Biology subjects

Biswas, A.

Publications and source records attributed to Biswas, A..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Growth-factor ligand functionalization enhances cellular and in vivo uptake of DNA nanodevices

Epidermal Growth Factor (EGF) and Transforming Growth Factor beta (TGF-{beta}) are two important classes of growth factor that regulates cell growth, cell proliferation, differentiation, immune responses, and extracellular matrix generation. Using a short peptide-based ligand coupled to DNA nanocages, we present the enhanced internalization of a receptor-mediated peptide-DNA nanocage. We used here tdDNA as a delivery vehicle. Our study in cellular and in vivo showed excellent internalization, cell growth, and inhibition. We expect that a tdDNA-modified receptor-binding peptides could become a valuable scaffold for use as a cellular programming and regenerative material.

bioengineering↗

bioRxiv2025

Inhibiting ezrin triggers formin-mediated actin remodelling reducing cellular mechano-protection

Ezrin plays a crucial role in linking the cortical actin cytoskeleton to the plasma membrane in animal cells. Inactivated by small molecule ezrin inhibitors (EzrInh), ezrin is known to regulate cellular functions like adhesion and motility. However, whether ezrin plays any significant role in protecting cells against mechanical stresses is less explored. We use hypo-osmotic shock (HS) to challenge cells and study the mechano-protective role of ezrin. Inhibition of ezrin phosphorylation led to increased cell rupture rates on hypo-shock, with a greater impact at later time points ([~] 10 min). The time scales match with that of enhanced tension contrast at edges at the basal plane. We also observed a lowered relative retraction rate at protrusions created by hypo-shock and a less contractile mid-plane cortex - both indicate the role of a weakening of the cortex by EzrInh in compromising membrane integrity on hypo-shock. Concomitantly, EzrInh also increased stress fibres (SFs), traction forces and cell spreading clearly indicative of additional cellular pre-stress. Utilizing formin inhibitor (SMIFH2), we showed that formin-mediated actin polymerization was critical for the SF response to EzrInh while it also prevented the subsequent EzrInh-treatment from enhancing cell rupture rates. Together EzrInh reduced mechano-protection in cells by tilting of balance of actins organization from the cortex to SF enhancing formin-mediated SF assembly. HighlightsO_LIHypo-osmotically shocked CHO cells rupture more on ezrin inhibition C_LIO_LIEzrin inhibition weakens contractility of cortical actin but enhances stress fibre numbers at the base C_LIO_LIHypo-osmotic shock creates basal protrusions that are also retracted. C_LIO_LIRetractive potential in cells is weakened by ezrin inhibition C_LIO_LIFormin inhibitor prevents net increase in stress fibres by inhibition of ezrin C_LIO_LIOn pre-treatment with formin inhibitor, subsequent inhibition of ezrin doesnot render cells more vulnerable to hypo-osmotic shock C_LI

biophysics↗

bioRxiv2025

Nuclear Receptor Transcription factors promote axon regeneration in the Adult Corticospinal Tract

Transcription factors are potent levers for neural repair, but which factors govern regenerative capacity in the corticospinal tract remains largely unknown. By intersecting developmental RNA-seq with ATAC-seq footprinting, we identified two nuclear-receptor transcription factors, NR2F1 and NR2F6, neither previously linked to CNS axon growth, whose chromatin occupancy at pro-growth enhancers is progressively lost as neurons mature. Forced expression of either factor significantly increased neurite outgrowth in single-neuron tracing assays, and each drove strong cross-midline sprouting after pyramidotomy and long-tract CST regeneration after complete thoracic crush, with concordant recovery of hip-rise kinematics and grip strength. Parallel multi-omic profiling (CUT&RUN, snRNA-seq and Ribo-seq) of both factors together with NR2F6 Hi-C revealed distinct mechanisms: NR2F1 reactivated chromatin-remodeling and cytoskeletal programs, whereas NR2F6, via a conserved corepressor domain, re-occupied developmental enhancers, reorganized three-dimensional chromatin architecture into new topologically associating domains, and imposed a transient translational down-shift in which growth-relevant modules were selectively preserved through translational buffering. Together, these data identify NR2F nuclear receptors as regulators of corticospinal regeneration, acting through enhancer redeployment, translational reprogramming and three-dimensional genome reorganization.

neuroscience↗

bioRxiv2025

Latitude Matters: A Global Phylogeographic Perspective on Climate-Driven Demographic Responses in Tarantulas

AimTo investigate how past climate change has shaped the genetic diversity and demographic responses of tarantulas across latitudes, and to test whether climate-demography relationships vary with latitude. LocationGlobal; spanning tropical to temperate regions. TaxonTarantulas (family Theraphosidae). MethodsWe compiled mitochondrial Cytochrome oxidase I (COI) sequences for 48 tarantula species worldwide, including newly generated sequences, to estimate nucleotide diversity ({pi}) and Tajimas D. Species distribution models (SDMs) were constructed under present-day and Last Glacial Maximum (LGM) climatic conditions to quantify changes in habitat suitability since the LGM. Using generalized linear models (GLMs), we tested whether genetic and demographic metrics were associated with latitude and climate-driven habitat change, and whether their relationship varied with latitude. ResultsPairwise correlations among latitude, habitat change, and genetic metrics showed no significant associations. However, GLMs revealed a significant interaction: the effect of habitat suitability change on Tajimas D was strongly positive at high latitudes but negative or negligible at low latitudes. This indicates that demographic responses to past climate change varied latitudinally. Several high-latitude species showed genetic signatures of demographic expansion and range increase since the LGM. Main conclusionsOur results support the hypothesis that species at higher latitudes experience stronger demographic fluctuations due to historical climate change, aligning with Darwins early predictions. Moreover, patterns of demographic growth in temperate taxa suggest that some species may benefit from recent warming, consistent with Janzens climatic variability hypothesis. These findings demonstrate that climate-driven genetic and demographic responses in tarantulas are shaped by latitude, highlighting the importance of integrating phylogeography with ecological niche modeling to understand species resilience under climate change.

evolutionary biology↗

bioRxiv2025

De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential

Predicting the precise positions of water molecules at the protein interface remains a formidable challenge, fueling active research in this field. Here, we present a novel approach based on molecular dynamics simulations that utilizes statistical thermodynamic signatures of water at protein interfaces to improve the accuracy of water placement in cryo-EM maps, with apoferritin as a model benchmark system. The interaction energy of solvent with the protein is insufficient to distinguish between high- and lower-consensus water positions, consistent with reports of earlier work. Instead, we employ a detailed statistical thermodynamic analysis based on the excess chemical potential (WT) - a measure of the thermodynamic balance between the interaction energy of an interfacial water molecule with the protein and its free energy of interaction with all of the other solvent molecules. WT is proportional to the log ratio of the local density of water molecules at the protein interface to the bulk density. 85% of the top 100 water locations with the most favorable excess chemical potential values are observed in one or more high resolution Cryo-EM maps deposited in the PDB, and 70% of the top 200 water locations indexed by excess chemical potential are observed in the cryo-EM maps. This work paves the way for the development of a cryo-EM refinement tool that integrates molecular dynamics simulations with cryo-EM data for high-resolution modeling of water networks.

biochemistry↗

bioRxiv2025

Intracellular formate is a critical mediator of the antimicrobial fate of Salmonella Typhimurium Against meropenem and ciprofloxacin

Salmonella enterica serovar Typhimurium (STM) employs various strategies to endure antibiotic stress, but the contribution of central metabolites to resistance remains insufficiently characterized. In this work, we identify intracellular formate, produced by pyruvate-formate lyase (PflB), as a key determinant of STM susceptibility to meropenem and ciprofloxacin. Deletion of pflB disrupts cellular pH homeostasis, impairing efflux pump function, increasing reactive oxygen species, and causing membrane depolarization, collectively heightening sensitivity to antibiotics. Supplementing extracellular formate reverses these phenotypes. Mechanistically, pH imbalance activates the RpoE-csrB regulatory pathway, leading to reduced expression of efflux pump genes acrB and tolC, while extracellular formate engages the BarA/SirA two-component system to further influence the CsrA/csrB network. Disrupting the formate pool interferes with efflux-dependent resistance, revealing a previously unrecognized signalling function for intracellular metabolites. Overall, our results position formate as a metabolic driver of antibiotic outcomes in STM and highlight it as a potential target for mitigating resistance.

microbiology↗

bioRxiv2025

Sewing the future of cotton: a multi-omics study combining nanomechanics, transcriptomics, and phenotypic traits

Cellulose microfibrils that are essential for mechanical strength and overall quality of cotton fibers. This study quantifies and compares the nanoscale structural and mechanical properties of cellulose microfibrils such as microfibril dimensions, crossover count and angles, roughness, and Youngs modulus for two popular cotton species: Gossypium hirsutum (Gh) and Gossypium barbadense (Gb) fibers across four growth stages (8, 12, 18, and 22 days post-anthesis) using atomic force microscopy (AFM). Our results revealed for the first time that Gb fibers exhibit a better alignment, finer dimensions, and higher stiffness compared to Gh fibers at nanoscale, resulting in smoother fiber surfaces, and improved quality at macroscale. We are also the first to develop machine-learning models to predict macroscale phenotypic traits specifically boll length and cellulose content using nanoscale features alone and in combination with multi-omics modalities, substantially enhancing the predictive accuracy and highlighting opportunities for robust cross-species modeling of cotton fiber traits.

biophysics↗

bioRxiv2025

RNA Mango-based Sensors for Lead

Lead (Pb2+) toxicity poses a serious threat to human health and remains a global concern; therefore, there is a critical need for the development of easy-to-use and cost-effective tools for the rapid monitoring of Pb2+. In this study, we demonstrate the potential of the RNA Mango aptamer as a sensitive and selective sensor for Pb2+. Our findings reveal that trace amounts of Pb2+ induce the formation of the G-quadruplex motif in RNA Mango, which facilitates dye binding and activates fluorescence. A detailed investigation of the fluorescence properties of RNA Mango with three different dyes, TO1-Biotin, TO3-Biotin, and Thioflavin-T, in the presence of Pb2+ shows that RNA Mango has the highest binding affinity for Pb2+ in combination with TO1-Biotin, with a KD value as low as [~]100 nM. In the presence of Pb2+, RNA Mango has sub-micromolar affinity for all three dyes, showing the tightest binding to TO1-Biotin (KD [~]40 nM). Mango lead sensors detect low nanomolar concentrations of Pb2+ with limits of detection of 2 - 16 nM, which are significantly lower than its allowable limit in drinking water. RNA Mango exhibits remarkable selectivity toward Pb2+ and can detect lead in tap water samples. This work reports a new class of simple and inexpensive fluorescence-based sensors for lead and expands the repertoire of RNA-based lead sensors.

biochemistry↗

bioRxiv2025

Hierarchical Heterogeneities in Spatio-Temporal Dynamics of the Cytoplasm

The physical properties of the cytoplasm fundamentally constrain the dynamics and fidelity of cellular processes. Endogenous fluctuations carry signatures of these properties, yet how their collective dynamics across mesoscopic spatiotemporal scales relate to cytoplasmic heterogeneity and organization remains poorly understood. Here, we use differential dynamic microscopy (DDM) to quantify these fluctuations in eukaryotic cytoplasms. In Xenopus laevis egg extracts, we identify signatures of subdiffusive fractional Brownian motion (fBm) and non-Gaussian displacement distributions, consistent with a crowded, heterogeneous environment. We introduce an empirical model combining fBm with an inverse Gaussian diffusivity distribution, enabling robust estimation of fractional diffusivities and scaling exponents across conditions. Denser cytoplasm exhibits lower fractional diffusivity and scaling exponent, while energy addition induces non-stationary dynamics. Stabilization of microtubule networks introduces a secondary timescale, rationalized by a two-state fBm model separating cytosolic and network-associated contributions. In HeLa cells, the framework reveals comparable scaling exponents but lower diffusivities than in egg extract. Upon microtubule depolymerization, the dynamics become slower yet more Brownian-like. This highlights dual roles of the cytoskeleton as confinement but also as fluidizer of the cytoplasm. These results establish label-free DDM as an interpretable, collective, multiscale readout of how composition, activity, and cytoskeletal organization shape hierarchical cytoplasmic dynamics.

biophysics↗

bioRxiv2025

Synthesis and In Vitro Assessment of Triazole-Based Compounds as Potential Inhibitors of Herpes Simplex Virus Type 1

A library of novel 1,2,4-triazole derivatives fused with a pyrazine moiety (5a-5t) was successfully synthesized and evaluated for their therapeutic potential against HSV-I virus and oxidative stress. These compounds were assessed for anti-inflammatory, antioxidant, and anti-HSV activities, demonstrating encouraging biological profiles. In particular, compounds 5f and 5t exhibited markedly improved antiviral efficacy compared to the reference drug, Acyclovir. The antioxidant capacity was also notable, with compound 5b showing exceptional radical scavenging potential. To better understand the interaction at the molecular level, docking studies were conducted, indicating that these molecules could potentially inhibit HSV1, a key enzyme required for viral replication. Also, in silico testing was conducted for assessing drug-likeness, ADME characteristics, and stability of metabolism which was helpful for optimizing further lead designs. Although the experimental methods were accurately implemented, some human error such as timing during administration of the compounds, measuring, and other tasks may have slight variations which are not entirely avoidable. These possible blunders are, however, unlikely to change significantly the observed trends. Ultimately, the study emphasizes these new hybrids of triazole-pyrazine as potential precursors for the synthesis of powerful anti-HSV-I and possibly antibacterial medicines, which require more advanced pharmacological and clinical research.

biochemistry↗

bioRxiv2025

A ribozyme ligase that requires a 3' terminal phosphate on its RNA substrate

Ribozymes played essential roles in catalyzing metabolic processes and facilitating genome replication in primordial RNA-based life. In vitro evolution has enabled the discovery of ribozymes that catalyze diverse chemical reactions, but it is likely that many catalytic activities of RNA remain to be uncovered. Expanding our understanding of the biochemical capabilities of RNA, especially new ribozyme functions related to RNA assembly, will help to refine models of primordial genome replication and, more broadly, the origin and evolution of early life. Here, we report the discovery of a novel ribozyme ligase that catalyzes the attack of the 2'-hydroxyl group of an RNA substrate on the 5'-triphosphate of a second RNA, but only when the substrate RNA possesses a 3'-phosphate vicinal to its nucleophilic 2'-hydroxyl group. This activity emerged unexpectedly during a directed evolution experiment designed to isolate ribozyme ligases that use 5'-triphosphorylated RNA oligonucleotides as substrates. Because the 3'-phosphate group on the RNA substrate does not directly participate in the ligation reaction, it would be extremely challenging to design a selection strategy to isolate ribozyme ligases with this unique reactivity. The ligases requirement for an RNA 3'-phosphate group on the substrate resembles enzymatic mechanisms found in protein-based RNA repair pathways. We propose that ribozyme-catalyzed ligation of 3'-phosphorylated RNA could have enabled the repair of cleaved RNA strands in primordial cells. We demonstrate that our in vitro evolved ribozymes ligate themselves specifically to 3'-phosphorylated RNA fragments present in heterogenous mixtures of cellular RNA, demonstrating their potential utility as enrichment reagents for profiling RNA cleavage products in transcriptomic studies. Our findings not only report a new catalytic reactivity in RNA but also provide insights into ribozyme evolution, primordial RNA repair, and potential applications in RNA sequencing.

biochemistry↗

bioRxiv2025

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

The emergence of drug resistance in the human immunodeficiency virus (HIV) remains a formidable challenge to the long-term efficacy of antiretroviral therapy (ART). A growing body of evidence highlights the critical role of epistasis, the dependence of mutational effects on the sequence context, in shaping the fitness landscape of HIV under ART-induced selection pressure. However, the biophysical origins of the epistatic interactions involved in engendering drug-resistance mutations (DRMs) remain unclear. Are the mutational correlations "intrinsic" to the properties of the protein, or do they arise because of drug binding? We use a Potts sequence-covariation statistical energy model built on patient-derived HIV-1 protein sequences to construct computational double mutant cycles that probe pairwise epistasis for all observed mutations across the three major HIV drug-target enzymes. We find that the strongest epistatic effects occur between mutations at residue positions that frequently mutate during the course of ART, termed resistance-associated positions. To investigate the structural origins of the strongest epistatic interactions, we perform [~]100 free energy perturbation molecular dynamics simulations, revealing that the primary contribution to the pairwise epistasis between DRMs arises from cooperative effects on protein stability and folding as an intrinsic consequence of the protein mutational landscape. The results collectively reinforce a mechanism of resistance evolution whereby viruses escape drug pressure by selectively engendering mutations at "intrinsically" coupled sites, allowing them to cooperatively ameliorate fitness detriments incurred by individual DRMs. SignificanceEpistasis refers to the phenomenon where the effect of a mutation on protein structure and function is dependent on the genetic sequence background of the mutation, resulting in the combined effect of mutations being non-additive. Epistasis plays a significant role in the evolution of drug resistance in viruses such as HIV under therapeutic selection pressure. We combine a protein sequence coevolutionary model and molecular dynamics free energy simulations to identify and probe the mechanistic origins of the strongest epistatic interactions connecting HIV drug-resistance mutations. The work establishes a foundation to probe the molecular bases of epistasis and predict the evolution of resistance predicated on the knowledge of epistatic interaction networks.

biophysics↗

bioRxiv2025

Optimizing SARS-CoV-2 RBD Boundaries for Enhanced E. coli Expression

The outbreak of Coronavirus Disease 2019 (COVID-19) has posed a significant risk to global health, warranting the formulation of efficient preventive and therapeutic measures to tackle its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of coronaviruses plays a pivotal role in viral attachment and entry into host cells. The receptor-binding domain (RBD) of the SARS-CoV-2 S protein has demonstrated a robust binding affinity to ACE2 receptors in humans. Consequently, it has become a prime target for therapeutic interventions using antibodies, vaccines, or other designed inhibitors. This paper presents an optimized RBD sequence that can be efficiently expressed in Escherichia coli and refolded to yield a functional protein. Using optimized refolding procedures, we obtained 10-12 mg of active protein from a one-liter LB culture. The biological activity of the refolded RBD was confirmed by monitoring its interaction with the designed LCB1 miniprotein ligand by surface plasmon resonance, wherein they exhibited significant affinity levels as reflected by their dissociation constants (KDs < 10 nM). The resulting RBD could be an ideal target for designing potent COVID-19 antivirals. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/633331v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@14e13b4org.highwire.dtl.DTLVardef@efb1f8org.highwire.dtl.DTLVardef@8d155dorg.highwire.dtl.DTLVardef@75a591_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Disruptive changes in tissue microenvironment prime oncogenic processes at different stages of carcinogenesis in lung

Carcinogenesis is characterized not only by the uncontrolled growth of malignant cells but also by the disruption of the normal balance of cellular processes and intercellular interactions in the microenvironment that overcome the constraints of tissue homeostasis and support malignant growth. We profiled benign pulmonary dysplasia, carcinoma in situ, and invasive lung carcinomas at single-cell resolution to identify composite changes in cellular processes, signaling, and interactions among tumor-immune-stromal cells in the microenvironment in progressively advanced disease stages. We developed OncoTerrain, a hyperparameter-tuned model that captured synergistic multimodal signatures of an increasingly perturbed microenvironment in malignant disease stages and identified composite microenvironmental changes that supported cancer hallmarks. Key cancer-related changes in transcriptional states, cellular processes, and intercellular interactions involving immune, fibroblast, and stromal cell types preceded tumor initiation and were often synergistic. The microenvironment of increasingly malignant tissues was characterized by immune avoidance, ECM remodeling, and altered cell mobility. There were changes in cell states in fibroblasts, macrophages, and their inter-cellular interactions with other cell types, whereas T-cell activation occurred late. The in-situ carcinomas showed variations in the composite microenvironmental states that corroborated their pathology, which was not apparent at the genome level. A subset of those harbored populations of tumor and non-tumor cells with aggressive characteristics in some but not all aspects of hallmarks of carcinogenesis in the lung. We suspect that the variation in the coordination of microenvironmental cues may influence why some but not all in-situ tumors progress to the advanced stages.

genomics↗

bioRxiv2024

Projections between the globus pallidus externa and cortex span motor and non-motor regions

The globus pallidus externa (GPe) is a heterogenous nucleus of the basal ganglia, with intricate connections to other basal ganglia nuclei, as well as direct connections to the cortex. The anatomic, molecular and electrophysiologic properties of cortex-projecting pallidocortical neurons are not well characterized. Here we show that pallidocortical neurons project to diverse motor and non-motor cortical regions, are organized topographically in the GPe, and segregate into two distinct electrophysiological and molecular phenotypes. In addition, we find that the GPe receives direct synaptic input back from deep layers of diverse motor and non-motor cortical regions, some of which form reciprocal connections onto pallidocortical neurons. These results demonstrate the existence of a fast, closed-loop circuit between the GPe and the cortex which is ideally positioned to integrate information about behavioral goals, internal states, and environmental cues to rapidly modulate behavior.

neuroscience↗

bioRxiv2024

Using phage display for rational engineering of a higher affinity humanized 3-phosphohistidine-specific antibody

Histidine phosphorylation (pHis) is a non-canonical post-translational modification (PTM) that is historically understudied due to a lack of robust reagents that are required for its investigation, such as high affinity pHis-specific antibodies. Engineering pHis-specific antibodies is very challenging due to the labile nature of the phosphoramidate (P-N) bond and the stringent requirements for selective recognition of the two isoforms, 1-phosphohistidine (1-pHis) and 3-phosphohistidine (3-pHis). Here, we present a strategy for in vitro engineering of antibodies for detection of native 3-pHis targets. Specifically, we humanized the rabbit SC44-8 anti-3-pTza (a stable 3-pHis mimetic) mAb into a scaffold (herein referred to as hSC44) that was suitable for phage display. We then constructed six unique Fab phage-displayed libraries using the hSC44 scaffold and selected high affinity 3-pHis binders. Our selection strategy was carefully designed to enrich antibodies that bound 3-pHis with high affinity and had specificity for 3-pHis versus 3-pTza. hSC44.20N32FL, the best engineered antibody, has an [~]10-fold higher affinity for 3-pHis than the parental hSC44. Eleven new Fab structures, including the first reported antibody-pHis peptide structures were solved by X-ray crystallography. Structural and quantum mechanical calculations provided molecular insights into 3-pHis and 3-pTza discrimination by different hSC44 variants and their affinity increase obtained through in vitro engineering. Furthermore, we demonstrate the utility of these newly developed high-affinity 3-pHis-specific antibodies for recognition of pHis proteins in mammalian cells by immunoblotting and immunofluorescence staining. Overall, our work describes a general method for engineering PTM-specific antibodies and provides a set of novel antibodies for further investigations of the role of 3-pHis in cell biology. Significance StatementHistidine phosphorylation is an elusive PTM whose role in mammalian cell biology is largely unknown due to the lack of robust tools and methods for its analysis. Here we report the development of antibodies with unprecedented affinity and specificity towards 3-pHis and present the first crystal structures of a pHis peptide in complex with an antibody. Finally, we show how these antibodies can be used in standard molecular biology workflows to investigate pHis-dependent biology.

synthetic biology↗

bioRxiv2024

TRiC/CCT Chaperonin Governs RNA Polymerase II Activity in the Nucleus to Support RNA Homeostasis

The chaperonin TRiC/CCT is a large hetero-oligomeric ringed-structure that is essential in eukaryotes. While present in the nucleus, TRiC/CCT is typically considered to function in the cytosol where it mediates nascent polypeptide folding and the assembly/disassembly of protein complexes. Here, we investigated the nuclear role of TRiC/CCT. Inactivation of TRiC/CCT resulted in a significant increase in the production of nascent RNA leading to the accumulation of noncoding transcripts. The influence on transcription was not due to cytoplasmic TRiC/CCT-activities or other nuclear proteins as the effect was observed when TRiC/CCT was evicted from the nucleus and restricted to the cytoplasm. Rather, our data support a direct role of TRiC/CCT in regulating RNA polymerase II activity, as the chaperonin modulated nascent RNA production both in vivo and in vitro. Overall, our studies reveal a new avenue by which TRiC/CCT contributes to cell homeostasis by regulating the activity of nuclear RNA polymerase II.

molecular biology↗

bioRxiv2024

Leveraging weighted quartet distributions for enhanced species tree inference from genome-wide data

Species tree estimation from genes sampled from throughout the whole genome is challeng-ing in the presence of gene tree discordance, often caused by incomplete lineage sorting (ILS), where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and theoretical guarantees of robustness to arbitrarily high amounts of ILS. ASTRAL, the most widely used quartet-based method, aims to infer species trees by maximizing the number of quartets in the gene trees that are consistent with the species tree. An alternative approach (as in wQFM) is to infer quartets for all subsets of four species and amalgamate them into a coherent species tree. While summary methods can be highly sensitive to gene tree estimation errors-especially when gene trees are derived from short alignments-quartet amalgamation offers an advantage by potentially bypassing the need for gene tree estimation. However, greatly understudied is the choice of weighted quar-tet inference method and downstream effects on species tree estimations under realistic model conditions. In this study, we investigated a broad range of methods for generating weighted quartets and critically assessed their impact on species tree inference. Our results on a collec-tion of simulated and empirical datasets suggest that amalgamating quartets weighted based on gene tree frequencies (GTF) typically produces more accurate trees than leading quartet-based methods like ASTRAL and SVDquartets. Further enhancements in GTF-based weighted quar-tet estimation were achieved by accounting for gene tree uncertainty, through the utilization of a distribution of trees for each gene (instead of a single tree), by employing traditional nonpara-metric bootstrapping methods or Bayesian MCMC sampling. Our study provides evidence that the careful generation and amalgamation of weighted quartets, as implemented in methods like wQFM, can lead to significantly more accurate trees compared to widely employed methods like ASTRAL, especially in the face of gene tree estimation errors.

bioinformatics↗