Biology subjects

Gokhale, C. S.

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

6 recordsLinked to original sources

bioRxiv2018

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↗

bioRxiv2018

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↗

bioRxiv2018

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↗

bioRxiv2018

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↗

bioRxiv2017

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↗

bioRxiv2017

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↗