Biology subjects

Gopalakrishnan, S.

Publications and source records attributed to Gopalakrishnan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Ancient environmental DNA reveals the distinct fingerprints of whaling and climate change on Antarctic marine biodiversity

The Southern Ocean is a disproportionately large contributor to Earth system processes, playing a crucial role in the global transport of carbon, oxygen and heat. It also hosts enormous seasonal biological productivity that supports diverse endemic marine biodiversity. Industrial whaling in the first half of the 20th century and recent human-driven climate change have both profoundly altered Antarctic ecosystems, but ecological surveys of these impacts are limited to well-known taxa in the short period since monitoring began. Here, we analysed five sediment records to reconstruct more than two centuries of ecosystem change across the Western Antarctic Peninsula, spanning periods before and during major human impacts. Environmental DNA metabarcoding of these records revealed substantial biodiversity shifts, with change accelerating in recent decades. We find a significant role for both climate change and whaling in restructuring communities, identifying unique variance in whole-community change explained by each driver. Moreover, we find a negative association between whaling and metazoan families which feed from the water column, suggesting that pre-whaling ecosystems had greater pelagic productivity. Overall, our results reveal baseline Antarctic biodiversity from long before observational records and identify a distinct fingerprint of human drivers in this fragile, rapidly changing ecosystem.

ecology↗

bioRxiv2026

Joint QTL mapping reveals patterns of pleiotropy across structured environments in budding yeast

Quantitative trait locus (QTL) mapping studies in model organisms have long been used to infer the structure of genotype-phenotype maps. However, prior work has largely focused on analyzing the genetic architecture of complex traits individually. Here, we sought to instead infer genotype-phenotype maps for a large set of related phenotypes simultaneously. To do so, we used bulk assays to measure the competitive fitness of each of 100,000 individuals from a large budding yeast QTL mapping panel across a set of 101 phenotypes related by a ``hub-and-perturbation'' pattern, and then used a forward search approach to jointly infer the genetic basis of all phenotypes together. Our results reveal complex patterns of pleiotropy in the genetic architecture of these traits. We find that these patterns of pleiotropy reflect the structure of the environmental relationships as well as functional information about individual variants and the interactions between them. This suggests that high-throughput QTL mapping across structured environments can help uncover biologically meaningful genetic interactions, along with their variation across related environmental contexts.

evolutionary biology↗

bioRxiv2026

Molecular Engineering of Silk via Fatty Acid Esterification for Water-Stable, Anti-fouling, Biocompatible, Implantable Materials

Biopolymers offer attractive properties for implantable materials, but their limited aqueous and enzymatic stability constrains long-term performance in biological environments. Silk fibroin is mechanically tunable and thermoplastically processable, yet remains susceptible to swelling in aqueous environments, which can impact mechanical properties. Here, we establish fatty acid esterification as a strategy to transform silk into a hydrophobic, water-stable, yet still bioresorbable material (FAsilk). Fatty acid functionalization significantly increased resistance to aqueous swelling and enzymatic degradation while preserving structural and mechanical integrity and thermoplastic processability. The resulting FAsilk biomaterials also reduced microbial contamination, blood clot formation, and macrophage adhesion relative to native silk, due to the change in hydrophobicity, while maintaining cytocompatibility and hemocompatibility. Subcutaneous implantation in mice demonstrated favorable biological responses, including minimal impact on body weight and no significant pro-inflammatory responses, indicating no adverse effects on animal health. Thus, fatty acid functionalization enables silk to combine hydrophobicity and aqueous stability with processability and biodegradability, providing a mechanically robust materials platform for bioresorbable implants, including medical devices, tissue-engineered grafts and drug delivery systems.

bioengineering↗

bioRxiv2026

The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

One of the most devastating events in human history, the Black Death (c.1347-1353), marked the beginning of the Second Plague Pandemic. After initially receding, plague returned in intermittent outbreaks throughout Europe, beginning with the pestis secunda. Despite its significance, the post-Black Death epidemiology of Yersinia pestis remains poorly understood. Here, we report 23 new Y. pestis genomes recovered from Second Plague Pandemic contexts across Scandinavia, the Netherlands, Iceland, and Armenia, spanning approximately 270 years. Applying a reproducible mutation-filtering pipeline to assess genetic diversity, we report both Black Death and post-Black Death lineages and document multiple waves of plague at individual cemetery sites. We identify four pestis secunda genomes, including three from Armenia, supporting the eastward dissemination of this lineage prior to its disappearance from Europe. We also resolve a previously under-characterised Branch 1A sub-lineage of Y. pestis and provide the first genomic evidence of plague in Iceland, resolving longstanding uncertainty over its presence on the island. Finally, by calling variants against a reconstructed ancestral reference, we identify clade-defining mutations, including nonsynonymous changes in metabolic and biofilm-related genes with predicted structural effects that may have contributed to shaping the epidemiological dynamics of the Second Plague Pandemic.

genetics↗

bioRxiv2026

Habitat discontinuity and fidelity to migratory routes shape narwhal genetic structure and diversity

Rapid Arctic warming is reshaping marine ecosystems and altering the evolutionary trajectories of ice-associated species. Narwhals (Monodon monoceros) are Arctic endemics that are thought to be vulnerable to climate change. We present the first nuclear genomic assessment of narwhals across their distribution to evaluate population structure, demographic history, local adaptation, inbreeding and genetic load. Using genomes from 117 individuals, we identified three populations: Canadian Arctic Archipelago/West Greenland, Northeast Greenland/Svalbard and Southeast Greenland. Demographic reconstructions indicated low effective population size over at least 600,000 years, followed by population growth during the last glacial period. Our results suggest that population structure is maintained by habitat discontinuities and fidelity to migration routes. The latter may promote local adaptation, as genes related to long-term memory were found in regions putatively under selection in Canadian Arctic Archipelago/West Greenland narwhals, which undertake the longest migrations. Genome-wide diversity was uniformly low across populations. Inbreeding levels were inversely related to estimated population sizes. The small and rapidly declining Southeast Greenland population exhibited elevated recent inbreeding. Deleterious mutations were primarily masked in heterozygous genotypes, raising concerns for this population. Together, our results demonstrate that past climate, habitat discontinuities and migration fidelity jointly structure narwhal populations.

evolutionary biology↗

bioRxiv2026

Progressive matrix stiffening of tyramine-modified silk fibroin hydrogels governs stage-specific pulmonary fibroblast activation

Fibrosis is a progressive and often fatal pathological process characterized by excessive extracellular matrix deposition, tissue stiffening, and irreversible organ dysfunction. Effective antifibrotic therapies remain limited by the lack of in vitro models that recapitulate the full spectrum of fibrotic disease progression. Here, we leverage tyramine-modified silk fibroin (SF-TA) hydrogels to investigate normal human lung fibroblasts (NHLF) responses to progressively stiffening environments relevant to pulmonary fibrosis. Two hydrogel formulations with distinct stiffening profiles over 14 days were prepared: a gradual-stiffening 0% SF-TA formulation reaching [~]20 kPa, and a rapidly stiffening 50% SF-TA formulation reaching [~]60 kPa. NHLFs were cultured on both formulations, with and without TGF{beta} (5 ng/mL), for 14 days and assessed for viability, metabolic activity, cytokine and collagen secretion, cytoskeletal organization, and mechanotransductive gene expression. The 0% SF-TA hydrogels drove sustained fibroblast proliferation and elevated secretion of IL-6, IL-8, and MCP-1, consistent with early inflammatory fibrosis. The 50% SF-TA hydrogels induced a metabolic plateau without senescence, suppressed inflammatory cytokine secretion, and, in the presence of TGF{beta}, led to significant upregulation of ACTA2 and CTGF, alongside -SMA stress fiber incorporation, consistent with established myofibroblast persistence. Both conditions produced comparable secreted collagen output by day 14. Together, these findings establish dynamically stiffening SF-TA hydrogels as a tunable platform for investigating stage-dependent fibroblast activation and mechanobiological progression in fibrosis.

bioengineering↗

bioRxiv2026

Human Genome-Scale Models of Metabolism and Gene Expression Reveal Resource Constraints of Cancer Cell Lines

Genome-scale metabolic models (M-models) provide mechanistic insight into intracellular metabolism by simulating fluxes subject to nutrient and energy resource constraints. However, they cannot account for a major component of resource allocation, since they do not explicitly account for the cost of producing and maintaining enzymes. Genome-scale models of metabolism and gene expression (ME-Models) address this by including gene expression reactions, but these have only been developed for prokaryotes due to the additional complexity and challenges of modeling eukaryotes. Here, we present the human ME-Model, which encodes transcription, translation, complex formation, and turnover reactions for all enzymes catalyzing metabolic reactions, and couples these processes to constrain metabolic fluxes. We introduce humanME, a Python package to build and analyze human ME-Models. With this, we constructed 16 cancer cell line ME-Models. We found that resource constraints improve growth-rate predictions, and that ME-Model flux predictions are more biologically plausible and efficient. Moreover, transcriptional fluxes recapitulate RNA-Seq expression levels, with discrepancies revealing potential trade-offs involving multiple cellular objectives. Finally, the ME-Model recapitulates the Warburg effect, with increasing growth rate inducing glycolytic shifts, in part due to machinery costs of the electron transport chain. Altogether, we show ME-modeling can mechanistically link gene expression, resource allocation, and metabolism in human cells, substantially expanding the predictive scope of constraint-based models.

systems biology↗

bioRxiv2026

Laboratory yeast crosses reveal limited epistasis in the genetic basis of complex traits

Mapping the genetic basis of complex traits is complicated by the presence of epistatic interactions between loci. While work in molecular genetics identifies numerous specific genetic interactions, statistical analyses of quantitative traits frequently conclude that additive (nonepistatic) models explain most heritable variation. However, these conclusions are typically limited by the narrow range of genetic relatedness(e.g. in F1 offspring of a biparental or circular cross). Here, we use a barcoded panel of Saccharomyces cerevisiae genotypes with a broad range of relatedness to quantify the effects of epistasis on the genetic architecture of seven complex traits. We find limited contributions of epistasis to the genetic basis of these traits. These results indicate that epistasis beyond that detected in standard yeast crosses may exist, yet it contributes little to phenotypic variance in these systems.

genetics↗

bioRxiv2025

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution

Quantitative genetics approaches designed to understand the evolution of traits have helped improve our understanding of the genetic basis of adaptation. However, they often overlook crucial aspects of adaptation, including the long-term temporal evolutionary dynamics, the predictability of evolutionary outcomes, the influence of past evolution on future evolutionary trajectories (contingency), and the diversity of molecular mechanisms underlying adaptation. Experimental evolution has been a useful tool for answering these questions, but extracting fundamental principles and predictive features of evolutionary outcomes from these datasets remains challenging due to the large number of covariates and confounding effects, such as differences in experimental setup, species lifestyle, gene content, and evolution rate. Here, we sought to circumvent these challenges by comparing distant yeast species that share several evolutionary features but differ mainly in evolutionary history and genome architecture, i.e. Saccharomyces cerevisiae and Schizosaccharomyces pombe. Thus, we evolved 10 populations of the fission yeast for 10,000 generations in the same conditions as a pre-existing budding yeast dataset (i.e. high-sugar media and hypoxic conditions), allowing us to observe repeatable evolutionary outcomes within species but diverse molecular mechanisms and targets of adaptation across species. The most frequent adapting route in these conditions involved upregulating fermentation genes and downregulating the glycolysis gene pyk1, which has not previously been observed in S. cerevisiae evolved populations or in wild Kluyveromyces lactis, but similar evolutionary paths have been observed in Schizosaccharomyces japonicus and in clinically relevant populations, such as some cancer cells. This suggests that parallelism is pervasive in the tree of life and that mechanisms of adaptation can be shared among closely related or distant species. Despite similar gene content and identical environments, recurrent adaptation across S. pombe populations involved different genes than in S. cerevisiae and was mostly detectable at the transcriptomic level. This suggests that trans-regulatory effects may play an important role in adaptation on short evolutionary timescales and that differences in evolutionary outcomes between these species may be attributed to contingency.

evolutionary biology↗

bioRxiv2025

Multi-omics time-series analysis in microbiome research: a systematic review

Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and characterizing temporal variation simultaneously across multiple scales, from specific molecular interactions to entire ecosystems, is crucial for uncovering biological mechanisms and understanding the emergence of complex phenotypes. With the increasing number of studies incorporating multi-omics data sampled over time, it has become clear that integrated approaches are pivotal for these efforts. However, standard data analytical practices in longitudinal multi-omics are still shaping up and many of the available methods have not yet been widely evaluated and adopted. Thus, we performed a systematic literature review on data science methods for longitudinal multi-omics, with a particular focus on microbiome research.

bioinformatics↗

bioRxiv2025

Genetic differentiation in Anopheles stephensi from India and Ethiopia: insights from mitochondrial genome analysis

Anopheles stephensi is a primary malaria vector, particularly in urban areas of South Asia and the Middle East. Its recent spread into Africa has raised significant interest in understanding its genetic structure and evolutionary history. This study presents a comprehensive analysis of 98 mitochondrial genomes of An. stephensi from India, Pakistan, and Ethiopia, providing critical insights into the species genetic diversity patterns. High genetic diversity was observed among Indian samples, with two distinct genetic ancestries identified. While one ancestry was more prevalent in specific geographical regions, both lineages were found across all study sites, suggesting the co-existence of multiple lineages within these areas. Further analysis revealed significant genetic differentiation between Indian and Ethiopian populations, with limited overlap in shared mutations. Although some Ethiopian samples showed genetic relatedness to the SDA500 strain from Pakistan (used in genome sequencing by the Broad Institute), the majority of Ethiopian samples showed distinct genetic ancestry. The distinctiveness of Ethiopian populations, compared to other countries outside of Africa, was also reflected in the COI datasets analyzed in this study. However, further expanding the mitogenome dataset to include additional wild samples from regions such as Pakistan, Iran, Saudi Arabia, Sri Lanka and other African countries will provide a more comprehensive understanding of An. stephensis invasion history. Overall, the findings of this study highlight the significant genetic differentiation between Ethiopian and Indian An. stephensi populations, and existence of multiple lineages in Ethiopia indicating multiple independent introductions from different countries.

zoology↗

bioRxiv2025

A community-consensus reconstruction of Chinese Hamster metabolism enables structural systems biology analyses to decipher metabolic rewiring in lactate-free CHO cells

Genome-scale metabolic models (GEMs) are indispensable for studying and engineering cellular metabolism. Here, we present iCHO3K, a community-consensus, manually-curated reconstruction of the Chinese Hamster metabolic network. In addition to accounting for 11004 reactions associated with 3597 genes, iCHO3K includes 3489 protein structures and structural descriptors for >70% of its 7377 metabolites, enabling deeper exploration of the link between molecular structure and cellular metabolism. We used iCHO3K to contextualize transcriptomics and metabolomics data from a CHO cell line in which lactate secretion is abolished. We found the reduced glycolytic flux and enhanced TCA cycle flux were accompanied by an elevated NADH and PEP levels in these cells, consistent with experimental measurements. Leveraging iCHO3Ks structural annotations, we identified candidate binding interactions of NADH and PEP with glycolytic enzymes showing model-predicted differential flux, suggesting novel allosteric regulation associated with the observed decrease in glucose uptake and glycolysis. Overall, iCHO3K offers a valuable framework for systematic integration of omics data, improved flux predictions, and structure-guided insights, thus advancing CHO cell engineering and enhancing biomanufacturing efficiency.

systems biology↗

bioRxiv2025

The information content of species: formal definitions of pangenome complexity track with bacterial lifestyle

Genes and other genomic elements have variable presence absence patterns across most bacterial species. Pangenome fluidity is often invoked to measure this genome flux. Fluid pangenomes contain genes found only in subsets of species strains. Tighter pangenomes contain more genes that define a shared core. Species definitions are often tied to this pangenome diversity. In any global comparative framework, pangenomes must be calculated across all known species. But defining pangenomes is fraught with computational and biological challenges, requiring assembly, annotation, alignment, and phylogenetics of millions of orthologs. We offer an alternate view that de-centers the gene and emphasizes the raw information content of sequences. Information is data that reduces uncertainty. Tight pangenomes, with elements repeated across every strain in a species ensemble, contain more complete information. In contrast, fluid pangenomes have more uncertainty, higher complexity, and higher information diversity. Bacterial lifestyle has been shown to drive this information diversity. For example, challenging environments often increase information diversity by encouraging the accrual of auxiliary genes. Here, we employ agile complexity metrics to quantify this increase. Ensembles of free-living, motile, and non-pathogenic species have high genomic complexity. Ensemble complexity decreases in species bound to specific hosts. Because we eliminate annotation and alignment, our method is fast enough to evaluate species across all known bacterial genomes. The approach democratizes classification and our results highlight how broad the term "species" has become.

genomics↗

bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗

bioRxiv2024

Ancient environmental DNA indicates limited human impact on marine biodiversity in pre-industrial Iceland

Human activities are affecting marine biodiversity globally by accelerating extinction rates, altering ecosystem conditions, and changing community structures. These changes can only be understood through establishing the ecosystem state prior to significant anthropogenic impact, and by disentangling the anthropogenic effect from natural climatic changes. Here, we reconstruct marine biodiversity in Iceland across three millennia (1315 BCE-1785 CE), encompassing periods of climatic fluctuation and human settlement, to explore the comparative effect of natural and anthropogenic forces on marine biodiversity. We performed 18S metabarcoding of ancient environmental DNA from two sediment cores collected from northern Icelandic shelf seas, integrating local climatic records, population estimates and zooarchaeological remains from published sources to estimate the influence of climatic and anthropogenic impacts. Against the backdrop of increasing human populations and marine exploitation, we observe no large-scale taxonomic shifts or anthropogenic biodiversity changes across the period. In contrast, we found a positive correlation between herring (Clupea harengus) detection rates and proxy-reconstructed sea surface temperature, suggesting a role for climate in shaping marine biodiversity. Overall, our data suggest that despite impacts on terrestrial ecosystems and the development of a substantial export fishery across the study period, Icelandic society may have had a limited effect on marine biodiversity.

ecology↗

bioRxiv2024

Complex genomic ancestry in southern regions and drivers of continental-level genetic diversity in the wolves of Asia

Gray wolves (Canis lupus) in Asia encompass most of the species global genetic diversity and many endangered populations. However, a clear understanding of the evolutionary history of wolves from many parts of Asia, especially southern regions, is lacking. We used 98 whole genomes of wolves sampled across Eurasia to better resolve their evolutionary history by investigating phylogenetic and gene flow histories across the genome, and to characterize their demographic history and genetic diversity. The strongest barriers to gene flow coincided with boundaries separating the three major extant wolf lineages - Indian, Tibetan, and Holarctic. Wolves in the central Asian mountain ranges belonged to the Holarctic lineage, and despite their geographic adjacency only share minimal ancestry with the Tibetan lineage. In contrast, wolves from eastern Asia share population-wide ancestry with the Tibetan lineage, which may reflect an unsampled lineage similar, but not exactly to, the modern-day Tibetan lineage. Wolves from southwestern Asia also share population-wide ancestry with the Indian lineage, likely due to old (>6kya) admixture events. Long-term historical declines over the last 100,000 years, geographic isolation, and recent inbreeding have resulted in the Indian and Tibetan wolves having some of the lowest levels of genetic diversity and highest realized genetic loads. In contrast, adjacent populations exhibit some of the highest genetic diversity, due in part to admixture along contact zones. Our study illustrates how using multiple approaches that consider heterogenous signals across the genome can more fully resolve the historical and contemporary processes that have led to present-day species diversity.

evolutionary biology↗

bioRxiv2024

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R2>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

evolutionary biology↗

bioRxiv2024

Fine-scale oceanographic processes shape marine biodiversity patterns in the Galapagos Islands

Uncovering the drivers that shape biodiversity patterns is critical to understand ecological and evolutionary dynamics. Despite evidence that biodiversity composition is influenced by processes at different spatial scales, little is known about the role of fine-scale oceanographic processes on the structure of marine communities. This is particularly important in biodiversity hotspot regions, where small changes in environmental conditions may lead to substantial changes in species composition. We combined ocean modelling and 12S environmental DNA (eDNA) metabarcoding, targeting teleost and elasmobranch species, to explore if oceanographic processes influenced biogeographic patterns around the biodiverse Galapagos Islands. We first detected significant differences in eDNA-measured community structure across the archipelagos diverse seascape. We found no significant relationship between Lagrangian particle tracking metrics and nektonic biodiversity, and thus developed a novel metric to measure the cumulative seawater flow resistance between pairs of geographic sites. This metric explained a significant proportion of variation in eDNA-measured beta dissimilarity between sites, comparable in influence to important abiotic drivers, such as temperature and geographic distance between sites. Cumulatively, our results indicate that marine communities are particularly sensitive to changes in local current systems, and suggest that fine-scale oceanographic processes may have an underappreciated role in structuring marine communities globally.

ecology↗