Phylogenetic analysis of marginal Asiatic black bears reveals a recent Iranian–Himalayan divergence and has implications for taxonomy and conservation

Abstract

A small population of Asiatic black bear-known as the Baluchistan black bear-survives in the western limit of the species' range in Iran, where the species is rare, difficult to monitor and occupy an atypical habitat with extreme environmental conditions. Through the use of noninvasively collected samples, we analyzed mitochondrial DNA control region sequences to evaluate the phylogenetic relationships and divergence time between the Baluchistan Iranian black bear population and other Asian populations. Phylogenetic analyses indicate that Baluchistan and Nepalese (Himalayan) populations are monophyletic, with their divergence time estimated at circa 120 thousand years ago. The results reveal the low level of mitochondrial DNA variability in this small and marginal population, as is the case for many bear populations living in areas with similar conditions. The divergence time between the populations from Iran and Nepal dates to the Late Pleistocene, pointing to a transitional period between colder (glacial) and warmer (interglacial) conditions that allowed forests to expand and opened new habitats to population expansions. Pending further genetic and morphological corroboration, these preliminary results suggest that all Baluchistan and Himalayan (Nepalese) black bears might be considered as synonymous under the prior U. t. thibetanus trinomial (with gedrosianus just as junior synonym). Conservation efforts on this small and endangered population remain poor, and further measures are required to guarantee its long-term survival in Iran. Keywords Baluchistan black bear • Ursus thibetanus gedrosianus • Himalayan black bear • Late pleistocene • Subspecies taxonomy • Ursus thibetanus Handling editor: Paul Grobler. Leili Khalatbari and Michael J. Jowers have contributed equally. Hadi Fahimi deceased.

The relevance of pedigrees in the conservation genomics era

“…Since the late 1960’s, conservation genetics has grown from a handful of techniques into a fully‐fledged discipline that uses genetic information to inform the conservation management of threatened species worldwide (Avise, 2008 ). This field has developed a substantive toolbox applied to understand phylogenetics and species delimitation (Coimbra et al, 2021 ; Yusefi et al, 2020 ), population structure and demographics (Coimbra et al, 2020 ), natural community profiling (Young et al, 2020 ), and the level of standing genetic variation within and among populations (Zhang et al, 2020 ). Much discussion regarding the conservation genetic toolbox has been dedicated to the types of variants that are used for genetic inference, and for good reason: in a relatively short time frame, the field has experienced remarkable growth, from detecting variants using allozyme protein electrophoresis to detecting hundreds of thousands of variants through high throughput sequencing (HTS) approaches (Hohenlohe et al, 2021 ).…”

The relevance of pedigrees in the conservation genomics era.

“…The conservation genetics toolbox Since the late 1960's, conservation genetics has grown from a handful of techniques into a fully-fledged discipline that uses genetic information to inform the conservation management of threatened species worldwide (Avise 2008). This field has developed a substantive toolbox applied to understand phylogenetics and species delimitation (e.g., Yusefi et al, 2020;Coimbra et al, 2021), population structure and demographics (e.g., Coimbra et al, 2020), natural community profiling (e.g., Young et al, 2020), and the level of standing genetic variation within and among populations (e.g., Zhang, Luan, Ren, Hu, & Yin, 2020). Much discussion regarding the conservation genetic toolbox has been dedicated to the types of variants that are used for genetic inference, and for good reason: in a relatively short time frame, the field has experienced remarkable growth, from detecting variants using allozyme protein electrophoresis to detecting hundreds of thousands of variants through high throughput sequencing (HTS) approaches (Hohenlohe, Funk, & Rajora, 2021).…”