Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia

Abstract

Knowledge of genetic diversity and population structure is critical for conservation and management planning at the population level within a species’ range. Many brown bear populations in Central Asia are small and geographically isolated, yet their phylogeographic relationships, genetic diversity, and contemporary connectivity are poorly understood. To address this knowledge gap, we collected brown bear samples from the Gobi Desert (n = 2360), Altai, Sayan, Khentii, and Ikh Khyangan mountains of Mongolia (n = 79), and Deosai National Park in the Himalayan Mountain Range of Pakistan (n = 5) and generated 927 base pairs of mitochondrial DNA (mtDNA) sequence data and genotypes at 13 nuclear DNA microsatellite loci. We documented high levels of mtDNA and nDNA diversity in the brown bear populations of northern Mongolia (Altai, Sayan, Buteeliin nuruu and Khentii), but substantially lower diversity in brown bear populations in the Gobi Desert and Himalayas of Pakistan. We detected 3 brown bear mtDNA phylogeographic groups among bears of the region, with clade 3a1 in Sayan, Khentii, and Buteeliin nuruu mountains, clade 3b in Altai, Sayan, Buteeliin nuruu, Khentii, and Ikh Khyangan, and clade 6 in Gobi and Pakistan. Our results also clarified the phylogenetic relationships and divergence times with other brown bear mtDNA clades around the world. The nDNA genetic structure analyses revealed distinctiveness of Gobi bears and different population subdivisions compared to mtDNA results. For example, genetic distance for nDNA microsatellite loci between the bears in Gobi and Altai (F ST = 0.147) was less than that of the Gobi and Pakistan (F ST = 0.308) suggesting more recent male-mediated nuclear gene flow between Gobi and Altai than between Gobi and the Pakistan bears. Our results provide valuable information for conservation and management of bears in this understudied region of Central Asia and highlight the need for special protection and additional research on Gobi brown bears.

An evaluation of noninvasive sampling techniques for Malayan sun bears

“…Microsatellite markers with smaller fragment sizes than used in this study may successfully amplify even partially degraded samples. Given recent advances in optimized multiplex PCR protocols for samples holding very small quantities of DNA (Sharma et al 2013, Tumendemberel et al 2019, our findings hold much promise for future studies of genetic structure, connectivity, and population size in sun bears.…”

Long‐term monitoring using DNA sampling reveals the dire demographic status of the critically endangered Gobi bear

“…We assumed an open population between primary sampling sessions (2009,2013,2017), and specified individuals were at risk of mortality (i.e., 1 − φ) for four years between primary sessions which in practice implements a ϕ = (ϕ 4 ) 1/4 correction to get real parameter estimates to reflect annual probabilities. Because the population was completely isolated (McLellan et al 2017, Tumendemberel et al 2019, and bears were not known to permanently leave the study area, the open aspect of this model can be interpreted as births and deaths while excluding immigration and emigration. Closure was assumed between secondary sampling occasions with 2009, 2013, and 2017 having four, five, and six secondary sampling seasons, respectively.…”

“…Because our interest was in estimating survival (φ), we fit the final set of models including the additive and interaction effects on φ while holding π as intercept-only. We fit all the models with fixed temporary emigration parameters (γ 0 = 1, γ" = 0) because the Gobi bear population appears to be geographically closed based on genetic (Tumendemberel et al 2019) and telemetry data (Gobi bear project, unpublished data).…”

A small neighborhood well-organized: seasonal and daily activity patterns of the community of large and mid-sized mammals around waterholes in the Gobi Desert, Mongolia

“…The area is protected since 1975, to protect representative samples of the Central Asian desert and semi-desert ecosystems together with their unique flora and fauna, and has been included in the World Network of Biosphere Reserves since 1990, being one of the largest biosphere reserves in the world [ 59 ]. A special focus was placed on large mammals, particularly wild Bactrian camel ( Camelus ferus ), brown bear ( Ursus arctos ; see [ 38 , 73 ] for recent proposed changes in its taxonomical status), snow leopard ( Panthera uncia ), argali wild sheep ( Ovis ammon ), and Asiatic wild ass or khulan ( Equus hemionus ), all of which are listed in the Mongolian Red List of Mammals and the Mongolian Red Book ([ 17 , 68 ]; Table 1 ). The GGASPA covers 4.419 million ha, with elevations ranging from 525 to 2683 m.a.s.l., and encompasses both large, mostly unvegetated depressions, extensive hilly areas, and several mountain ranges (Atas Bogd, Tsaagan Bogd, Eej Uul, and Edren).…”