Biology subjects

Bhat, A. S.

Publications and source records attributed to Bhat, A. S..

11 recordsLinked to original sources

bioRxiv2026

Internal evolutionary conflicts: a conceptual synthesis and mathematical primer

Internal evolutionary conflicts arise when elements within an organism have diverging fitness interests. Examples range from meiotic drive and cytoplasmic male sterility to transposable elements and supernumerary B chromosomes. While once treated as genetic curiosities, they are now seen as widespread and major drivers of eukaryotic genome evolution. Yet their study remains fragmented, with no clear entry point not only for those who wish to gain an overview of theoretical advances, or those who wish to construct models of their own. Here, we discuss ways in which internal evolutionary conflicts have been modelled and develop a common population genetic framework for building such models. The framework provides explicit criteria for what counts as conflict, distinguishing it from fitness trade-offs, and formalises how and when internal conflicts arise. By treating different cases within the same structure, it shows that these diverse phenomena share a common logic.

evolutionary biology↗

bioRxiv2026

Stochastic failure accumulation as a foundation for exponential mortality and selective disappearance

Most organisms become increasingly likely to die as they grow older, a phenomenon known as demographic senescence. Despite this statement saying nothing about the particular shape of a mortality curve, the Gompertz-Makeham law remains remarkably accurate in a broad range of species. We develop a general mathematical framework in which individuals are modelled as comprising a fixed number of interacting intra-organismal sub-systems, each characterised by stochastic failure and repair rates, such that the number of failed sub-systems follows a birth-death process. In many organisms, failure begets failure because sub-systems are typically interdependent. We use diffusion approximations to demonstrate that this interdependence generically produces Gompertz-Makeham mortality curves. Since individuals who die can no longer age, observed cohorts become increasingly composed of lucky individuals that avoided death by (stochastically) taking paths in failure space associated with lower mortality despite no intrinsic differences in their quality. Selective disappearance of unlucky individuals generates deviations from Gompertz-Makeham predictions at advanced ages, producing a late-life mortality plateau. We show that while these deviations must always exist, they may often be too small to detect, either because the failure accumulation process is stereotyped or because detection requires unreasonably large cohort sizes. Our work establishes Gompertz-Makeham curves arising from stochastic failure accumulation as a null expectation in organisms with many interdependent sub-systems.

ecology↗

bioRxiv2024

Spatial structure could explain the maintenance of alternative reproductive tactics in tree cricket males

Trait polymorphisms are widespread in nature, and explaining their stable co-existence is a central problem in ecology and evolution. Alternative reproductive tactics, in which individuals of one or more sex exhibit discrete, discontinuous traits in response to reproductive competition, represent a special case of trait polymorphism in which the traits are often complex, behavioural, and dynamic. Thus, studying how alternative reproductive tactics are maintained may provide general insights into how complex trait polymorphisms are maintained in populations. We construct a spatially explicit individual-based model inspired from extensively collected empirical data to address the mechanisms behind the co-existence of three behavioural alternative reproductive tactics in males of a tree cricket (Oecanthus henryi). Our results show that the co-existence of these tactics over ecological time scales is facilitated by the spatial structure of the landscape they inhabit, which serves to equalize the otherwise unequal mating benefits of the three tactics. We also show that this co-existence is unlikely if spatial aspects of the system are not considered. Our findings highlight the importance of spatial dynamics in understanding ecological and evolutionary processes and underscore the power of integrative approaches that combine models inspired from empirical data.

animal behavior and cognition↗

bioRxiv2024

Eco-evolutionary dynamics for finite populations and the noise-induced reversal of selection

Theoretical studies from diverse areas of population biology have shown that demographic stochasticity can substantially impact evolutionary dynamics in finite populations, including scenarios where traits that are disfavored by natural selection can nevertheless increase in frequency through the course of evolution. Here, we analytically describe the eco-evolutionary dynamics of finite populations from demographic first principles to investigate how noise-induced effects can alter the evolutionary fate of populations in which total population size may vary stochastically over time. Starting from a generic birth-death process describing a finite population of individuals with discrete traits, we derive a set of stochastic differential equations (SDEs) that recover well-known descriptions of evolutionary dynamics such as the replicator-mutator equation, the Price equation, and Fishers fundamental theorem in the infinite population limit. For finite populations, our SDEs reveal how stochasticity can predictably bias evolutionary trajectories to favour certain traits, a phenomenon we call noise-induced biasing. We show that noise-induced biasing acts through two distinct mechanisms that we call the direct and indirect mechanisms. While the direct mechanism can be identified with classic bet-hedging theory, the indirect mechanism is a more subtle consequence of frequency and density-dependent demographic stochasticity. Our equations reveal that noise-induced biasing may lead to evolution proceeding in a direction opposite to that predicted by natural selection in the infinite population limit. By extending and generalizing some standard equations of population genetics, we thus describe how demographic stochasticity appears alongside and interacts with the more well-understood forces of natural selection and neutral drift to determine the eco-evolutionary dynamics of finite populations of non-constant size.

evolutionary biology↗

bioRxiv2023

Mutualism Destabilizes Communities, but Competition Pays the Price

A classic result in theoretical ecology states that an increase in the proportion of cooperative interactions in unstructured ecological communities leads to a loss of stability to external perturbations. However, the fate and composition of the species that constitute an unstable ecological community following such perturbations remains relatively unexplored. In this paper, we use an individual-based model to study the population dynamics of unstructured communities following external perturbations to species abundances. We find that while increasing the number of cooperative interactions does indeed increase the probability that a community will experience an extinction following a perturbation, the entire community is rarely wiped out following a perturbation. Instead, only a subset of the ecological community is driven to extinction, and the species that go extinct are more likely to be those engaged in a greater number of competitive interactions. Thus, the resultant community formed after a perturbation has a higher proportion of cooperative interactions than the original community. We show that this result can be explained by studying the dynamics of the species engaged in the highest number of competitive interactions: After an external perturbation, those species that compete with such a top competitor are more likely to go extinct than expected by chance alone, whereas those that are engaged in cooperative interactions with such a species are less likely to go extinct than expected by chance alone. Our results provide a potential explanation for the ubiquity of cooperative interactions in nature despite the known negative effects of cooperation on community stability.

ecology↗

bioRxiv2022

Studying the age of onset and detection of Chronic Myeloid Leukemia using a three-stage stochastic model

Chronic Myeloid Leukemia (CML) is a biphasic malignant clonal disorder that progresses, first with a chronic phase, where the cells have enhanced proliferation only, and then to a blast phase, where the cells have the ability of self-renewal. It is well-recognized that the Philadelphia chromosome (which contains the BCR-ABL fusion gene) is the "hallmark of CML". However, empirical studies have shown that the mere presence of BCR-ABL may not be a sufficient condition for the development of CML, and further modifications related to tumor suppressors may be necessary. Accordingly, we develop a three-mutation stochastic model of CML progression, with the three stages corresponding to the non-malignant cells with BCR-ABL presence, the malignant cells in the chronic phase and the malignant cells in the blast phase. We demonstrate that the model predictions agree with age incidence data from the United States. Finally, we develop a framework for the retrospective estimation of the time of onset of malignancy, from the time of detection of the cancer.

systems biology↗

bioRxiv2022

Allopatric montane wren-babblers exhibit similar song notes but divergent vocal sequences

The songs of passerine birds consist of notes temporally arranged into vocal sequences following syntactic structures, and function both in courtship and territorial defense. Geographic barriers are important drivers of avian speciation, and also influence the divergence of song. However, there is relatively little quantitative study of the relationship between geographic barriers and the syntactic structure of vocal sequences. Here, we investigate interspecific divergence in song notes and syntax within a genus of allopatric montane Asian wren-babblers (Spelaeornis). Employing a robust quantitative analytical framework and song recordings from publicly accessible databases, we find that Spelaeornis appear to have undergone diversification in song syntax without divergence in note parameters. Broadly, we find three different syntactic structures across the eight species in the genus, each occurring in a different geographic region in Asia, with two species apparently exhibiting intermediate syntax. Species within the genus appear to possess similar song notes, but subgroups confined to different geographic regions (eg: hills south of the Brahmaputra river) arrange these notes according to different syntactic rules to construct songs. Our computational framework to examine signal structure and diversification across multiple scales of signal organization has potential implications for our understanding of speciation, signal evolution and more broadly in fields such as linguistic diversification.

animal behavior and cognition↗

bioRxiv2021

Behavioral context shapes vocal sequences in two anuran species with different repertoire sizes

Acoustic signals in animals serve to convey context-dependent information to receivers. Birds and mammals combine diverse sounds into complex sequences to communicate, but these sequences largely remain understudied in other taxa. Anuran vocalizations are a prominent feature of their life history, and function in defense of territories and to attract mates. However, despite the spectacular diversity of anurans in tropical regions of the world, vocal diversity and communication strategies remain relatively poorly studied. Specifically, studies of vocal sequences and context-dependent vocal patterns in frogs remain few. Here, we investigated the context-dependent vocal repertoire and the use of vocal sequences by two anuran species belonging to different lineages, both endemic to the hyper-diverse Western Ghats of India. By recording vocal sequences both when frogs were alone and in the presence of a territorial rival, we present evidence that both species modify their vocal repertoire according to context. Specifically, one species appends notes to generate more complex sequences, whereas the other shifts to different note types, resulting in different sequences for different contexts. Thus, despite differences in repertoire size, both frog species are capable of adjusting the temporal sequence of vocalizations to communicate in different contexts. This study highlights the need for further studies of insular frogs, to understand how diversification across these continental islands has influenced the evolution of vocal repertoires, vocal sequence patterns and communication systems. Lay SummaryAnimals employ complex sequences of acoustic signals to communicate in diverse behavioral contexts. Here, we demonstrate that two frog species with different vocal repertoires both modify the sequence of note emissions in the presence of a territorial rival. These patterns demonstrate that anurans are capable of complex shifts in the patterns of their vocalization, to communicate different messages to different receivers. Our findings demonstrate the value of studying behavioral diversity in tropical regions.

animal behavior and cognition↗

bioRxiv2020

A colony-level optimisation model provides a potential mechanism for the evolution of novel castes in eusocial ant colonies

Ant species often have multiple morphologically distinct castes within a single colony. Given that most of these castes are involved in non-reproductive tasks, and since such individuals thus never reproduce, the question of how ant castes can evolve is a non-trivial one. Over the years, several models have been proposed in order to explain the evolution of castes in ant colonies. Here, we attempt to answer this question using an economics-based approach, developing an optimization model that implements adaptation and selection at the colony level. We argue that due to the nature of ant colonies, selection is shifted to the group level, and, due to this, individual ants are sheltered from negative selection. We show that our framework can explain the evolution of novel castes in ant colonies, and discuss the novelty of our model with regard to previous models that have been proposed. We also show that our model is consistent with several empirical observations of ant colonies.

evolutionary biology↗

bioRxiv2018

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

BackgroundPan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy. Moreover, sequencing errors often inflate the number of taxa present. Pacific Biosciences (PacBios) long-read technology in particular suffers from high error rates per base. Herein we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome data\n\nResultsAnalysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity. Examination of a 250-plus species mock community demonstrated correct species-level classification of >90% of taxa and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed. Propiniobacterium acnes (recently renamed Cutibacterium acnes [1]) was the predominant species throughout, but was found at distinct relative abundances by site.\n\nConclusionsOur microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt) overcomes deficits of standard marker gene based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.

bioinformatics↗

bioRxiv2018

Microbiome-TP53 Gene Interaction in Human Lung Cancer

BackgroundLung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesized that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from controls (n=33) and cancer cases (n=143), we conducted 16S rRNA bacterial gene sequencing, with RNA-seq data from lung cancer cases in The Cancer Genome Atlas (n=1112) serving as the validation cohort.\n\nResultsOverall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma (SCC) specifically, a separate group of taxa were identified, in which Acidovorax was enriched in smokers (P =0.0013). Acidovorax temporans was identified by fluorescent in situ hybridization within tumor sections, and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibited higher abundance among the subset of SCC cases with TP53 mutations, an association not seen in adenocarcinomas (AD).\n\nConclusionsThe results of this comprehensive study show both a microbiome-gene and microbiome-exposure interactions in SCC lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can damage epithelial function, have a unique bacterial consortia which is higher in relative abundance in smoking-associated SCC. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.

cancer biology↗