architecture and design, philosophy of science, and systems biology, this paper aims to explore the interconnections between built, social, biotic, and health processes with key attention to the moderating roles of the built environment. The focus is part diagnostic and part prescriptive. Initially, we specify failures in COVID-19 representational infrastructure and practice in accounting for built environment and social process impacts on public health factors. By presenting three intertwined problems with scientific representation in COVID-19 modeling and data-gathering, we examine to what extent current scientific practices fail to robustly account for the complex intersections between built, biotic, social, and health processes. We suggest that resolving the presented problems requires the development of new conceptual precedents for the analysis of causal relations in changing contexts. The second focal point is prescriptive. By discussing conceptual developments that spotlight relations—e.g., ‘context’, ‘nudge’, ‘affordance’, and ‘interface’—we organize the numerous moderating roles of built environment contexts, and we suggest practical applications to ongoing public health practices—such as, cautioning against nudge policies. Ultimately, we argue that the built environment can be represented not only as a single variable (or handful of discrete variables) but also as an interface that reorganizes multiple causal landscapes—concurrently, deregulating factors and leaving others unaffected. Because of the difficulty of representing emergent properties, relevant to differential built environment burden and inequitable health outcomes, we provide ways to visualize the built environment as interface in multidimensional form. We conclude that adequately representing the various moderating roles of the built environment goes a step beyond how to represent complexity, and it requires asking a deeper normative question: who ought to be involved in representing complexity.
... Moreover, organisms undergoing metamorphosis exhibit drastic changes in performance as morphology changes (Pechenik et al., 1998). The framework of adaptive landscapes provides an explanatory model for understanding how genotypic and, thus, phenotypic combinations within a population affect fitness (Wright, 1932), yet researchers must be explicit in defining the phenotypic space and limitations of the landscape of their framework (Pigliucci, 2008). ...
As frogs undergo metamorphosis from tadpole to adult, they may be susceptible to decreases in locomotor performance and survival during stages in which the tail and limbs are both present. Because these alternative axial and appendicular propulsive systems might interfere with each other, performance might be better when only one or the other system predominates. This framework, termed the ‘adaptive peak hypothesis’ emerged from studies of generalist anuran taxa with biphasic life histories in which aquatic larvae transition to terrestrial adults. However, it is not clear that such patterns apply to taxa with different patterns of ontogenetic environmental transitions.
We evaluated the relationship between morphology, locomotor performance and survival versus predators across metamorphic stages of a fully aquatic frog, the pipid Xenopus laevis . We measured escape performance from individuals of four developmental stages spanning possession of just a tail, the presence of both tail and legs and resorption of the tail, and then conducted selection trials in which equal numbers of individuals of all stages were exposed to an aquatic predator (cichlid fish). After collecting survivors from these trials, we calculated linear and nonlinear selection gradients for a suite of morphological traits.
Unlike generalist frogs, we found that both locomotor performance and survival increased across metamorphic stages of X. laevis . Linear selection gradients favoured tadpoles with longer hindlimbs, longer and narrower bodies, and shorter tails—patterns that generally parallel trends during metamorphic growth. Nonlinear selection showed that longer hindlimbs were favoured as body length increased and the positive effect of forelimb length was reduced as tail length increased.
The relationship between hindlimb and body length aligns with expected changes in growth postmetamorphosis where postmetamorphic individuals are expected to have greater survival. However, longer forelimbs are generally associated with decreased locomotor performance, suggesting that alternative mechanisms of selection may be acting on the forelimbs of Xenopus through development.
Overall, our results indicate that the generality of the adaptive peak framework, as applied to amphibian metamorphosis, can be impacted by specifics of life history patterns across species.
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... No obstante, es un proceso que debe ser equilibrado y llevarse a cabo en la presencia de otras fuerzas evolutivas. Como lo dijo Wright (1932), "…la evolución depende de un cierto balance entre sus factores. Debe haber una mutación genética, pero una velocidad excesiva produce una serie de fenómenos, no evolución; debe haber selección, pero un proceso demasiado severo destruye el campo de variabilidad y, por lo tanto, la base para una adicional ventaja". ...
Resumen: La mutación es una característica inherente del material genético e implica un cambio en su composición y función, por lo que se considera la fuente última de la variabilidad genética. Estos cambios pueden ser diversos y no todos son perjudiciales, también los hay favorables, o incluso neutrales, pero, en cualquier caso, la aparición de estos cambios es un evento raro o de muy baja frecuencia. Dentro de aquellas mutaciones que no matan a los individuos, pueden surgir nuevos genes y, por lo tanto, nuevas funciones que pueden incrementar la adaptabilidad y alcanzar una mayor capacidad de dejar mayor descendencia.
Abstract: Mutation is an inherent characteristic of genetic material and implies a change in its composition and function, thus becoming the ultimate source of genetic variability. These changes can be diverse and not all of them are bad, there are also good ones, or even neutral ones, but, in any case, the appearance of these changes is a rare or very low frequency event. Within those mutations that do not kill individuals, new genes can arise and, therefore, new functions that can increase adaptability and achieve a greater ability to leave more offspring.
... Alternatively, images may be interpreted in a more concrete way, with clear connections to causality. This point about two different scientific usages of pictures has been made by Fusco et al. (2014) in relation to the landscape visualizations of Wright (1932) in evolution and Waddington (1940Waddington ( , 1957 in development. It has also been made by Nuño de la Rosa (2018) in relation to pictures of particular embryonic stages, and the advances made in contemplating transitions between these stages that have derived from time-lapse and other modern imaging techniques. ...
D’Arcy Thompson’s drawings showing coordinated differences between the shape of an individual of one species and the shape of an individual of another have been reproduced and discussed countless times. However, while they have been widely regarded as inspirational, their interpretation in causal terms has proved difficult, and there is as yet no consensus on this matter. Here, I approach these Thompsonian transformations from a particular angle, namely their dimensional insufficiency. I argue that this problem must be solved before the issue of causality can be considered. This approach leads to the conclusion that Thompsonian transformations—or “morphological transformations”—have not taken place in evolution, and logically can never do so, because they involve the direct conversion of the adult form of one species into that of another. In contrast, “developmental transformations” do occur in the short term, within the lifetime of a single individual. And “evolutionary transformations” occur in the long term, in a context that can be described, following Scott Gilbert, as five-dimensional. I argue that these two kinds of transformation—developmental and evolutionary—have different causal agencies. I consider the possible nature of these agencies and, related to that, the way in which Thompson’s work connects with Darwinian evolutionary theory.
... The determinants of neutral flat-fitness landscapes versus performance-trait associations are a long-standing controversy in biology (Carroll, 2001) and other disciplines (Arthur & Sibani, 2017;Cobey & Lipsitch, 2012). Throughout the 20th century, theories that attempted to understand the evolution of species traits (Wright, 1932), molecular biochemistry (Monod, 1971) and population genetics (Kreitman, 1996), as well as the ecology of individuals (Losos, 2017) and population dynamics (Royama, 1992), converged on F I G U R E 3 Diversity of plant traits and their representation in temporary ponds. (a) Principal coordinate analysis (PCoA) summarizing the multicollinearity in species traits. ...
Biodiversity emerges from niche mechanisms, in which the combination of traits determines species performance, and populations drift because of the inherent stochasticity of community assembly processes. Population biology dictates that small and isolated communities are more prone to show stochastic assemblages. However, a reduced mass effect in isolated communities may promote trait selection. In addition, large and connected communities have a larger species pool, higher functional redundancy, lower population sizes and more random recruitment, which also fosters stochasticity in community assembly. These contradictory expectations demand empirical analyses.
Plant metacommunities in temporary ponds are assembled by the action of strong environmental filters and cover wide ranges of local community sizes and connectivity, representing ideal systems for identifying determinants of trait‐selection processes. Using a deviance partition method introduced by the theory of community assembly by trait selection, we evaluated the role of plant traits in local community assemblies along 60 communities from a 14‐year plant survey of temporary ponds.
Variation in pond size, hydroperiod, connectitivity and heterogeneity determined a selection gradien in traits related to drought resistance, life history and disperal strategies; and also in the strength of trait‐mediated community assembly. The taxonomic and functional diversity of a pond and its physical heterogeneity fostered stochasticity in the assembly of the community, which also presented a hump‐shaped association with connectivity. The pond area increased taxonomic richness but decreased functional diversity, determining negative and positive indirect effects on stochasticity.
Synthesis . Diversity provides the raw material for trait selection putatively reducing stochasticity, but here diversity was positively related to stochasticity. Having enough functional diversity, larger redundancy and lower population sizes in diverse communities is probably fostering stochastic assemblages. The hump‐shaped association between stochasticity and connectivity supports a larger role of trait selection in isolated systems due to a weak mass effect, but also on connected communities in which a set of more optimal traits for the selection scenario could be available. In the ongoing state of ecosystem fragmentation, these empirical trends contribute to the mechanistic understanding of the connection between landscape structure and biodiversity assembly.
... Although some models for the evolution of recombination plasticity did explore finite-size setups, 98 The evolutionary interplay between spatial structure and recombination has been addressed in several models assuming constant recombination. Since Wright's classic works, 125,126 it has been argued that spatial structure allows populations with frequent recombination to navigate rugged fitness landscapes. More recently, Cooper and ...
Meiotic recombination is one of the main sources of genetic variation, a fundamental factor in the evolutionary adaptation of sexual eukaryotes. Yet, the role of variation in recombination rate and other recombination features remains underexplored. In this review, we focus on the sensitivity of recombination rates to different extrinsic and intrinsic factors. We briefly present the empirical evidence for recombination plasticity in response to environmental perturbations and/or poor genetic background and discuss theoretical models developed to explain how such plasticity could have evolved and how it can affect important population characteristics. We highlight a gap between the evidence, which comes mostly from experiments with diploids, and theory, which typically assumes haploid selection. Finally, we formulate open questions whose solving would help to outline conditions favoring recombination plasticity. This will contribute to answering the long-standing question of why sexual recombination exists despite its costs, since plastic recombination may be evolutionary advantageous even in selection regimes rejecting any non-zero constant recombination.
... more effectively. The first observation can be understood and interpreted using Wright's shifting balance 425 theory, since through either decreased effective selection or increasing hindrance to gene flow, an increase in 426 the relative force of drift leads to an increased window in which the final beneficial mutation can rescue the 427 mutant lineage (Wright et al., 1932). ...
Spatially-resolved datasets are revolutionizing knowledge in molecular biology, yet are under-utilized for questions in evolutionary biology. To gain insight from these large-scale datasets of spatial organization, we need mathematical representations and modeling techniques that can both capture their complexity, but also allow for mathematical tractability. Specifically, it is hard to link previous deme-based or lattice-based models with datasets exhibiting complex patterns of spatial organization and the role of heterogeneous population structure in shaping evolutionary dynamics is still poorly understood. Evolutionary graph theory utilizes the mathematical representation of networks as a proxy for population structure and has started to reshape our understanding of how spatial structure can direct evolutionary dynamics. However, previous results are derived for the case of a single mutation appearing in the population. Complex traits arise from interactions among multiple genes and these interaction can result in rugged fitness landscapes, where evolutionary dynamics can vastly differ from the dynamics of stepwise fixation. Here, we develop a unifying theory of how heterogenous population structure shapes evolutionary dynamics on rugged fitness landscapes. We show that even a simple extension to a two- mutational landscape can exhibit evolutionary dynamics not observed in deme-based models and that cannot be predicted using previous single-mutation results. We also show how to link these models to spatially-resolved datasets and build the networks of the stem cell niches of the bone marrow. We show that these cellular spatial architectures reduce the probability of neoplasm initiation across biologically relevant mutation rate and fitness distributions.
... It is obvious that the image of a metapopulation distributed across a terrain with weak genetic connections, and life histories that are survival peaks with troughs between them, corresponds in many ways to Sewall Wright's shifting balance theory of evolution [25][26][27]. The local adaptations of different salmon life histories spawning in local reaches of a shifting river system provide a context highly generative for evolutionary adaptations. ...
We view the history of the Columbia River Basin through a resilience lens from the point of view of salmonids, as keystone species for the river basin ecosystems and social systems. We rely on the concept of multiple stable states as depicted in a stability landscape, as a scientific theory, but equally as a metaphor and a mental model. Using evidence-based plausibility arguments concerning the existence, creation, and potential critical transitions between regimes, we describe change over centuries. We argue that a critical transition occurred taking the state of the system from its historic regime into a novel regime stabilized by new social feedbacks and institutional configurations. By using a state space defined by four variables used in policy deliberations for salmon recovery we tie our results to historical and contemporary management issues. Knowledge of (a) which regime is currently occupied and (b) which critical transitions between regimes are possible are both crucial to effective policy formation. We draw distinctions between positions held by federal agencies, tribal agencies, and civil society organizations as to the current state of affairs and policy recommendations, raising questions about the appropriate use of decision support systems in the public process for decision making.
... The concept of the adaptive landscape was first proposed by Wright (1932) and has become a "standard imagination prosthesis for evolutionary theorists. It has proven its worth in literally thousands of applications, including many outside evolutionary theory" (Dennett 1996: 190;see discussion in McGhee 2007). ...
Contributors explore common elements in the evolutionary histories of both human and insect agriculture resulting from convergent evolution.
During the past 12,000 years, agriculture originated in humans as many as twenty-three times, and during the past 65 million years, agriculture also originated in nonhuman animals at least twenty times and in insects at least fifteen times. It is much more likely that these independent origins represent similar solutions to the challenge of growing food than that they are due purely to chance. This volume seeks to identify common elements in the evolutionary histories of both human and insect agriculture that are the results of convergent evolution. The goal is to create a new, synthetic field that characterizes, quantifies, and empirically documents the evolutionary and ecological mechanisms that drive both human and nonhuman agriculture.
The contributors report on the results of quantitative analyses comparing human and nonhuman agriculture; discuss evolutionary conflicts of interest between and among farmers and cultivars and how they interfere with efficiencies of agricultural symbiosis; describe in detail agriculture in termites, ambrosia beetles, and ants; and consider patterns of evolutionary convergence in different aspects of agriculture, comparing fungal parasites of ant agriculture with fungal parasites of human agriculture, analyzing the effects of agriculture on human anatomy, and tracing the similarities and differences between the evolution of agriculture in humans and in a single, relatively well-studied insect group, fungus-farming ants.
Contributors
Duur K. Aanen, Niels P. R. Anten, Peter H. W. Biedermann, Jacobus J. Boomsma, Laura T. Buck, Guillaume Chomicki, Tim Denham, R. Ford Denison, Dorian Q. Fuller, Richard Gawne, Nicole M. Gerardo, Thomas C. Harrington, Ana Ješovnik, Judith Korb, Chase G. Mayers, George R. McGhee, Kenneth Z. McKenna, Lumila P. Menéndez, Peter N. Peregrine, Ted R. Schultz
... Additionally, the positional relationship between encoded sequences within the latent space suggests an attractive model for studying sequence evolution and phylogenetic relationships, hearkening back to older theories of evolutionary landscapes 56 where genes were imagined as points on landscapes of high and low fitness. One way of understanding the latent space organization is shown in the upper section of Fig. 1b with a vector plot, where at each pixel coordinate, a maximum probability sequence is generated and then reencoded through the encoder, yielding vectors of coordinate change. ...
Variational autoencoders are unsupervised learning models with generative capabilities, when applied to protein data, they classify sequences by phylogeny and generate de novo sequences which preserve statistical properties of protein composition. While previous studies focus on clustering and generative features, here, we evaluate the underlying latent manifold in which sequence information is embedded. To investigate properties of the latent manifold, we utilize direct coupling analysis and a Potts Hamiltonian model to construct a latent generative landscape. We showcase how this landscape captures phylogenetic groupings, functional and fitness properties of several systems including Globins, β-lactamases, ion channels, and transcription factors. We provide support on how the landscape helps us understand the effects of sequence variability observed in experimental data and provides insights on directed and natural protein evolution. We propose that combining generative properties and functional predictive power of variational autoencoders and coevolutionary analysis could be beneficial in applications for protein engineering and design.
... The simplest way to understand how this process drives phenotypic (and species) diversification is through the classic Simpson's "adaptive landscape" (Simpson 1944). In this concept, inspired by Wright's fitness landscapes for gene frequencies (Wright 1932), fitness is visualized as the height of a surface that, in turn, varies as a function of the values of two or more phenotypic traits (Simpson 1944). In this way, the combination of trait values that allow higher fitness are visualized as 'peaks' in the surface while those combinations of trait values that determine low fitness are visualized as 'valleys' (Fig. 6). ...
Amphibians constitute one of the major branches of the vertebrate tree of life, with nearly 8,400 extant species currently inhabiting most terrestrial and freshwater habitats in temperate and tropical landmasses worldwide. The extant amphibians (Lissamphibia) encompass three orders of markedly distinct morphologies and life styles. The most diverse of these are the Anura (frogs and toads) that have short, tailless bodies with long, powerful hind limbs for jumping. Less diverse Caudata (salamanders and newts) have slender bodies with proportionally paired limbs and long tails. And the smallest group are the Gymnophiona (caecilians) that have elongated, limbless bodies adapted for burrowing. Extant amphibians have a long evolutionary history that probably extends back more than 300 million years ago, and are key for understanding the colonization of terrestrial environments by early tetrapods. This chapter discusses the state-of-knowledge of the origin and ancestry, phylogeny and evolution, and diversification of extant amphibians. Since the beginning of the XXI century, the vast accumulation of data from multiple sources (molecular, genomic, paleontological, morphological, ecological, behavioural, biogeographical) as well as the spread of integrative approaches have shed light on long hotly debated issues on the origin and evolution of this important group of vertebrates.
... The pattern described above can best be visualized via an analogy to the concept of fitness landscapes coming from the biological sciences. Viewing behavioral, cultural, and cognitive performances as complex, multidimensional fitness landscapes draws on S. Wright's (1932Wright's ( , 1982 work on biological systems. His complex landscapes feature several adaptive peaks and valleys of different heights, corresponding to local fitness maxima and minima. ...
The behavioral origins of Homo sapiens can be traced back to the first material culture produced by our species in Africa, the Middle Stone Age (MSA). Beyond this broad consensus, the origins, patterns, and causes of behavioral complexity in modern humans remain debated. Here, we consider whether recent findings continue to support popular scenarios of: (1) a modern human 'package,' (2) a gradual and 'pan-African' emergence of behavioral complexity, and (3) a direct connection to changes in the human brain. Our geographically structured review shows that decades of scientific research have continuously failed to find a discrete threshold for a complete 'modernity package' and that the concept is theoretically obsolete. Instead of a continent-wide, gradual accumulation of complex material culture, the record exhibits a predominantly asynchronous presence and duration of many innovations across different regions of Africa. The emerging pattern of behavioral complexity from the MSA conforms to an intricate mosaic characterized by spatially discrete, temporally variable, and historically contingent trajectories. This archaeological record bears no direct relation to a simplistic shift in the human brain but rather reflects similar cognitive capacities that are variably manifested. The interaction of multiple causal factors constitutes the most parsimonious explanation driving the variable expression of complex behaviors , with demographic processes such as population structure, size, and connectivity playing a key role. While much emphasis has been given to innovation and variability in the MSA record, long periods of stasis and a lack of cumulative developments argue further against a strictly gradualistic nature in the record. Instead, we are confronted with humanity's deep, variegated roots in Africa, and a dynamic metapopulation that took many millennia to reach the critical mass capable of producing the ratchet effect commonly used to define contemporary human culture. Finally, we note a weakening link between 'modern' human biology and behavior from around 300 ka ago.
... Darwin's evolutionary theory states that heritable phenotypic variation provides the foundation on which natural selection operates, allowing organisms to evolve. 1 Nonetheless, maintaining phenotypic diversity may have fitness costs under typical growth conditions, especially if divergent phenotypes deviate from optimal fitness. 2 It is crucial for a population to maintain high fitness so that it can compete with other populations under normal conditions, but it must also harbor enough phenotypic diversity to allow it to survive under stressful conditions. ...
Enhanced phenotypic diversity increases a population’s likelihood of surviving catastrophic conditions. Hsp90, an essential molecular chaperone and a central network hub in eukaryotes, has been observed to suppress or enhance the effects of genetic variation on phenotypic diversity in response to environmental cues. Because many Hsp90-interacting genes are involved in signaling transduction pathways and transcriptional regulation, we tested how common Hsp90-dependent differential gene expression is in natural populations. Many genes exhibited Hsp90-dependent strain-specific differential expression in five diverse yeast strains. We further identified transcription factors (TFs) potentially contributing to variable expression. We found that on Hsp90 inhibition or environmental stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual strains can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.
... Adaptive landscapes have the potential to become powerful tools for predicting evolution [1]. Persistent selection under a constant environment confines the viable mutational space available to populations, restricting their ability to acquire neutral or deleterious changes that would move them 'sideways' or 'downwards' on the landscape and instead drives them upward to realize the local fitness optimum [2]. This means that once an adapting population has set upon a path, possessing complete knowledge of the landscape and adaptive context can allow an observer to predict which trajectories are more likely to be taken [3]. ...
Predicting how a population will likely navigate a genotype–phenotype landscape requires consideration of selection in combination with mutation bias, which can skew the likelihood of following a particular trajectory. Strong and persistent directional selection can drive populations to ascend toward a peak. However, with a greater number of peaks and more routes to reach them, adaptation inevitably becomes less predictable. Transient mutation bias, which operates only on one mutational step, can influence landscape navigability by biasing the mutational trajectory early in the adaptive walk. This sets an evolving population upon a particular path, constraining the number of accessible routes and making certain peaks and routes more likely to be realized than others. In this work, we employ a model system to investigate whether such transient mutation bias can reliably and predictably place populations on a mutational trajectory to the strongest selective phenotype or usher populations to realize inferior phenotypic outcomes. For this we use motile mutants evolved from ancestrally non-motile variants of the microbe Pseudomonas fluorescens SBW25, of which one trajectory exhibits significant mutation bias. Using this system, we elucidate an empirical genotype–phenotype landscape, where the hill-climbing process represents increasing strength of the motility phenotype, to reveal that transient mutation bias can facilitate rapid and predictable ascension to the strongest observed phenotype in place of equivalent and inferior trajectories.
This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
... Here we attempt to meet this challenge via the notion of landscape, a visual metaphor used in evolutionary and developmental biology, to map out similarly complex phenomena and operationalize a dynamic, contingent field of action. Sewall Wright (1932) developed the concept of adaptive landscapes to chart the relationship of fitness (reproductive success) to possible genotypes in a population under particular environmental conditions. As shown in Figure 1, peaks and valleys on the landscape represent gene combinations associated with higher (+) and lower (-) fitness. ...
Practices occupy the intersection of human behavior with its personal and societal dimensions, operating in social theory as bridges between high‐order cultural features and on‐the‐ground dynamics that reciprocally shape the conditions of everyday life and animate human experience. Yet precisely how this bridging occurs remains underspecified. We address that gap in this and a companion article (Worthman, Cummings, and Lende 2023). This article situates practices in dynamic action space, while the second details how those dynamics work and applies them to questions of inequity, resilience, and contemplative practice. We trace a spectrum of practices from mundane activities to formal rituals and self‐transformational pursuits. We then situate them within a socioecological framework, drawing on the visual metaphor of Charles Waddington's epigenetic landscape to represent fields of possible practices or action landscapes that are contingent, situated, and dynamically configured to constitute the middle ground bridging social actors and lived experience with sociocultural worlds.
... Adaptive landscapes are central to evolutionary theory, forming a conceptual bridge between micro-and macroevolution. [1][2][3][4] Evolution by natural selection across an adaptive landscape should drive lineages toward fitness peaks, shaping the distribution of phenotypic variation within and among clades over evolutionary timescales. 5 The location and breadth of these peaks in phenotypic space can also evolve, 4 but whether phylogenetic comparative methods can detect such patterns has largely remained unexplored. ...
Adaptive landscapes are central to evolutionary theory, forming a conceptual bridge between micro- and macroevolution.1,2,3,4 Evolution by natural selection across an adaptive landscape should drive lineages toward fitness peaks, shaping the distribution of phenotypic variation within and among clades over evolutionary timescales.5 The location and breadth of these peaks in phenotypic space can also evolve,4 but whether phylogenetic comparative methods can detect such patterns has largely remained unexplored.6 Here, we characterize the global and local adaptive landscape for total body length in cetaceans (whales, dolphins, and relatives), a trait that spans 5 orders of magnitude, across their ∼53 million year evolutionary history. Using phylogenetic comparative methods, we analyze shifts in long-term mean body length7 and directional changes in average trait values8 for 345 living and fossil cetacean taxa. Remarkably, we find that the global macroevolutionary adaptive landscape of cetacean body length is relatively flat, with very few peak shifts occurring after cetaceans entered the oceans. Local peaks are more numerous and manifest as trends along branches linked to specific adaptations. These results contrast with previous studies using only extant taxa,9 highlighting the vital role of fossil data for understanding macroevolution.10,11,12 Our results indicate that adaptive peaks are dynamic and are associated with subzones of local adaptations, creating moving targets for species adaptation. In addition, we identify limits in our ability to detect some evolutionary patterns and processes and suggest that multiple approaches are required to characterize complex hierarchical patterns of adaptation in deep time.
... Interestingly, our analysis revealed that once the populations had evolved a mode of communication based on the timing of signal onset-delay and/or signal duration, none of them were able to switch to the more efficient system of communication via signal amplitude. A likely reason for this is that switching from one system of communication to the other would require passing through a valley of lower performance values [29] where each population would have to abandon their original mode of communication to develop the other. This problem is likely to be particularly acute in the case of communication systems because changes in either the signaling or response strategy would destroy the communication system that is already in place and result in performance decrease [30,31]. ...
Displaced communication, whereby individuals communicate regarding a subject that is not immediately present (spatially or temporally), is one of the key features of human language. It also occurs in a few animal species, most notably the honeybee, where the waggle dance is used to communicate the location and quality of a patch of flowers. However, it is difficult to study how it emerged given the paucity of species displaying this capacity and the fact that it often occurs via complex multimodal signals. To address this issue, we developed a novel paradigm in which we conducted experimental evolution with foraging agents endowed with neural networks that regulate their movement and the production of signals. Displaced communication readily evolved but, surprisingly, agents did not use signal amplitude to convey information on food location. Instead, they used signal onset-delay and duration-based mode of communication, which depends on the motion of the agent within a communication area. When agents were experimentally prevented from using these modes of communication, they evolved to use signal amplitude instead. Interestingly, this mode of communication was more efficient and led to higher performance. Subsequent controlled experiments suggested that this more efficient mode of communication failed to evolve because it took more generations to emerge than communication grounded on the onset-delay and length of signaling. These results reveal that displaced communication is likely to initially evolve from non-communicative behavioral cues providing incidental information with evolution later leading to more efficient communication systems through a ritualization process.
... If so, then this view is historically unfounded. Sewall Wright, indisputably a core architect of the Modern Synthesis, placed multilevel selection firmly in the centre of his understanding of the evolutionary process, in the form of the "shifting balance" view of adaptive evolution (Wright 1932). This concerned the rate-rather than the purpose-of adaptation. ...
Dickins has made some thoughtful suggestions as to why the important contributions of inclusive fitness theory have not been more celebrated by the proponents of the Extended Evolutionary Synthesis, considering the extent to which inclusive fitness theory has accommodated and illuminated—and, indeed, been motivated by—their “laundry list” of supposedly neglected evolutionary factors. We agree that this oversight could be explained, in part, by their seeing inclusive fitness as a “monist” alternative to a more “pluralist” multilevel selection that was not part of the Modern Synthesis. Here we clarify that multilevel selection and inclusive fitness are not competing explanations, but rather they address orthogonal issues, concerning the process of selection and the purpose of adaptation, respectively. We discuss the sense in which inclusive fitness is “monist” in providing the only generally correct adaptive maximand, but also “pluralist” in the sense of accommodating a diversity of adaptive agents. We also emphasise that multilevel selection was, in fact, part of the Modern Synthesis and, indeed, its inadequacies as a theory of organismal adaptation provided a crucial motivation for the concept of inclusive fitness.
... Surrogate Model of Landscape. The concept of the protein fitness landscape, which describes the relationship between a protein's sequence and its fitness score, has been used in protein engineering since 1932 [11], which provides a graphical representation of protein sequence and function. Exploring the entire protein fitness landscape can be difficult due to the time and cost involved, especially for large proteins with complex structure. ...
Protein sequence design is a challenging problem in protein engineering, which aims to discover novel proteins with useful biological functions. Directed evolution is a widely-used approach for protein sequence design, which mimics the evolution cycle in a laboratory environment and conducts an iterative protocol. However, the burden of laboratory experiments can be reduced by using machine learning approaches to build a surrogate model of the protein landscape and conducting in-silico population selection through model-based fitness prediction. In this paper, we propose a new method based on Batch Bayesian Optimization (Batch BO), a well-established optimization method, for protein sequence design. By incorporating Batch BO into the directed evolution process, our method is able to make more informed decisions about which sequences to select for artificial evolution, leading to improved performance and faster convergence. We evaluate our method on a suite of in-silico protein sequence design tasks and demonstrate substantial improvement over baseline algorithms.
... In August 1932, Dobzhansky took part in the Sixth International Congress of Genetics held in Ithaca, New York. There he heard Sewall Wright's report on evolutionary mechanisms based on his well known article of 1931 (Wright 1931(Wright , 1932. The report would later greatly influence Dobzhansky (Provine 1981). ...
Theodosius Dobzhansky was one of the principal ‘founding fathers' of the modern ‘synthetic theory of evolution' and the ‘biological species' concept, first set forth in his classic book, Genetics and the Origin of Species (1937). Much of the discussion of Dobzhansky’s work by historians has focused on English-accessible sources, and has emphasized the roles of the Morgan School, and figures such as Sewall Wright, and Leslie C. Dunn. This article uses Dobzhansky’s Russian articles that are unknown to English-speaking readers, and his late 1920s to early 1930s correspondence with colleagues and friends in the Soviet Union, to clarify some of the Russian influences on Dobzhansky’s evolving evolutionary views, particularly the development of his views on species and speciation. For Dobzhansky, as for Darwin, the problem of species and speciation was crucial for his theoretical explanation of evolution.
... Antigen diversification in a microbial pathogen can be conceptualized, modeled, and predicted with fitness landscapes. The idea of a fitness (or adaptive) landscape was first used as a metaphor by Sewall Wright in 1932 to describe the relationship between genotype and fitness [10]. Akin to topographic maps, these three-dimensional fitness landscapes plot possible genotype combinations along the x and y axes, and fitness (or a fitness proxy) on the z axis. ...
Driven by host–pathogen coevolution, cell surface antigens are often the fastest evolving parts of a microbial pathogen. The persistent evolutionary impetus for novel antigen variants suggests the utility of novelty-seeking algorithms in predicting antigen diversification in microbial pathogens. In contrast to traditional genetic algorithms maximizing variant fitness, novelty-seeking algorithms optimize variant novelty. Here, we designed and implemented three evolutionary algorithms (fitness-seeking, novelty-seeking, and hybrid) and evaluated their performances in 10 simulated and 2 empirically derived antigen fitness landscapes. The hybrid walks combining fitness- and novelty-seeking strategies overcame the limitations of each algorithm alone, and consistently reached global fitness peaks. Thus, hybrid walks provide a model for microbial pathogens escaping host immunity without compromising variant fitness. Biological processes facilitating novelty-seeking evolution in natural pathogen populations include hypermutability, recombination, wide dispersal, and immune-compromised hosts. The high efficiency of the hybrid algorithm improves the evolutionary predictability of novel antigen variants. We propose the design of escape-proof vaccines based on high-fitness variants covering a majority of the basins of attraction on the fitness landscape representing all potential variants of a microbial antigen.
Cancer genomes are almost invariably complex with genomic alterations cooperating during each step of carcinogenesis. In cancers that lack a single dominant oncogene mutation, cooperation between the inactivation of multiple tumor suppressor genes can drive tumor initiation and growth. Here, we shed light on how the sequential acquisition of genomic alterations generates oncogene-negative lung tumors. We couple tumor barcoding with combinatorial and multiplexed somatic genome editing to characterize the fitness landscapes of three tumor suppressor genes NF1, RASA1, and PTEN, the inactivation of which jointly drives oncogene-negative lung adenocarcinoma initiation and growth. The fitness landscape was surprisingly accessible, with each additional mutation leading to growth advantage. Furthermore, the fitness landscapes remained fully accessible across backgrounds with the inactivation of additional tumor suppressor genes. These results suggest that while predicting cancer evolution will be challenging, acquiring the multiple alterations that drive the growth of oncogene-negative tumors can be facilitated by the lack of constraints on mutational order.
Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the 'neutral mutation-random drift' hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist-selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?
Seasons impose different selection pressures on organisms through contrasting environmental conditions. How such seasonal evolutionary conflict is resolved in organisms whose lives span across seasons remains underexplored. Through field experiments, laboratory work, and citizen science data analyses, we investigate this question using two closely related butterflies (Pieris rapae and P. napi). Superficially, the two butterflies appear highly ecologically similar. Yet, the citizen science data reveal that their fitness is partitioned differently across seasons. Pieris rapae have higher population growth during the summer season but lower overwintering success than do P. napi. We show that these differences correspond to the physiology and behavior of the butterflies. Pieris rapae outperform P. napi at high temperatures in several growth season traits, reflected in microclimate choice by ovipositing wild females. Instead, P. rapae have higher winter mortality than do P. napi. We conclude that the difference in population dynamics between the two butterflies is driven by seasonal specialization, manifested as strategies that maximize gains during growth seasons and minimize harm during adverse seasons, respectively.
When looking for a solution, deterministic methods have the enormous advantage that they do find global optima. Unfortunately, they are very CPU intensive, and are useless on untractable NP-hard problems that would require thousands of years for cutting-edge computers to explore. In order to get a result, one needs to revert to stochastic algorithms that sample the search space without exploring it thoroughly. Such algorithms can find very good results, without any guarantee that the global optimum has been reached; but there is often no other choice than using them. This chapter is a short introduction to the main methods used in stochastic optimization.
The relationship between science and religion is a topic that runs rife with misconceptions, misunderstandings and debates. Are science and religion always in conflict? Is Darwin's theory of evolution through natural selection atheistic? How does history shape current debates around science and religion? This book explores these questions in a neutral and balanced way, focusing on the Christianity-evolution relationship. It shows that two paradigms – the world as an organism and the world as a machine – have critically informed and guided the discussions. The author uses his deep understanding of the history and philosophy of science, particularly Darwinian evolutionary theory and its controversies through the past 150 years, to bring fresh ideas to the debate and to wider discussions such as environmental issues and hate. Understanding the Christianity-Evolution Relationship provides a lively and informative analysis and lays out multiple views so that readers can make their own judgements to increase their understanding.
Evolutionary dynamics are subject to constraints ranging from limitations on what is physically possible to limitations on the pathways that evolution can take. One set of evolutionary constraints, known as 'demographic constraints', constrain what can occur evolutionarily due to the demographic or dynamical consequences of evolution leading to conditions that make populations susceptible to extinction. These demographic constraints can limit the strength of selection or the rates of environmental change populations can experience while remaining extant and the trait values a population can express. Here we further hypothesize that the population demographic and dynamic consequences of evolution also can constrain the eco-evolutionary pathways that populations can traverse by defining ecological boundaries represented by areas of likely extinction. We illustrate this process using a model of predator evolution. Our results show that the populations that persist over time tend to be those whose eco-evolutionary dynamics have avoided ecological boundaries representing areas of likely extinction due to stochastic deviations from a deterministic eco-evolutionary expectation. We term this subset of persisting pathways viable eco-evolutionary pathways. The potential existence of ecological boundaries constraining evolutionary pathways has important implications for predicting evolutionary dynamics, interpreting past evolution, and understanding the role of stochasticity and ecological constraints on eco-evolutionary dynamics.
The evolution of antibiotic-resistant bacterial populations underpins the ongoing antibiotic resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained, and whether it can be predictable.
Biological adaptations appear designed for a purpose, and so they result from a “creative process” almost by definition. Traditional evolutionary theory assigns a special role in this process to natural selection, with theorists invoking selection both to explain the appearance of purpose, and to predict what the purpose of adaptations will be. At the same time, traditional theory recognizes that many other factors might influence the evolution of adaptations. These factors might, for example, increase evolvability and accelerate adaptation, or bias evolution towards a subset of the possible adaptive outcomes. Such factors are also creative in a sense, but not in the same sense as natural selection. Challenges to traditional theory have sometimes championed organisms as a neglected source of creativity in evolution. This could be interpreted as the radical claim that non-human organisms—like people—are novel sources of purpose in nature, generating apparently designed outcomes that are not directed at reproductive success. But it might also be interpreted as the uncontroversial claim that organisms—like many other things—sometimes act in a way that accelerates adaptation or makes some adaptive outcomes more probable than others. Ambiguity about their claims has led to theories attracting unwarranted enthusiasm and unwarranted scepticism, and distracts us from the criteria by which the theories should be judged.KeywordsAdaptationEvolvabilityGenetic assimilationNiche construction
Astyanax mexicanus
Mycobacterium tuberculosis
Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines emergent function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes -- analogs to fitness landscapes -- that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically-inferred landscapes quantitatively predict community functions from knowledge of strain presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species, and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes are typically not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show this observation is generic across many ecological models, suggesting community-function landscapes can be applied broadly across many contexts. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.
In this chapter, we evaluate debates surrounding calls for an Extended Evolutionary Synthesis in light of the Darwinian core of evolutionary theory, which was somewhat broader than the Modern Synthesis. We suggest that Darwin’s nuanced operationalization of natural selection rested upon two innovations: the atomization of individuals into trait-variants, and a reconceptualization of heredity in terms of transmission of trait-variants. Darwin also implicitly differentiated between the causes and consequences of selection, noting that while selection acts on individuals, it is actually trait-variants that are consequently differentially transmitted, and the species that is eventually modified. This is important because the individual, with inherencies and agency, is largely relevant only when examining the causes of selection, with trait-variants being the more appropriate unit for studying its consequences. Consequently, we emphasize the importance of restricting the use of ‘fitness’ to one-step change in trait-variant frequency, instead of also using it for lifetime reproductive success of individuals, or even trait-variants. Fitness, thus defined, is always inclusive, circumventing much unnecessary debate. We also present a schematization of explananda in evolutionary biology and suggest a framework for the comparative evaluation of factors affecting evolutionary change. We further suggest that the controversial ‘gene’s eye view of evolution’ is best seen as not one, but two distinct views, one Fisherian and the other Dawkinsian, and that conflating them has led to considerable unnecessary debate. In conclusion, we suggest that it is helpful to view received evolutionary thought as an evolving set of explanations, intertwined with one another to varying degrees, rather than a distinct, static Modern Synthesis. This leads to our viewing various processes and factors affecting the origin, dynamics and patterns of prevalence of variants at various levels of biological organization, as representing differing but complementary parts of a complex, nuanced, multifarious and evolving standard evolutionary theory.KeywordsModern synthesisNatural selectionTrait-variantsDarwinian fitnessReproductive outputTransmission fidelityTransmission efficiencyGene’s eye view of evolution
The last decades have seen frequent calls for a more extended evolutionary synthesis (EES) that will supposedly overcome the limitations in the current evolutionary framework with its intellectual roots in the Modern Synthesis (MS). Some radical critics even want to entirely abandon the current evolutionary framework, claiming that the MS (often erroneously labelled “Neo-Darwinism”) is outdated, and will soon be replaced by an entirely new framework, such as the Third Way of Evolution (TWE). Such criticisms are not new but have repeatedly re-surfaced every decade since the formation of the MS, and they were particularly articulated by developmental biologist Conrad Waddington and paleontologist Stephen Jay Gould. Waddington, Gould, and later critics argued that the MS was too narrowly focused on genes and natural selection, and that it ignored developmental processes, epigenetics, paleontology and macroevolutionary phenomena. More recent critics partly recycle these old arguments and argue that non-genetic inheritance, niche construction, phenotypic plasticity and developmental bias necessitate major revision of evolutionary theory. Here I discuss these supposed challenges, taking a historical perspective and tracing the arguments by critics back to Waddington and Gould. I dissect the old claims by Waddington, Gould and more recent critics that the MS was excessively gene centric and became increasingly “hardened” over time and narrowly focused on natural selection. Recent critics have consciously or unconsciously exaggerated the long-lasting influence of the MS on contemporary evolutionary biology and have underestimated many post-Synthesis developments, particularly Neutral Theory, evolutionary quantitative genetics and the power and generality of the Price Equation. Critics have also painted a biased picture of the MS as a more monolithic research tradition than it ever was and have downplayed the pluralistic nature of contemporary evolutionary biology, particularly the long-lasting influence of Sewall Wright with his emphasis on gene interactions and stochasticity. I argue that some of the criticisms of the MS and contemporary evolutionary biology are primarily meta-scientific, revealing the underlying identity politics of critics when pushing their alternative research agendas. It is still unclear what their proposed alternative research frameworks would entail and why the existing theoretical framework is insufficient. Finally, I outline and visualize the conceptually split landscape of contemporary evolutionary biology, with four different stably coexisting analytical frameworks: adaptationism, mutationism, neutralism and selectionism. I suggest that the field can accommodate the challenges raised by critics, although structuralism (“Evo Devo”) and macroevolution remain to be conceptually integrated within mainstream evolutionary theory.KeywordsDevelopmental biasExtended evolutionary synthesisModern synthesisMacroevolutionMutationismNeo-DarwinismNiche constructionNon-genetic inheritancePopulation geneticsPhenotypic plasticityQuantitative geneticsThird way of evolution
From one point of view, the passions aroused by the gene’s-eye view are difficult to explain. As Ågren (2021; this volume) shows clearly, the methods of Williams (1966) and Dawkins (1976) continue to be useful for many problems (e.g., Boomsma 2016: R1254)—even Dawkins’ throwaway remarks about green beards (1976: 96; Hamilton 1964: 25) still generate valuable science (e.g., Gruenheit et al. 2017; Gardner and West 2010); and yet the methods were never more than a part of the biologist’s toolkit (Dawkins 1982: Ch. 1; Williams 1992: 31; Grafen 1992; Kitcher 2001: 407; Haig 2012; Boomsma 2016). In any case, as Ågren also shows, the gene’s-eye view differs only subtly from one sort of organism-centered approach (e.g., Hamilton 1964; Brockmann et al. 1979; Grafen 1999). Many of the initial disputes about the gene’s-eye view were cleared up long ago by Williams (1985) and especially Lloyd (1988, 2001), who showed how different biologists, interested in different questions, had been using terms like “unit of selection” to mean different things (Maynard Smith 2001). But consider the following, from a review of Ågren (2021) in the journal Evolution:Why would disclaimers like this seem necessary? Winther’s framing, so puzzling from one point of view, does I think make better sense if we consider the contributions of two giants of evolutionary genetics: R. A. Fisher and R. C. Lewontin.KeywordsGene’s-eye-viewAdaptationR. A. FisherR. C. Lewontin
Explaining the emergence of diversity and the coexistence of competing types has long been one of the main goals of ecological theory. Rugged fitness landscapes have often been used to explain diversity through the presence of local peaks, or adaptive zones, in the fitness landscape acting as available niches for different species. Alternatively, niche-packing and theories based on limiting similarity describe frequency-dependent selection leading to the organic differentiation of a continuous phenotype space into multiple coexisting types. By combining rugged carrying capacity landscapes with frequency-dependent selection, here we investigate the effects of ruggedness on adaptive diversification and stably maintained diversity. We show that while increased ruggedness often leads to a decreased opportunity for adaptive diversification, it is the shape of the global carrying capacity function, not the local ruggedness, that determines the diversity of the ESS and the total diversity a system can stably maintain.
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