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Gokhale, C. S.

Publications and source records attributed to Gokhale, C. S..

30 records · Page 2Linked to original sources

A unifying approach to gene drive

Synthetic gene drive technologies aim to spread transgenic constructs into wild populations even when they impose organismal fitness disadvantages. The extraordinary diversity of plausible drive mechanisms and the range of selective parameters they may encounter makes it very difficult to convey their relative predicted properties, particularly where multiple approaches are combined. The sheer number of published manuscripts in this field, experimental and theoretical, the numerous techniques resulting in an explosion in the gene drive vocabulary hinder the regulators point of view. We address this concern by defining a simplified parameter based language of synthetic drives. Employing the classical population dynamics approach, we show that different drive construct (replacement) mechanisms can be condensed and evaluated on an equal footing even where they incorporate multiple replacement drives approaches. Using a common language, it is then possible to compare various model properties, a task desired by regulators and policymakers. The generalization allows us to extend the study of the invasion dynamics of replacement drives analytically and, in a spatial setting, the resilience of the released drive constructs. The derived framework is available as a standalone tool. Besides comparing available drive constructs, our tool is also useful for educational purpose. Users can also explore the evolutionary dynamics of future hypothetical combination drive scenarios. Thus, our results appraise the properties and robustness of drives and provide an intuitive and objective way for risk assessment, informing policies, and enhancing public engagement with proposed and future gene drive approaches.

evolutionary biology↗

Consequences of combining life-history traits with sex-specific differences

Males and females evolved distinct life-history strategies, reflected in diverse inter-linked life-history traits. The sex that allocates more resources towards offspring relies on an increased life span, and long life requires an efficient immune system. The other sex needs to attract mates and thus allocates its resources towards ornamentation, which may negatively correlate with investment into the immune defense. Such sex-specific resource allocation trade-offs are not always strictly female or male-specific but may depend on the overall resources allocated towards life-history traits. Informed by experimental data, we designed a theoretical framework that combines multiple life-history traits. We disentangled specific life-history strategies from particular sex, allowing us to include species with reversed sex-roles and male parental investment. We computed the lifetime reproductive success (combining fitness components from diverse sex-specific life-history traits) observing a strong bias in adult sex ratio depending on sex-specific resource allocation towards life-history traits. Overall, our work provides a generalized method to combine various life-history traits with sex-specific differences to calculate lifetime reproductive success. The results explain specific population-level empirical observations as a consequence of sexual dimorphism in life-history traits.

evolutionary biology↗

Eco-evolutionary dynamics of Plasmodium genotypes under mass drug administration

Mass Drug Administration (MDA) is regarded as a potential strategy for locally interrupting transmission of human malaria under specific circumstances. However, insights on how MDA affects the eco-evolutionary dynamics of different Plasmodium species are not well known. We provide a computational model where the ecologically explicit life cycle of the parasite is implemented. Since the parasite inhabits two different ecological niches - human host and the mosquito - it undergoes different selection pressures during its reproduction. We use the model to perform an evolutionary analysis of the dynamics of resistance alleles under atovaquone, chloroquine and combined atovaquone-chloroquine drug treatments. Our study shows how the reduced viability of resistant parasites in the mosquito affects the spread of resistance and transmission interruption in treated human populations. Overall, results confirm that the disadvantage of drug-resistant genotypes in the mosquito vector is a good tool to achieve malaria control goals under MDA programmes.\n\nAuthor summaryEvery year there are millions of new malaria cases reported worldwide. The cause of the disease is the infection by Plasmodium, a protozoan which is transmitted between humans through the bite of a mosquito. Antimalarials have existed since long, but Plasmodium has evolved resistance to the treatment, making it necessary to develop new strategies to heal the infected humans. Lately, it has been pointed out that mosquitoes could be our allies when using drugs such as atovaquone, which resistant parasites have difficulties to reproduce in the mosquito. Here we study the scenarios in which these drugs, used in Mass Drug Administration (MDA) programmes, can interrupt the transmission of malaria in local treated populations.

evolutionary biology↗

On a mechanistic process of macroparasite aggregation

Parasite aggregation, a recurring pattern in macroparasite infections, is considered one of the "laws" of parasite ecology. Few hosts have a large number of parasites while most hosts have a low number of parasites. Phenomenological models of host-parasite systems thus use the negative-binomial distribution. However, to infer the mechanisms of aggregation, a mechanistic model that does not make any a priori assumptions is essential. Here we formulate a mechanistic model of parasite aggregation in hosts without assuming a negative-binomial distribution. Our results show that a simple model of parasite accumulation still results in an aggregated pattern, as shown by the derived mean and variance of the parasite distribution. By incorporating the derived statistics in host-parasite interactions, we can predict how aggregation affects the population dynamics of the hosts and parasites through time. Thus, our results can directly be applied to observed data as well as can inform the designing of statistical sampling procedures. Overall, we have shown how a plausible mechanistic process can result in the often observed phenomenon of parasite aggregation occurring in numerous ecological scenarios, thus providing a basis for a "law" of ecology.

ecology↗

Eco-evolutionary spatial dynamics of non-linear social dilemmas

Spatial dynamics can promote the evolution of cooperation. While dispersal processes have been studied in simple evolutionary games, real-world social dilemmas are much more complicated. The public good, in many cases, does not increase linearly as per the investment in it. When the investment is low, for example, every additional unit of the investment may help a lot to increase the public good, but the effect vanishes as the number of investments increase. Such non-linear behaviour is the norm rather than an exception in a variety of social as well as biological systems. We take into account the non-linearity in the payoffs of the public goods game as well as the natural demographic effects of population densities. Population density has also been shown to impact the evolution of co-operation. Coupling these non-linear games and population size effect together with an explicitly defined spatial structure brings us one step closer to the complexity of real eco-evolutionary spatial systems. We show how the non-linearity in payoffs, resulting in synergy or discounting of public goods can alter the effective rate of return on the cooperative investment. Synergy or discounting in public goods accumulation affects the resulting spatial structure, not just quantitatively but in some cases, drastically changing the outcomes. In cases where a linear payoff structure would lead to extinction, synergy can support the coexistence of cooperators and defectors. The combined eco-evolutionary trajectory can thus be qualitatively different in cases on non-linear social dilemmas.

evolutionary biology↗

On the innovation and evolution of predatory tactics

Predator-prey systems are ubiquitous across ecological systems. Typical ecological models focus on the dynamics of predator-prey populations. Eco-evolutionary models integrate arms race or Red-Queen like dynamics. The roles of the predator and prey species are always assumed to be static. Nevertheless, sometimes predators can bite off more than they can chew. For example, predators that encounter multiple or dangerous prey types may need to develop new predatory tactics to capture prey. We explore the dynamics of predator-prey dynamics when the prey can injure or kill the predator. This common ecological scenario places pressure on the predator to develop novel predatory tactics to both capture prey and avoid counter-attack from prey. Taking a bottom-up approach, we develop the Holling function mechanistically and then implement it in a model of innovationselection dynamics inspired by economic theory. We show how an interdisciplinary approach can be used to explain the emergence of complex predatory behaviours. Notably, our study shows why predators may hunt dangerous prey even when safe prey are available. In a broader context, we demonstrate how a multidisciplinary approach combining ecology, evolution and economics improves our understanding of a complex behavioural trait.

animal behavior and cognition↗

Eco-evolutionary agriculture: a study in crop rotations

Since its origins, thousands of years ago, agriculture has been challenged by the presence of evolving plant pathogens. In response, current practices have started relying on computational tools to design efficient prospective planning, but further efforts for multi-criteria assessment are needed. Here, we present a methodology for developing cultivation strategies optimal for control or eradication of pathogens. This approach can integrate both, traditionally used criteria in crop rotations and the analysis of host-pathogen coevolution systems where hosts are artificially selected. Our analysis shows that prospective planning can maximise cash yield in the long run by investing consecutively in soil quality during initial sea-sons. Importantly, rational application of crop rotation patterns can minimise yield loss in infected fields, despite the evolution of pathogen virulence. Our results provide strategies for optimal resource investment for increased food production and lead to further insights into minimisation of pesticide use in a society demanding efficient agriculture.

evolutionary biology↗

Environmental disturbances compromise synthetic symbiosis

By virtue of complex interactions, the behaviour of mutualistic systems is difficult to study and nearly impossible to predict. We have developed a theoretical model of a modifiable experimental yeast system that is amenable to exploring self-organised cooperation while considering the production and use of specific metabolites. Leveraging the simplicity of an artificial yeast system, a simple model of mutualism, we develop and test the assumptions and stability of this theoretical model. We examine how one-off, recurring and permanent changes to an ecological niche affect a cooperative interaction and identify an ecological \"Goldilocks zone\" in which the mutualism can survive. Moreover, we explore how a factor like the cost of mutualism - the cellular burden of cooperating - influences the stability of mutualism and how environmental changes shape this stability. Our results highlight the fragility of mutualisms and suggest the use of synthetic biology to stave off an ecological collapse.

evolutionary biology↗

Disentangling eco-evolutionary effects on trait fixation

In population genetics, fixation of traits in a demographically changing population under frequency-independent selection has been extensively analysed. In evolutionary game theory, models of fixation have typically focused on fixed population sizes and frequency-dependent selection. A combination of demographic fluctuations with frequency-dependent interactions such as Lotka-Volterra dynamics has received comparatively little attention. We consider a stochastic, competitive Lotka-Volterra model with higher order interactions between two traits. The emerging individual based model allows for stochastic fluctuations in the frequencies of the two traits and the total population size. We calculate the fixation probability of a trait under differing competition coefficients. This fixation probability resembles qualitatively the deterministic evolutionary dynamics. Furthermore, we partially disentangle the selection effects into their ecological and evolutionary components. We find that changing the evolutionary selection strength also changes the population dynamics and vice versa. Thus, a clean separation of the ecological and evolutionary effects is not possible. The entangled eco-evolutionary processes thus cannot be ignored when determining fixation properties in a co-evolutionary system.

evolutionary biology↗

Ecological feedback on diffusion dynamics

Spatial patterns are ubiquitous across different scales of organization. Animal coat pattern, spatial organization of insect colonies, and vegetation in arid areas are prominent examples from such diverse ecologies. Typically, pattern formation has been described by reaction-diffusion equations, which considers individuals dispersing between sub-populations of a global pool. This framework applied to public goods game nicely showed the endurance of populations via diffusion and generation of spatial patterns. However, how the spatial characteristics, such as diffusion, are related to the eco-evolutionary process as well as the nature of the feedback from evolution to ecology and vice versa, has been so far neglected. We present a thorough analysis of the ecologically driven evolutionary dynamics in a spatially extended version of ecological public goods games. We show how these evolutionary dynamics feedback into shaping the ecology thus together determining the fate of the system.

evolutionary biology↗

Social Dilemma In The External Immune System Of The Red Flour Beetle? It Is A Matter Of Time

Sociobiology has revolutionized our understanding of interactions between organisms. Interactions may present a social dilemma where the interests of individual actors do not align with those of the group as a whole. Viewed through a sociobiological lens, nearly all interactions can be described in terms of their costs and benefits and a number of them then resemble a social dilemma. Numerous experimental systems, from bacteria to mammals, have been proposed as models for studying such dilemmas. Here we make use of the external immune system of the red flour beetle, Tribolium castaneum, to investigate how the experimental duration can affect whether the external secretion comprises a social dilemma or not. Some beetles (secretors) produce a costly quinone-rich external secretion that inhibits microbial growth in the surrounding environment, providing the secretors with direct personal benefits. However, since the antimicrobial secretion acts in the environment of the beetle it is potentially also advantageous to other beetles (non-secretors), who avoid the cost of producing the secretion. We test experimentally if the secretion qualifies as a public good. We find that in the short term, costly quinone secretion can be interpreted as a public good presenting a social dilemma where the presence of secretors increases the fitness of the group. In the long run, the benefit to the group of having more secretors vanishes and actually becomes detrimental to the group. Therefore, in such semi-natural environmental conditions, it turns out that qualifying a trait as social can be a matter of timing.

evolutionary biology↗

Discovering Complete Quasispecies In Bacterial Genomes

Mobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs within a genome are an evolving populations because they replicate and mutate. We know the exact composition of this population and the sequence of each member of a REPIN population, in contrast to most other biological populations. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to ten different REPIN populations from ten different bacterial strains and estimate duplication rates. We find that our estimated duplication rates range from about 5 x 10-9 to 37 x 10-9 duplications per generation per genome. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size and we also see an example of competition between two REPIN populations.

evolutionary biology↗