Biology subjects

Agashe, D.

Publications and source records attributed to Agashe, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Mutation bias influences the emergence and effects of antibiotic resistance

Evolution of antibiotic resistance is a major global public health problem. Rapid emergence of antibiotic resistance is often linked to hypermutator bacteria with defective DNA repair, leading to high mutation rates that are broadly advantageous. However, depending on which DNA repair pathway is dysfunctional, mutators may sample only specific types of mutations at a higher rate. Thus, their mutation spectrum can be biased towards specific mutation types, influencing the identity of resistance mutations. Under strong antibiotic selection, an overall high mutation rate should generally shorten the time to sample a resistance mutation and increase the probability of resistance. However, recent work suggests that the mutation rate for specific types of mutations in target genes that drive high resistance is more important than the overall mutation rate. To systematically test this prediction, we exposed Escherichia coli mutators with varying mutation rates and spectra to antibiotics targeting different cellular functions. For each strain, we determined the highest antibiotic concentration at which resistance could emerge overnight, quantifying both the magnitude and probability of resistance. High level antibiotic resistance was generally better predicted by specific rather than overall mutation rate, and resistance mutations matched the mutation spectrum of the respective mutator. Despite the varying magnitude of resistance, at the highest antibiotic concentration survived by each strain, the respective resistance mutations were generally costly in the absence of antibiotic. Given that mutators often arise in laboratory, natural, and clinical settings under antibiotic selection, we suggest that their mutation spectra deserve more attention.

evolutionary biology↗

bioRxiv2026

Codon degeneracy contributes to divergent fitness effects of rare tRNAs with A-starting anticodons

Transfer RNA (tRNA) repertoires vary greatly across genomes, shaped by genetic drift and selection. A peculiar pattern across prokaryotes is the near-complete absence of tRNAs with unmodified adenine at the 34th (wobble) position (i.e., tRNAANN). Each of these tRNAs are just a single mutation away from several other tRNAs. Hence, their persistent absence suggests fundamental but hitherto unclear constraints. We engineered 36 Escherichia coli strains expressing tRNAs carrying each theoretically possible ANN anticodon to determine their functionality and fitness effects. Notably, there was no evidence of broad toxicity due to these tRNAs. All five tRNAANN tested underwent post-transcriptional maturation and all seven tested compensated for the deletion of their respective native tRNABNN (carrying G, C or U at the 34th position), demonstrating that tRNAANN are translationally active. Furthermore, tRNAANN from four-fold degenerate (4D) codon boxes were unmodified and were generally neutral or beneficial, whereas tRNAANN from two-fold degenerate (2D) boxes underwent A34-to-I34 modification and were more likely to impair fitness. We suggest superwobbling by tRNAANN -- decoding an entire four-codon set -- as one mechanism underlying these differential fitness effects. Maximal degeneracy in 4D boxes buffers or exploits tRNAANN superwobbling via synonymous decoding, whereas constrained degeneracy in 2D boxes renders it deleterious, likely through amino acid misincorporation. Thus, these differential fitness effects, sharpens the paradox of neutral or beneficial yet absent 4D tRNAANN, while beginning to empirically unravel underlying causes for the absence of 2D tRNAANN.

evolutionary biology↗

bioRxiv2025

Crowding drives terminal investment in a generalist pest

Apart from genotype and environment, several fitness related traits of individuals are also influenced by the conditions experienced by their parents, i.e., by parental effects. To uncover the underlying physiological or molecular mechanisms, most studies analyze specific drivers in isolation, such as parental age or the degree of crowding experienced by the parents. However, potential interaction effects between different aspects of parental context are poorly understood. We analyzed the combined effect of parental age and population density on the number, fitness and physiology of offspring, in the red flour beetle Tribolium castaneum. Both factors independently reduce fitness, leading us to predict that old parents from high density should produce fewer offspring of the lowest quality. Surprisingly, older parents exposed to crowding produced more eggs than expected. These eggs were larger, had higher survival in an optimal as well as a suboptimal resource, and were provisioned with more lipids. This result is consistent with terminal reproductive investment in response to high density. The interaction between two ecologically relevant contexts -- ageing and crowding -- thus drives terminal investment via nutrient provisioning, perhaps contributing to the success of this generalist pest.

evolutionary biology↗

bioRxiv2025

Mutation bias is a key predictor of adaptation rate

A growing body of work indicates that mutation bias -- whereby some types of mutations occur more often than others -- can influence the genetic basis of adaptation and the distribution of fitness effects of new mutations, with potentially important evolutionary consequences. Specifically, reversing an ancestral mutation bias (e.g., in Escherichia coli, shifting from a transition-biased to a transversion-biased mutation spectrum) enhances access to under-sampled variants, increasing the supply of beneficial mutations. However, the effect of mutation bias relative to other factors influencing adaptation remains unclear. By experimentally evolving wild type and mutator E. coli strains in different growth media, we show that mutation bias reversal facilitates early adaptation, altering the genetic basis of adaptation and the type of mutations accumulated under selection. Together, mutation bias, mutation rate, and initial fitness correctly predicted relative adaptation rates for any pair of strains. Our results highlight multiple ways in which mutational processes can shape genetic and phenotypic outcomes of adaptation.

evolutionary biology↗

bioRxiv2025

Ecological drift drives microbiome variation in the red flour beetle

Many eukaryotes harbor complex microbial communities that provide significant benefits to the host. However, recent work demonstrates substantial variation in microbiota across hosts and over time, though the causes and consequences of this instability are not always clear. We describe large temporal, among-individual and across-population variation in the microbiome of the red flour beetle Tribolium castaneum, a widespread pest of stored grain flour and a laboratory model organism. Across 5 years, the total load and composition of the bacterial community of laboratory beetle populations fluctuated dramatically, cycling between a few dominant taxa and hundreds of rare taxa. We show that this ecological drift is caused by a lack of maternal microbial transmission and large microbial load fluctuations in flour, which is the primary reservoir of microbial inocula. Newly hatched larvae (from eggs) and newly eclosed adults (from pupae) acquire microbes from ingested flour containing conspecific feces. The flour microbiome fluctuates with host population density and stage structure, with larval feces increasing microbial load and antimicrobial secretions from adults decreasing it. Periodic flour replacement during population maintenance also dramatically decreases flour bacterial load, contributing to stochasticity in microbial colonization. The resulting drift was associated with unstable fitness benefits for beetles, though we cannot disentangle cause vs. effect. Our work thus represents a case study of significant ecological drift even in a highly controlled laboratory environment. We suggest that such unstable microbial communities and variable host benefits may not be uncommon, and offer an opportunity to analyze early stages of the evolution and ecology of host-microbial interactions.

ecology↗

bioRxiv2025

Cost of altered translation accuracy shapes adaptation to antibiotics in E. coli

Protein synthesis, while central to cellular function, is error-prone. The resulting mistranslation is generally costly, but we do not know how these costs compare or interact with the costs imposed by external selection pressures such as antibiotics. We also do not know whether and how these costs are compensated during evolution. It is important to answer these questions, since mistranslation is ubiquitous and antibiotic exposure, widespread. We quantified the growth cost of genetically increasing and decreasing mistranslation rates, and exposure to low antibiotic concentrations, in Escherichia coli. Mistranslation costs were generally lower than the cost imposed by antibiotics, and exacerbated in a strain-specific manner under antibiotic exposure. All strains quickly compensated the antibiotic cost during experimental evolution, via antibiotic- and genotype-specific mutations. In contrast, mistranslation costs were significantly reduced only in some cases, without clear causal mutations. Control populations that evolved without antibiotics consistently compensated the cost of accuracy, and evolved increased antibiotic resistance as a by-product. Our work demonstrates that even when the cost of mistranslation is weak, altered translation accuracy can shape adaptive outcomes and underlying genetic mechanisms, with strong collateral fitness effects for apparently unrelated phenotypes such as antibiotic resistance.

evolutionary biology↗

bioRxiv2025

Founders predict trait evolution and population dynamics after evolutionary rescue

Evolutionary rescue helps populations survive environmental change, but the phenotypic and demographic factors associated with rescue dynamics and its long-term effects remain unclear. We experimentally evolved 10 wild-collected populations of flour beetles from across India in a suboptimal corn resource for 70 generations (>5 years), collecting >10,000 population census points book-ended by measurements of fitness-related traits for 30 experimental lines. Despite clear ancestral trait differences, all lines showed highly parallel evolutionary rescue within 20 generations. Long-term average population size varied across source populations and was positively correlated with ancestral development rate, which increased convergently across populations and emerged as the single best predictor of population performance during and after evolutionary rescue. Notably, specific demographic events during rescue (such as the rate of population decline and recovery) were uncorrelated both with ancestral trait distributions and post-rescue adaptation. Our results support prior work showing founder traits as key predictors of adaptation, and highlight their role in long-term adaptation and trait evolution following evolutionary rescue. SIGNIFICANCE STATEMENTUnderstanding how populations adapt to sudden environmental change is vital given accelerating biodiversity declines, the rise of antimicrobial resistance and climate change. We chart evolutionary rescue -- where rapid adaptation prevents extinction -- in flour beetles across 70 generations. Using >10,000 census points and measuring fitness in ancestors, their offspring and in evolved lines, we show that larval development rate is the strongest correlate of long-term population success across diverse wild-collected populations. The effect of ancestral variation is dynamic and disassociated from finer-grained details of the rescue. All populations show highly parallel evolutionary rescue, with convergent evolution in key traits. These findings have direct implications for predicting species survival after environmental change, ranging from conservation to pest and pathogen management.

evolutionary biology↗

bioRxiv2024

Divergence and convergence in epiphytic and endophytic phyllosphere bacterial communities of rice landraces

Phyllosphere-associated microbes can significantly alter host plant fitness, with distinct functions provided by bacteria inhabiting the epiphytic (external surface) vs. endophytic niches (internal leaf tissue). Hence, it is important to understand the assembly and stability of these phyllosphere communities, especially in field conditions. Broadly, epiphytic communities should encounter more environmental changes and immigration, whereas endophytic microbiomes should face stronger host selection. We analysed the structure and stability of leaf phyllosphere microbiomes of four traditionally cultivated rice landraces and one commercial variety from northeast India grown in the field for three consecutive years, supplemented with opportunistic sampling of 8 other landraces. Epiphytic and endophytic bacterial communities shared dominant core genera such as Methylobacterium and Sphingomonas. Consistent with an overall strong environmental effect, both communities varied more across sampling years than across host landraces. Seeds sampled from a focal landrace did not support vertical transmission of phyllosphere bacteria, suggesting that both types of communities are assembled anew each generation. Despite these points of convergence, epiphytic communities had distinct composition and significantly higher microbial load, and were more rich, diverse, modular, and unstable than endophytic communities. Finally, focused sampling of one landrace across developmental stages showed that the divergence between the two types of communities arose primarily at the flowering stage. Thus, our results show both convergent and divergent patterns of community assembly and composition in distinct phyllosphere niches in rice, identifying key bacterial genera and host developmental stages that may aid agricultural interventions to increase rice yield.

microbiology↗

bioRxiv2024

Genome assembly and annotation of the red flour beetle (Tribolium castaneum) from India

The largest insect order, Coleoptera, includes several economically important beetles that also serve as major model species for biological research. Perhaps foremost among these is the red flour beetle, a global pest of stored grains and flour whose genome was sequenced in 2008. However, the currently available reference genome (Tcas5.2) is incomplete, fragmented and contains many gaps, and the Y chromosome is not assembled. Here we present inTcas1, an updated genome assembly and annotation of T. castaneum collected from India, assembled using both short and long read sequencing, and annotated using two transcriptome datasets. We report that inTcas1 has fewer gaps, less fragmentation, and many new genes and new isoforms of previously annotated genes. This new resource provides a useful update, comparison, and reference for new beetle genome assemblies. The first Y chromosome assembly for this species also provides critical data to study the evolution of insect sex chromosomes and sex determination systems. SIGNIFICANCEWe present here an improved T. castaneum genome assembly (inTcas1) for beetles sampled from India, including the first Y chromosome of this important pest and laboratory model species. The new genome should facilitate more comprehensive analysis of Coleoptera genome and transcriptome datasets, especially beetle populations from Asia - the previously available genome, Tcas5.2, was assembled using the GA2 strain from USA. The updated genome should also facilitate analyses of genome evolution, including sex determination and sex chromosome dynamics; and the new gene annotations can expand the genetic toolkit for this beetle.

genomics↗

bioRxiv2024

Physical confinement selectively favours bacterial growth based on cell shape

How are bacterial communities altered by changes in their microenvironment? Evidence from homogeneous liquid or flat plate cultures implicates biochemical cues -- such as variation in nutrient composition 1,2, response to chemoattractants and toxins 3,4, and inter-species signalling 5,6 -- as the primary modes of bacterial interaction with their microenvironment. However, these systems fail to capture the effect of physical confinement on bacteria in their natural habitats. Bacterial niches like the pores of soil, mucus, and infected tissues are disordered microenvironments with material properties defined by their internal pore sizes and shear moduli7-11. Here, using three-dimensional matrices that match the viscoelastic properties of gut mucus, we test how altering the physical properties of their microenvironment influences bacterial growth under confinement. We find that low aspect-ratio bacteria form compact, spherical colonies under confinement while high aspect-ratio bacteria push their progenies further outwards to create elongated colonies with a higher surface area, enabling increased access to nutrients. As a result, the population level growth of high aspect-ratio bacteria is more robust to increased physical confinement compared to that of low aspect-ratio bacteria. Thus, our results capture experimental evidence showing that physical constraints can play a selective role in bacterial growth based on cell shape.

biophysics↗

bioRxiv2024

Mutation bias alters the distribution of fitness effects of mutations

Mutation bias is an important factor determining the diversity of genetic variants available for selection. As adaptation proceeds and some beneficial mutations are fixed, new beneficial mutations become rare, limiting further adaptation. The depletion of beneficial mutations is especially stark within the mutational class favoured by the existing mutation bias. Recent theoretical work predicts that this problem may be alleviated by a change in the direction of mutation bias (i.e., a bias reversal). If populations sample previously underexplored types of mutations, the distribution of fitness effects (DFE) of mutations should shift towards more beneficial mutations. Here, we test this prediction using Escherichia coli, which has a transition mutation bias, with [~]54% single-nucleotide mutations being transitions compared to the unbiased expectation of [~]33% transitions. We generated mutant strains with a wide range of mutation biases, from 97% transitions to 98% transversions, either reinforcing or reversing the wild type transition bias. Quantifying DFEs of [~]100 single mutations obtained from mutation accumulation experiments for each strain, we find strong support for the theoretical prediction. Strains that oppose the ancestral bias (i.e., with a strong transversion bias) have DFEs with the highest proportion of beneficial mutations, whereas strains that exacerbate the ancestral transition bias have up to 10-fold fewer beneficial mutations. Such dramatic differences in the DFE should drive large variation in the rate and outcome of adaptation, suggesting an important and generalized evolutionary role for mutation bias shifts.

evolutionary biology↗

bioRxiv2023

Density dependent survival drives variation in density dependent population growth of an insect pest

Several ecological processes - from population dynamics to species co-existence - are driven by density dependence (DD) in population growth rate. Thus, to predict and manage ecological outcomes, we need a deep understanding of which factors and demographic traits drive variation in DD. In the insect pest Tribolium castaneum, we found large variation in DD across habitats but not across source populations. We modeled DD in population growth as the product of DD in fecundity and survival, experimentally estimating each parameter. Across habitats, survival parameters varied more than fecundity, including in simulations with varying parameter values. Thus, DD in survival drives variation in density-dependent population growth, and should evolve rapidly under strong density-dependent selection. Our general framework combining detailed experiments and simulations with a simple model can be used for other species to better understand the causes and consequences of density dependent population growth.

ecology↗

bioRxiv2022

ES30L: A large subunit rRNA expansion segment enriched in mammals and birds

Ribosomes, the molecular machines that are central to protein synthesis, have gradually been gaining prominence for their regulatory role in translation. Eukaryotic cytosolic ribosomes are typically larger than bacterial ones, partly due to multi-nucleotide insertions at specific conserved positions in the ribosomal RNAs (rRNAs). Such insertions called expansion segments (ESs) are present primarily on the ribosomal surface, with their role in translation and its regulation remaining under-explored. One such ES in the ribosomal large subunit (LSU) is ES30L, which is present only in mammals and birds among eukaryotes. In this study, we show that ES30L possesses complementarity to many protein-coding transcripts in humans and that the complementarity is enriched around the start codon, hinting at a possible role in translation regulation. Further, our in silico analysis analyses and pull-down assays indicate that ES30L may bind to secondary structures in the 5 UTR of several transcripts and RNA binding proteins (RBPs) that are essential for translation. Thus, we have identified a potential regulatory role for ES30L in translation.

molecular biology↗

bioRxiv2022

Disruption of flour beetle microbiota limits experimentally evolved immune priming response, but not pathogen resistance

Host-associated microbiota play a fundamental role in the training and induction of different forms of immunity, including inducible as well as constitutive components. However, direct experiments analysing the relative importance of microbiota during evolution of different immune functions are missing. We addressed this gap by using experimentally evolved lines of Tribolium castaneum that either produced inducible immune memory-like responses (immune priming) or constitutively expressed basal resistance (without priming), as mutually exclusive strategies against Bacillus thuringiensis infection. We disrupted the microbial communities in these evolved lines and estimated the impact on the beetles ability to mount a priming response vs basal resistance. Populations that had evolved immune priming lost the ability to mount a priming response upon microbiota disruption. Microbiota manipulation also caused a drastic reduction in their reproductive output and post-infection longevity. In contrast, in pathogen-resistant beetles, microbiota manipulation did not affect post-infection survival or reproduction. The divergent evolution of immune responses across beetle lineages was thus associated with divergent reliance on the microbiome. Whether the latter is a direct outcome of differential pathogen exposure during selection or reflects evolved immune functions remains unclear. We hope that our results will motivate further experiments to understand the mechanistic basis of these complex evolutionary associations between microbiota, host immune strategies, and fitness outcomes.

evolutionary biology↗

bioRxiv2022

The layered costs and benefits of translational redundancy

The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful, and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and posttranscriptional modification. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species evolutionary history with feasts and famines.

evolutionary biology↗

bioRxiv2022

IMPACT OF PHYLLOSPHERE METHYLOBACTERIUM ON HOST RICE LANDRACES

The genus Methylobacterium includes widespread plant-associated bacteria that dominate the plant phyllosphere (occupying leaf surfaces), consume plant-secreted methanol, and can produce plant growth promoting metabolites. However, despite the potential to increase agricultural productivity, their impact on host fitness in the natural environment is relatively poorly understood. Here, we conducted field experiments with three traditionally cultivated rice landraces from north eastern India. We inoculated seedlings with native vs. non-native phyllosphere Methylobacterium strains, finding significant impacts on plant growth and grain yield. However, these effects were variable: whereas some Methylobacterium isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium. Host plant benefits were not consistently associated with Methylobacterium colonization, altered phyllosphere microbiome composition, changes in early expression of plant stress response pathways, or bacterial auxin production. We provide the first clear demonstration of the benefits of phyllosphere Methylobacterium for rice yield under field conditions, and highlight the need for further analysis to understand the mechanisms underlying these benefits. Given that the host landrace-Methylobacterium relationship is not generalizable, future agricultural applications will require careful testing to identify coevolved host- bacterium pairs that may enhance the productivity of high-value rice varieties.

microbiology↗

bioRxiv2021

Selection bias in mutation accumulation

Mutation accumulation (MA) experiments, in which de novo mutations are sampled and subsequently characterized, are an essential tool in understanding the processes underlying evolution. In microbial populations, MA protocols typically involve a period of population growth between severe bottlenecks, such that a single individual can form a visible colony. While it has long been appreciated that the action of positive selection during this growth phase cannot be eliminated, it is typically assumed to be negligible. Here, we quantify the effect of both positive and negative selection in MA studies, demonstrating that selective effects can substantially bias the distribution of fitness effects (DFE) and mutation rates estimated from typical MA protocols in microbes. We then present a simple correction for this bias which applies to both beneficial and deleterious mutations, and can be used to correct the observed DFE in multiple environments. Finally, we use simulated MA experiments to illustrate the extent to which the MA-inferred DFE differs from the underlying true DFE, and demonstrate that the proposed correction accurately reconstructs the true DFE over a wide range of scenarios. These results highlight that positive selection during microbial MA experiments is in fact not negligible, but can be corrected to gain a more accurate understanding of fundamental evolutionary parameters.

evolutionary biology↗

bioRxiv2021

Fitness Landscapes Reveal Context-Dependent Benefits of Oviposition Choice

Resource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Are such context-dependent behaviours adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition choice reflects distinct, context-specific local fitness peaks. Manipulating female egg allocation in a habitat containing optimal and suboptimal resource patches, we measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference). Females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components that are linked in a tradeoff. With increasing age and prior exposure to competition, they produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naive females produce many slow-developing offspring, beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts. Preprint available at - https://www.biorxiv.org/content/10.1101/2021.05.27.445916v1.full Citation - Vrinda Ravi Kumar, Gaurav Agavekar, Deepa Agashe; bioRxiv 2021.05.27.445916; doi: https://doi.org/10.1101/2021.05.27.445916

ecology↗