Biology subjects

Chattopadhyay, B.

Publications and source records attributed to Chattopadhyay, B..

6 recordsLinked to original sources

bioRxiv2026

Genetic introgression is a catalyst for diversification in an Old World fruit bat radiation

Genetic introgression, the exchange of genes between closely related species, was once thought to be rare and counterproductive to species differentiation until more recent evidence showed that introgression is pervasive in nature and may even facilitate the transfer of important functional traits among species. However, evidence for the role of introgression in facilitating speciation in natural systems is rare. In this study, we investigated the role of introgression in accelerating trait sharing and speciation in a poorly understood group of South and Southeast Asian fruit bats of the genus Cynopterus using genome-wide DNA from 93 individuals, including both fresh and historic museum specimens. We uncovered substantial new species level diversity within the genus and retrieved multiple strong signatures of complex genetic introgression, including two putative events of hybrid speciation within this radiation. In the genomic areas implicated in most of these introgression events, we identified a locus potentially linked to sperm integrity and fusion of egg and sperm. Further, we observed high between-species divergence in an area of the genome linked to skull development. The Cynopterus radiation augments a small but growing list of examples showing that genetic introgression - rather than forming an impediment against differentiation - is likely to boost and reinforce diversification processes, for example through the transfer of functional loci that may facilitate innovations. Our study also highlights the importance of museum collections in understanding cryptic diversity and speciation in complex biogeographic settings.

evolutionary biology↗

bioRxiv2025

Anthropogenic habitats shape gut microbiome composition in Southern Indian bats

BackgroundAnthropogenic habitat modification and associated resources can exert selection pressures on wildlife and their microbiomes, altering their diversity, resulting in homogenization and making them resemble the human microbiome. Diet is an important predictor of the microbiomes of volant vertebrates, mainly for birds, but for bats, results remain inconclusive. In spite of Indias exceptional bat diversity, there is little understanding of how their microbiomes respond to anthropogenic habitats. Therefore, we investigated the trends of taxonomic and functional diversity and their relationships with host feeding-guild and phylogeny for six wide-ranging bat species across six anthropogenically modified sites in Southern India by generating 16S barcode sequences from their fecal samples. ResultsEubacteria dominated samples with diet-specific taxonomic composition. Frugivore microbiomes contained large proportions of Cyanobacteria, possibly sourced from consumed plant matter or polluted drinking-water sources, and Lactobacillales dominated insectivore microbiomes, while Gammaproteobacteria were abundant regardless of host feeding guild. We found human pathogens in our samples possibly transferred from polluted water to the guts of bats foraging in nearby areas. We observed diet-specific taxonomic, phylogenetic, and functional composition. However, functional composition incorporating abundances displayed a high degree of overlap across feeding-guilds, suggesting functional homogenisation of microbiomes across feeding guilds, possibly due to anthropogenicity. Sample-wise diversity indices were significantly different with respect to diet only when samples from the same roost were not pooled together. However, in all cases, microbiomes from the same diet types displayed significant taxonomic and phylogenetic similarity to each other. Lastly, we observed limited concordance of microbiome diversity with chiropteran phylogeny. ConclusionsBecause of these potential signatures of pollution on bat microbiomes such as pathogens, we recommend their monitoring, especially because Cyanobacteria play a known role in bat and human disease. Our study is one of the first to study microbiome composition and function from bat species common around human inhabitation in South India, and establishes baselines in this region.

evolutionary biology↗

bioRxiv2024

Tropical island endemic birds' demographic responses to climate are modulated by habitat availability and species traits

Climate change and associated habitat fluctuations can expedite the diversification of insular lineages or lead to isolation and extinction. Tropical island birds are a model system to assess responses to climate change owing to their insular nature and ability to diversify rapidly. While there is some understanding of the diversification of tropical island avian clades, we are yet to understand the vulnerability of these species to climate change. Long-term species genetic diversity and historical demography are critical predictors of this. Therefore, we investigated the sensitivity of tropical island endemic birds to climate change and analysed how species traits determine these responses by comparing species traits with demographic histories and paleohabitat fluctuations during the Last Glacial Period (LGP). From publicly available whole genome and paleoclimatic datasets, we reconstructed tropical island endemics past demographic histories (effective population size (Ne)) using Pairwise Sequential Markovian Coalescent (PSMC) (n = 23) and suitable habitat (n = 29) during the LGP and the Holocene. We observed that most species experienced an increase in suitable habitat between the Last Interglacial and the Last Glacial Maximum. However, a concomitant increase in Ne was only observed in the hyper-diverse passerine clade, attesting to their ability to rapidly diversify. Overall, diet specialists and large-bodied species showed a decrease in Ne during the LGP. Our results indicate that species traits dictate tropical island endemics demographic responses to climate, and a plastic response to habitat availability could be a consequence of clades abilities to rapidly occupy new niches and diversify. Further, our analyses revealed that most species entered the Holocene with low effective population sizes. Given that tropical island endemics have small geographic ranges and are groups vulnerable to climate change, special efforts are necessary to conserve them. We recommend that conservation management policies add components like historical demography and species traits while assessing extinction threats for island populations.

evolutionary biology↗

bioRxiv2024

Identification of distinct rodent-associated adenovirus lineages from a mixed-use landscape in the Western Ghats biodiversity hotspot

Shifts in land-use patterns and increased human-livestock-wildlife interactions have generated numerous possibilities for pathogen spillover. This demands increased efforts of pathogen surveillance in wildlife, especially in changing landscapes with high biodiversity. We investigated adenovirus diversity in small mammals, an understudied host taxon, from a forest-plantation mosaic in the Western Ghats biodiversity hotspot. Using PCR-based screening followed by Sanger sequencing and phylogenetic analyses, we attempted to detect and characterize adenovirus diversity in seven species of small mammals. We observed high prevalence (up to 38.8%) and identified five lineages of adenoviruses with unique mutations in the endemic and dominant small mammal species, Rattus satarae. These lineages significantly differed from other known Murine adenoviruses (p-distance > 25%), indicating the likelihood of novel adenovirus diversity in this endemic small mammal. Collectively, our results highlight the potential for unexplored diversity of DNA viruses like adenovirus in poorly explored host taxa inhabiting human-used landscapes and its zoonotic implications.

evolutionary biology↗

bioRxiv2021

Historical climate change and megafaunal extinctions linked to genetic diversity declines in shorebirds

Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in breeding area predicted by environmental niche modelling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Demise of ecosystem-engineering megafauna which maintained open habitats would have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.

evolutionary biology↗

bioRxiv2020

Western Ghats Myrtaceae are not Gondwana elements but likely dispersed from south-east Asia

Gondwana break-up is one of the key sculptors of the global biogeographic pattern including Indian subcontinent. Myrtaceae, a Gondwana family, demonstrates a high diversity across Indian Western Ghats. A rich paleo-records in Deccan Intertrappean bed in India strive to reconcile two contending hypothesis of origin and diversification of Myrtaceae in India, namely Gondwana elements floated on peninsular India or lineages invading from south-east Asia. In this study, we have reconstructed the biogeographic history of Myrtaceae of Western Ghats of India combining fossil-calibrated phylogeny, ancestral area reconstruction, and comparing various dispersal models. Phylogenetic reconstructions divided lineages into multiple clades at the tribal level that mostly is in agreement with previous descriptions. Dated tree indicated a presumable Gondwanan origin of Myrtaceae (95.7 Ma). The Western Ghats taxa are relatively younger and seem to have arrived either through long-distance oceanic dispersal in middle Eocene (Rhodomyrtus tomentosa), and Miocene (Eugenia) or through major overland dispersals throughout Miocene (Syzygium). However, late Cretaceous fossilsin India lends support to the existence of proto-Myrtaceae on floating peninsular India. Taken together, we conclude that Myrtaceae lineages on the biotic ferry were perhaps extirpated by Deccan volcanism leaving a little or no trace of living Gondwanan link, while the Western Ghats was likely enriched by dispersed elements either from south-east Asia or from South America.

genomics↗