Biology subjects

Pandit, R.

Publications and source records attributed to Pandit, R..

9 recordsLinked to original sources

bioRxiv2025

Width of Range Overlap in Congeneric Bird Species Pairs Along An Elevational Gradient In The Eastern Himalayas

We investigated the distribution of range overlap between contiguous pairs of congeneric bird species along a 200-2800 m elevational gradient in the eastern Himalayas. Over a 3-year field survey between from 2012 to 2014 we recorded 15867 birds comprising 245 species in elevational intervals of 50 m. From this data set, we selected 107 congeneric pairs and fit a logistic curve to the abundance ratio versus elevation data to estimate the width of transition zone over which the species ratio changes from 90% to 10%. We found that the distribution of the transition widths range from < 50 m (about a quarter of the pairs) to more than 500 m. This lack of physical exclusion suggests that there is considerable niche separation between closely related species. For a smaller subset of species pairs with better quality data and model fit we investigated the correlation between the degree of range overlap (transition width) on the one hand, and phylogenetic distance and morphological trait difference on the other. We found a significant correlation with mass, beak width and wing size, but not with tarsus length, beak length and phylogenetic distance. This suggests that mass beak width and wing size may play an important role in niche differentiation in the area.

ecology↗

bioRxiv2025

Molecular Surveillance Identifies Evidence of Getah Virus (GETV) in Mosquito Vectors in Alabama, USA

The Getah virus (GETV) is a mosquito-borne RNA virus in the Togaviridae family and the Alphavirus genus, associated with severe disease outbreaks in livestock across Asia-Pacific regions. Since its first isolation in Malaysia in 1955, GETV has been reported in Eurasia and the South Pacific, yet documented cases in the United States remain exceptionally rare, leaving major gaps in regional vector competence and surveillance data. To evaluate the potential of local mosquito populations as GETV carriers, field collections were conducted in Montgomery and Pike Road neighborhoods of Alabama from 2023 to 2024, capturing multiple mosquito species for molecular screening. Initial real-time qPCR assays on 200 pooled and individual samples suggested that approximate 30% of specimens demonstrated possible GETV carriage potential. To validate viral presence, two distinct primer sets were designed to amplify viral genome fragments. Mosquito RNA was reverse-transcribed into cDNA, followed by conventional PCR. The first PCR, targeting [~]280 bp, produced single or multiple amplicon bands in 32% of samples via gel electrophoresis. These positive cDNAs were re-amplified with a second primer pair targeting a [~]430 bp fragment from a separate genomic region, yielding confirmatory bands in 30% of specimens. Amplified products were purified and Sanger sequenced, revealing approximate 95% nucleotide similarity to the wild-type GETV reference genome. This study delivers the first field-based molecular evidence supporting GETV detection in Alabama mosquitoes, signaling either localized emergence or potential introduction of the virus. These findings underscore the need for expanded vector competence profiling, arboviral surveillance, and livestock disease preparedness in the southeastern United States, strengthening both public health readiness and state-level vector monitoring strategies.

microbiology↗

bioRxiv2023

Tropical montane gradients elucidate the contributions of functional traits to competitive and environmental fitness

Functional traits can be classified as alpha or beta, based on their relative importance in determining a species competitive and environmental fitness, respectively. However, the link between a trait and its contribution to a particular aspect of fitness is not always straight-forward. We investigated phylogenetic and functional diversity for bird communities along a 200-2800 m elevational transect in the eastern Himalayas. We hypothesized that beta traits, associated with environmental tolerances, would exhibit a directional change in mean values, while alpha traits, linked to competitive strategies, would show a decrease in dispersion with elevation. Our findings showed that most functional traits exhibited a decrease in dispersion with elevation. However, surprisingly, the mean values of these traits also exhibited a significant relationship with elevation, suggesting their involvement in both competitive and environmental fitness. Furthermore, we observed that morphological traits, traditionally considered beta traits associated with environmental tolerance, were influenced more strongly by resource availability and habitat structure rather than aspects of temperature or air density. These results challenge the simplistic classification of traits as either alpha or beta. We suggest that future studies should carefully analyze the variation in mean values and dispersion of individual traits before assigning them solely to a particular category of fitness. The results contribute to a broader understanding of the complex interactions between functional traits, fitness, and environmental conditions in Himalayan bird communities.

ecology↗

bioRxiv2023

Unravelling Genomic Origin of Lumpy Skin Disease Virus in Recent Outbreaks

Lumpy skin disease virus (LSDV) belongs to the genus Capripox virus and family Poxviridae. LSDV was endemic in most of Africa, Middle east and Turkey, but since 2015, several outbreaks have been reported in Asian countries. In this study we used Whole Genome Sequence (WGS) approach to investigate the origin of the outbreak and understand the genomic landscape of the virus. Our study showed that the LSDV strain of 2022 outbreak exhibited many genetic variations, compared to the Reference Neethling strain sequence and the previous field strains from India. A total of 1819 variations were found in 22 genome sequences, which includes 399 extragenic mutations, 153 insertion frameshift mutations, 234 deletion frameshift mutations, 271 Single nucleotide polymorphisms (SNPs) and 762 silent SNPs. 38 genes have more than 2 variations per gene and these genes belong to viral-core protein, viral binding proteins, replication and RNA polymerase proteins. We highlight the importance of several SNPs in various genes which may play an essential role in pathogenesis of LSDV. Phylogenetic analysis performed on all whole genome sequences of LSDV showed two types of variants in India. One group of the variant with fewer mutations was found to lie closer to the LSDV 2019 strain from Ranchi while the other group clustered with previous Russian outbreaks from 2015. Our study highlights the importance of genomic characterization of viral outbreaks to not only monitor the frequency of mutations but also address its role in pathogenesis of LSDV as the outbreak continues.

microbiology↗

bioRxiv2023

DNA metabarcoding using new rbcL and ITS2 metabarcodes collectively enhance detection efficiency of medicinal plants in single and polyherbal formulations

With the widespread adoption of barcoding and next-generation sequencing, metabarcoding is emerging as a potential tool for detecting labelled and unlabelled plant species in herbal products. In this study, newly designed rbcL and ITS2 metabarcode primers were validated for metabarcoding using in-house mock controls of medicinal plant gDNA pools and biomass pools. The applicability of the multi-barcode sequencing approach was evaluated on 17 single drugs and 15 polyherbal formulations procured from the Indian market. The rbcL metabarcode demonstrated detection efficiencies of 86.7% and 71.7% in gDNA plant pools and biomass mock controls, respectively, while the ITS2 metabarcode demonstrated 82.2% and 69.4%. In the gDNA plant pool and biomass pool mock controls, the cumulative detection efficiency increased by 100% and 90%, respectively. A total of 79% cumulative detection efficiency of both metabarcodes was observed in single drugs, while 76.3% was observed in polyherbal formulations. An average fidelity of 83.6% was observed for targeted plant species present within mock controls as well as in herbal formulations. Our results demonstrated the applicability of multilocus strategies in metabarcoding as a potential tool for detecting labelled and unlabelled plant species in herbal formulations.

molecular biology↗

bioRxiv2022

Comprehensive analysis using DNA metabarcoding, PCR, and HPLC unveils the adulteration in Brahmi herbal products

BackgroundThe herbal products market is expanding and creating a bottleneck for raw materials. Hence, economically motivated adulteration has a high prevalence. DNA barcoding and species-specific PCR assays are now revolutionising the molecular identification of herbal products and are included in a number of pharmacopoeias for the identification of raw materials. High-throughput sequencing with barcoding advances toward metabarcoding, which enables the identification of unintentionally or intentionally unlabelled plant material present in herbal products. Brahmi is one of the most commercially significant and nootropic botanicals, with great controversy over the terms "Brahmi" being used to describe both Bacopa monneri (BM) and Centella asiatica (CA) species. PurposeThis study evaluates DNA-based methods for Brahmi herbal products with the traditional HPLC-based analytical approach in order to assess their effectiveness. MethodsWe employed a species-specific PCR assay, DNA metabarcoding using rbcL minibarcode, and HPLC to detect the presence of the Brahmi (either BM or CA) in eighteen market samples. All the methods have been validated using in-house blended formulations. ResultsComprehensive analysis of all three methods revealed the presence of 22.2%, 55.6%, and 50.0% of Brahmi by PCR assay, DNA metabarcoding, and HPLC, respectively, in Brahmi market formulations, whereas blended formulations only exhibited targeted plant species with all three methods. ConclusionSpecies-specific PCR can be used as a cost-effective and rapid method to detect the presence of the Brahmi, while in high-throughput methods, DNA metabarcoding can be used to detect the presence of widespread adulterated botanicals, and further, bioactive compounds could be detected by HPLC. These results emphasise the need for quality control of the marketed Brahmi herbal products as well as the implementation of all methodologies in accordance with fit for purpose.

molecular biology↗

bioRxiv2022

Testing a theoretical framework for the environment-species abundance paradigm: a new approach to the Abundant Centre Hypothesis

The linkage between environment, a species fitness and its abundance is central to the theory of evolution. So far, all studies of this linkage have been heuristic and empirical due to an inability to determine fitness either experimentally (independent of abundance) or theoretically (from species-environment interaction). One category of such studies involves the Abundant Centre Hypothesis which posits that a species abundance rises to a maximum at the centre of its range. We argue that the confusing mix of results from ACH studies arises from ignoring the central premise that the abundance distribution cannot be independent of the environment. First, we employed a theoretical framework to identify an environmental context (an elevational transect; 200-2800 m in the eastern Himalayas) likely to favour ACH. We then improved upon some previously identified conceptual and methodological shortcomings of ACH studies. Using systematically collected bird data (245 species; 15867 records) from that transect we found that the community average abundance profile is symmetric, as expected by ACH. Notwithstanding which, the abundance profiles of individual species showed a small degree of asymmetry which was correlated with elevation. This elevational dependence may be due to the hard elevational limits at the lower and upper ends of the mountain, as expected from theoretical considerations. We also showed that the average abundance profile shape is close to gaussian, while ruling out uniform and inverted-quadratic shapes. This work demonstrates that selecting a particular category of environmental contexts can help in integrating theoretical tools into a field dominated by empirical studies. Such a union should spur the development of more detailed and testable theoretical models for better insights in an important field.

ecology↗

bioRxiv2021

Comparative analysis of two NGS platforms and different databases for analysis of AMR genes

The use of antibiotics in human medicine and livestock production has contributed to the widespread occurrence of antimicrobial resistance (AMR). Recognizing the relevance of AMR to human and livestock health, it is important to assess the occurrence of genetic determinants of resistance in medical, veterinary, and public health settings in order to understand risks of transmission and treatment failure. Advances in Next Generation Sequencing (NGS) technologies have had a significant impact on research in microbial genetics and microbiome analyses. Now, strategies for high throughput sequencing from panels of PCR amplicons representing known AMR genes offer opportunities for targeted characterization of complex microbial populations. Aim of the present study was to compare the Illumina MiSeq and Ion Torrent S5 Plus sequencing platforms for use with the Ion AmpliSeq AMR Research Panel in a veterinary/public health setting. All samples were processed in parallel for the two sequencing technologies, subsequently following a common bioinformatics workflow to define the occurrence and abundance of AMR gene sequences. Regardless of sequencing platform, the results were closely comparable with minor differences. The Comprehensive Antibiotic Resistance Database (CARD), QIAGEN Microbial Insight - Antimicrobial Resistance (QMI-AR), Antimicrobial resistance database (AR), and CARD-CLC databases were compared for analysis, with the most genes identified using CARD. Drawing on these results we describe an end-to-end workflow for AMR gene analysis using NGS.

bioinformatics↗

bioRxiv2021

Taxonomic scale dependency of Bergmann's patterns: A cross-scale comparison of hawkmoths and birds along a tropical elevational gradient

Bergmanns rule predicts a larger body size for endothermic organisms in colder environments. The multiplicity of patterns and processes is expected because body size and temperature are two most fundamental factors on which many physiological, ecological and evolutionary processes depend, affecting all levels of biological organization, from individuals to communities. The confounding results from previous studies may be due to the differences in taxonomic (intraspecific, interspecific and community) and spatial (latitudinal vs elevational) scales. We compared Bergmanns patterns for endotherms (Aves) and ectotherms (Lepidoptera: Sphingidae) along a same 2.6 km elevational transect in the eastern Himalayas. Using a large data spanning 3,302 hawkmoths (76 morpho-species) and 15,746 birds (245 species), we compared the patterns at the intraspecific (hawkmoths only), interspecific and community scales. At the interspecific scale, we account for phylogenetic non-independence in body mass by using a heirarchical linear mixed effects model for hawkmoths, and a phylogenetic generalised least squares model for birds. We assess the importance of using abundance-weighted metrics at the community scales, after accounting for spatial auto-correlation in communities. Hawkmoths exhibited positive Bergmanns pattern at the intraspecific and abundance-weighted community scale. Intraspecific variation accounted for a substantial 33% variation at the community level. Contrary to this, birds exhibited a strong converse-Bergmanns pattern at interspecific and community scales, both with- and without-abundance. Overall, all metrics which incorporate local traits and/or species abundances show stronger correlations than when this information is lacking. The multiplicity of patterns at a single location provides the opportunity to disentangle the relative contribution of individual- and species-level processes by integrating data across multiple nested taxonomic scales for the same taxa. We suggest that future studies of Bergmanns patterns should explicitly address taxonomic- and spatial-scale dependency, with species relative abundance and intraspecific trait variation as essential ingredients especially at short elevational scales.

ecology↗