The grizzly bear (
ssp.
) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data ...were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96.1% were found to be complete within the assembly. An automated annotation of the genome identified 19,848 protein coding genes. Our study shows that the combination of the two sequencing modalities that we used is sufficient for the construction of highly contiguous reference quality mammalian genomes. The assembled genome sequence and the supporting raw sequence reads are available from the NCBI (National Center for Biotechnology Information) under the bioproject identifier PRJNA493656, and the assembly described in this paper is version QXTK01000000.
Landscape genetic analyses of wildlife populations can exclude variation in a broad suite of potential spatiotemporal correlates, including consideration of how such variation might have similarly ...influenced people over time. Grizzly bear (Ursus arctos) populations in what is now known as coastal British Columbia, Canada, provide an opportunity to examine the possible effects of a complex set of landscape and human influences on genetic structure. In this collaboration among the Nuxalk, Haíɫzaqv, Kitasoo/Xai'xais, Gitga'at, and Wuikinuxv First Nations and conservation scientists, we characterized patterns of genetic differentiation in the grizzly bear, a species of high cultural value, by genotyping 22 microsatellite loci from noninvasively collected hair samples over a 23,500 km² area. We identified three well-differentiated groups. Resistance surfaces, which incorporated past and present human use, settlement, and landscape resistant features, could not explain this pattern of genetic variation. Notably, however, we detected spatial alignment between Indigenous language families and grizzly bear genetic groups. Grizzly bears sampled within an area represented by a given language family were significantly similar to those sampled within that language family (P = 0.001) and significantly divergent to those sampled outside the language family (P = 0.001). This spatial co-occurrence suggests that grizzly bear and human groups have been shaped by the landscape in similar ways, creating a convergence of grizzly bear genetic and human linguistic diversity. Additionally, grizzly bear management units designated by the provincial government currently divide an otherwise continuous group and exclude recently colonized island populations that are genetically continuous with adjacent mainland groups. This work provides not only insight into how ecological and geographic conditions can similarly shape the distribution of people and wildlife but also new genetic evidence to support renewed, locally led management of grizzly bears into the future.
Biodiversity loss from climate and land use change is a global occurrence, but is of particular concern in more prominent biodiverse and sensitive areas such as the Hindu Kush Himalayan (HKH) region. ...This region harbors two species of geographically separated brown bear (Ursus arctos) - the Tibetan (U. a. pruinosus) and Himalayan brown bear (U. a. isabellinus). Both serve as important umbrella species, providing many ecological benefits to their surrounding ecosystems. However, how these two species from the same taxonomic group but with distinct geographical ranges, will respond to climate and land use change is poorly understood. The aim of this study was to predict the potential impacts of future climate and land use change on the distribution and dispersal paths of Tibetan and Himalayan brown bears in the HKH region. We applied MaxEnt modeling to predict the distribution of the two bear species both currently and for the year 2070, using three General Circulation Models and three scenarios of climate and land use change. We then identified potential dispersal paths using Circuit Theory. Results showed that both species would be negatively affected by the climate and land use change expected in the 2070s. In all three climate scenarios, their distribution areas would both shrink and shift to higher altitudes. Throughout the HKH region, Tibetan and Himalayan brown bears were predicted to lose over 34% and 32% of currently inhabited area under the most severe climate scenario, respectively. In addition, results showed that the density of dispersal paths for Tibetan brown bear would decrease while dispersal resistance would increase, and that dispersal paths for Himalayan brown bears would shift to higher latitudes. To protect these species, the currently suitable distribution areas and dispersal paths should be considered as priority protected areas. Our findings provide a scientific basis for allocating protected areas in the HKH region that are effective under the context of global climate change, and for establishing transboundary cooperation in the HKH region.
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•Brown bears' distribution range, dispersal paths and climate refugia were identified in the Hindu Kush Himalayan region.•Brown bears would be negatively affected by climate and land use change.•Brown bears' distribution range would shrink and shift to higher altitudes.•Climate and land use change would degrade brown bears' dispersal paths.•Brown bears' dispersal paths would shift to higher latitudes.
Reduction in population size, with its predicted effects on population fitness, is the most alarming anthropogenic impact on endangered species. By introducing compatible individuals, genetic rescue ...(GR) is a promising but debated approach for reducing the genetic load unmasked by inbreeding and for restoring the fitness of declining populations. Although GR can improve genetic diversity and fitness, it can also produce loss of ancestry, hampering local adaptation, or replace with introduced variants the unique genetic pools evolved in endemic groups. We used forward genetic simulations based on empirical genomic data to assess fitness benefits and loss of ancestry risks of GR in the Apennine brown bear (Ursus arctos marsicanus). There are approximately 50 individuals of this isolated subspecies, and they have lower genetic diversity and higher inbreeding than other European brown bears, and GR has been suggested to reduce extinction risks. We compared 10 GR scenarios in which the number and genetic characteristics of migrants varied with a non‐GR scenario of simple demographic increase due to nongenetic factors. The introduction of 5 individuals of higher fitness or lower levels of deleterious mutations than the target Apennine brown bear from a larger European brown bear population produced a rapid 10–20% increase in fitness in the subspecies and up to 22.4% loss of ancestry over 30 generations. Without a contemporary demographic increase, fitness started to decline again after a few generations. Doubling the population size without GR gradually increased fitness to a comparable level, but without losing ancestry, thus resulting in the best strategy for the Apennine brown bear conservation. Our results highlight the importance for management of endangered species of realistic forward simulations grounded in empirical whole‐genome data.
Consecuencias en la aptitud y pérdida de ascendencia del oso pardo de los Apeninos después de un rescate genético simulado
Resumen
La reducción del tamaño poblacional, con los previsibles efectos sobre su aptitud, es el impacto antropogénico más alarmante sobre las especies amenazadas. Mediante la introducción de individuos compatibles, el rescate genético (RG) es una estrategia prometedora para reducir la carga genética revelada por la endogamia y restaurar la aptitud de las poblaciones en declive, aunque todavía se debate la eficiencia de esta. Aunque el RG puede mejorar la diversidad genética y la aptitud, también puede producir pérdida de ascendencia, lo que puede dificultar la adaptación local, o sustituir con variantes introducidas por los migrantes los acervos genéticos únicos que han evolucionado en grupos endémicos. En este trabajo realizamos simulaciones genéticas a futuro basadas en datos genómicos empíricos para evaluar los beneficios del RG en términos de aptitud y los riesgos de la pérdida de ascendencia en el oso pardo de los Apeninos (Ursus arctos marsicanus). Quedan aproximadamente 50 individuos de esta subespecie aislada que cuentan con una menor diversidad genética y un mayor nivel de endogamia comparado con otros osos pardos europeos y se ha sugerido que el RG podria reducir el riesgo de extinción de esta población. Comparamos 10 escenarios de RG en los que variaban el número y las características genéticas de los osos migrantes con un escenario sin RG con aumento demográfico causado por factores no genéticos. La introducción de 5 individuos procedentes de una población europea de oso pardo con mayor aptitud o niveles menores de mutaciones deletéreas que el oso pardo de los Apeninos produjo un rápido aumento de la aptitud del 10–20% en la subespecie y hasta un 22.4% de pérdida de ascendencia durante 30 generaciones. En las simulaciones sin un aumento demográfico, la aptitud empezó a disminuir de nuevo después de unas pocas generaciones. La duplicación del tamaño de la población sin RG aumentó gradualmente la aptitud hasta un nivel comparable al de algunos escenarios de RG, pero sin pérdida de ascendencia, por lo que parece ser la mejor estrategia para la conservación del oso pardo de los Apeninos. Nuestros resultados resaltan la importancia que tienen las simulaciones realistas a futuro basadas en datos empíricos del genoma completo para la gestión de especies amenazadas.
Animal personality traits and the emergence of behavioural syndromes, i.e. between-individual correlation of behaviours, are commonly quantified from behavioural observations in controlled ...environments. Subjecting large and elusive wildlife to controlled test situations is, however, rarely possible, suggesting that ecologists should exploit alternative measures of behaviours for quantifying differences between individuals. Our goal was to test whether movement and space use data can be used to quantify behavioural syndromes in the wild. We quantified six behaviours from GPS and dual motion sensor tracking devices of 46 adult female brown bears followed in southcentral Sweden over the summer and early autumn. As well as daily travel distance, an indicator for activity, and daily displacement, an indicator for exploration, we quantified four behaviours that increase a bear's likelihood of encountering humans and could thus serve as indicators for boldness: diurnality, selection for roads and selection for two open habitat types, bogs and clearcuts, with low lateral cover. We tested (1) whether behaviours showed repeatable between-individual variation (animal personality) and (2) whether behaviours were correlated between individuals and thus formed a behavioural syndrome. Repeatability of behaviours ranged from 0.16 to 0.61 confirming between-individual variation in movement, activity and space use. A multivariate mixed model revealed significant positive correlations between travel distance, displacement and diurnality, suggesting the existence of an activity–exploration and potentially partial boldness syndrome in our bear population. Selection for exposed or human-frequented habitats were uncorrelated with the activity–exploration syndrome and with each other, albeit there was a trend for stronger road avoidance by bears that readily used clearcuts. We show that large tracking data sets can be used to quantify between-individual correlation in spatial behaviours. We suggest that delineating behavioural types from wildlife tracking data will be of increasing interest because of the importance of animal personality for ecological processes, wildlife conservation and human–wildlife coexistence.
•We tested whether bears showed personality in remotely quantified behaviours.•Bears showed repeatability in movement, diurnality and habitat selection.•Movement behaviours and diurnality were significantly correlated between individuals.•Habitat selection behaviours were uncorrelated with the movement activity syndrome.•Movement data are useful to assess animal personalities and behavioural syndromes.
Increased popularity of recreational activities in natural areas has led to the need to better understand their impacts on wildlife. The majority of research conducted to date has focused on ...behavioral effects from individual recreations, thus there is a limited understanding of the potential for population-level or cumulative effects. Brown bears (Ursus arctos) are the focus of a growing wildlife viewing industry and are found in habitats frequented by recreationists. Managers face difficult decisions in balancing recreational opportunities with habitat protection for wildlife. Here, we integrate results from empirical studies with expert knowledge to better understand the potential population-level effects of recreational activities on brown bears. We conducted a literature review and Delphi survey of brown bear experts to better understand the frequencies and types of recreations occurring in bear habitats and their potential effects, and to identify management solutions and research needs. We then developed a Bayesian network model that allows managers to estimate the potential effects of recreational management decisions in bear habitats. A higher proportion of individual brown bears in coastal habitats were exposed to recreation, including photography and bear-viewing than bears in interior habitats where camping and hiking were more common. Our results suggest that the primary mechanism by which recreation may impact brown bears is through temporal and spatial displacement with associated increases in energetic costs and declines in nutritional intake. Killings in defense of life and property were found to be minimally associated with recreation in Alaska, but are important considerations in population management. Regulating recreation to occur predictably in space and time and limiting recreation in habitats with concentrated food resources reduces impacts on food intake and may thereby, reduce impacts on reproduction and survival. Our results suggest that decisions managers make about regulating recreational activities in time and space have important consequences for bear populations. The Bayesian network model developed here provides a new tool for managers to balance demands of multiple recreational activities while supporting healthy bear populations.
В статье приведен анализ численности бурого медведя Ursus arctos Linnaeus на о. Завьялова и дано описание возможных путей миграции между островом, материковой частью побережья и другими островами с ...учетом преобладающих морских течений, ветров и ледовых условий. В результате наблюдений с катеров и аэроучета установлено, что на острове обитают бурые медведи всех возрастных и половых групп. Определено, что на всей площади острова, кроме скал, плотность бурого медведя обычна, так же как и для схожего по природным условиям побережья северной части Охотского моря.
•We extracted unpaved roads from RapidEye imagery with 87 % precision and 89 % recall.•Post-processing improved initial predictions produced by the neural network.•Results changed the public road ...database by 20 % through additions and removals.
Accurate and current road network data is fundamental to land management and emergency response, yet challenging to produce for unpaved roads in rural and forested regions using traditional cartographic approaches. Automatic extraction of roads from satellite imagery using deep learning is a promising alternative gaining increasing attention, however most efforts have focused on urban paved roads and used very high spatial resolution imagery, which is less frequently available for rural regions. Additionally, road extraction routines still struggle to produce a fully-connected, vectorized road network. In this study covering a large forested area in Western Canada, we developed and evaluated a routine to automatically extract unpaved road pixels using a convolutional neural network (CNN), and then used the CNN outputs to update a pre-existing government road network and evaluate if and how it would change. To cover the large spatial extent mapped in this study, we trained the routine using moderately high-resolution satellite imagery from the RapidEye constellation and a ground-truth dataset collected with smartphones by organizations already operating and driving in the region. Performance of the road extraction was comparable to results achieved by others using very high-resolution imagery; recall accuracy was 89–97%, and precision was 85–91%. Using our approach to update the pre-existing road network would result in both removals and additions to the network, totalling over 1250 km, or about 20 % of the roads previously in the network. We discuss how road density estimates in the study area would change using this updated network, and situate these changes within the context of ongoing efforts to conserve grizzly bears, which are listed as a Threatened species in the region. This study demonstrates the potential of remote sensing to maintain current and accurate rural road networks in dynamic forest landscapes where new road construction is prevalent, yet roads are also frequently de-activated, reclaimed or otherwise not maintained.
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