Sequencing and annotation of the endangered wild buffalo (Bubalus arnee) mitogenome for taxonomic assessment

Pacha, Ankit Shankar; Nigam, Parag; Pandav, Bivash; Mondol, Samrat

doi:10.1007/s11033-021-06165-8

Cited by 6 publications

(4 citation statements)

References 28 publications

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“…Historical persecutions and domestication of the wild buffaloes have led to their extinction from their former range. Using samples of wild and domestic buffaloes from across their range, our results strengthen earlier studies that indicated northeast and central Indian wild buffaloes to be genetically similar compared to many domesticated water buffaloes within India (Mishra & Gaur 2019; Pacha et al 2021). The close genetic association of wild buffaloes from northeast and central India based on mitochondrial data is suggestive of common maternal lineages of these populations.…”

Section: Discussionsupporting

confidence: 86%

“…Megaherbivores were ubiquitous and likely abundant across terrestrial ecosystems until very recently, when humans selectively eliminated them at continental scales (Surovell et al 2005;Sandom et al 2014;Dembitzer et al 2022) a process that is still widely ongoing (Chase et al 2016). Megaherbivores are keystone species as they influence ecosystems by modifying species composition, nutrient cycling, primary productivity, fire, and water regimes (Owen-Smith 1988). Increasingly, research is linking their decline (Smith et al 2018) to a cascade of co-extinctions (Keesing & Young 2014), trophic degradation (Estes et al 2011), altered fire regimes (Rule et al 2012;Karp et al 2021), an increase in invasive species (Mungi et al 2023b), and a lasting anthropogenic impact on the biosphere (Malhi et al 2016;Enquist et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Evaluating the potential for reintroducing the endangered wild water buffalo (Bubalus arnee) in Kanha National Park, central India

Bora,

Vardhan,

Vijh

et al. 2024

Restoration Ecology

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Reintroducing megafauna to their historic range is an effective strategy to halt their extinctions and restore ecosystems. Wild water buffalo (Bubalus arnee) is an endangered megaherbivore that is lost from 95% of its range. About 90% of its global population (less than 4000) resides within India, in two isolated populations: northeast and central India. The central Indian population is on the verge of extinction and warrants urgent conservation interventions. We assess the potential and provide a strategy for reintroducing buffaloes in Kanha National Park, India. Habitat suitability using the global occurrence of buffalo revealed low‐lying grasslands with least human pressure found in Kanha (390 km2) to be suitable. Within this suitable range, we evaluated vegetation composition, forage biomass, and potential carrying capacity. Multidimensional ordination classified these suitable sites into moist and dry grassland clusters. Moist grasslands were found to better suit reintroduction due to lower grazing pressure, higher productivity, and availability of perennial water sources. Distinct matriarchal clades of swamp and river buffalo were observed. Within the river buffalo clade, Indian wild buffaloes formed a distinct cluster with close proximity between northeast and central Indian samples, suggesting northeast buffaloes could be sourced for a founding population in Kanha. Following IUCN guidelines, we discuss the reintroduction strategy that could sustain approximately 200 buffaloes in the area and subsequently expand to other suitable habitats in central India. If implemented as proposed, recovery of this lost ecosystem engineer will help to restore grasslands, and swamp habitats, as well as contribute to its global conservation efforts.

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Section: Discussionsupporting

confidence: 86%

Section: Introductionmentioning

confidence: 99%

Evaluating the potential for reintroducing the endangered wild water buffalo (Bubalus arnee) in Kanha National Park, central India

Bora,

Vardhan,

Vijh

et al. 2024

Restoration Ecology

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“…Upon scrutiny, it was observed that both Hangul mitogenomes from GenBank were identical and therefore only one of the sequences ( ) was used in all analyses. Three sequences from Bovidae group: wild buffalo ( Bubalus arnee ) ( Pacha et al, 2021 ), Indian gaur ( Bos gaurus ) ( Hassanin et al, 2012 ) and Cape buffalo ( Boselaphus tragocamelus ) ( Hassanin et al, 2012 ) were used as outgroup in this analysis. MEGA v7 was used to estimate inter-sequence mean pairwise genetic distance ( Kumar, Stecher & Tamura, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens

Ahmad,

Shankar Pacha,

Yahya Naqash

et al. 2023

PeerJ

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Background The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species. Methods Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park. Results The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.

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“…Therefore, the taxonomic status of the domestic water buffalo types is still debated and they were considered as two subspecies by some authors [10,11] or different species by others [9,[13][14][15]. sequence [16], we reconstructed the phylogenetic relationship between the three water buffalo types and the other members of genus Bubalus based on the whole mitogenome sequence. The phylogenetic tree included: lowland anoa (Bubalus depressicornis), mountain anoa (Bubalus quarlesi) in addition to the wild, river and swamp water buffalo types.…”

Section: Introductionmentioning

confidence: 99%

Mitogenome Analyses of Water Buffalo: Closeness of the Genetic Architecture of River Buffalo and Wild Buffalo (Bubalus arnee) Excludes Swamp Buffalo

Hassan

Youssef

El-Ghor

et al. 2022

Egyptian Journal of Veterinary Sciences

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With the recent availability of the wild water buffalo (Bubalus arnee) mitogenome W ATER buffalo species belongs to genus Bubalus and involves the wild and the domestic types. Domestic water buffaloes are reclassified into river and swamp types.Here, we have reconstructed the phylogenetic relationship between members of water buffalo species based on mitogenome sequences. The phylogenetic tree included lowland anoa, mountain anoa in addition to wild, river and swamp water buffalo types. Results indicated the paraphyly of water buffalo species since lowland anoa and mountain anoa were clustered with river and wild water buffalo in a separate clade, leaving swamp buffalo at the outside. Results also indicated close genetic architecture between the mitogenomes of river and wild water buffalo types. These findings may indicate that river buffalo and swamp buffalo belong to two distinct species and that river buffalo and not swamp buffalo is a descendant of wild water buffalo. Mitogenome analysis provided more information about the taxonomic status of water buffalo types and verified their relationship with the members of genus Bubalus.

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Sequencing and annotation of the endangered wild buffalo (Bubalus arnee) mitogenome for taxonomic assessment

Cited by 6 publications

References 28 publications

Evaluating the potential for reintroducing the endangered wild water buffalo (Bubalus arnee) in Kanha National Park, central India

Evaluating the potential for reintroducing the endangered wild water buffalo (Bubalus arnee) in Kanha National Park, central India

Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens

Mitogenome Analyses of Water Buffalo: Closeness of the Genetic Architecture of River Buffalo and Wild Buffalo (Bubalus arnee) Excludes Swamp Buffalo

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