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Arvind, C.

Publications and source records attributed to Arvind, C..

11 recordsLinked to original sources

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↗

Female song and breeding phenology of the Nilgiri Flycatcher (Eumyias albicaudatus) in the Shola Sky Islands

Assessing breeding phenology using singing intensity can potentially provide insights into a species' responses to climate or habitat change. Although male passerines are known to sing elaborate songs during the breeding season, females of several tropical passerines also sing. The Nilgiri Flycatcher (Eumyias albicaudatus) is an endemic dimorphic songbird found in the southern Western Ghats of India. Despite its limited distribution and its ecological significance as an indicator species of cloud forests, very little is known about its vocal behaviour and breeding ecology. To examine sex-specific differences in vocalisation patterns, we analysed 294 male and 102 female focal songs from two pairs of birds. We then used data from a year-long automated recorder placed near a breeding pair to study the species' singing phenology using the BirdNET Analyser. The two sexes broadly produced similar songs, although males' songs included more notes at a faster pace. The sex-specific detectors failed due to this high similarity among songs of the two sexes, but we were able to automate species-level detection (F1-score = 0.795 at a confidence threshold of 0.1). We found strong seasonality in vocal activity, with peaks in singing during the breeding season, and identified a diurnal peak at dawn. More data are required to parameterise differences in annual vocal activity between the sexes. These detection patterns provide a framework for a landscape-wide examination of Nilgiri Flycatcher phenology and occurrence. This study suggests that automatic detectors can be a reliable tool for assessing singing phenology in birds and provide insights into breeding periods.

ecology↗

Distinct, asynchronous processes underlie cultural and genetic variation in a bird species with a complex song repertoire

Dialects in birdsongs represent population clusters and cultural diversity. Cultural and genetic variation in animals, however, do not always evolve along the same trajectory. Few studies have tested this in a wild songbird with a continuous learning strategy. Songbirds (oscine Passeriformes) with a continual learning window exhibit great song diversity and may show cultural differentiation that outpaces genetic divergence. We investigate cultural and genetic variation in a tropical endemic songbird in a topographically and climatically complex sky-island landscape of the Western Ghats of India. We combine fine-scale acoustic, behavioural, and genetic data: from 90 individuals (10,816 songs), analysed using frequency-temporal parameters and a linguistic method for syntax; a playback experiment with 136 trials to compare behavioural responses to local and non-local songs; and blood samples from 242 individuals (10,638 SNPs) to infer genetic population structure. We find no difference in songs across locations and individuals in the time-frequency domain, but only in syntax. One-third of notes, the smallest vocal units, are widely shared across all individuals in their distribution. Longer note combinations result in greater individual differences within populations, but only form small differences between populations. Geographic distance strongly predicts genetic but not song syntactic differences, and playback experiments show equal responses to local and non-local songs. Thus, strong individual signatures but weak local-level dialects are generated by a shared note repertoire and associated combinatorial syntax. We highlight that cultural transmission may operate at fine social scales, decoupled from genetic structure, which is strongly driven by isolation-by-distance. Significance statementWhether learned behaviours exhibit patterns similar to those of inherited genes remains a long-standing question in evolutionary biology. Birdsong has a strong cultural component paralleling human language, yet most knowledge comes from birds with a narrow learning window. Open-ended learners, who acquire new songs throughout life like humans, are poorly documented in the wild. We studied such a songbird restricted to the tropical cloud montane forests of southern India. Songs appear acoustically similar across populations but differ in how basic units are ordered (syntax), while individuals are more distinct from each other in longer note combinations than populations are. Genetic similarity decreased with geographic distance. Culturally learned traits can thus evolve independently of genetic structure, showing how learning decouples behaviour from geography-driven genetic ancestry.

evolutionary biology↗

Song complexity in suboscine birds: evolutionary drivers and ecological constraints

Acoustic signal complexity varies widely in the animal kingdom for reasons that remain unclear. In birds, it is widely proposed that vocal complexity evolves as an honest signal of individual quality driven by sexual selection. Other hypotheses related to social interactions include competition for ecological resources (social selection) and intra-group communication in group- living animals, both of which may favour signal complexity. However, these hypotheses are rarely explored at macroevolutionary scales, particularly in the context of constraints on sound production, transmission and detection, leading to ongoing uncertainty about the evolutionary origins of complex vocal signals. Using Bayesian phylogenetic models, we test whether different forms of social communication and ecological constraints predict the temporal and spectral complexity of songs in 1,288 species of suboscine passerine birds. We found that song complexity was reduced by sexual selection, along with other limiting factors including large body size and dense vegetation. Conversely, territoriality boosted the temporal complexity of songs. These findings challenge the common assumption that sexual selection is the main driver of increased signal complexity, and instead highlight the role of social selection as a key component of multiple inter-related drivers and constraints.

evolutionary biology↗

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↗

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↗

Changes in habitat connectivity for range-restricted birds reflect patterns of woodland invasion

Habitat fragmentation and landscape change are common causes of concern for species persistence, especially for habitat specialists. The composition of the matrix surrounding habitat fragments influences connectivity between them, which affects gene flow across the landscape. This can further impact populations in various ways. The Shola Sky Island landscapes naturally comprise a biphasic, forest-grassland mosaic ecosystem unique to the high-altitude regions of the Western Ghats of India. Earlier, this mosaic consisted of patches of native cloud forests embedded in a large grassland matrix. Over the last few decades, however, extensive invasion (up to 60%) of timber species into native grasslands has inverted this mosaic, i.e., small patches of grasslands are nested in a woodland matrix. We attempt to study the effects of these modifications on functional habitat connectivity in this region by modelling species movement using a circuit theory-based algorithm. We do this for seven Shola endemic, range-restricted bird species; six forest-specialist and one grassland-specialist species, based on a decade of field data. We consider a range of species-environment relationships and dispersal capacities for a past, relatively uninvaded landscape and a present, highly modified landscape. We used bird occupancy data (presence/absence from a total of 720 grid cells from targeted occupancy surveys for forest species and 744 presence locations for grassland species from occupancy surveys combined with opportunistic records) along with remotely sensed landscape, vegetation, climatic and topographic variables. We find that connectivity has increased overall for forest specialists, but has reduced for the grassland species. This pattern is concordant with regions where woodland cover from invasive timber species has expanded over approximately two decades. We also identify species-specific areas of low and high connectivity, which may have implications for gene flow within the landscape. This would help focus conservation efforts and predict how future landscape change might affect species persistence.

ecology↗

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↗

High-quality genome assembly of the endemic threatened White-bellied Sholakili Sholicola albiventris (Muscicapidae: Blanford, 1868) from the Shola Sky Islands, India.

The White-bellied Sholakili (Sholicola albiventris) is an endemic, elevational restricted species occurring in the Shola Sky Islands of the Western Ghats of India. This unique understory bird, with a complex vocal repertoire, exhibits impacts of gene flow due to anthropogenic habitat fragmentation. Here, we present the first genome assembly for Sholicola albiventris, which was assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.083 Gbp, consisting of 975 scaffolds with an N50 of 68.64Mbp and L50 of 6. Our genome assemblys completeness is supported by a high number of BUSCOs (99.9%) and a total of 4887 ultraconserved element (UCE) loci retrieved. We also report the complete mitochondrial genome comprising 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. We identified 11.82% of the nuclear genome as repetitive and 36,000 putative genes, with 12017 genes functionally annotated. Our assembly showed a great synteny between Taeniopygia guttata and Gallus gallus chromosome level assemblies. This reference will be pivotal for investigating landscape connectivity, sub-population genetics, local adaptation, and conservation genetics of this high-elevation, range-restricted endemic bird species.

genomics↗

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↗

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↗