scholarly journals Using bear rub data and spatial capture-recapture models to estimate trend in a brown bear population

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Katherine C. Kendall ◽  
Tabitha A. Graves ◽  
J. Andrew Royle ◽  
Amy C. Macleod ◽  
Kevin S. McKelvey ◽  
...  

AbstractTrends in population abundance can be challenging to quantify during range expansion and contraction, when there is spatial variation in trend, or the conservation area is large. We used genetic detection data from natural bear rubbing sites and spatial capture-recapture (SCR) modeling to estimate local density and population growth rates in a grizzly bear population in northwestern Montana, USA. We visited bear rubs to collect hair in 2004, 2009—2012 (3,579—4,802 rubs) and detected 249—355 individual bears each year. We estimated the finite annual population rate of change 2004—2012 was 1.043 (95% CI = 1.017—1.069). Population density shifted from being concentrated in the north in 2004 to a more even distribution across the ecosystem by 2012. Our genetic detection sampling approach coupled with SCR modeling allowed us to estimate spatially variable growth rates of an expanding grizzly bear population and provided insight into how those patterns developed. The ability of SCR to utilize unstructured data and produce spatially explicit maps that indicate where population change is occurring promises to facilitate the monitoring of difficult-to-study species across large spatial areas.

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 598 ◽  
Author(s):  
Gregory A. Taylor ◽  
Heather Kirk ◽  
Lauren Coombe ◽  
Shaun D. Jackman ◽  
Justin Chu ◽  
...  

The grizzly bear (Ursus arctos ssp. horribilis) 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.


2021 ◽  
Author(s):  
◽  
Michelle McLellan

<p>Identifying the mechanisms causing population change is essential for conserving small and declining populations. Substantial range contraction of many carnivore species has resulted in fragmented global populations with numerous small isolates in need of conservation. Here I investigate the rate and possible agents of change in two threatened grizzly bear (Ursus arctos) populations in southwestern British Columbia, Canada. I use a combination of population vital rates estimates, population trends, habitat quality analyses, and comparisons to what has been described in the literature, to carefully compare among possible mechanisms of change. First, I estimate population density, realized growth rates (λ), and the demographic components of population change for each population using DNA based capture-recapture data in both spatially explicit capture-recapture (SECR) and non-spatial Pradel robust design frameworks. The larger population had 21.5 bears/1000km2 and between 2006 and 2016 was growing (λPradel = 1.02 ± 0.02 SE, λsecr = 1.01 ± 4.6 x10-5 SE) following the cessation of hunting. The adjacent but smaller population had 6.3 bears/1000km2 and between 2005 and 2017 was likely declining (λPradel = 0.95 ± 0.03 SE, λsecr = 0.98 ± 0.02 SE). Estimates of apparent survival and recruitment indicated that lower recruitment was the dominant factor limiting population growth in the smaller population.  Then I use data from GPS-collared bears to estimate reproduction, survival and projected population change (λ) in both populations. Adult female survival was 0.96 (95% CI: 0.80-0.99) in the larger population (McGillvary Mountains or MM) and 0.87 (95% CI: 0.69-0.95) in the small, isolated population (North Stein-Nahatlatch or NSN). Cub survival was also higher in the MM (0.85, 95%CI: 0.62-0.95) than the NSN population (0.33, 95%CI: 0.11-0.67). This analysis identifies both low adult female survival and low cub survival as the demographic factors associated with population decline in the smaller population. By comparing the vital rates from these two populations with other small populations, I suggest that when grizzly bear populations are isolated, there appears to be a tipping point (de Silva and Leimgruber 2019) around 50 individuals, below which adult female mortality, even with intensive management, becomes prohibitive for population recovery. This analysis provides the first detailed estimates of population vital rates for a grizzly bear population of this size, and this information has been important for subsequent management action. To determine whether bottom-up factors (i.e. food) are limiting population growth and recovery in the small isolated population I use resource selection analysis from GPS collar data. I develop resource selection functions (RSF) for four dominant foraging seasons: the spring-early summer season when bears feed predominantly on herbaceous plants and dig for bulbs, the early fruit season where they feed on low elevation berries and cherries, the huckleberry season and the post berry season when foraging behaviours are most diverse but whitebark pine nuts are a relatively common food source. The differences in overall availability of high-quality habitats for different food types, especially huckleberries, between populations suggests that season specific bottom-up effects may account for some differences in population densities. Resource selections are a very common tool used for estimating resource distribution and availability, however, their ability to estimate food abundance on the ground are usually not tested. I assessed the accuracy of the resulting RSF models for predicting huckleberry presence and abundance measured in field plots. My results show that berry specific models did predict berry abundance in previously disturbed sites though varied in accuracy depending on how the models were categorized and projected across the landscape. Finally, I combine spatially explicit capture-recapture methods and models developed from resource selection modelling to estimate the effect of seasonal habitat availability and open road density, as a surrogate for top-down effects, on the bear density in the two populations. I found that population density is most strongly connected to habitats selected during a season when bears fed on huckleberries, the major high-energy food bears eat during hyperphagia in this area, as well as a large baseline difference between populations. The abundance of high-quality huckleberry habitat appears to be an important factor enabling the recovery of the larger population that is also genetically connected to other bears. The adjacent, smaller and genetically isolated population is not growing. The relatively low abundance of high-quality berry habitat in this population may be contributing to the lack of growth of the population. However, it is likely that the legacy of historic mortality and current stochastic effects, inbreeding effects, or other Allee effects, are also contributing to the continued low density observed. While these small population effects may be more challenging to overcome, this analysis suggests that the landscape can accommodate a higher population density than that currently observed.</p>


2021 ◽  
Author(s):  
◽  
Michelle McLellan

<p>Identifying the mechanisms causing population change is essential for conserving small and declining populations. Substantial range contraction of many carnivore species has resulted in fragmented global populations with numerous small isolates in need of conservation. Here I investigate the rate and possible agents of change in two threatened grizzly bear (Ursus arctos) populations in southwestern British Columbia, Canada. I use a combination of population vital rates estimates, population trends, habitat quality analyses, and comparisons to what has been described in the literature, to carefully compare among possible mechanisms of change. First, I estimate population density, realized growth rates (λ), and the demographic components of population change for each population using DNA based capture-recapture data in both spatially explicit capture-recapture (SECR) and non-spatial Pradel robust design frameworks. The larger population had 21.5 bears/1000km2 and between 2006 and 2016 was growing (λPradel = 1.02 ± 0.02 SE, λsecr = 1.01 ± 4.6 x10-5 SE) following the cessation of hunting. The adjacent but smaller population had 6.3 bears/1000km2 and between 2005 and 2017 was likely declining (λPradel = 0.95 ± 0.03 SE, λsecr = 0.98 ± 0.02 SE). Estimates of apparent survival and recruitment indicated that lower recruitment was the dominant factor limiting population growth in the smaller population.  Then I use data from GPS-collared bears to estimate reproduction, survival and projected population change (λ) in both populations. Adult female survival was 0.96 (95% CI: 0.80-0.99) in the larger population (McGillvary Mountains or MM) and 0.87 (95% CI: 0.69-0.95) in the small, isolated population (North Stein-Nahatlatch or NSN). Cub survival was also higher in the MM (0.85, 95%CI: 0.62-0.95) than the NSN population (0.33, 95%CI: 0.11-0.67). This analysis identifies both low adult female survival and low cub survival as the demographic factors associated with population decline in the smaller population. By comparing the vital rates from these two populations with other small populations, I suggest that when grizzly bear populations are isolated, there appears to be a tipping point (de Silva and Leimgruber 2019) around 50 individuals, below which adult female mortality, even with intensive management, becomes prohibitive for population recovery. This analysis provides the first detailed estimates of population vital rates for a grizzly bear population of this size, and this information has been important for subsequent management action. To determine whether bottom-up factors (i.e. food) are limiting population growth and recovery in the small isolated population I use resource selection analysis from GPS collar data. I develop resource selection functions (RSF) for four dominant foraging seasons: the spring-early summer season when bears feed predominantly on herbaceous plants and dig for bulbs, the early fruit season where they feed on low elevation berries and cherries, the huckleberry season and the post berry season when foraging behaviours are most diverse but whitebark pine nuts are a relatively common food source. The differences in overall availability of high-quality habitats for different food types, especially huckleberries, between populations suggests that season specific bottom-up effects may account for some differences in population densities. Resource selections are a very common tool used for estimating resource distribution and availability, however, their ability to estimate food abundance on the ground are usually not tested. I assessed the accuracy of the resulting RSF models for predicting huckleberry presence and abundance measured in field plots. My results show that berry specific models did predict berry abundance in previously disturbed sites though varied in accuracy depending on how the models were categorized and projected across the landscape. Finally, I combine spatially explicit capture-recapture methods and models developed from resource selection modelling to estimate the effect of seasonal habitat availability and open road density, as a surrogate for top-down effects, on the bear density in the two populations. I found that population density is most strongly connected to habitats selected during a season when bears fed on huckleberries, the major high-energy food bears eat during hyperphagia in this area, as well as a large baseline difference between populations. The abundance of high-quality huckleberry habitat appears to be an important factor enabling the recovery of the larger population that is also genetically connected to other bears. The adjacent, smaller and genetically isolated population is not growing. The relatively low abundance of high-quality berry habitat in this population may be contributing to the lack of growth of the population. However, it is likely that the legacy of historic mortality and current stochastic effects, inbreeding effects, or other Allee effects, are also contributing to the continued low density observed. While these small population effects may be more challenging to overcome, this analysis suggests that the landscape can accommodate a higher population density than that currently observed.</p>


2020 ◽  
Author(s):  
Michelle McLellan ◽  
BN McLellan ◽  
R Sollmann ◽  
CT Lamb ◽  
CD Apps ◽  
...  

© 2019 Elsevier Ltd We conducted DNA capture-recapture monitoring of grizzly bears (Ursus arctos) from 5 to 17 years after hunting was stopped in two adjacent but genetically distinct populations in southwestern British Columbia, Canada. We used spatial capture-recapture and non-spatial Pradel robust design modelling to estimate population density, trends, and the demographic components of population change for each population. The larger population had 21.5 bears/1000 km 2 and was growing (λ Pradel = 1.02 ± 0.02 SE; λ secr = 1.01 ± 4.6 × 10 −5 SE) following the cessation of hunting. The adjacent smaller population had 6.3 bears/1000 km 2 and was likely declining (λ Pradel = 0.95 ± 0.03 SE; λ secr = 0.98 ± 0.02 SE). Estimates of apparent survival and apparent recruitment indicated that lower recruitment was the dominant factor limiting population growth in the smaller population. Factors limiting reproductive rates and population density could include poor habitat quality, particularly the abundance of high-energy foods, genetic Allee effects due to a long period of population isolation, or demographic effects affecting infanticide rates. The cessation of hunting was insufficient to promote population recovery for the low density, isolated population. Our research highlights the importance of considering mortality thresholds in addition to small population effects and habitat quality when recovering large carnivore populations.


2020 ◽  
Author(s):  
Michelle McLellan ◽  
BN McLellan ◽  
R Sollmann ◽  
CT Lamb ◽  
CD Apps ◽  
...  

© 2019 Elsevier Ltd We conducted DNA capture-recapture monitoring of grizzly bears (Ursus arctos) from 5 to 17 years after hunting was stopped in two adjacent but genetically distinct populations in southwestern British Columbia, Canada. We used spatial capture-recapture and non-spatial Pradel robust design modelling to estimate population density, trends, and the demographic components of population change for each population. The larger population had 21.5 bears/1000 km 2 and was growing (λ Pradel = 1.02 ± 0.02 SE; λ secr = 1.01 ± 4.6 × 10 −5 SE) following the cessation of hunting. The adjacent smaller population had 6.3 bears/1000 km 2 and was likely declining (λ Pradel = 0.95 ± 0.03 SE; λ secr = 0.98 ± 0.02 SE). Estimates of apparent survival and apparent recruitment indicated that lower recruitment was the dominant factor limiting population growth in the smaller population. Factors limiting reproductive rates and population density could include poor habitat quality, particularly the abundance of high-energy foods, genetic Allee effects due to a long period of population isolation, or demographic effects affecting infanticide rates. The cessation of hunting was insufficient to promote population recovery for the low density, isolated population. Our research highlights the importance of considering mortality thresholds in addition to small population effects and habitat quality when recovering large carnivore populations.


2018 ◽  
Vol 2 (3) ◽  
pp. 84-92
Author(s):  
R. Obour, D. Amankwaa, A. Asare

Protected Areas (PAs) are created for the protection and maintenance of biological diversity, but many of Ghana’s PAs are subjectto severe pressures and threats, the main pressures being the illegal extraction of natural resources. Rattans are indisputablyone of the most important Non-Timber Forest Products (NTFPs) in Ghana’s Protected Areas that is without doubt one of thereasons for which it has drawn the attention of researchers. In this study the illegal rattan extraction patterns in the AnkasaConservation Area (ACA) in Ghana was inspected. Simple random sampling and Snowball sampling techniques were used. Datacollection employed the use of semi-structured questionnaires, interviews and field enumeration of rattans as well as an analysisof Effective Patrol Man-days (EPMDS) from 2004 to 2012. The results showed a significant positive correlation (r = 0.75, p<0.05, r2 = 0.557) between patrol effort and rattan extraction encounters. In addition, there was a general reduction in illegalrattan extraction encounters from 2004 to 2012 at a rate of 4.3 per year. The highest illegal rattan extraction incidences wererecorded in 2006 (76 encounters), 2005 (35 encounters), 2008 (22 encounters), 2004 (18 encounters) and the least incidencewere recorded in both 2010 (3 encounters) and 2011 (3 encounters).The research also revealed that Eremospatha macrocarpawas the most extracted rattan species followed by Laccosperma secundiflorum. The major rattan extraction and trade routesoriginate in the northern parts and in the area east of the reserve and also south of Draw River Forest Reserve. Generally, rattanpoaching in Ankasa Conservation Area has declined, but there are still human incursions in the northern part of the reserve. Thestudy recommended an intensification of patrols in the north of the reserve. Also, enrichment planting and Agroforestry practicesof inter-cropping rattans with seasonal crops should be pursued vigorously for the local communities.


1984 ◽  
Vol 52 (3) ◽  
pp. 545-560 ◽  
Author(s):  
R. Giugliano ◽  
D. J. Millward

1. Male weanling rats were fed on diets either adequate (55 mg/kg), or severely deficient (0.4 mg/kg) in zinc, either ad lib. or in restricted amounts in four experiments. Measurements were made of growth rates and Zn contents of muscle and several individual tissues.2. Zn-deficient rats exhibited the expected symptoms of deficiency including growth retardation, cyclic changes in food intake and body-weight.3. Zn deficiency specifically reduced whole body and muscle growth rates as indicated by the fact that (a) growth rates were lower in ad lib.-fed Zn-deficient rats compared with rats pair-fed on the control diet in two experiments, (b) Zn supplementation increased body-weights of Zn-deficient rats given a restricted amount of diet at a level at which they maintained weight if unsupplemented, (c) Zn supplementation maintained body-weights of Zn-deficient rats fed a restricted amount of diet at a level at which they lost weight if unsupplemented (d) since the ratio, muscle mass:body-weight was lower in the Zn-deficient rats than in the pair-fed control groups, the reduction in muscle mass was greater than the reduction in body-weight.4. Zn concentrations were maintained in muscle, spleen and thymus, reduced in comparison to some but not all control groups in liver, kidney, testis and intestine, and markedly reduced in plasma and bone. In plasma, Zn concentrations varied inversely with the rate of change of body-weight during the cyclic changes in body-weight.5. Calculation of the total Zn in the tissues examined showed a marked increase in muscle Zn with a similar loss from bone, indicating that Zn can be redistributed from bone to allow the growth of other tissues.6. The magnitude of the increase in muscle Zn in the severely Zn-deficient rat, together with the magnitude of the total losses of muscle tissue during the catabolic phases of the cycling, indicate that in the Zn-deficient rat Zn may be highly conserved in catabolic states.


2018 ◽  
Vol 18 (19) ◽  
pp. 14637-14651 ◽  
Author(s):  
Yingjie Zhang ◽  
Wei Du ◽  
Yuying Wang ◽  
Qingqing Wang ◽  
Haofei Wang ◽  
...  

Abstract. The North China Plain (NCP) has experienced frequent severe haze pollution events in recent years. While extensive measurements have been made in megacities, aerosol sources, processes, and particle growth at urban downwind sites remain less understood. Here, an aerosol chemical speciation monitor and a scanning mobility particle sizer, along with a suite of collocated instruments, were deployed at the downwind site of Xingtai, a highly polluted city in the NCP, for real-time measurements of submicron aerosol (PM1) species and particle number size distributions during May and June 2016. The average mass concentration of PM1 was 30.5 (±19.4) µg m−3, which is significantly lower than that during wintertime. Organic aerosols (OAs) constituted the major fraction of PM1 (38 %), followed by sulfate (25 %) and nitrate (14 %). Positive matrix factorization with the multilinear engine version 2 showed that oxygenated OA (OOA) was the dominant species in OA throughout the study, on average accounting for 78 % of OA, while traffic and cooking emissions both accounted for 11 % of OA. Our results highlight that aerosol particles at the urban downwind site were highly aged and mainly from secondary formation. However, the diurnal cycle also illustrated the substantial influence of urban emissions on downwind sites, which are characterized by similar pronounced early morning peaks for most aerosol species. New particle formation and growth events were also frequently observed (58 % of the time) on both clean and polluted days. Particle growth rates varied from 1.2 to 4.9 nm h−1 and our results showed that sulfate and OOA played important roles in particle growth during clean periods, while OOA was more important than sulfate during polluted events. Further analyses showed that particle growth rates have no clear dependence on air mass trajectories.


Author(s):  
Courtney Quinn ◽  
Dylan Harries ◽  
Terence J. O’Kane

AbstractThe dynamics of the North Atlantic Oscillation (NAO) are analyzed through a data-driven model obtained from atmospheric reanalysis data. We apply a regularized vector autoregressive clustering technique to identify recurrent and persistent states of atmospheric circulation patterns in the North Atlantic sector (110°W-0°E, 20°N-90°N). In order to analyze the dynamics associated with the resulting cluster-based models, we define a time-dependent linear delayed map with a switching sequence set a priori by the cluster affiliations at each time step. Using a method for computing the covariant Lyapunov vectors (CLVs) over various time windows, we produce sets of mixed singular vectors (for short windows) and approximate the asymptotic CLVs (for longer windows). The growth rates and alignment of the resulting time-dependent vectors are then analyzed. We find that the window chosen to compute the vectors acts as a filter on the dynamics. For short windows, the alignment and changes in growth rates are indicative of individual transitions between persistent states. For long windows, we observe an emergent annual signal manifest in the alignment of the CLVs characteristic of the observed seasonality in the NAO index. Analysis of the average finite-time dimension reveals the NAO− as the most unstable state relative to the NAO+, with persistent AR states largely stable. Our results agree with other recent theoretical and empirical studies that have shown blocking events to have less predictability than periods of enhanced zonal flow.


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