Biology subjects

Priklopil, T.

Publications and source records attributed to Priklopil, T..

8 recordsLinked to original sources

bioRxiv2025

Adaptation of protein stability to thermally heterogeneous environments

Proper protein folding is essential for biological function, and its disruption can lead to disease, reduced fitness, or death. The ability of a protein to maintain its folded conformation is thus critical for life, making it a key target of adaptive evolution. However, protein stability is sensitive to environmental factors, particularly temperature, which can threaten phenotypic integrity and organismal survival under thermal changes. Despite its importance, the influence of complex thermal environments - characterized here by mean temperature, thermal fluctuations, and environmental heterogeneity - on the evolution of protein stability remains poorly understood. To address this, we developed a mathematical framework that combines two well-established models: a population genetic model describing species distributed across habitats with distinct thermal environments, and a thermodynamic model of protein stability incorporating temperature-dependent enthalpy and entropy contributions. We focus on two-state proteins that alternate between folded and unfolded states and assume that allelic fitness is maximized in proteins that achieve an optimal balance between flexibility and rigidity. Using this framework, we performed an invasion analysis of mutations (sensu adaptive dynamics framework) affecting three thermodynamic parameters that fully determine protein stability profiles. Where possible, we derived analytical expressions for evolutionarily optimal thermodynamic parameters and complemented these with numerical solutions. Our results show that mean temperature and thermal fluctuations have orthogonal effects on thermodynamic parameters, underscoring the need to consider both when studying protein stability adaptation. We further examined thermally heterogeneous environments, where subpopulations connected by migration experience different mean temperatures, identifying conditions that favor either local (specialist) or global (generalist) adaptation. Our results may explain why one thermodynamic parameter shows little association with thermal adaptation and suggest that local adaptation is more likely for proteins with stability profiles limited to narrow temperature ranges. Additionally, our analysis reveals whether a locally adapted protein originated in a colder or warmer habitat. Finally, we identified trade-offs in thermodynamic parameters that influence local or global adaptation. This study offers key predictions about protein evolution in complex thermal environments and lays the groundwork for developing practical tools to understand how temperature shapes adaptation and biodiversity.

evolutionary biology↗

bioRxiv2025

The role of asymmetric migration on local adaptation: an analysis of the classic two-habitat migration model

We explore how migration and selection interact to shape local adaptation, revisiting the notion that increased gene flow typically suppresses genetic differentiation and local adaptation. Instead, we demonstrate that migration can both suppress and facilitate local adaptation, depending on the symmetry or asymmetry of migration rates between populations. This duality is examined in two scenarios within a single-locus theory: one in which local adaptation of a pair of alleles is maintained under arbitrary patterns of antagonistic selection, and another in which local adaptation develops through the recurrent invasion and fixation of alleles with weak selective effects on a continuous phenotype. For both scenarios, we analyze the classic two-habitat migration model, providing a novel examination of its dynamics. When migration is symmetric, an equal increase in migration rates impedes local adaptation by forcing both variant alleles to spend more time in non-local habitats where they are disfavored. In contrast, when migration rates increase asymmetrically, leading to skewed gene flow, both alleles spend more time in the same habitat, disadvantaging the non-local allele but favoring the locally adapted one. Thus, both increasing and decreasing migration rates can favor or hinder local adaptation, depending on the interplay between migration patterns and selection, underscoring the importance of migration heterogeneity in shaping local adaptation dynamics.

evolutionary biology↗

bioRxiv2024

Explicit derivation of the standard fitting technique for two-state protein transitions using differential scanning calorimetry data

This paper has three main objectives. First, we aim to derive from first principles a linear heat capacity model for proteins exhibiting two-state conformational transition dynamics, which includes, as a special case, the constant heat capacity model frequently referenced in the literature. Second, we present a protocol for inferring the Gibbs free energy of protein folding by fitting the linear heat capacity model to differential scanning calorimetry data. Third, we demonstrate this protocol using Mathematica software, applying it to real datasets and comparing the linear and constant heat capacity models. While most of our derivations are well established in the literature, we provide a step-by-step bridge from mathematical modeling to application, addressing a practical gap in existing resources that benefits researchers.

molecular biology↗

bioRxiv2022

On the interpretation of the operation of natural selection in class-structured populations

Biological adaptation is the outcome of allele-frequency change by natural selection. At the same time, populations are usually class structured as individuals occupy different states such as age, sex, or stage. This is known to result in the differential transmission of alleles through non-heritable fitness differences called class transmission, also affecting allele-frequency change even in the absence of selection. How does one then isolate the allele-frequency change due to selection from that owing to class transmission? We decompose one-generational allele-frequency change in terms of effects of selection and class transmission, and show how reproductive values can be used to reach a decomposition between any two distant generations of the evolutionary process. This provides a missing relationship between multigenerational allele-frequency change and the operation of selection. It also allows to define a measure of fitness summarizing the effect of selection in a multigenerational evolutionary process, which connects asymptotically to invasion fitness.

evolutionary biology↗

bioRxiv2021

Metacommunities, fitness and gradual evolution

We analyze the evolution of a multidimensional quantitative trait in a class structured focal species interacting with other species in a wider metacommunity. The evolutionary dynamics in the focal species as well as the ecological dynamics of the whole metacommunity is described as a continuous time process with birth, physiological development, dispersal, and death given as rates that can depend on the state of the whole metacommunity. This can accommodate complex local community and global metacommunity environmental feedbacks owing to inter- and intra-specific interactions, as well as local environmental stochastic fluctuations. For the focal species, we derive a fitness measure for a mutant allele affecting class-specific trait expression. Using classical results from geometric singular perturbation theory, we provide a detailed proof that if the effect of the mutation on phenotypic expression is small ("weak selection"), the large system of dynamical equations needed to describe selection on the mutant allele in the metacommunity can be reduced to a single ordinary differential equation on the arithmetic mean mutant allele frequency that is of constant sign. This invariance on allele frequency entails the mutant either dies out or will out-compete the ancestral resident (or wild) type. Moreover, the directional selection coefficient driving arithmetic mean allele frequency can be expressed as an inclusive fitness effect calculated from the resident metacommunity alone, and depends, as expected, on individual fitness differentials, relatedness, and reproductive values. This formalizes the Darwinian process of gradual evolution driven by random mutation and natural selection in spatially and physiologically class structured metacommunities.

evolutionary biology↗

bioRxiv2020

Hamilton's rule, gradual evolution, and the optimal (feedback) control of reaction norms and other function-valued traits

Most traits expressed by organisms, such as gene expression profiles, developmental trajectories, behavioural sequences and reaction norms are function-valued traits (colloquially "phenotypically plastic traits"), since they vary across an individuals age and in response to various internal and/or external factors (state variables). Furthermore, most organisms live in populations subject to limited genetic mixing and are thus likely to interact with their relatives. We here formalise selection on genetically determined function-valued traits of individuals interacting in a group-structured population, by deriving the marginal version of Hamiltons rule for function-valued traits. This rule simultaneously gives a condition for the invasion of an initially rare mutant function-valued trait and its ultimate fixation in the population (invasion thus implies substitution). Hamiltons rule thus underlies the gradual evolution of function-valued traits and gives rise to necessary first-order conditions for their uninvadability (evolutionary stability). We develop a novel analysis using optimal control theory and differential game theory, to simultaneously characterise and compare the first-order conditions of (i) open-loop traits - functions of time (or age) only, and (ii) closed-loop (state-feedback) traits - functions of both time and state variables. We show that closed-loop traits can be represented as the simpler open-loop traits when individuals do no interact or when they interact with clonal relatives. Our analysis delineates the role of state-dependence and interdependence between individuals for trait evolution, which has implications to both life-history theory and social evolution.

evolutionary biology↗

bioRxiv2019

Invasion implies substitution in ecological communities with class-structured populations

Long-term evolution of quantitative traits is classically and usefully described as the directional change in phenotype due to the recurrent fixation of new mutations. A formal justification for such continual evolution ultimately relies on the "invasion implies substitution"-principle. Here, whenever a mutant allele causing a small phenotypic change can successfully invade a population, the ancestral (or wild-type) allele will be replaced, whereby fostering gradual phenotypic change if the process is repeated. It has been argued that this principle holds in a broad range of situations, including spatially and demographically structured populations experiencing frequency and density dependent selection under demographic and environmental fluctuations. However, prior studies have not been able to account for all aspects of population structure, leaving unsettled the conditions under which the "invasion implies substitution"-principle really holds. In this paper, we start by laying out a program to explore and clarify the generality of the "invasion implies substitution"-principle. Particular focus is given on finding an explicit and functionally constant representation of the selection gradient on a quantitative trait. Using geometric singular perturbation methods, we then show that the "invasion implies substitution"-principle generalizes to well-mixed and scalar-valued polymorphic multispecies ecological communities that are structured into finitely many demographic (or physiological) classes. The selection gradient is shown to be constant over the evolutionary timescale and that it depends only on the resident phenotype, individual growth-rates, population steady states and reproductive values, all of which are calculated from the resident dynamics. Our work contributes to the theoretical foundations of evolutionary ecology.

evolutionary biology↗

bioRxiv2018

Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system

Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a recognition system common in flowering plants.

evolutionary biology↗