Biology subjects

Basu, D. N.

Publications and source records attributed to Basu, D. N..

7 recordsLinked to original sources

bioRxiv2026

TRACKING THE COMPOSITION AND STABILITY OF MICROBIOME ACROSS INDIAN SOCIAL HONEYBEES FORAGING IN A HOMOGENOUS RESOURCE LANDSCAPE

Microbial communities are essential for host health and ecosystem stability. However, whether host identity or shared foraging resources shapes microbiome structure among co-occurring species remains poorly understood. We studied bacterial and fungal communities of four Indian honeybee species in a mustard monoculture resource condition, integrating behavioural observation-based pollinator data with microbial co-occurrence networks derived from metabarcoding. Microbiome composition was linked to host identity rather than foraging behaviour, bee abundance, or landscape use. While core bacterial taxa were shared, relationships among bacterial cobionts, unlike those among fungal genera, remained species-specific. Microbial diversity, along with community structure and function, influenced network stability, with a highly modular microbial network of Apis cerana exhibiting more resilience to simulated perturbations. In summary, host-specific filtering shaped the microbiome more than resource homogenisation, with closely related species facing unique risks of microbial collapse, with broader implications for vulnerability to microbiome imbalance, environmental stress, and emerging infections.

ecology↗

bioRxiv2025

ADAPTATION AGAINST LONG-TERM PROTEIN DEPRIVATION TRADES OFF WITH IMMUNOCOMPETENCE AND THE ABILITY TO SURVIVE PATHOGENIC INFECTIONS

Insufficient protein intake, leading to malnutrition, is a major global health concern that compromises the immune system and increases susceptibility to diseases. In scenarios where protein availability is constrained, organisms may experience strong selection to efficiently allocate their resources between immunity vs other energy-demanding processes, such as reproduction, resulting in evolutionary trade-offs. Additionally, in many species, protein deficiency has a more significant impact on female reproduction than on males, potentially leading to pronounced sexually dimorphic trade-offs involving immunity and infection outcomes. However, there are no experiments to test these possibilities. In this work, we demonstrate that in Drosophila melanogaster populations selected for increased early-life reproduction under protein limitations, evolved virgin females indeed suffered a greater reduction in their resistance to the pathogen Providencia rettgeri and showed lower survival following infection than males, corroborating our expectations. However, mating resulted in a loss of sexually dimorphic infection outcomes, causing both sexes to exhibit nearly identical infection costs and reduced infection tolerance compared to their ancestral, unselected populations. Moreover, several immune components, including the Toll- and IMD-mediated inducible immune pathways, were either less upregulated or more downregulated in the selected flies, which may contribute to their heightened susceptibility to pathogens. Downregulation in key metabolic pathways and genes related to phagocytosis, melanisation and ROS-mediated defence after infection in selected flies can also be associated with their increased pathogen vulnerability. Taken together, our work thus reveals the reproductive status- and sex-specific plasticity of immune investments and post-infection health in response to evolutionary constraints under chronic protein deprivation.

evolutionary biology↗

bioRxiv2024

Microbiota drives the sexually dimorphic infection outcomes in mealworm beetles

Sexually dimorphic responses to pathogenic infections in animals may stem from sex-specific differences in their life history and immune investment. Recent evidence highlights that such sex-specific variations in immune responses can also be critically regulated by microbiota. However, direct experiments to test how microbiota jointly impacts sex-specific immunity and vulnerability to pathogens are still limited. To this end, we used Tenebrio molitor beetles to first establish that sexes appear to differ in their microbiota composition and infection responses. Females were more vulnerable to bacterial infections and carried a higher bacterial load than males. When we depleted the microbiome, only females improved their post-infection survival, leading to a loss of sex-specific infection outcomes. Males, on the other hand, remained unaffected. Microbiota reconstitution (via feeding on faecal matter) of microbiota-depleted females increased their susceptibility to infection again, restoring the sexual dimorphism. We thus found a causal association between microbiome and infection responses. We also found reduced expression of an antimicrobial peptide tenecin 1 in females, which could be associated with their higher infection susceptibility, but such immune gene-vs-phenotypic associations were not consistent across microbiota manipulations. Immune strategies that are required to mediate the causal links between microbiome and infection response might thus vary with microbiota manipulations, warranting future investigations.

evolutionary biology↗

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

PATHOGEN GROWTH AND VIRULENCE DYNAMICS DRIVE THE HOST EVOLUTION AGAINST COINFECTIONS

Coinfections, or the simultaneous infection of hosts by multiple pathogens, are widespread in nature with significant negative impacts on global health. Can hosts evolve against such coinfections as effectively as they would against individual pathogens? Also, what roles do individual pathogens play during such evolution? Here, we combined theoretical models and experiments with Tribolium castaneum populations evolving against two coinfecting bacterial pathogens, with contrasting growth and virulence dynamics, to reveal that fast-growing pathogens inflicting rapid mortality surges (i.e., fast-acting) restrict adaptive success against coinfections. While hosts rapidly evolved better survival against slow-growing bacteria causing long-lasting infections, evolution against coinfection was significantly delayed and resembled slow adaptation against fast-acting pathogens. Moreover, limited scopes of immunomodulation against fast-acting pathogens during coinfections can drive the observed adaptive patterns. Overall, we provide new insights into how adaptive dynamics and mechanistic bases against coinfections are critically regulated by individual pathogens growth and virulence dynamics.

evolutionary biology↗

bioRxiv2022

An interactive pipeline for multitrait evolutionary analysis in a phylogenetic framework

Comparative phylogenetic studies based on 2D image data can reveal macroevolutionary patterns and processes by integrating phylogenetic and ecological analyses. The advent of high-throughput imaging facilities has led to the accumulation of large image datasets; however, large-scale data extraction and analysis using these resources can be labour- and computation-intensive. Moreover, there are few standardized methods to analyse multitrait image-based data in a phylogenetic framework. Several packages in the R statistical environment offer utilities for processing and analysing large-scale image data. Techniques for the comparative phylogenetic analysis of multitrait data have also been introduced in other packages. However, most of these approaches are specialized for discrete purposes, and there is a lack of streamlined and efficient methodological pipelines integrating features across packages. Here, we present multEvol, an interactive pipeline for the extraction and phylogenetic analysis of shape and colour pattern data from 2D images in the R statistical computing environment. Using this pipeline, shape outlines and colour pattern data for multiple colours can be extracted, visualised, and compared in a phylogenetic framework. Using various utilities provided in the phytools, RNiftyReg, Momocs, patternize, convevol, and geiger packages, we introduce an interactive interface that allows user inputs for iterative data extraction. This pipeline provides an efficient method for the bulk processing of images of biological specimens from museum collections. As such, it has potential applications in the large-scale morphometric analysis of museum specimens to reveal macroevolutionary patterns in ecology, evolution and integrative biology.

evolutionary biology↗

bioRxiv2020

CARCASS SCAVENGING RELAXES CHEMICAL-DRIVEN FEMALE INTERFERENCE COMPETITION

Female-female nonsexual interference competition is rapidly emerging as a major fitness determinant of biased sex-ratio groups with high female density. How do females overcome such competition? We used adult flour beetle Tribolium castaneum to answer this question, where females from female-biased groups suppressed each others fecundity by secreting toxic quinones from their stink glands, revealing a chemical-driven interference competition. The added natal resource did not alleviate these fitness costs. Females also did not disperse more at high female-density. Hence, the competition was neither limited by the total resource availability nor the inability to avoid chemical interference. Instead, protein sequestered via scavenging of nutrient-rich carcasses relaxed the female competition, by increasing their fecundity and reducing the quinone content. Even infected carcasses were scavenged to extract fitness benefits, despite the infection-risk. Finally, individual stink gland components triggered carcass-scavenging to increase fecundity, indicating a potentially novel chemical feedback loop to reduce the competition.

ecology↗