Biology subjects

Robin, V. V.

Publications and source records attributed to Robin, V. V..

13 recordsLinked to original sources

bioRxiv2026

Disparities in avian genomic resources highlight gaps across the Global South

Avian genomes have proliferated rapidly in recent years while expanding our knowledge of genomic evolution. However, evaluating bird sampling across the tree of life and across their distributions is necessary to assess their contributions to global bird diversity and diversification patterns. We evaluated all available avian genome assemblies across geography, taxonomy, conservation status, and time. The 1,712 species with at least one genome assembly represent only ~15% of recognized avian diversity. Although all orders were represented, 24 bird families (all restricted to the Global South) lacked any genome assembly, and only ~37% (N= 2,397) of recognized genera had genomic representation. Nearly 78% of the most evolutionarily distinct and globally endangered (EDGE) lineages lacked a genome. Genomic resources are concentrated in temperate regions of the Global North, whereas species-rich tropical regions in Africa, South America, and Southeast Asia remain severely underrepresented relative to their diversity. Even after accounting for conservation status, evolutionary distinctiveness, and ecology, Global South species had roughly fourfold lower odds of having a genome than Global North species. Notably, the post-2021 surge in genome sequencing has counter-intuitively widened this gap. Together, our results highlight persistent gaps in genomic resources across the Global South and the need to collectively address these global knowledge gaps via collaborative efforts.

genomics↗

bioRxiv2025

Avian elevational migration patterns in the Western Ghats, as revealed by participatory science and systematic surveys.

Elevational migration is globally exhibited by montane bird species through elevational range shifts to track seasonal changes in weather patterns and resources. Studies investigating the patterns and mechanisms of such elevational shifts have been limited in spatial scale owing to the difficulty of sampling data across montane gradients. Here, we integrated data from the worlds largest participatory science project (eBird) with systematic surveys to examine patterns and mechanisms that may explain bird elevational range shifts in the Nilgiri Hills of the Western Ghats Biodiversity Hotspot. We calculate the extent of shifts in elevational ranges for birds present year-round in the Nilgiris between the hottest and coldest months and quantify the associations between these shifts and species traits using phylogenetic generalized least squares regressions. We found that 77% (54/70) of the species investigated showed seasonal shifts in their elevational ranges. Birds in the Nilgiris showed nearly equal proportions of downslope (37%) and upslope (33%) winter shifts. All species had significant range overlap between seasons but employed different shifting strategies. Species with narrow thermal regimes predominantly shifted downslope in winter (niche tracking), while those with the widest thermal regimes shifted upslope (niche switching), revealing that species adapt to climatic variability through contrasting thermal strategies. Our results suggest that climatic constraints, specifically thermal regime, could be a major driver of seasonal shifts in elevational ranges of birds in the Nilgiris. Understanding these elevational shift strategies is critical for conservation planning in tropical montane systems facing accelerating climate change.

ecology↗

bioRxiv2025

Genome assemblies for seven families of birds from the Global South

Tropical regions are biodiversity-rich, yet remain underrepresented in the availability of genomic resources, as is evident in the Western Ghats of India, a biodiversity hotspot with high endemism. Here, we present high-quality, de novo genome assemblies for seven birds, representing seven families distributed in the Western Ghats: Black-naped Monarch (Monarchidae: Hypothymis azurea), Indian Yellow Tit (Paridae: Machlolophus aplonotus), Brown-cheeked Fulvetta (Leiothrichidae: Alcippe poioicephala), Malabar Trogon (Trogonidae: Harpactes fasciatus), Blue-bearded Bee-eater (Meropidae: Nyctyornis athertoni), Malabar Whistling-Thrush (Muscicapidae: Myophonus horsfieldii), Orange-headed Thrush (Turdidae: Geokichla citrina). Using a hybrid Oxford Nanopore long reads - Illumina short reads approach, we assembled genomes with sizes ranging from 1.03 to 1.13 Gbp. All assemblies demonstrated high contiguity and completeness (BUSCO scores >97%, UCEs >4799). Repeat masking identified [~]10% of the genomes as interspersed repeats, and functional annotations yielded an average of 9,619 protein-coding genes per species. Comparative analysis showed our assemblies had significantly higher contiguity than the median of existing avian genomes on NCBI (Wilcoxson test, p = 0.00226). Our genome assemblies fill a key geographic and taxonomic gap in the genomic data and provide a foundational resource for evolutionary and ecological research in the Old-World tropics.

genomics↗

bioRxiv2025

Linguistic Rules of Syntax and Sharing in the Complex Songs of a Tropical Passerine

1. Birdsong offers a powerful model to study the evolution of complex communication systems. While most song syntax and sharing research focuses on temperate species with fixed repertoires, we know far less about tropical songbirds with large, open-ended vocal systems. 2. We examined song structure and cultural transmission in the White-bellied Sholakili Sholicola albiventris, a tropical passerine endemic to the Shola Sky Islands of southern India. We studied song complexity and spectro-temporal variation using over 6,000 songs from 17 color-banded males across five years. We analyzed the song syntax using sequence-based metrics, including Levenshtein Distances and N-gram models. 3. Our results reveal high syntactic variability across short and long timescales, with stable note-type cores and structured expansions of combinatorial sequences. Higher-order N-gram turnover was rapid and strongly individual-specific, while broadly sharing the population-level note pool. Song sharing was significantly higher among neighbors than non-neighbors. 4. Using Generalized Additive Models, we explain how social and ecological factors, including neighbor count, territory area, repertoire size, N-gram usage, and the spectro-temporal structure of N-grams, determine consistency across years and sharing across individuals. This study highlights parallels between human linguistics and syntactic organization in the complex songs of a tropical passerine.

animal behavior and cognition↗

bioRxiv2025

Host niche breadth differentially modulates the effects of anthropogenic disturbance across generalist and specialist parasites

Anthropogenic disturbances in natural habitats increase the risk of emerging infectious diseases in free-ranging host communities. Hence, understanding the processes driving such patterns is critical towards One Health. While anthropogenic disturbance is known to promote habitat-generalist host species through biotic homogenisation, generalist parasites (wider host breadth) also respond positively to the disturbed habitats. We hypothesise that generalist parasites are more likely to infect generalist hosts. We tested this hypothesis in a sky island system where generalist (Plasmodium) and specialist (Haemoproteus) haemosporidian parasites infect a range of bird hosts in disturbed and natural forest patches. We used a natural experiment framework to control for climatic differences (similar elevation) and habitat quality (same habitat type, but varying disturbance matrix). We collected 1106 samples from the field and examined the genus-level parasite prevalence and the host specificity of individual parasite lineages. Our results suggest that the generalist (Plasmodium) parasites are more prevalent in generalist birds, irrespective of disturbance. However, the specialist (Haemoproteus) parasites were more prevalent in specialist birds in natural forests than in disturbed forests. Among the individual parasite lineages, we found the host specificity to be associated with the degree of habitat specialisation of their host species. Our results provide evidence for the tendency of generalist parasites to infect generalist host species - a potential mechanism for a higher risk of emerging infectious diseases in human-dominated regions. We emphasise the role of host ecology in understanding the impact of anthropogenic disturbance on parasite prevalence in free-ranging host communities.

ecology↗

bioRxiv2025

Spatial patterns of diversity in forest birds of peninsular India

Biodiversity is structured via complex interactions among ecological, geological, and climatic processes. Regions with high heterogeneity in climate and topography are known to harbor fine scale patterns in diversity which are often overlooked in global scale analyses. Here, we investigate spatial phylogenetic patterns of forest bird diversity across peninsular India, a region with high topographic and climatic heterogeneity. Using a comprehensive global bird phylogeny, we employ metrics such as Phylogenetic Diversity (PD), Phylogenetic Endemism (PE), and their relative forms (RPD, RPE) to quantify evolutionary history and endemism of forest birds in peninsular India. We examine the roles of contemporary climate, historic climatic stability, and topography in shaping these patterns. Our results reveal a strong gradient in diversity, with the southern Western Ghats acting as a major hotspot for both taxonomic and phylogenetic diversity and endemism. We detect distinct ecological and phylogenetic community structures across the peninsula, likely shaped by regional species pools and biogeographic barriers. Areas with greater topographic complexity, higher precipitation, and greater historic climatic stability were found to support high diversity. Our study provides critical insights for biogeography in this understudied yet highly biodiverse region for forest birds.

ecology↗

bioRxiv2024

Playback-aided surveys and acoustic monitoring in the detection of the Endangered Forest Owlet Athene blewitti

Long-term monitoring of populations of rare, endangered species is often challenging. Both the availability of baseline historical datasets and appropriate methods for long-term monitoring are often limited. Anthropogenic climate change and landscape change can impact species distributions significantly, sometimes resulting in a distributional shift of species and, in some cases, driving species to extinction. The Forest Owlet is an endangered bird that was considered extinct but was rediscovered after 113 years in 1997. Since its rediscovery, followed by the description of its calls, there have been regular sightings of the species from newer locations, leading to its down-listing in the IUCN Red List from Critically Endangered to Endangered. One area of interest is the Dang region in Gujarat, India, where there have been no historical records despite previous ornithological studies, but there are several recent records. Through field surveys, we repurpose data from the last three decades (1990, 2000, and 2019) to explore if this bird currently occurs in previous study sites where it was not recorded. The period has seen the rise of acoustic data, and we assess if new survey techniques using playback of its call could increase its detection. Additionally, we examined any changes in landscape and climate in this region across the same period. We also developed an acoustic detection framework for detecting the Forest Owlet from co-occurring sympatric owlets using Automated Recording Units (ARU) and sound-analysis software. We assessed appropriate detection distances from vocalizing birds on the field to design a spacing grid for future surveys of the species. We could locate the Forest Owlet from the resurveys at locations where previous studies three decades ago had not. We also find a significant change in the landscape - loss of native forests and increased agriculture, along with a significant change in climatic variables - mean maximum temperature and mean rainfall. Although the detection of the Forest Owlet is higher when accompanied by playback of its call, there is considerable variation across the landscape. Our acoustic detector comparison led us to a detection strategy for long-term monitoring - different approaches for songs and calls, and an effective detection distance of 300m in its habitat. Although the species responds to climate and habitat change, our study cannot determine the cause of the increased reports of this endangered species. All possibilities remain; the increase in the recent records of the species could be from variable detection or changes in climate and land use. However, we do find increased detections with newer survey techniques with bioacoustics, and we recommend they be used with care for future baseline studies that are urgently required.

ecology↗

bioRxiv2022

Patterns of secondary invasion in the understory of exotic, invasive timber stands

Current climate and land cover change threaten global mountaintops with increased spread of invasive species. Long-established plantations of exotic and invasive trees on these mountaintops can alter their surroundings, further increasing invader-facilitated or secondary invasion. Identifying the ecological conditions that promote such specific associations can help develop better management interventions. The Western Ghatss Shola Sky Islands (>1400m MSL) host vast stretches of exotic and invasive tree plantations that sustain colonisation of other invasive woody, herbaceous and fern species in their understories. Here we analysed vegetation and landscape variables from 232 systematically-placed plots in randomly selected grids using NMDS and Phi Coefficient approaches, to examine patterns of association (positive interactions) between secondary understory invasive species with specific exotic and invasive overstory species. We also conducted GLMM with zero inflation to determine the influence of environmental variables where such associations occur. We find that secondary invasion of multiple species under the canopy of other exotic invasives is widespread across the Shola Sky Islands. Stands of Eucalyptus host the colonisation of 70% of non-native invasive species surveyed across the Shola Sky Islands. In particular, Lantana camara invasion is strongly associated with Eucalyptus stands. We also found that climatic variables affect the colonisation of understorey woody invasive species, while invasion by exotic herbaceous species is associated with the density of road networks.. Canopy cover impacts all invasives negatively, while incidence of fire was negatively associated with invasion by Lantana spp and the Pteridium spp. While the restoration of natural habitats largely targets the highly invasive Acacia, less invasive Eucalyptus and Pine are often not included. Our study suggests that retaining such exotic species in natural habitats, particularly protected areas, can hinder ongoing restoration efforts by facilitating further invasions by multiple woody and herbaceous species.

ecology↗

bioRxiv2021

Song Richness Index: A measure to understand the diversity and repetition of notes in a birdsong

Birdsong plays an important role in mate attraction and territorial defense. Many birds, especially Passerines, produce varying sequences of multiple notes resulting in complex songs. Studying the diversity of notes within these songs can give insights into an individuals reproductive fitness. We first looked at the previously described and commonly used diversity measures to understand the possible case-specific limitations. We then developed a new diversity measure-Song Richness Index (SRI). We compared SRI with three measures of diversity using all possible combinations of notes to understand the case-specific advantages and limitations of all approaches. Simulating all possible combinations gave us insights into how each diversity measure works in a real scenario. SRI showed an advantage over conventional measures of diversity like Note Diversity Index (NDI), Shannons Equitability (SH), and Simpsons Diversity (SI), especially in the cases where songs are made up of only one type of repetitive note.

animal behavior and cognition↗

bioRxiv2021

Demographic changes of a tropical understory bird in naturally patchy montane habitats in southern India

The occurrence, density and survival of a species often depend on various aspects of the habitat that it occupies including patch size and disturbance. The demography of most threatened tropical species largely remain unstudied but could provide valuable information about their biology and insights for their conservation. Our study examined the effect of patch size and disturbance on different demographic parameters of an understory, threatened, endemic bird, the white-bellied shortwing in the tropical biodiversity hotspot of the Western Ghats in India. We sampled eight plots on a sky-island using mist-nets for four years in a Robust design mark-recapture framework. Based on model selection using AIC values, the model with survival as a function of disturbance fits the data better than models with abundance or with these parameters modeled as functions of forest patch size. Shortwing density and sex ratio were not different across forest patch sizes or differing disturbance regimes. However, the survival rate of the species significantly decreased with increasing disturbance but was not related to forest patch size. Our study is possibly the first to provide critical baseline information on the demography of a tropical understory species from this region.

ecology↗

bioRxiv2021

Spectrogram cross-correlation can be used to measure the complexity of bird vocalizations

O_LIBirdsong is an important signal in mate attraction and territorial defense. Quantifying the complexity of these songs can shed light on individual fitness, sexual selection, and behavior. Several techniques have been used to quantify song complexity and be broadly categorized into diversity indices, measures of stationary probabilities, and measures of sequential variations. However, these methods are unable to account for important acoustic features like the frequency bandwidth and the variety in the shape of syllables which are an integral part of these vocal signals. This study proposes a new complexity measure that considers intra-song note variability and calculates a weighted index for birdsongs using spectral cross-correlation. C_LIO_LIWe compared the previously described methods to understand the advantages and limitations based on the factors that would be affecting the complexity of songs. We developed a new method- Note Variability Index (NVI), which incorporates the spectral features of notes while quantifying complexity. This measure alleviates the need for manual annotations of notes that can be error-prone. We used Spectrogram Cross-Correlation (SPCC) to compare notes within a song and used the output values to quantify song complexity. C_LIO_LITo check for the efficacy of the new method, we generated synthetic songs to caricature extremes in song complexity and compared selected conventional complexity measures along with the NVI. We provide case-specific limitations of these methods. Additionally, to examine the efficacy of this new method in real-world scenarios, we used natural birdsongs from multiple species across the globe with varying song structures to compare conventional methods with NVI. C_LIO_LITo our knowledge, NVI is the only song complexity method that captures the variation of spectral features of notes in songs where the conventional methods fail to distinguish between similar song structures with different note types. As NVI does not need a manual classification of notes, it can be easily implemented for any type of birdsong with existing sound analysis softwares; it is very quick, avoids the possible biases in note classification, and can possibly be automated for large datasets in the future. C_LI

ecology↗

bioRxiv2021

Testing the efficacy of hyperspectral (AVIRIS-NG), multispectral (Sentinel-2) and radar (Sentinel-1) remote sensing images to detect native and invasive non-native trees

Invasive alien species (IAS) threaten tropical grasslands and native biodiversity and impact ecosystem service delivery, ecosystem function, and associated human livelihoods. Tropical grasslands have been dramatically and disproportionately lost to invasion by trees. The invasion continues to move rapidly into the remaining fragmented grasslands impacting various native grassland-dependent species and water streamflow in tropical montane habitats. The Shola Sky Islands of the Western Ghats host a mosaic of native grasslands and forests; of which the grasslands have been lost to exotic tree invasion (Acacias, Eucalyptus and Pines) since the 1950s. The invasion intensities, however, differ between these species wherein Acacia mearnsii and Pinus patula are highly invasive in contrast to Eucalyptus globulus. These disparities necessitate distinguishing these species for effective grassland restoration. Further, these invasive alien trees are highly intermixed with native species, thus requiring high discrimination abilities to native species apart from the non-native species. Here we assess the accuracy of various satellite and airborne remote sensing sensors and machine learning classification algorithms to identify the spatial extent of native habitats and invasive trees. Specifically, we test Sentinel-1 SAR and Sentinel-2 multispectral data and assess high spatial and spectral resolution AVIRIS-NG imagery identifying invasive species across this landscape. Sensor combinations thus include hyperspectral, multispectral and radar data and present tradeoffs in associated costs and ease of procurement. Classification methods tested include Support Vector Machine (SVM), Classification and Regression Trees (CART) and Random Forest (RF) algorithms implemented on the Google Earth Engine platform. Results indicate that AVIRIS-NG data in combination with SVM recover the highest classification skill (Overall -98%, Kappa-0.98); while CART and RF yielded < 90% accuracy. Fused Sentinel-1 and Sentinel-2 produce 91% accuracy, while Sentinel-2 alone yielded 91% accuracy with RF and SVM classification; but only with higher coverage of ground control points. AVIRIS-NG imagery was able to accurately (97%) demarcate the Acacia invasion front while Sentinel-1 and Sentinel-2 data failed. Our results suggest that Sentinel-2 images could be useful for detecting the native and non-native forests with more ground truth points, but hyperspectral data (AVIRIS-NG) permits distinguishing, native and non-native tree species and recent invasions with high precision using limited ground truth points. We suspect that large areas will have to be mapped and assessed in the coming years by conservation managers, NGOs to plan restoration, or to assess the success of restoration activities, and several data procurement and analysis steps may have to be simplified.

ecology↗

bioRxiv2019

Local extinction of a montane, endemic grassland bird driven by landscape change across its global distribution

ContextTropical montane habitats support high biodiversity, and are hotspots of endemism, with grasslands being integral components of many such landscapes. The montane grasslands of the Western Ghats have seen extensive land-use change over anthropogenic timescales. The factors influencing the ability of grassland-dependent species to persist in habitats experiencing loss and fragmentation, particularly in montane grasslands, are poorly known.\n\nObjectivesWe studied the relationship between the Nilgiri pipit Anthus nilghiriensis, a threatened endemic bird that typifies these montane grasslands, and its habitat, across most of its global distribution. We examined what habitat features make remnants viable habitat, which is necessary for effective management.\n\nMethodsWe conducted 663 surveys in 170 sites and used both single-season occupancy modelling and N-mixture modelling to account for processes influencing detection, presence, and abundance.\n\nResultsElevation had a positive influence on species presence, patch size had a moderate positive influence and patch isolation a moderate negative influence. Species abundance was positively influenced by elevation and characteristics related to habitat structure, and negatively influenced by the presence of invasive woody vegetation.\n\nConclusionsThe strong effect of elevation on the highly range-restricted Nilgiri pipit makes it vulnerable to, and an indicator of, climate change. This highly range-restricted species is locally extinct at several locations and persists at low densities in remnants of recent fragmentation, suggesting an extinction debt. Our findings indicate a need to control and reverse the spread of exotic woody invasives to preserve the grasslands themselves and the specialist species dependent upon them.

ecology↗