Biology subjects

Rajamani, N.

Publications and source records attributed to Rajamani, N..

6 recordsLinked to original sources

bioRxiv2026

Food acquisition patterns of the three-striped palm squirrel are influenced by interactions: variation in foraging response across an urban-rural gradient

Urbanisation significantly alters the habitat and resources accessible to urban animals. Synanthropic animals adapt by exploiting available resources and modulating abundance across the urban habitat matrix. Urban arboreal mammals, such as palm squirrels, encountering altered foraging resources in green spaces and across the matrix, develop strategies to maximise their fitness, including modulating food selection, spatial microhabitat use, and social interactions. We examined whether squirrel abundance affects foraging patterns and whether social interactions at the feeding site regulated individuals' exploratory tendencies. We conducted cafeteria experiments with F. palmarum in rural and urban areas around Tirupati, India and tested for differences in responses to novelty, food selection, and dominance interactions among individuals. We observed a preferential bias towards processed food and approach tendencies were stronger in urban individuals. Urban regions marked with a higher density of squirrels, were associated with higher competitive interactions showing transient social despots of dominance, leading to increased exploration by non-dominant individuals. On the contrary, a lower density of squirrels in rural areas, leads to reduced dominance interactions and subsequent lack of exploration. The potential exploration and consumption of novel resources feeds into the urban loop which enhances population in urban areas, whereas the opposite effect is observed in rural areas. This study highlights how urban commensal organisms, such as squirrels, adopt behaviours to maximise resource utilisation which is modulated by social interactions and can potentially determine the population dynamics in changing landscapes.

ecology↗

bioRxiv2026

A precise atlas of the human subcortex

Clinical interventions and neuroimaging in the subcortex require anatomical definitions that exceed the resolution and anatomical detail of currently available deformable brain atlases. Here, we introduce a high-resolution human brain atlas comprising 95 manually segmented grey and white matter structures as well as 82 white matter tracts compiled from a multitude of resources including ex-vivo MRI, histology, fibre dissections, and neuroanatomy textbooks. The atlas is defined at an isotropic resolution of 100 m and can be precisely deformed to individual subject brain anatomy. By providing precise definitions of both grey and white matter structures within and around the basal ganglia, thalamus, subthalamus, midbrain and cerebellum, the atlas provides a foundational resource for stereotactic surgery and subcortical brain imaging research, as well as for development of next-generation neuromodulation strategies.

neuroscience↗

bioRxiv2025

Evolution of burrowing and associated behavioral traits in Lagomorphs

Burrowing is a complex behavior that has evolved repeatedly across animal lineages, yet its evolutionary origins and ecological correlates remain poorly understood in many mammalian groups. The order Lagomorpha, comprising pikas (Ochotonidae), rabbits and hares (Leporidae) exhibits remarkable diversity in lifestyle, sociality, and life history, making it an ideal system to study the evolution of burrowing behavior. Here, we reconstruct the most comprehensive dated phylogeny of Lagomorphs to date, encompassing 84 of 102 extant species, including newly sequenced genomes of Ochotona nubrica and O. ladacensis. Using ancestral state reconstruction and phylogenetically informed comparative analyses, we examine how burrowing behavior relates to morphology, climate, habitat, sociality, and fecundity. Our results reveal that burrowing evolved multiple times independently within Lagomorphs, with the ancestral state of Ochotonids inferred as burrowing and that of Leporids as semi-fossorial or form-dwelling. Contrary to expectations, burrowing species did not show distinct hind-limb adaptations or associations with extreme or variable climates. However, burrowing behavior was significantly correlated with sociality, and both burrowing and social species exhibited higher fecundity, suggesting an energetic and reproductive advantage linked to group-living in fossorial taxa. These findings highlight a recurrent evolutionary association between burrowing, sociality, and reproductive investment: the burrowing, sociality and fecundity triangle. This underscores the importance of integrating behavioral and ecological data to understand the adaptive evolution of lifestyle traits in mammals.

evolutionary biology↗

bioRxiv2025

Asian pika populations track local glaciation events through the Pleistocene

BackgroundThe Pleistocene glaciation cycles (2.6 mya - 11 kya) were major climatic events that shaped diversity and community assemblages on Earth. Cold-adapted, high-elevation specialists are expected to have responded negatively to warm interglacial periods, with populations contracting and being pushed up the elevational gradient, leading to isolated populations on mountain tops. During the cool glacial maximums, they are expected to have been distributed at both low and high elevations, with populations expanding and facilitating gene flow across mountains. Pikas (Ochotonidae) are poorly studied high-elevation specialist Lagomorphs being extirpated at alarming rates due to climate change. Insights into their historical demography and current effective population size are crucial in determining their current population status to inform conservation planning. ResultsWe use de novo assembly to construct partial genomes of three Asian pika species (Ochotona ladacensis, O. nubrica, and O. macrotis) that differ in their life history, lifestyle, and social behaviors. We use a combination of species distribution modeling (SDM) projected back in time, in addition to inferring historical demographic patterns using a pairwise sequentially Markovian coalescent (PSMC) approach. Our SDMs predicted the largest bio-climatic niches for all three species during the last glacial maximum (LGM [~]20 kya), and the smallest niches at the last interglacial (LIG[~]120 kya), agreeing well with the elevational shift hypothesis. Our PSMC models for the populations in the Changthang Biotic province (CBP), revealed largely synchronous oscillations of populations sampled in geological timescales but displayed contrasting temporal patterns of population spikes when compared with SDMs. The largest effective population sizes of all species examined on the CBP were inferred to pre-date both the LGM and LIG and were placed around the MIS-6 ([~] 191 kya). After the MIS-6 local glaciation event, populations were inferred to have been through a deep bottleneck, correlating well with local glaciation patterns on this plateau. ConclusionOur study illustrates the power of using complementary approaches to infer historical demography in mountainous landscapes with complex glaciation histories. While SDMs appropriately describe species responses to historical climate across the geographic range of species, PSMCs are more informative about local population dynamics when subject to large degrees of population differentiation. All three species of pikas responded similarly to historical glaciation events on the CBP that differ from the rest of the world and other parts of the Himalayas and likely have very low effective population sizes at current timescales. This is one of the first few studies to examine the population demography of small mammals on the Indo-Tibetan Plateau and has the potential to inform species and population-specific conservation planning in the Himalayas. It is very likely that small mammals such as pikas, marmots and voles on the CBP have low effective population sizes due to historical inbreeding during the LIG and the lack of a glaciation rescue during the LGM. This highlights the need for conservation measures for small mammals on the landscape.

genomics↗

bioRxiv2024

Cortical beta oscillations map to shared brain networks modulated by dopamine

Brain rhythms can facilitate neural communication for the maintenance of brain function. Beta rhythms (13-35 Hz) have been proposed to serve multiple domains of human ability, including motor control, cognition, memory and ewmotion, but the overarching organisational principles remain unknown. To uncover the circuit architecture of beta oscillations, we leverage normative brain data, analysing over 30 hours of invasive brain signals from 1772 channels from cortical areas in epilepsy patients, to demonstrate that beta is the most distributed cortical brain rhythm. Next, we identify a shared brain network from beta dominant areas with deeper brain structures, like the basal ganglia, by mapping parametrised oscillatory peaks to whole-brain functional and structural MRI connectomes. Finally, we show that these networks share significant overlap with dopamine uptake as indicated by positron emission tomography. Our study suggests that beta oscillations emerge in cortico-subcortical brain networks that are modulated by dopamine. It provides the foundation for a unifying circuit-based conceptualisation of the functional role of beta activity beyond the motor domain and may inspire an extended investigation of beta activity as a feedback signal for closed-loop neurotherapies for dopaminergic disorders.

neuroscience↗

bioRxiv2020

U-Net Model for Brain Extraction on Non-human Primates

Brain extraction (a.k.a. skull stripping) is a fundamental step in the neuroimaging pipeline as it can affect the accuracy of downstream preprocess such as image registration, tissue classification, etc. Most brain extraction tools have been designed for and applied to human data and are often challenged by non-human primates (NHP) data. Amongst recent attempts to improve performance on NHP data, deep learning models appear to outperform the traditional tools. However, given the minimal sample size of most NHP studies and notable variations in data quality, the deep learning models are very rarely applied to multi-site samples in NHP imaging. To overcome this challenge, we used a transfer-learning framework that leverages a large human imaging dataset to pretrain a convolutional neural network (i.e. U-Net Model), and then transferred this to NHP data using a small NHP training sample. The resulting transfer-learning model converged faster and achieved more accurate performance than a similar U-Net Model trained exclusively on NHP samples. We improved the generalizability of the model by upgrading the transfer-learned model using additional training datasets from multiple research sites in the Primate Data-Exchange (PRIME-DE) consortium. Our final model outperformed brain extraction routines from popular MRI packages (AFNI, FSL, and FreeSurfer) across a heterogeneous sample from multiple sites in the PRIME-DE with less computational cost (20s~10min). We also demonstrated the transfer-learning process enables the macaque model to be updated for use with scans from chimpanzees, marmosets, and other mammals (e.g. pig). Our model, code, and the skull-stripped mask repository of 136 macaque monkeys are publicly available for unrestricted use by the neuroimaging community at https://github.com/HumanBrainED/NHP-BrainExtraction.

neuroscience↗