Kunal Arekar

Interests

Teaching

Data mining, Bayesian modelling, evolutionary biology

Research

Evolutionary genomics, evolutionary ecology, biogeography, population genetics, adaptation genomics, conservation genomics, disease ecology, urban ecology

Courses

Scholarly Contributions

Journals/Publications

• Hameed, S., Ali, M., Manu, S., Arekar, K., Khaleel, M., Bashir, T., & Umapathy, G. (2024). Genetic Diversity, Geographical Structure, and Demographic History of the Kashmir Gray Langur (Semnopithecus ajax). International Journal of Primatology. doi:10.1007/s10764-024-00455-1
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  Genetic diversity allows species to survive in a dynamic environment where selective criteria are ever-changing. As a result, the long-term survival of a species can be affected by its levels of genetic diversity. The Kashmir gray langur, Semnopithecus ajax, is an Endangered primate species endemic to the northwestern Himalaya. It has a fragmented distribution, is exposed to severe anthropogenic and climatic pressures, and has received little scientific attention. We investigated patterns of genetic diversity, population structure, and demographic history in wild populations of the Kashmir gray langur in the Kashmir Himalaya. We sampled 15 langur groups by using noninvasive sampling for scat collection and also obtained a tissue sample from a dead langur for whole-genome sequencing. We sequenced a mt-DNA fragment encompassing part of the noncoding D-loop region (728 bp) for 63 samples and protein-coding Cytochrome b (775 bp) for 37 samples. We generated whole-genome data by using PCR-free shotgun sequencing. We also reconstructed the demographic history of the Kashmir gray langur through coalescent analysis using MSMC2. We observed (± SD) lower haplotype (Hd = 0.207 ± 0.088) and nucleotide (π = 0.00126 ± 0.00077) diversity in Cytochrome b (693 bp) gene sequences than in noncoding partial D-loop (625 bp) gene sequences (Hd = 0.878 ± 0.026 and π = 0.00735 ± 0.002). Concatenated alignment (Cytochrome b and D-loop, 1318 bp) defined 21 unique haplotypes with haplotype diversity of 0.935 ± 0.024 and nucleotide diversity of 0.00532 ± 0.00193. The haplotype network and maximum likelihood phylogenetic tree revealed strong signatures of genetic differentiation among geographic populations, with the Jhelum River appearing to be a prominent barrier to gene flow between these populations. We found no evidence of isolation-by-distance. Mean genome-wide heterozygosity was very low (0.00034). We estimated the long-term effective population size to be 8,702 individuals; however, the most recent estimate indicated a lower value of 1,844 individuals. Our study emphasizes the need for habitat connectivity to mitigate the negative impacts of habitat loss and fragmentation on the genetic diversity of terrestrial and arboreal animals inhabiting the Himalayan ecosystems, particularly habitat specialist species.
• Arekar, K., Tiwari, N., Sambandam, S., Khaleel, M., & Karanth, P. (2022). Geography vs. past climate: the drivers of population genetic structure of the Himalayan langur. BMC Ecology and Evolution, 22(1). doi:10.1186/s12862-022-02054-1
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  Background: Contemporary species distribution, genetic diversity and evolutionary history in many taxa are shaped by both historical and current climate as well as topography. The Himalayas show a huge variation in topography and climatic conditions across its entire range, and have experienced major climatic fluctuations in the past. However, very little is known regarding how this heterogenous landscape has moulded the distribution of Himalayan fauna. A recent study examined the effect of these historical events on the genetic diversity of the Himalayan langurs in Nepal Himalaya. However, this study did not include the samples from the Indian Himalayan region (IHR). Therefore, here we revisit the questions addressed in the previous study with a near complete sampling from the IHR, along with the samples from the Nepal Himalaya. We used the mitochondrial Cytochrome-b (Cyt-b, 746 bp) region combined with multiple phylogeographic analyses and palaeodistribution modelling. Results: Our dataset contained 144 sequences from the IHR as well as the Nepal Himalaya. Phylogenetic analysis showed a low divergent western clade nested within high divergent group of eastern lineages and in the network analysis we identified 22 haplotypes over the entire distribution range of the Himalayan langurs. Samples from the Nepal Himalaya showed geographically structured haplotypes corresponding to different river barriers, whereas samples from IHR showed star-like topology with no structure. Our statistical phylogeography analysis using diyABC supported the model of east to west colonisation of these langurs with founder event during colonisation. Analysis of demographic history showed that the effective population size of the Himalayan langurs decreased at the onset of last glacial maximum (LGM) and started increasing post LGM. The palaeodistribution modelling showed that the extent of suitable habitat shifted from low elevation central Nepal, and adjoining parts of north India, during LGM to the western Himalaya at present. Conclusion: The current genetic diversity and distribution of Himalayan langurs in the Nepal Himalaya has been shaped by river barriers, whereas the rivers in the IHR had relatively less time to act as a strong genetic barrier after the recent colonisation event. Further, the post LGM expansion could have had confounding effect on Himalayan langur population structure in both Nepal Himalaya and IHR.
• Arekar, K., Parigi, A., & Karanth, K. (2021). Understanding the convoluted evolutionary history of the capped-golden langur lineage (Cercopithecidae: Colobinae)†. Journal of Genetics, 100(2). doi:10.1007/s12041-021-01329-8
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  The phylogenetic position of the capped and golden langur (CG) lineage has been ambiguous owing to the discordance between phylogenies from multiple molecular markers. Previous molecular studies have hypothesised that this discordance likely arises from either a hybridization event that took place between the Indian genus Semnopithecus and the Southeast Asian genus Trachypithecus or from incomplete lineage sorting (ILS). Distinguishing between hybridization and ILS is challenging and these processes can lead to serious difficulties in inferring phylogenies. In this study, we used genetic markers (nine nuclear and eight mitochondrial) in conjunction with coalescent based species tree approach and a test for hybridization using posterior predictive checking to better understand the evolutionary origin of the CG lineage. Both the concatenated nuclear as well as the mitochondrial dataset recovered congruent relationships where CG lineage was sister to Trachypithecus. However, nuclear species tree estimated using different multispecies coalescent methods suggested an opposite result, i.e. CG lineage was sister to Semnopithecus. Hybridization analysis strongly indicates gene flow between Semnopithecus and Trachypithecus that likely gave rise to the hybrid CG lineage. Further, the CG lineage is morphologically intermediate between Semnopithecus and Trachypithecus with respect to skull and body measurements. In light of the above evidences, we argue that the CG lineage needs to be elevated to a new genus of its own. Taxonomic and conservation implications of these results are also discussed.
• Arekar, K., Sathyakumar, S., & Karanth, K. (2021). Integrative taxonomy confirms the species status of the Himalayan langurs, Semnopithecus schistaceus Hodgson, 1840. Journal of Zoological Systematics and Evolutionary Research, 59(2). doi:10.1111/jzs.12437
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  Taxonomy is replete with groups where the species identity and classification remain unresolved. One such group is the widely distributed Hanuman langur (Colobinae: Semnopithecus). For most part of the last century, the Hanuman langur was considered to be a single species with multiple subspecies. Nevertheless, recent studies using an integrative taxonomy approach suggested that this taxon is a complex, with at least three species. However, these studies did not include the Himalayan population of the Hanuman langur whose taxonomic status remains unresolved. The Himalayan population of Hanuman langurs has been classified as a distinct species with multiple subspecies or been subsumed into other species. These classification schemes are wholly based on morphological characters which are sometimes insufficient to delimit different species. Here, we have integrated data from multiple sources viz. morphology, DNA, and ecology to resolve the taxonomy of the Himalayan langur and to understand its distribution limit. Our results with three lines of evidence corresponding to three different species concepts show that Himalayan langur is a species distinct from Semnopithecus entellus of the plains. Additionally, these results did not show any support for splitting of the Himalayan langur into multiple subspecies. Our study supports the classification proposed by Hill (Ceylon Journal of Science, XXI, 1939) and we recommend Semnopithecus schistaceus Hodgson, 1840 as species name for the Himalayan langur and subsume all the known subspecies into it.
• Karanth, K., Gautam, S., Arekar, K., & Divya, B. (2019). Phylogenetic diversity as a measure of biodiversity: Pros and Cons. Journal of the Bombay Natural History Society, 116. doi:10.17087/jbnhs/2019/v116/120848
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  Species richness is predominantly used as one of the fundamental measures of biodiversity for prioritization of areas for conservation. However, species richness often underestimates true diversity, as it does not take into account the evolutionary histories of the species in an area. In this regard, phylogenetic diversity, which incorporates information regarding species relationships in calculating diversity, has been proposed as an alternative. Here we compare species richness and phylogenetic diversity of mammals in nine sanctuaries to explore the importance and use of evolutionary relationships in characterizing diversity. Our analyses suggest that even though species richness and phylogenetic diversity are correlated, they are often decoupled. Importantly, areas with low species richness might harbour high phylogenetic diversity and vice-versa. We recommend the use of both the diversity measures for a holistic understanding of biodiversity and for prioritization of areas for conservation.