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Biology subjects

Sethuraman, A.

Publications and source records attributed to Sethuraman, A..

At least 19 recordsLinked to original sources
bioRxiv2026

Effects of Reduced Watering Regimes on Hops Growth and Rhizospheric Microbial Communities

Marked by shifts in historic climatic patterns, the effects of climate change have begun to disrupt biological life worldwide. In agricultural systems, the abiotic effects of climate change such as increased temperatures and reduced rainfall extend beyond crop yield and can be felt at the ecological level through microbial community shifts associated at the interface of the root/soil matrix, known as the rhizosphere. Shifts in rhizospheric community composition have been known to greatly impact crop health, making common garden studies examining the totality of climate related impacts on crops of the utmost importance. Using a combination of both phenotypic and metabarcoding data collected from the rhizosphere, we present a multi-month drought tolerance experiment using the cash crop Humulus lupulus (hops) and five of its cultivars; Cascade, Centennial, Chinook, Comet and CTZ. Statistical analyses of phenotypic data revealed that hops displayed a differential impact on reduced watering strategies while rhizospheric data revealed more consistent patterns of association between microbes and cultivar type. We hope results from our study can be used to further expand our knowledge on the impact of future climate change and necessary reduced watering strategies on agricultural systems, providing insight into potential mechanisms of response for drought tolerance in crop systems.

plant biology↗
bioRxiv2026

CoalMiner: a coalescent model generator for fastsimcoal2

Demographic inference using the Site Frequency Spectrum (SFS) is often constrained by the number and complexity of models tested. Here we present a coalescent model generator called CoalMiner for use with fastsimcoal2. CoalMiner utilizes a decision tree framework to generate biologically plausible models, with user input dictating the number and ranges of demographic parameters and histories, which can then be plugged into the fastsimcoal2 pipeline. Using extensive simulations and empirical data, we show that CoalMiner is an effective helper tool to explore demographic model space. CoalMiner is written in Python and is freely available on GitHub: https://github.com/raywray/coalminer with numerous vignettes and tutorials.

evolutionary biology↗
bioRxiv2026

GhostHunter: A Multi-Test Framework for Detecting Ghost Introgression

Withdrawal StatementThe authors have withdrawn this manuscript because of several factual errors in it. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

evolutionary biology↗
bioRxiv2025

SaVor - A Reproducible Structural Variant Calling and Benchmarking Platform from Short-Read Data

Structural variations (SVs) are differences in genomic regions that are larger than 1 kilobase-pair (Kbp) between individuals, and can arise from errant DNA repair mechanisms, whole genome duplications, and transposable element activity across the genome. Recent advances, optimizations, and cost reductions in next generation sequencing technologies have facilitated the exponential increase in the amount of available short read genomic data. Here we present SaVor, a flexible, reproducible SV calling workflow that accepts single or multi-lane short-read paired-end Illumina sequence data, or BAM files as input to generate a consensus SV call-set based on user-provided merge parameters. We tested SaVor on 1,165 Arabidopsis thaliana whole genome sequences and benchmarked its performance on a set of SVs derived from the same accessions using Lumpy. Intersection calls i.e. SVs supported by 3 SV callers showed the highest precision (>0.91) while union calls supported by at least 1 caller showed the highest recall (>0.88). We found that the former suffers from decreased recall (<0.51) and the latter decreased precision (<0.57). Depending on the merge strategy, trade-offs in recall and precision need to be considered for downstream analyses of SV call-sets from short-read data. SaVor is an open-source Snakemake pipeline and is available on GitHub at https://github.com/ChabbyTMD/SaVor

bioinformatics↗
bioRxiv2025

Hidden in Plain Sight. How Ks histogram dynamics can reveal and obscure ancient whole genome duplications.

Polyploidy is a significant force in angiosperm evolution, of great interest to evolutionary biologists and crop scientists. The mode of origin of a polyploid lineage is a continuum, ranging from whole genome duplication (WGD) from within the same species (autopolyploidy), to a WGD derived from hybridization between two (or more) distinct species (allopolyploidy). The polyploid mode of origin impacts many aspects of genome evolution, including patterns of chromosomal inheritance, homeologous exchange rate, and post-WGD diploidization. Here, we develop a novel polyploid genome simulation engine DemographiKS to demonstrate that the Ks histogram, one of the most broadly utilized methods for inferring WGD events, is highly sensitive to evolutionary parameters relating to the mode of origin, as well as demographic parameters such as migration events, population bottlenecks and expansions. Our results show that that the location of the Ks peak may correspond to the time of parental divergence (for allopolyploids); might be hidden at Ks=0 (for autopolyploids under a population contraction); may correspond to the mean time of coalescence of the diploid ancestor (for autopolyploids under a population expansion), or the time of most recent migration between the parental species (for allopolyploids). We also fit simulated Ks histograms to polyploid genomes from four well-studied plant lineages on the polyploid continuum (Coffea arabica, Zea mays, Populus trichocarpa, and Saccharum spontaneum), demonstrating that WGD simulations may be used to corroborate inferred demographies. In summary, we demonstrate that Ks histograms are information-rich, computationally tractable, and can be utilized to corroborate detailed evolutionary histories inferred by other methods.

genomics↗
bioRxiv2025

A Comprehensive Catalog of Telomere Content Variation Across Human Populations

Quantifying telomere content across global human populations is critical to understanding the evolutionary biology of senescence and has implications for the field of biogerontology. Here, we analyzed 26 global human populations from Phase 3 of the 1000 Genomes Project and observed that differences in telomere content vary significantly across different human populations. Most notably, African-ancestry populations in the Americas: ACB (African Caribbean in Barbados) and ASW ((African Ancestry in Southwest USA) showed significantly different telomere content compared to both continental African populations and populations from other ancestries (p < 10-5) However, we did not observe significant differences (p > 0.05) in telomere content between sexes across and within different populations. We also report that out of the five superpopulations (separated by continental ancestry), humans of American ancestry show significant difference in telomere content with all other superpopulations (p < 0.001 for all comparisons), whereas humans of East Asian and South Asian ancestry show no significant differences with other superpopulations (p > 0.05). Our analysis suggests that the extent of telomere content variation is likely influenced by complex interactions between genomic and environmental factors. The pipeline to catalog telomere content variation is publicly available via: https://github.com/paribytes/TeloTales.

genomics↗
bioRxiv2025

MULTICLUST - Fast multinomial clustering of multiallelic genotypes to infer genetic population structure

Identifying population structure from multilocus genotype data is key to down-stream genetic analyses, including analysis of genome-wide association (GWAS), genetic genealogy and phylogenetics, in the fields of conservation, forensics, evolution and more. While inference of population structure has been dominated by Bayesian methods, maximum likelihood methods have some benefits in terms of reliability, consistency and efficiency. Here we extend the methods of Tang et al. [53] and Alexander et al. [2] to handle multi-allelic (e.g., SNP, STR, allozyme) and polyploid loci with missing data to infer genetic admixture proportions and subpopulation allele frequencies. Comparative analyses of our method, MULTICLUST, and STRUCTURE [42] on both simulated and empirical data indicate comparable, fast, reproducible, and accurate estimates of population admixture proportions and allele frequencies using MULTICLUST.MULTICLUST is implemented in the C programming language and is publicly accessible via www.github.com/arunsethuraman/multiclust.

evolutionary biology↗
bioRxiv2025

A Novel Machine Learning Approach for Tumor Detection Based on Telomeric Signatures

Cancer remains one of the most complex diseases faced by humanity, with over 200 distinct types, each characterized by unique molecular profiles that demand specialized therapeutic approaches (Tomczak et al., 2015). Prior studies have shown that both short and long telomere lengths are associated with elevated cancer risk, underscoring the intricate relationship between telomere length variation and tumorigenesis (The Telomeres Mendelian Randomization Collaboration et al., 2017). To investigate this relationship, we developed a supervised machine learning model trained on telomeric read content, genomic variants, and phenotypic features to predict tumor status. Using data from 33 cancer types within The Cancer Genome Atlas (TCGA) program, our model achieved an accuracy of 82.62% in predicting tumor status. The trained model is available for public use and further development through the projects GitHub repository: https://github.com/paribytes/TeloQuest. This work represents a novel, multidisciplinary approach to improving cancer diagnostics and risk assessment by integrating telomere biology with Biobank-scale genomic and phenotypic data. Furthermore, we highlight the potential of telomere length variation as a meaningful predictive biomarker in oncology.

bioinformatics↗
bioRxiv2024

Evolutionary history and rhizosphere microbial community composition in domesticated hops (Humulus lupulus L.)

Humulus lupulus L., commonly known as hops, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hops have undergone intense artificial selection with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavor and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. Previous studies have individually explored differences between cultivars, aiming to identify markers that can quickly and cost-effectively differentiate between cultivars. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study aims to explore the global population structure and domestication history of 98 hops cultivars. Additionally, we assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial community compositions between US and non-US based cultivars. Contrary to previous studies, our study revealed that worldwide hop cultivars cluster into four primary subpopulations; Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modeling the evolutionary history of domesticated hops reveals an early divergence of the common ancestors of modern US cultivars around 2800 ybp, and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations. Furthermore, cultivars of US origin were shown to overall outperform non-US cultivars in both growth rates and usage of dissolvable nitrogen and display novel microbial composition.

evolutionary biology↗
bioRxiv2024

Accurately Inferring Ancient Auto and Allopolyploidization Events using Forward-time Simulations

Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history of angiosperms. To understand how these cycles occur, much work has been done to model the genomic consequences and evolutionary significance of WGD. The machinations of diploidization are strongly influenced by the mode of speciation (allo or autopolyploidy). However, there is no discrete boundary between allo and autopolyploidy, which is best described as a continuum. Here we present a forward-time polyploid genome evolution simulator called SpecKS. SpecKS models polyploid speciation as originating from a 2D continuum, whose dimensions account for both the level of genetic differentiation between the ancestral parental genomes, as well the time lag between ancestral speciation and their subsequent reunion in the derived polyploid. Using extensive simulations, we demonstrate that changes in initial conditions along either dimension of the 2D continuum deterministically affect the shape of the Ks histogram. Our findings indicate that the error in the common method of estimating WGD time from the Ks histogram peak scales with the degree of allopolyploidy, and we present an alternative, accurate estimation method that is independent of the degree of allopolyploidy. Lastly, we use SpecKS to derive tests that infer both the lag time between parental divergence and WGD time, and the diversity of the ancestral species, from an input Ks histogram. We apply the latter test to transcriptomic data from over 200 species across the plant kingdom, the results of which are concordant with the prevailing theory that the majority of angiosperm lineages are derived from diverse parental genomes and may be of allopolyploid origin.

evolutionary biology↗
bioRxiv2023

Go west: population genomics reveals unexpected population fluctuations and little gene flow in Western Hemisphere populations of the predatory lady beetle, Hippodamia convergens

The convergent lady beetle, Hippodamia convergens, is used extensively in augmentative biological control of aphids, thrips, and whiteflies across its native range in North America, and was introduced into South America in the 1950s. Overwintering H. convergens populations from its native western range in the United States are commercially collected and released across its current range in the eastern U.S., with little knowledge of the effectiveness of augmentative biological control using H. convergens. Here we use a novel ddRADseq-based SNP/haplotype discovery approach to estimate its range-wide population diversity, differentiation, and recent evolutionary history. Our results indicate (1) significant population differentiation among eastern U.S., western U.S., and South American populations of H. convergens, with (2) little to no detectable recent admixture between them, despite repeated population augmentation, and (3) continued recent population size expansion across its range. These results contradict previous findings using microsatellite markers. In light of these new findings, the implications for the effectiveness of augmentative biological control using H. convergens are discussed. Additionally, because quantifying the non-target effects of augmentative biological control is a difficult problem in migratory beetles, our results could serve as a foundation cornerstone in improving and predicting the efficacy of future releases of H. convergens across its range.

evolutionary biology↗
bioRxiv2023

Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in Anza Borrego Desert

Here we describe the metagenome composition, community functional annotation, and diversity of prokaryotic microbial species derived from calcareous stromatolite formations discovered in the dry stream bed of the open-canopy, ephemeral San Felipe Creek in the Anza Borrego Desert. In this environment, resident microbes must be able to adapt to the harsh conditions of extreme heat, high UV light, desiccation and fluctuating solubilization/precipitation and hydration/evaporation. Metagenomic analysis revealed a community capable of carrying out complete nitrogen fixation and assimilatory nitrate reduction, forming biofilms and quorum sensing, and potentially forming thick-walled akinetes as desiccation-resistant stages. Nitrogen cycling is likely to play a fundamental role in mediating both the structure of the stromatolite microbial community and the mineral precipitation/dissolution. The viruses present in the stromatolites, particularly Nodularia and Mycobacterium phages are also likely to impact community population dynamics and activity. Stromatolite community members possess different morphological and physiological strategies to cope with desiccation stress. Metagenomic signatures were found for scytonemin, carotenoids, synthesis of potential microsporine-like amino acids; genes involved in microalgal desiccation tolerance, including those encoding aquaporins, chaperones, antioxidants; and enzymes responsible for the synthesis of trehalose, sucrose, and polyamines. The stromatolite ecosystem provides a diverse array of microniches where different functional guilds can develop complex metabolite exchange with the substrate supporting their life in extreme conditions. Metagenome analyses revealed several genes that might enable a specialized and unique group of endolithic cyanobacteria including Chroococcidiopsis, Hyella, Myxosarcina, and Pleurocapsa to derive metals and important nutrients from rocks, being potentially destructive for the calcareous formations. Our study revealed environmental adaptations of freshwater microbial communities in desert stream stromatolites which may provide valuable insights into Precambrian paleoenvironments, which are little known.

genomics↗
bioRxiv2023

Shared patterns of population genomic variation and phenotypic response across rapid range expansions in two invasive lady beetle species

Non-native lady beetle species have often been introduced, with variable success, into North America for biological control of aphids, scales, whiteflies, and other agricultural pests. Two predatory lady beetle species, Propylea quatuordecimpunctata and Hippodamia variegata, both originating from Eurasia, were first discovered near Montreal, Quebec, in North America in 1968 and 1984, respectively, and have since expanded into northeastern North America and the midwestern United States. In this study, we estimate the range-wide population structure, establishment and range-expansion, and recent evolutionary history of these species of non-native lady beetles using reduced representation genotyping-by-sequencing via ddRADseq. In addition, we quantified the responses to a key abiotic factor, photoperiod, that regulates adult reproductive diapause in these two species and may influence their latitudinal distribution and spread in North America. Our analyses detect (1) non-significant genetic differentiation and divergence among North American populations, (2) evidence of reduced contemporary gene flow within the continental US, (3) significant phenotypic differences in diapause induction despite genetic similarities across sampled populations.

evolutionary biology↗
bioRxiv2022

Like mother, like daughter? Phenotypic plasticity, environmental covariation, and heritability of size in a parthenogenetic wasp

Dinocampus coccinellae (Hymenoptera:Braconidae, Euphorinae) is a solitary, generalist Braconid parasitoid wasp that reproduces through thelytokous parthenogenesis, an asexual process in which diploid daughters emerge from unfertilized eggs, and parasitizes over fifty diverse species of coccinellid ladybeetles worldwide as hosts. Here we utilized a common garden and reciprocal transplant experiment using parthenogenetic lines of D. coccinellae presented with three different host ladybeetle species of varying sizes, across multiple generations to investigate heritability, plasticity, and environmental covariation of body size in D. coccinellae. We expected positively correlated parent-offspring parasitoid regressions, indicative of heritable size variation, from unilineal (parent and offspring reared on same host species) lines, since these restrict environmental variation in phenotypes. In contrast, because multilineal (parent and offspring reared on different host species) lines would induce phenotypic plasticity of clones reared in varying environments, we expected negatively correlated parent-offspring parasitoid regressions. Our results indicate (1) little heritable variation in body size, (2) strong independence of offspring size on the host environment, (3) a consistent signal of size-host tradeoff wherein small mothers produced larger offspring, and vice versa, independent of host environment. We then model the evolution of size and host-shifting under a constrained fecundity advantage model of Copes Law using a Hidden Markov Model, showing that D. coccinellae likely has considerable fitness advantage to maintain phenotypic plasticity in body size despite parthenogenetic reproduction.

evolutionary biology↗
bioRxiv2021

Genome of the parasitoid wasp Dinocampus coccinellae reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior

Dinocampus coccinellae (Hymenoptera: Braconidae) is a generalist parasitoid wasp that parasitizes >50 species of predatory lady beetles (Coleoptera: Coccinellidae), with thelytokous parthenogeny as its primary mode of reproduction. Here we present the first high quality genome of D. coccinellae using a combination of short and long read sequencing technologies, followed by assembly and scaffolding of chromosomal segments using Chicago+ HiC technologies. We also present a first-pass ab initio genome annotation, and resolve timings of divergence and evolution of (1) solitary behavior vs eusociality, (2) arrhenotokous vs thelytokous parthenogenesis, and (3) rates of gene loss and gain among Hymenopteran lineages. Our study finds (1) at least two independent origins of eusociality and solitary behavior among Hymenoptera, (2) two independent origins of thelytokous parthenogenesis from ancestral arrhenotoky, and (3) accelerated rates of gene duplications, loss, and gain along the lineages leading to D. coccinellae. Our work both affirms the ancient divergence of Braconid wasps from ancestral Hymenopterans and accelerated rates of evolution in response to adaptations to novel hosts, including polyDNA viral co-evolution.

genomics↗
bioRxiv2020

Chronic intake of high dietary sucrose induces sexually dimorphic metabolic adaptations in liver and adipose tissue

Almost all effective treatments for non-alcoholic fatty liver disease (NAFLD) involve reduction of adiposity, which suggests the metabolic axis between liver and adipose tissue is essential to NAFLD development. Since excessive dietary sugar intake may be an initiating factor for NAFLD, we have characterized the metabolic effects of liquid sucrose intake at concentrations relevant to typical human consumption in mice. We report that sucrose intake induces sexually dimorphic effects in liver, adipose tissue, and the microbiome; differences concordant with steatosis severity. We show that when steatosis is decoupled from impairments in insulin responsiveness, sex is a moderating factor that influences sucrose-driven lipid storage and the contribution of de novo fatty acid synthesis to the overall hepatic triglyceride pool. Our findings provide physiologic insight into how sex influences the regulation of adipose-liver crosstalk and highlight the importance of extrahepatic metabolism in the pathogenesis of diet-induced steatosis and NAFLD.

physiology↗
bioRxiv2019

The Pop-gen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

Here we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

bioinformatics↗