First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages

Abstract

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focusing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species’ distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ∼290 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; “Mainland clade”), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand (“Sunda clade”). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbour a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.

Application of Next-Generation Sequencing Technology in Southeast Asia: A Practical Framework for Advancing Wildlife Conservation

“…Thus, the issue of illegal wildlife trade and mislabelling species can combat the challenges in biodiversity loss [40]. With the sensitivity of NGS technology to sequence challenging specimens such as museum specimen or non-invasive samples via metabarcoding, it can potentially increase the accuracy and overcome the limitation by Sanger sequencing [40][41][42]. This is also supported where genetic non-invasive sample can provide a valuable information for population monitoring and allow the inferences of population density and key behavioural traits which is cost-effectiveness for wildlife study [43][44][45].…”

Corrigendum

“…In the recent article by Kunde et al (2023), the authors would like to add the following funding information:…”