@article {160485, title = {Founders predict trait evolution and population performance after evolutionary rescue in the red flour beetle.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 Sep 09}, pages = {e2506244122}, abstract = {

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 y), 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.

}, keywords = {Adaptation, Physiological, Animals, Biological Evolution, Coleoptera, India, Phenotype, Population Density, Population Dynamics}, issn = {1091-6490}, doi = {10.1073/pnas.2506244122}, author = {Ravi Kumar, Vrinda and Buddh, Shyamsunder and Singhal, Shivansh and Prakash, Arun and Agashe, Deepa} } @article {150944, title = {Cell shape affects bacterial colony growth under physical confinement.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Nov 08}, pages = {9561}, abstract = {

Evidence from homogeneous liquid or flat-plate cultures indicates that biochemical cues are 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 moduli. Here, we use three-dimensional matrices that match the viscoelastic properties of gut mucus to test how altering the physical properties of their microenvironment influences the growth of bacteria under confinement. We find that low aspect\ ratio (spherical) bacteria form compact, spherical colonies under confinement while high aspect\ ratio (rod-shaped) 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 growth of high aspect\ ratio bacteria is, under the tested conditions, more robust to increased physical confinement compared to that of low aspect\ ratio bacteria. Thus, our experimental evidence supports that environmental physical constraints can play a selective role in bacterial growth based on cell shape.

}, keywords = {Bacteria, Cell Shape, Escherichia coli}, issn = {2041-1723}, doi = {10.1038/s41467-024-53989-6}, author = {Sreepadmanabh, M and Ganesh, Meenakshi and Sanjenbam, Pratibha and Kurzthaler, Christina and Agashe, Deepa and Bhattacharjee, Tapomoy} } @article {152586, title = {Confronting risks of mirror life.}, journal = {Science}, volume = {386}, year = {2024}, month = {2024 Dec 20}, pages = {1351-1353}, abstract = {

Broad discussion is needed to chart a path forward.

}, keywords = {Artificial Life, Bacteria, Biosecurity, Risk, Stereoisomerism}, issn = {1095-9203}, doi = {10.1126/science.ads9158}, author = {Adamala, Katarzyna P and Agashe, Deepa and Belkaid, Yasmine and Bittencourt, Daniela Matias de C and Cai, Yizhi and Chang, Matthew W and Chen, Irene A and Church, George M and Cooper, Vaughn S and Davis, Mark M and Devaraj, Neal K and Endy, Drew and Esvelt, Kevin M and Glass, John I and Hand, Timothy W and Inglesby, Thomas V and Isaacs, Farren J and James, Wilmot G and Jones, Jonathan D G and Kay, Michael S and Lenski, Richard E and Liu, Chenli and Medzhitov, Ruslan and Nicotra, Matthew L and Oehm, Sebastian B and Pannu, Jaspreet and Relman, David A and Schwille, Petra and Smith, James A and Suga, Hiroaki and Szostak, Jack W and Talbot, Nicholas J and Tiedje, James M and Venter, J Craig and Winter, Gregory and Zhang, Weiwen and Zhu, Xinguang and Zuber, Maria T} } @article {149953, title = {Divergence and convergence in epiphytic and endophytic phyllosphere bacterial communities of rice landraces.}, journal = {mSphere}, year = {2024}, month = {2024 Oct 30}, pages = {e0076524}, abstract = {

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 fluctuations and frequent immigration, whereas endophytic microbiota should face stronger host selection. As a result, we expect greater variability in epiphytic than endophytic communities. We analyzed the structure and stability of leaf phyllosphere microbiota of four traditionally cultivated rice landraces and one commercial variety from northeast India grown in the field for 3 consecutive years, supplemented with opportunistic sampling of eight other landraces. Epiphytic and endophytic bacterial communities shared dominant core genera such as and . 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.IMPORTANCEPhyllosphere (leaf-associated) microbes significantly impact plant fitness, making it crucial to understand how these communities are assembled and maintained. While many studies have analyzed epiphytic (surface) phyllosphere communities, we have a relatively poor understanding of endophytic communities which colonize the very distinct niche formed inside leaf tissues. We found that across several rice landraces, both communities are largely colonized by the same core genera, indicating divergence at the species level across the two leaf niches and highlighting the need to understand the mechanisms underlying this divergence. Surprisingly, both epiphytic and endophytic communities were only weakly shaped by the host landrace, with a much greater role for environmental factors that likely vary over time. Thus, microbiome-based agricultural interventions for increasing productivity could perhaps be generalized across rice varieties but would need to account for the temporal instability of the microbiota. Our results thus highlight the importance of data sets such as ours-with extensive sampling across landraces and years-for understanding phyllosphere microbiota and their applications in the field.

}, issn = {2379-5042}, doi = {10.1128/msphere.00765-24}, author = {Sanjenbam, Pratibha and Agashe, Deepa} } @article {140651, title = {Mutational signatures in wild type Escherichia coli strains reveal predominance of DNA polymerase errors.}, journal = {Genome Biol Evol}, year = {2024}, month = {2024 Feb 24}, abstract = {

While mutational processes operating in the Escherichia coli genome have been revealed by multiple laboratory experiments, the contribution of these processes to accumulation of bacterial polymorphism and evolution in natural environments is unknown. To address this question, we reconstruct signatures of distinct mutational processes from experimental data on E. coli hypermutators, and ask how these processes contribute to differences between naturally occurring E. coli strains. We show that both mutations accumulated in the course of evolution of wild type strains in nature and in the lab-grown non-mutator laboratory strains are explained predominantly by the low fidelity of DNA polymerases II and III. By contrast, contributions specific to disruption of DNA repair systems cannot be detected, suggesting that temporary accelerations of mutagenesis associated with such disruptions are unimportant for within-species evolution. These observations demonstrate that accumulation of diversity in bacterial strains in nature is predominantly associated with errors of DNA polymerases.

}, issn = {1759-6653}, doi = {10.1093/gbe/evae035}, author = {Garushyants, Sofya K and Sane, Mrudula and Selifanova, Maria V and Agashe, Deepa and Bazykin, Georgii A and Gelfand, Mikhail S} } @article {134602, title = {Alteration of diet microbiota limits the experimentally evolved immune priming response in flour beetles, but not pathogen resistance.}, journal = {J Evol Biol}, year = {2023}, month = {2023 Sep 01}, abstract = {

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 on diverse forms of evolved 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 divergent counterstrategies against Bacillus thuringiensis infection. We altered the microbial communities present in the diet (i.e. wheat flour) of these evolved lines using UV irradiation and estimated the impact on the beetle{\textquoteright}s ability to mount a priming response versus basal resistance. Populations that had evolved immune priming lost the ability to mount a priming response upon alteration of diet microbiota. 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 lines 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.

}, issn = {1420-9101}, doi = {10.1111/jeb.14213}, author = {Prakash, Arun and Agashe, Deepa and Khan, Imroze} } @article {123070, title = {Fitness landscapes reveal context-dependent benefits of oviposition behavior.}, journal = {Evolution}, volume = {77}, year = {2023}, month = {2022 Dec 08}, pages = {550-561}, abstract = {

Resource choice behavior has enormous fitness consequences and can drive niche expansion. However, individual behavioral choices are often mediated by context, determined by past experience. Do such context-dependent behaviors reflect maladaptive variation or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behavior reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviors (i.e., combinations of fecundity and resource preference) in a habitat containing optimal and suboptimal resource patches. We did this by experimentally manipulating egg allocation across patches, which allowed us to assess behaviors not typically observed in the laboratory. We found that females from different age and competition contexts exhibit distinct behaviors which optimize different fitness components, linked in a tradeoff. With prior exposure to strong competition and increasing age, females produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young na{\"\i}ve females produce significantly more (but slower developing) offspring, which is beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioral optimality and offers predictive power in novel contexts.

}, issn = {1558-5646}, doi = {10.1093/evolut/qpac035}, author = {Ravi Kumar, Vrinda and Agavekar, Gaurav and Agashe, Deepa} } @article {125200, title = {The layered costs and benefits of translational redundancy.}, journal = {Elife}, volume = {12}, year = {2023}, month = {2023 Mar 02}, abstract = {

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 a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of 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 downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species{\textquoteright} evolutionary history with feasts and famines.

}, keywords = {Biological Evolution, Cost-Benefit Analysis, Escherichia coli, Exercise, Gene Dosage}, issn = {2050-084X}, doi = {10.7554/eLife.81005}, author = {Raval, Parth K and Ngan, Wing Yui and Gallie, Jenna and Agashe, Deepa} } @article {134597, title = {Revisiting the Role of Genetic Variation in Adaptation}, journal = {AMERICAN NATURALIST }, year = {2023}, month = {09/2023}, abstract = {

Evolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of ge-netic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural pop-ulations. The 2022 Vice Presidential Symposium of the American So-ciety of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse or-ganisms, and addressed distinct aspects of how genetic variation influ-ences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fit-ness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful in-troduction to the field.

}, doi = {10.1086/726012}, author = {Agashe, Deepa and Sane, Mrudula and Singhal, Shivansh} } @article {129162, title = {Shifts in mutation spectra enhance access to beneficial mutations.}, journal = {Proc Natl Acad Sci U S A.}, volume = {120}, year = {2023}, month = {05/2023}, pages = {e2207355120}, abstract = {

Biased mutation spectra are pervasive, with wide variation in the magnitude of mutational biases that influence genome evolution and adaptation. How do such diverse biases evolve? Our experiments show that changing the mutation spectrum allows populations to sample previously undersampled mutational space, including beneficial mutations. The resulting shift in the distribution of fitness effects is advantageous: Beneficial mutation supply and beneficial pleiotropy both increase, while deleterious load reduces. More broadly, simulations indicate that reducing or reversing the direction of a long-term bias is always selectively favored. Such changes in mutation bias can occur easily via altered function of DNA repair genes. A phylogenetic analysis shows that these genes are repeatedly gained and lost in bacterial lineages, leading to frequent bias shifts in opposite directions. Thus, shifts in mutation spectra may evolve under selection and can directly alter the outcome of adaptive evolution by facilitating access to beneficial mutations.

}, doi = {10.1073/pnas.2207355120}, author = {Sane, Mrudula and Diwan, Gaurav D and Bhat, BA and Wahl, LM and Agashe, Deepa} } @article {123068, title = {Towards evolutionary predictions: Current promises and challenges.}, journal = {Evol Appl}, volume = {16}, year = {2023}, month = {2023 Jan}, pages = {3-21}, abstract = {

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.

}, issn = {1752-4571}, doi = {10.1111/eva.13513}, author = {Wortel, Meike T and Agashe, Deepa and Bailey, Susan F and Bank, Claudia and Bisschop, Karen and Blankers, Thomas and Cairns, Johannes and Colizzi, Enrico Sandro and Cusseddu, Davide and Desai, Michael M and van Dijk, Bram and Egas, Martijn and Ellers, Jacintha and Groot, Astrid T and Heckel, David G and Johnson, Marcelle L and Kraaijeveld, Ken and Krug, Joachim and Laan, Liedewij and L{\"a}ssig, Michael and Lind, Peter A and Meijer, Jeroen and Noble, Luke M and Okasha, Samir and Rainey, Paul B and Rozen, Daniel E and Shitut, Shraddha and Tans, Sander J and Tenaillon, Olivier and Teot{\'o}nio, Henrique and de Visser, J Arjan G M and Visser, Marcel E and Vroomans, Renske M A and Werner, Gijsbert D A and Wertheim, Bregje and Pennings, Pleuni S} } @article {106149, title = {Career challenges for young independent researchers in India}, journal = {CURRENT SCIENCE}, volume = {122}, year = {2022}, month = {01/2022}, pages = {135-143}, abstract = {

The scientific enterprise in India has grown dramatically in the past few decades, with research emerging as a viable and important career option for students of science. The country thus has a large population of young scientists in the early stages of establishing their independent research careers. While this demographic is arguably the most important group that will determine the future of scientific research in India, their status and concerns are poorly understood. The Indian National Young Academy of Sciences conducted a national survey to better understand and present the challenges faced by them. Through a structured questionnaire, we sought the views of researchers below 45 years of age. Here, we summarize the responses from 854 participants across multiple early career stages. We highlight key challenges faced by these scientists in establishing an independent research career, and suggest steps to address them.

}, doi = {10.18520/cs/v122/i2/135-143}, author = {Agashe, Deepa and Maheshwary, Sugandha and Pattanaik, Jitendra Kumar and Prakash, Jai and Bhatt, Pragya and Arya, S. S. and Chatterjee, Sriparna and Kumar, Pankaj and Singh, Paramdeep and Abbas, Nazia and Sharma, Chandra Shekhar and Chaudhuri, Chirasree Roy and Devi, Pooja} } @article {99928, title = {The costs and benefits of basal infection resistance vs immune priming responses in an insect.}, journal = {Dev Comp Immunol}, volume = {126}, year = {2022}, month = {2021 Sep 16}, pages = {104261}, abstract = {

In insects, basal pathogen resistance and immune priming can evolve as mutually exclusive strategies, with distinct infection outcomes. However, the evolutionary drivers of such diverse immune functions remain poorly understood. Here, we addressed this key issue by systematically analyzing the differential fitness costs and benefits of priming vs resistance evolution in Tribolium beetle populations infected with Bacillus thuringiensis. Surprisingly, resistant beetles had increased post-infection reproduction and a longer lifespan under both starving as well as fed conditions, with no other measurable costs. In contrast, priming reduced offspring early survival, development rate and reproduction. Priming did improve post-infection survival of offspring, but this added trans-generational benefit of immune priming might not compensate for its pervasive costs. Resistance was thus consistently more beneficial. Overall, our work demonstrates the evolutionary change in trans-generational priming response, and provides a detailed comparison of the complex fitness consequences of evolved priming vs resistance.

}, issn = {1879-0089}, doi = {10.1016/j.dci.2021.104261}, author = {Prakash, Arun and Agashe, Deepa and Khan, Imroze} } @article {110791, title = {Evolutionary jumps in bacterial GC content.}, journal = {G3 (Bethesda)}, year = {2022}, month = {2022 May 17}, abstract = {

Genomic GC content is a fundamental molecular trait linked with many key genomic features such as codon and amino acid use. Across bacteria, GC content is surprisingly diverse and has been studied for many decades; yet its evolution remains incompletely understood. Since it is difficult to observe GC content evolve on laboratory time-scales, phylogenetic comparative approaches are instrumental; but this dimension is rarely studied systematically in the case of bacterial GC content. We applied phylogenetic comparative models to analyse GC content evolution in multiple bacterial groups across two major bacterial phyla. We find that GC content diversifies via a combination of gradual evolution and evolutionary "jumps". Surprisingly, unlike prior reports that solely focused on reductions in GC, we found a comparable number of jumps with both increased and decreased GC content. Overall, many of the identified jumps occur in lineages beyond the well-studied peculiar examples of endosymbiotic and AT-rich marine bacteria, and do not support the predicted role of oxygen dependence. Our analysis of rapid and large shifts in GC content thus identifies new clades and novel contexts to further understand the ecological and evolutionary drivers of this important genomic trait.

}, issn = {2160-1836}, doi = {10.1093/g3journal/jkac108}, author = {Mahajan, Saurabh and Agashe, Deepa} } @article {115019, title = {Impact of Phyllosphere Methylobacterium on Host Rice Landraces}, journal = {MICROBIOLOGY SPECTRUM}, year = {2022}, month = {07/2022}, abstract = {

Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse.

The genus Methylobacterium includes widespread plant-associated bacteria that are abundant in the plant phyllosphere (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 northeastern India. We inoculated seedlings with native versus nonnative phyllosphere Methylobacterium strains and found 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 on its own. Host plant benefits were not consistently associated with Methylobacterium colonization and did not have altered phyllosphere microbiome composition, changes in the early expression of plant stress response pathways, or bacterial auxin production. We provide the first 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 was 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. IMPORTANCE Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse. We tested the effects of native, leaf-inhabiting bacteria (genus Methylobacterium) on traditionally cultivated rice varieties in a crop field. We found that inoculation with some bacteria increased rice grain production substantially while a nonnative bacterium reduced plant health. Overall, the effect of bacterial inoculation varied across pairs of rice varieties and their native bacteria. Thus, knowledge of evolved associations between specific bacteria hosted by specific rice varieties is necessary to develop ways to increase the yield of traditional rice landraces and preserve these important sources of cultural and genetic diversity.

}, doi = {10.1128/spectrum.00810-22}, author = {Sanjenbam, Pratibha and Shivaprasad, P. V and Agashe, Deepa} } @article {157118, title = {Impact of Phyllosphere on Host Rice Landraces.}, journal = {Microbiol Spectr}, volume = {10}, year = {2022}, month = {2022 Aug 31}, pages = {e0081022}, abstract = {

The genus includes widespread plant-associated bacteria that are abundant in the plant phyllosphere (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 northeastern India. We inoculated seedlings with native versus nonnative phyllosphere strains and found significant impacts on plant growth and grain yield. However, these effects were variable. Whereas some isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium on its own. Host plant benefits were not consistently associated with colonization and did not have altered phyllosphere microbiome composition, changes in the early expression of plant stress response pathways, or bacterial auxin production. We provide the first demonstration of the benefits of phyllosphere 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- relationship was 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. Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse. We tested the effects of native, leaf-inhabiting bacteria (genus ) on traditionally cultivated rice varieties in a crop field. We found that inoculation with some bacteria increased rice grain production substantially while a nonnative bacterium reduced plant health. Overall, the effect of bacterial inoculation varied across pairs of rice varieties and their native bacteria. Thus, knowledge of evolved associations between specific bacteria hosted by specific rice varieties is necessary to develop ways to increase the yield of traditional rice landraces and preserve these important sources of cultural and genetic diversity.

}, keywords = {epiphytes; grain yield; host fitness; host-bacterial interaction; phyllosphere; rice landraces.}, issn = {2165-0497}, doi = {10.1128/spectrum.00810-22}, author = {Sanjenbam, Pratibha and Shivaprasad, P V and Agashe, Deepa} } @article {105163, title = {Selection bias in mutation accumulation.}, journal = {Evolution}, year = {2022}, month = {2022 Jan 06}, abstract = {

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. 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; we also provide an example of these corrections applied to experimental data. 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. This article is protected by copyright. All rights reserved.

}, issn = {1558-5646}, doi = {10.1111/evo.14430}, author = {Wahl, Lindi M and Agashe, Deepa} } @article {88404, title = {The Impact of Mistranslation on Phenotypic Variability and Fitness.}, journal = {Evolution}, year = {2021}, month = {01/2021}, abstract = {

Phenotypic variation is widespread in natural populations, and can significantly alter population ecology and evolution. Phenotypic variation often reflects underlying genetic variation, but also manifests via non-heritable mechanisms. For instance, translation errors result in about 10\% of cellular proteins carrying altered sequences. Thus, proteome diversification arising from translation errors can potentially generate phenotypic variability, in turn increasing variability in the fate of cells or of populations. However, the link between protein diversity and phenotypic variability remains unverified. We manipulated mistranslation levels in Escherichia coli, and measured phenotypic variability between single cells (individual level variation), as well as replicate populations (population level variation). Monitoring growth and survival, we find that mistranslation indeed increases variation across E. coli cells, but does not consistently increase variability in growth parameters across replicate populations. Interestingly, although any deviation from the wild type (WT) level of mistranslation reduces fitness in an optimal environment, the increased variation is associated with a survival benefit under stress. Hence, we suggest that mistranslation-induced phenotypic variation can impact growth and survival and has the potential to alter evolutionary trajectories. This article is protected by copyright. All rights reserved.

}, doi = {10.1111/evo.14179}, author = {Samhita, Laasya and Raval, Parth K and Stephenson, G and Thutupalli, Shashi and Agashe, Deepa} } @article {74445, title = {Global mistranslation increases cell survival under stress in Escherichia coli.}, journal = {PLoS Genet}, volume = {16}, year = {2020}, month = {2020 Mar 09}, pages = {e1008654}, abstract = {

Mistranslation is typically deleterious for cells, although specific mistranslated proteins can confer a short-term benefit in a particular environment. However, given its large overall cost, the prevalence of high global mistranslation rates remains puzzling. Altering basal mistranslation levels of Escherichia coli in several ways, we show that generalized mistranslation enhances early survival under DNA damage, by rapidly activating the SOS response. Mistranslating cells maintain larger populations after exposure to DNA damage, and thus have a higher probability of sampling critical beneficial mutations. Both basal and artificially increased mistranslation increase the number of cells that are phenotypically tolerant and genetically resistant under DNA damage; they also enhance survival at high temperature. In contrast, decreasing the normal basal mistranslation rate reduces cell survival. This wide-ranging stress resistance relies on Lon protease, which is revealed as a key effector that induces the SOS response in addition to alleviating proteotoxic stress. The new links between error-prone protein synthesis, DNA damage, and generalised stress resistance indicate surprising coordination between intracellular stress responses and suggest a novel hypothesis to explain high global mistranslation rates.

}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1008654}, author = {Samhita, Laasya and Raval, Parth K and Agashe, Deepa} } @article {73639, title = {Phenotypic diversity of Methylobacterium associated with rice landraces in North-East India.}, journal = {PLoS One}, volume = {15}, year = {2020}, month = {2020}, pages = {e0228550}, abstract = {

The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. However, the impact of such host association on bacterial ecology and evolution is not well understood. Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most abundant and widespread plant-associated bacteria. In addition, many of these species impact plant fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East (NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and we expected that the divergent selection on hosts may have also generated divergence in associated Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent with our expectation, across spatial scales this phenotypic variation was largely explained by host landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed that at least some rice landraces gain an early growth advantage from their specific phyllosphere-colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and understand diversity in one of the most important food crops of the world.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0228550}, author = {Sanjenbam, Pratibha and Buddidathi, Radhika and Venkatesan, Radhika and Shivaprasad, P V and Agashe, Deepa} } @article {83642, title = {The red flour beetle Tribolium castaneum: A model for host-microbiome interactions.}, journal = {PLoS One}, volume = {15}, year = {2020}, month = {2020}, pages = {e0239051}, abstract = {

A large body of ongoing research focuses on understanding the mechanisms and processes underlying host-microbiome interactions, and predicting their ecological and evolutionary outcomes. To draw general conclusions about such interactions and understand how they are established, we must synthesize information from a diverse set of species. We analysed the microbiome of an important insect model-the red flour beetle Tribolium castaneum-which is a widespread generalist pest of stored cereals. The beetles complete their entire life cycle in flour, which thus serves multiple functions: habitat, food, and a source of microbes. We determined key factors that shape the T. castaneum microbiome, established protocols to manipulate it, and tested its consequences for host fitness. We show that the T. castaneum microbiome is derived from flour-acquired microbes, and varies as a function of (flour) resource and beetle density. Beetles gain multiple fitness benefits from their microbiome, such as higher fecundity, egg survival, and lifespan; and reduced cannibalism. In contrast, the microbiome has a limited effect on development rate, and does not enhance pathogen resistance. Importantly, the benefits are derived only from microbes in the ancestral resource (wheat flour), and not from novel resources such as finger millet, sorghum, and corn. Notably, the microbiome is not essential for beetle survival and development under any of the tested conditions. Thus, the red flour beetle is a tractable model system to understand the ecology, evolution and mechanisms of host-microbiome interactions, while closely mimicking the host species{\textquoteright} natural niche.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0239051}, author = {Agarwal, Aparna and Agashe, Deepa} } @article {53989, title = {Dimensions of ant diversity on a small tropical island}, journal = {INSECT CONSERVATION AND DIVERSITY}, volume = {12}, year = {2019}, month = {03/2019}, pages = {161-171}, abstract = {
  1. Recent appreciation of the multidimensional nature of biodiversity has prompted biologists to examine the taxonomic, functional, and phylogenetic attributes of natural communities. Simultaneous consideration of such multiple diversity dimensions provides valuable insights into various community assembly processes.
  2. We studied the alpha and beta components of ant diversity on a simple island landscape dominated by adjacent but abiotically distinct evergreen (humid \& dense canopy) and littoral (dry \& sparse canopy) forest habitats. We sought to (i) describe and examine interrelationships of ant diversity dimensions, and (ii) identify potential processes structuring ant communities by comparing the diversity patterns of observed and randomly generated communities.
  3. We found that the drier littoral habitat had lower ant species richness and non-random community composition, but had similar functional diversity as evergreen forests. This result is in contrast with previous studies comparing intact and human-altered habitats that reported severe loss of ant functional diversity with reduced richness. In our study, the functional similarity between habitats was maintained because communities in littoral forests were functionally overdispersed than expected by chance. We suggest that competition and/or thermal tolerance of ants may drive overdispersion of littoral ant communities.
  4. At the small spatial scale of our island, phylogenetic diversity was a poor predictor of habitat differences despite significant phylogenetic signal in functional traits and non-random functional diversity patterns. Our work highlights the need for a broad range of studies comparing multidimensional diversity in adjacent habitats that would provide a baseline for interpreting community-level changes due to anthropogenic pressures.
}, doi = {10.1111/icad.12326}, author = {Agavekar, Gaurav and Agashe, Deepa and Economo, EP} } @article {70232, title = {Disrupting butterfly caterpillar microbiomes does not impact their survival and development.}, journal = {Proc Biol Sci}, volume = {286}, year = {2019}, month = {2019 Dec 18}, pages = {20192438}, abstract = {

Associations with gut microbes are believed to play crucial roles in the physiology, immune function, development and behaviour of insects. However, microbiome sequencing has recently suggested that butterflies are an anomaly, because their microbiomes do not show strong host- and developmental stage-specific associations. We experimentally manipulated butterfly larval gut microbiota and found that disrupting gut microbes had little influence on larval survival and development. Larvae of the butterflies and that fed on chemically sterilized or antibiotic-treated host plant leaves had significantly reduced bacterial loads, and their gut bacterial communities were disrupted substantially. However, neither host species treated this way suffered a significant fitness cost: across multiple experimental blocks, treated and control larvae had similar survival, growth and development. Furthermore, re-introducing microbes from the excreta of control larvae did not improve larval growth and survival. Thus, these butterfly larvae did not appear to rely on specialized gut bacteria for digestion, detoxification, biomass accumulation and metamorphosis. Our experiments thus show that dependence on gut bacteria for growth and survival is not a universal phenomenon across insects. Our findings also caution that strategies which target gut microbiomes may not always succeed in controlling Lepidopteran pests.

}, issn = {1471-2954}, doi = {10.1098/rspb.2019.2438}, author = {Phalnikar, Kruttika and Kunte, Krushnamegh and Agashe, Deepa} } @article {54874, title = {Evolthon: A community endeavor to evolve lab evolution.}, journal = {PLoS Biol}, volume = {17}, year = {2019}, month = {2019 Mar}, pages = {e3000182}, abstract = {

In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate mutation rate evolve faster? What are ideal population sizes of evolving populations? There are endless strategies, beyond those that can be exposed by individual labs. We therefore arranged a community challenge, Evolthon, in which students and scientists from different labs were asked to evolve Escherichia coli or Saccharomyces cerevisiae for an abiotic stress-low temperature. About 30 participants from around the world explored diverse environmental and genetic regimes of evolution. After a period of evolution in each lab, all strains of each species were competed with one another. In yeast, the most successful strategies were those that used mating, underscoring the importance of sex in evolution. In bacteria, the fittest strain used a strategy based on exploration of different mutation rates. Different strategies displayed variable levels of performance and stability across additional challenges and conditions. This study therefore uncovers principles of effective experimental evolutionary regimens and might prove useful also for biotechnological developments of new strains and for understanding natural strategies in evolutionary arms races between species. Evolthon constitutes a model for community-based scientific exploration that encourages creativity and cooperation.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3000182}, author = {Kaminski Strauss, Sivan and Schirman, Dvir and Jona, Ghil and Brooks, Aaron N and Kunjapur, Aditya M and Nguyen Ba, Alex N and Flint, Alice and Solt, Andras and Mershin, Andreas and Dixit, Atray and Yona, Avihu H and Cs{\"o}rg{\H o}, B{\'a}lint and Busby, Bede Phillip and Hennig, Bianca P and P{\'a}l, Csaba and Schraivogel, Daniel and Schultz, Daniel and Wernick, David G and Agashe, Deepa and Levi, Dikla and Zabezhinsky, Dmitry and Russ, Dor and Sass, Ehud and Tamar, Einat and Herz, Elad and Levy, Emmanuel D and Church, George M and Yelin, Idan and Nachman, Iftach and Gerst, Jeffrey E and Georgeson, Joseph M and Adamala, Katarzyna P and Steinmetz, Lars M and R{\"u}bsam, Marc and Ralser, Markus and Klutstein, Michael and Desai, Michael M and Walunjkar, Nilima and Yin, Ning and Aharon Hefetz, Noa and Jakimo, Noah and Snitser, Olga and Adini, Omri and Kumar, Prashant and Soo Hoo Smith, Rachel and Zeidan, Razi and Hazan, Ronen and Rak, Roni and Kishony, Roy and Johnson, Shannon and Nouriel, Shira and Vonesch, Sibylle C and Foster, Simmie and Dagan, Tal and Wein, Tanita and Karydis, Thrasyvoulos and Wannier, Timothy M and Stiles, Timothy and Olin-Sandoval, Viridiana and Mueller, William F and Bar-On, Yinon M and Dahan, Orna and Pilpel, Yitzhak} } @article {68513, title = {Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies.}, journal = {PeerJ}, volume = {7}, year = {2019}, month = {2019}, pages = {e8058}, abstract = {

Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies-considered to be generalist predators-consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72\% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations.

}, issn = {2167-8359}, doi = {10.7717/peerj.8058}, author = {Deb, Rittik and Nair, Ashwin and Agashe, Deepa} } @article {59711, title = {Pathogen susceptibility and fitness costs explain variation in immune priming across natural populations of flour beetles.}, journal = {J Anim Ecol}, year = {2019}, month = {2019 May 27}, abstract = {

In many insects, individuals primed with low doses of pathogens early in life have higher survival after exposure to the same pathogen later in life. Yet, our understanding of the evolutionary and ecological history of priming of immune response in natural insect populations is limited. Previous work demonstrated population-, sex- and stage-specific variation in the survival benefit of priming response in flour beetles (Tribolium castaneum) infected with their natural pathogen Bacillus thuringiensis. However, the evolutionary forces responsible for this natural variation remained unclear. In the present work, we tested whether the strength of the priming response (measured as the survival benefit after priming and subsequent infection, relative to unprimed controls) was associated with multiple fitness parameters and immune components across 10 flour beetle populations collected from different locations in India. Our results suggest two major selective pressures that may explain the observed inter-population variation in priming: (a) Basal pathogen susceptibility - populations that were more susceptible to infection produced a stronger priming response, and (b) Short-term early reproductive success - populations where primed females produced more offspring early in life (measured over 2\ days) had lower survival benefit (measured over 120\ days), suggesting a potential trade-off between early reproduction and priming response. However, the negative association between survival and reproduction is limited to priming and infection in adults, but not in larvae. While other components of beetle fitness (starvation resistance and larval development) and immune function (haemolymph antibacterial activity and antimicrobial quinone secretion) also varied widely across populations, none of them was correlated with the variation in priming responses across populations. Our work is the first systematic empirical demonstration of multiple selective pressures that may govern the evolution of immune priming in the wild. We hope that this motivates further experiments to establish the role of pathogen-imposed selection and fitness costs in the evolution of priming in natural insect populations.

}, issn = {1365-2656}, doi = {10.1111/1365-2656.13030}, author = {Khan, Imroze and Prakash, Arun and Agashe, Deepa} } @article {43852, title = {Antagonistic pleiotropy for carbon use is rare in new mutations.}, journal = {Evolution}, year = {2018}, month = {2018 Aug 10}, abstract = {

Pleiotropic effects of mutations underlie diverse biological phenomena such as ageing and specialization. In particular, antagonistic pleiotropy ("AP": when a mutation has opposite fitness effects in different environments) generates tradeoffs, which may constrain adaptation. Models of adaptation typically assume that AP is common - especially among large-effect mutations - and that pleiotropic effect sizes are positively correlated. Empirical tests of these assumptions have focused on de novo beneficial mutations arising under strong selection. However, most mutations are actually deleterious or neutral, and may contribute to standing genetic variation that can subsequently drive adaptation. We quantified the incidence, nature, and effect size of pleiotropy for carbon utilization across 80 single mutations in Escherichia coli that arose under mutation accumulation (i.e., weak selection). Although \~{}46\% of the mutations were pleiotropic, only 11\% showed AP; among beneficial mutations, only \~{}4\% showed AP. In some environments, AP was more common in large-effect mutations; and AP effect sizes across environments were often negatively correlated. Thus, AP for carbon use is generally rare (especially among beneficial mutations); is not consistently enriched in large-effect mutations; and often involves weakly deleterious antagonistic effects. Our unbiased quantification of mutational effects therefore suggests that antagonistic pleiotropy may be unlikely to cause maladaptive tradeoffs.

}, issn = {1558-5646}, doi = {10.1111/evo.13569}, author = {Sane, Mrudula and Miranda, Joshua John and Agashe, Deepa} } @article {35861, title = {Dietary and developmental shifts in butterfly-associated bacterial communities.}, journal = {R Soc Open Sci}, volume = {5}, year = {2018}, month = {2018 May}, pages = {171559}, abstract = {

Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts.

}, issn = {2054-5703}, doi = {10.1098/rsos.171559}, author = {Phalnikar, Kruttika and Kunte, Krushnamegh and Agashe, Deepa} } @article {27663, title = {Female Density-Dependent Chemical Warfare Underlies Fitness Effects of Group Sex Ratio in Flour Beetles}, journal = {American Naturalist}, year = {2018}, month = {12/2017}, abstract = {

In animals, skewed sex ratios can affect individual fitness via sexual (e.g., intersexual conflict or intrasexual mate competition) or nonsexual (e.g., sex-specific resource competition) interactions. Because most analyses of sex ratio focus on sexual interactions, the relative importance of sexual versus nonsexual mechanisms remains unclear. We tested both mechanisms in the flour beetle Tribolium castaneum, where male-biased sex ratios increase female fitness relative to unbiased or female-biased groups. Although flour beetles show both sexual and nonsexual (resource) competition, we found that sexual interactions did not explain female fitness. Instead, female fecundity was dramatically reduced even after a brief exposure to flour conditioned by other females. Earlier studies suggested that secreted toxins might mediate density-dependent population growth in flour beetles. We identified ethyl benzoquinone and methyl benzoquinone (quinones) as components of adult stink glands that regulate female fecundity. In female-biased groups (i.e., at high female density), females upregulated quinones and suppressed each other{\textquoteright}s reproduction. In male-biased groups, low female density and associated low quinone levels maximized fecundity. Thus, females appear to use quinones as weapons for female-specific, density-dependent interference competition. Our results underscore the importance of nonsexual interference competition that may often underlie the fitness consequences of skewed sex ratios.

}, doi = {10.1086/695806}, author = {Khan, Imroze and Prakash, Arun and Issar, Swastika and Umarani, Mihir and Sasidharan, Rohit and Masagalli, JN and Lama, Prakash and Venkatesan, Radhika and Agashe, Deepa} } @article {29619, title = {Translational selection for speed is not sufficient to explain variation in bacterial codon usage bias.}, journal = {Genome Biol Evol}, year = {2018}, month = {2018 Jan 29}, abstract = {

Increasing growth rate across bacteria strengthens selection for faster translation, concomitantly increasing the total number of tRNA genes and codon usage bias (CUB: enrichment of specific synonymous codons in highly expressed genes). Typically, enriched codons are translated by tRNAs with higher gene copy numbers (GCN). A model of tRNA-CUB coevolution based on fast growth associated selection on translational speed recapitulates these patterns. A key untested implication of the coevolution model is that translational selection should favor higher tRNA GCN for more frequently used amino acids, potentially weakening the effect of growth associated selection on CUB. Surprisingly, we find that CUB saturates with increasing growth rate across γ-proteobacteria, even as the number of tRNA genes continues to increase. As predicted, amino acid specific tRNA GCN is positively correlated with the usage of corresponding amino acids, but there is no correlation between growth rate associated changes in CUB and amino acid usage. Instead, we find that some amino acids - Cysteine and those in the NNA/G codon family - show weak CUB that does not increase with growth rate, despite large variation in the corresponding tRNA GCN. We suggest that amino acid specific variation in CUB is not explained by tRNA GCN because GCN does not influence the difference between translation times of synonymous codons as expected. Thus, selection on translational speed alone cannot fully explain quantitative variation in overall or amino acid specific CUB, suggesting a significant role for other functional constraints and amino acid specific codon features.

}, issn = {1759-6653}, doi = {10.1093/gbe/evy018}, author = {Mahajan, Saurabh and Agashe, Deepa} } @article {35144, title = {Wobbling forth and drifting back: The evolutionary history and impact of bacterial tRNA modifications.}, journal = {Mol Biol Evol}, year = {2018}, month = {2018 May 28}, abstract = {

Along with tRNAs, enzymes that modify anticodon bases are a key aspect of translation across the tree of life. tRNA modifications extend wobble pairing, allowing specific ("target") tRNAs to recognize multiple codons and cover for other ("non-target") tRNAs, often improving translation efficiency and accuracy. However, the detailed evolutionary history and impact of tRNA modifying enzymes has not been analyzed. Using ancestral reconstruction of five tRNA modifications across 1093 bacteria, we show that most modifications were ancestral to eubacteria, but were repeatedly lost in many lineages. Most modification losses coincided with evolutionary shifts in non-target tRNAs, often driven by increased bias in genomic GC and associated codon use, or by genome reduction. In turn, the loss of tRNA modifications stabilized otherwise highly dynamic tRNA gene repertoires. Our work thus traces the complex history of bacterial tRNA modifications, providing the first clear evidence for their role in the evolution of bacterial translation.

}, issn = {1537-1719}, doi = {10.1093/molbev/msy110}, author = {Diwan, Gaurav D and Agashe, Deepa} } @article {14686, title = {Early-life inflammation, immune response and ageing.}, journal = {Proc Biol Sci}, volume = {284}, year = {2017}, month = {2017 Mar 15}, abstract = {

Age-related diseases are often attributed to immunopathology, which results in self-damage caused by an inappropriate inflammatory response. Immunopathology associated with early-life inflammation also appears to cause faster ageing, although we lack direct experimental evidence for this association. To understand the interactions between ageing, inflammation and immunopathology, we used the mealworm beetle Tenebrio molitor as a study organism. We hypothesized that phenoloxidase, an important immune effector in insect defence, may impose substantial immunopathological costs by causing tissue damage to Malpighian tubules (MTs; functionally equivalent to the human kidney), in turn accelerating ageing. In support of this hypothesis, we found that RNAi knockdown of phenoloxidase (PO) transcripts in young adults possibly reduced inflammation-induced autoreactive tissue damage to MTs, and increased adult lifespan. Our work thus suggests a causative link between immunopathological costs of early-life inflammation and faster ageing. We also reasoned that if natural selection weakens with age, older individuals should display increased immunopathological costs associated with an immune response. Indeed, we found that while old infected individuals cleared infection faster than young individuals, possibly they also displayed exacerbated immunopathological costs (larger decline in MT function) and higher post-infection mortality. RNAi-mediated knockdown of PO response partially rescued MTs function in older beetles and resulted in increased lifespan after infection. Taken together, our data are consistent with a direct role of immunopathological consequences of immune response during ageing in insects. Our work is also the first report that highlights the pervasive role of tissue damage under diverse contexts of ageing and immune response.

}, issn = {1471-2954}, doi = {10.1098/rspb.2017.0125}, author = {Khan, Imroze and Agashe, Deepa and Rolff, Jens} } @article {27662, title = {Experimental evolution of insect immune memory versus pathogen resistance.}, journal = {Proc Biol Sci}, volume = {284}, year = {2017}, month = {2017 Dec 20}, abstract = {

Under strong pathogen pressure, insects often evolve resistance to infection. Many insects are also protected via immune memory (immune priming), whereby sublethal exposure to a pathogen enhances survival after secondary infection. Theory predicts that immune memory should evolve when the pathogen is highly virulent, or when pathogen exposure is relatively rare. However, there are no empirical tests of these hypotheses, and the adaptive benefits of immune memory relative to direct resistance against a pathogen are poorly understood. To determine the selective pressures and ecological conditions that shape immune evolution, we imposed strong pathogen selection on flour beetle (Tribolium castaneum) populations, infecting them with Bacillus thuringiensis (Bt) for 11 generations. Populations injected first with heat-killed and then live Bt evolved high basal resistance against multiple Bt strains. By contrast, populations injected only with a high dose of live Bt evolved a less effective but strain-specific priming response. Control populations injected with heat-killed Bt did not evolve priming; and in the ancestor, priming was effective only against a low Bt dose. Intriguingly, one replicate population first evolved priming and subsequently evolved basal resistance, suggesting the potential for dynamic evolution of different immune strategies. Our work is the first report showing that pathogens can select for rapid modulation of insect priming ability, allowing hosts to evolve divergent immune strategies (generalized resistance versus specific immune memory) with potentially distinct mechanisms.

}, issn = {1471-2954}, doi = {10.1098/rspb.2017.1583}, author = {Khan, Imroze and Prakash, Arun and Agashe, Deepa} } @article {19200, title = {The road not taken: Could stress-specific mutations lead to different evolutionary paths?}, journal = {PLoS Biol}, volume = {15}, year = {2017}, month = {2017 Jun}, pages = {e2002862}, abstract = {

Organisms often encounter stressful conditions, some of which damage their DNA. In response, some organisms show a high expression of error-prone DNA repair machinery, causing a temporary increase in the genome-wide mutation rate. Although we now have a detailed map of the molecular mechanisms underlying such stress-induced mutagenesis (SIM), it has been hotly debated whether SIM alters evolutionary dynamics. Key to this controversy is our poor understanding about which stresses increase mutagenesis and their long-term consequences for adaptation. In a new study with Escherichia coli, Maharjan and Ferenci show that while only some nutritional stresses (phosphorous and carbon limitation) increase total mutation rates, each stress generates a unique spectrum of mutations. Their results suggest the potential for specific stresses to shape evolutionary dynamics and highlight the necessity for explicit tests of the long-term evolutionary impacts of SIM.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.2002862}, author = {Agashe, Deepa} } @article {11618, title = { Divergent immune priming responses across flour beetle life stages and populations }, journal = { ECOLOGY AND EVOLUTION }, volume = {6}, year = {2016}, month = {11/2016}, pages = {7847-7855}, abstract = {

Growing evidence shows that low doses of pathogens may prime the immune response in many insects, conferring subsequent protection against infection in the same developmental stage (within-life stage priming), across life stages (ontogenic priming), or to offspring (transgenerational priming). Recent work also suggests that immune priming is a costly response. Thus, depending on host and pathogen ecology and evolutionary history, tradeoffs with other fitness components may constrain the evolution of priming. However, the relative impacts of priming at different life stages and across natural populations remain unknown. We quantified immune priming responses of 10 natural populations of the red flour beetle Tribolium castaneum, primed and infected with the natural insect pathogen Bacillus thuringiensis. We found that priming responses were highly variable both across life stages and populations, ranging from no detectable response to a 13-fold survival benefit. Comparing across stages, we found that ontogenic immune priming at the larval stage conferred maximum protection against infection. Finally, we found that various forms of priming showed sex-specific associations that may represent tradeoffs or shared mechanisms. These results indicate the importance of sex-, life stage-, and population-specific selective pressures that can cause substantial divergence in priming responses even within a species. Our work highlights the necessity of further work to understand the mechanistic basis of this variability.

}, doi = {10.1002/ece3.2532}, author = {Khan, Imroze and Prakash, Arun and Agashe, Deepa} } @article {4892, title = {The Frequency of Internal Shine-Dalgarno-like Motifs in Prokaryotes.}, journal = {Genome Biol Evol}, volume = {8}, year = {2016}, month = {2016}, pages = {1722-33}, abstract = {

In prokaryotes, translation initiation typically depends on complementary binding between a G-rich Shine-Dalgarno (SD) motif in the 5{\textquoteright} untranslated region of mRNAs, and the 3{\textquoteright} tail of the 16S ribosomal RNA (the anti-SD sequence). In some cases, internal SD-like motifs in the coding region generate "programmed" ribosomal pauses that are beneficial for protein folding or accurate targeting. On the other hand, such pauses can also reduce protein production, generating purifying selection against internal SD-like motifs. This selection should be stronger in GC-rich genomes that are more likely to harbor the G-rich SD motif. However, the nature and consequences of selection acting on internal SD-like motifs within genomes and across species remains unclear. We analyzed the frequency of SD-like hexamers in the coding regions of 284 prokaryotes (277 with known anti-SD sequences and 7 without a typical SD mechanism). After accounting for GC content, we found that internal SD-like hexamers are avoided in 230 species, including three without a typical SD mechanism. The degree of avoidance was higher in GC-rich genomes, mesophiles, and N-terminal regions of genes. In contrast, 54 species either showed no signature of avoidance or were enriched in internal SD-like motifs. C-terminal gene regions were relatively enriched in SD-like hexamers, particularly for genes in operons or those followed closely by downstream genes. Together, our results suggest that the frequency of internal SD-like hexamers is governed by multiple factors including GC content and genome organization, and further empirical work is necessary to understand the evolution and functional roles of these motifs.

}, issn = {1759-6653}, doi = {10.1093/gbe/evw107}, author = {Diwan, Gaurav D and Agashe, Deepa} } @article {1028, title = {Immunosenescence and the ability to survive bacterial infection in the red flour beetle Tribolium castaneum.}, journal = {J Anim Ecol}, volume = {85}, year = {2016}, month = {01/2016}, pages = {291-301}, abstract = {

In most animals, ageing is associated with a decline in immune function (immune senescence). However, different components of the immune system seem to age differentially, and many studies do not measure the ultimate fitness consequences of immune function after infection. Previous work shows that immune function may be traded off with other fitness components such as reproduction. It is possible that age alters the nature of these trade-offs, particularly in conjunction with factors such as gender and mating that can also affect investment in immune function. We tested the impact of age, sex and mating on post-infection survivorship in Tribolium castaneum flour beetles, as well as the components of baseline constitutive innate immunity and external (secreted) immune function in uninfected individuals. We also tested whether the reproductive ability of uninfected females is traded off with immune function (baseline innate and external immunity) and post-infection survivorship across age groups. We found that age, sex and mating significantly affected immune components and infection outcome, although the magnitude and nature of the impact varied in each case. We found that older beetles were more susceptible to infection by the pathogen Bacillus thuringiensis even though major components of the constitutive innate immune defence (antibacterial and phenoloxidase activity) remained unchanged or improved with age. Thus, these aspects of innate immunity cannot explain the observed decline in post-infection survival of older beetles. We did not find trade-offs between the reproductive ability of uninfected females and their immune function. In contrast to innate immunity, external immunity showed an overall decline with age but was also affected by sex and mating. Finally, we show that bacterial infection alters external immunity via complex interactions between age, sex and mating status. Our work uncovers novel interactions between age, sex and mating that can determine the evolution and outcome of immunosenescence by affecting the time course of relative investment in different immune and fitness components.

}, issn = {1365-2656}, doi = {10.1111/1365-2656.12433}, author = {Khan, Imroze and Prakash, Arun and Agashe, Deepa} } @article {3547, title = {Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium.}, journal = {Mol Biol Evol}, year = {2016}, month = {2016 Feb 23}, abstract = {

Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically. We now show that during laboratory evolution, these variants rapidly regained fitness via parallel yet variant-specific, highly beneficial point mutations in the N-terminal region of fae. These mutations (including four synonymous mutations) had weak but consistently positive impacts on transcript levels, enzyme production, or enzyme activity. However, none of the proposed mechanisms (including internal ribosome pause sites or mRNA structure) predicted the fitness impact of evolved or additional, engineered point mutations. This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context.

}, issn = {1537-1719}, doi = {10.1093/molbev/msw035}, author = {Agashe, Deepa and Sane, Mrudula and Phalnikar, Kruttika and Diwan, Gaurav D and Habibullah, Alefiyah and Martinez-Gomez, Norma Cecilia and Sahasrabuddhe, Vinaya and Polachek, William and Wang, Jue and Chubiz, Lon M and Marx, Christopher J} } @article {4891, title = {Selection Maintains Apparently Degenerate Metabolic Pathways due to Tradeoffs in Using Methylamine for Carbon versus Nitrogen.}, journal = {Curr Biol}, volume = {26}, year = {2016}, month = {2016 Jun 6}, pages = {1416-26}, abstract = {

Microorganisms often encode multiple non-orthologous metabolic modules that catalyze the same reaction. However, little experimental evidence actually demonstrates a selective basis for metabolic degeneracy. Many methylotrophs-microorganisms that grow on reduced single-carbon compounds-like Methylobacterium extorquens AM1 encode two routes for methylamine oxidation: the periplasmic methylamine dehydrogenase (MaDH) and the cytoplasmic N-methylglutamate (NMG) pathway. In Methylobacterium extorquens AM1, MaDH is essential for methylamine growth, but the NMG pathway has no known physiological role. Here, we use experimental evolution of two isolates lacking (or incapable of using) MaDH to uncover the physiological challenges that need to be overcome in order to use the NMG pathway for growth on methylamine as a carbon and energy source. Physiological characterization of the evolved isolates revealed regulatory rewiring to increase expression of the NMG pathway and novel mechanisms to mitigate cytoplasmic ammonia buildup. These adaptations led us to infer and validate environmental conditions under which the NMG pathway is advantageous compared to MaDH. The highly expressed MaDH enables rapid growth on high concentrations of methylamine as the primary carbon and energy substrate, whereas the energetically expensive NMG pathway plays a pivotal role during growth with methylamine as the sole nitrogen source, which we demonstrate is especially true under limiting concentrations (\<1\ mM). Tradeoffs between cellular localization and ammonium toxicity lead to selection for this apparent degeneracy as it is beneficial to facultative methylotrophs that have to switch between using methylamine as a carbon and energy source or just a nitrogen source.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2016.04.029}, author = {Nayak, Dipti D and Agashe, Deepa and Lee, Ming-Chun and Marx, Christopher J} } @article {2209, title = {Evolutionary Biology}, journal = {Current Science}, volume = {108}, year = {2015}, pages = {1835-1873}, author = {Kunte, Krushnamegh and Agashe, Deepa} }