The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

Genetic and genomic monitoring with minimally invasive sampling methods

Iran lies at the southernmost range limit of brown bears globally. Therefore, understanding the habitat associations and patterns of population connectivity for brown bears in Iran is relevant for the species’ conservation. We applied species distribution modeling to predict habitat suitability and connectivity modeling to identify population core areas and corridors. Our results showed that forest density, topographical roughness, NDVI and human footprint were the most influential variables in predicting brown bear distribution. The most crucial core areas and corridor networks for brown bear are concentrated in the Alborz and Zagros Mountains. These two core areas were predicted to be fragmented into a total of fifteen isolated patches if dispersal of brown bear across the landscape is limited to 50,000 cost units, and aggregates into two isolated habitat patches if the species is capable of dispersing 400,000 cost units. We found low overlap between corridors, and core habitats with protected areas, suggesting that the existing protected area network may not be adequate for the conservation of brown bear in Iran. Our results suggest that effective conservation of brown bears in Iran requires protection of both core habitats and the corridors between them, especially outside Iran’s network of protected areas.

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Identifying priority core habitats and corridors for effective conservation of brown bears in Iran.

Gobi bear (Ursus arctos gobiensis, Sokolov, Orlov, 1992) is endangered and occurs only in isolated populations in the Southwestern part of Mongolia. It is listed in the Red book of Mongolia (1987, 1997, 2013) and is registered in Annex I of the Convention on international trade in endangered species (CITES, 1991). Hunting for the Gobi bear is prohibited by law in 1953, nowadays it is protected in the Great Gobi reserve. The article provides generalized information about habitat, behavior, diet, and mortality of Gobi bear. The research also touched upon the peculiarities of its historical distribution in Gobi (and the subsequent loss of habitat), movement, size, and taxonomic status. Previous analysis of mitochondrial DNA (Galbreath et al., 2007; McCarthy et al., 2009) showed that Gobi bear is similar to the subspecies Ursus arctos Preliminary analysis based on nuclear microsatellite markers indicates that Gobi bear is actually can be a separate subspecies of Ursus arctos gobiensis (Tumendemberel et al., 2015а). The analysis of 2835 places of encounters of five bears using GPS for the period from 2005 to 2009 has allowed estimating that within the Great Gobi reserve for the habitat of the Gobi bear suitable territory is about 23619.18 km2. The current habitat is likely reduced by 60% from historical range. Based on the telemetry data and the results of genetic analyses, the current distribution of bears in the Gobi desert was estimated. Adult females have moved around an area of about 514 km2 within 1009–1532 m above sea level around Shar Khuls oasis. Adult males moved through the area about 2465–2485 km2; altitudinal limits of 1122–1492 m. International Team Project on Gobi bear, together with researchers from the Gobi bear Fund, Institute of General and Experimental biology, Mongolian Academy of Sciences and the administration of the Great Gobi reserve in 2005 have used camera traps to estimate population size of Gobi bear. It is established that on the reserve territory at least 18 bears were including 7 males, 4 females, and 2 calves (Amgalan et al., 2005). Using genetic analyses (DNA microsatellites) from more than 1000 hair samples taken near 14 springs, it was calculated that during 2008–2009, these springs were visited by 22–31 individuals of Gobi bear, of which at least 14 males and 8 females (Tumendemberel et al., 2015).

Review of Gobi bear research (Ursus arctos gobiensis, Sokolov and Orlov, 1992)

Predicting the current and future suitable habitats of the main dietary plants of the Gobi Bear using MaxEnt modeling

Human–Bear Conflicts at the Beginning of the Twenty-First Century: Patterns, Determinants, and Mitigation Measures

Brown bears (Ursus arctos) inhabit much of the northern hemisphere, including portions of North America, Europe, and Asia. Whereas northern populations generally are healthy, their distribution becomes fragmented and conservation status more tenuous in their southern range. Many fragmented populations across southern Asia are poorly understood, and abundance and distribution data are minimal. One such population contains the Gobi bear, a brown bear surviving in the Great Gobi Strictly Protected Area of southwestern Mongolia. The number of bears in this area was assumed to be low, without data-based abundance estimates. Whereas bears frequent 3 oases complexes, it was not known to what extent bears moved or bred among these complexes, which span approximately 300 km. As part of a larger science-based conservation effort, we conducted a DNA-based mark–recapture population survey in 2009 to estimate abundance, inter-oases movements of individual bears and geneflow, and genetic variability. We placed...

https://bioone.org/journals/Ursus/volume-26/issue-2/URSUS-D-15-00001.1/Gobi-bear-abundance-and-inter-oases-movements-Gobi-Desert-Mongolia/10.2192/URSUS-D-15-00001.1.pdf

Gobi bear abundance and inter-oases movements, Gobi Desert, Mongolia

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 (FST = 0.147) was less than that of the Gobi and Pakistan (FST = 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.

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Tuya Tserenbataa

Papers

Gobi bear abundance and inter-oases movements, Gobi Desert, Mongolia

Review of Gobi bear research (Ursus arctos gobiensis, Sokolov and Orlov, 1992)

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

Gobi Bear Population Survey 2009