Age-structured Jolly-Seber model expands inference and improves parameter estimation from capture-recapture data.

Understanding the influence of individual attributes on demographic processes is a key objective of wildlife population studies. Capture-recapture and age data are commonly collected to investigate hypotheses about survival, reproduction, and viability. We present a novel age-structured Jolly-Seber model that incorporates age and capture-recapture data to provide comprehensive information on population dynamics, including abundance, age-dependent survival, recruitment, age structure, and population growth rates. We applied our model to a multi-year capture-recapture study of polar bears (Ursus maritimus) in western Hudson Bay, Canada (2012-2018), where management and conservation require a detailed understanding of how polar bears respond to climate change and other factors. In simulation studies, the age-structured Jolly-Seber model improved precision of survival, recruitment, and annual abundance estimates relative to standard Jolly-Seber models that omit age information. Furthermore, incorporating age information improved precision of population growth rates, increased power to detect trends in abundance, and allowed direct estimation of age-dependent survival and changes in annual age structure. Our case study provided detailed evidence for senescence in polar bear survival. Median survival estimates were lower (<0.95) for individuals aged <5 years, remained high (>0.95) for individuals aged 7-22 years, and subsequently declined to near zero for individuals >30 years. We also detected cascading effects of large recruitment classes on population age structure, which created major shifts in age structure when these classes entered the population and then again when they reached prime breeding ages (10-15 years old). Overall, age-structured Jolly-Seber models provide a flexible means to investigate ecological and evolutionary processes that shape populations (e.g., via senescence, life expectancy, and lifetime reproductive success) while improving our ability to investigate population dynamics and forecast population changes from capture-recapture data.

Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas.

BACKGROUND: The gut microbiome is essential for the host's health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda's gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis. RESULTS: Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways. CONCLUSION: Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome's functional characteristics; however, it needs further studies to ascertain the study outcomes.

Gene expression profiles during postnatal development of the liver and pancreas in giant pandas.

Giant pandas are unique Carnivora with a strict bamboo diet. To investigate the molecular mechanism of giant panda nutrient metabolism from newborn to adult, the gene expression profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using RNA-seq. We found a total of 3,211 hepatic and 3,343 pancreatic differentially expressed genes (DEGs) from three comparisons between suckling and no feeding, adult and no feeding, and adult and suckling groups. Few differences in gene-expression profiles were exhibited between no feeding and suckling groups in both tissues. GO and KEGG analyses were performed to further understand the biological functions of the DEGs. In both the liver and pancreas, genes related mainly to cell cycle processes were highly up-regulated in newborn samples whereas genes related to metabolism and immunity were up-regulated in adult giant pandas. The high expression of metabolism-related genes in adult samples probably helps to fulfill the metabolic function requirements of the liver and pancreas. In contrast, several vital genes involved in cholesterol metabolism and protein digestion and absorption were over-expressed in newborn samples. This may indicate the importance of cholesterol metabolism and protein digestion and absorption processes in giant panda infancy.

Identifying reliable indicators of fitness in polar bears.

Animal structural body size and condition are often measured to evaluate individual health, identify responses to environmental change and food availability, and relate food availability to effects on reproduction and survival. A variety of condition metrics have been developed but relationships between these metrics and vital rates are rarely validated. Identifying an optimal approach to estimate the body condition of polar bears is needed to improve monitoring of their response to decline in sea ice habitat. Therefore, we examined relationships between several commonly used condition indices (CI), body mass, and size with female reproductive success and cub survival among polar bears (Ursus maritimus) measured in two subpopulations over three decades. To improve measurement and application of morphometrics and CIs, we also examined whether CIs are independent of age and structural size-an important assumption for monitoring temporal trends-and factors affecting measurement precision and accuracy. Maternal CIs and mass measured the fall prior to denning were related to cub production. Similarly, maternal CIs, mass, and length were related to the mass of cubs or yearlings that accompanied her. However, maternal body mass, but not CIs, measured in the spring was related to cub production and only maternal mass and length were related to the probability of cub survival. These results suggest that CIs may not be better indicators of fitness than body mass in part because CIs remove variation associated with body size that is important in affecting fitness. Further, CIs exhibited variable relationships with age for growing bears and were lower for longer bears despite body length being related to cub survival and female reproductive success. These results are consistent with findings from other species indicating that body mass is a useful metric to link environmental conditions and population dynamics.

Splitting hairs: dietary niche breadth modelling using stable isotope analysis of a sequentially grown tissue.

Stable isotope data from durable, sequentially grown tissues (e.g. hair, claw, and baleen) is commonly used for modelling dietary niche breadth. The use of tissues grown over multiple months to years, however, has the potential to complicate isotopic niche breadth modelling, as time-averaged stable isotope signals from whole tissues may obscure information available from chronologically resolved stable isotope signals in serially sectioned tissues. We determined if whole samples of brown bear guard hair produced different isotopic niche breadth estimates than those produced from subsampled, serially sectioned samples of the same tissue from the same set of individuals. We sampled guard hair from brown bears (Ursus arctos) in four regions of Alaska with disparate biogeographies and dietary resource availability. Whole hair and serially sectioned hair samples were used to produce paired isotopic dietary niche breadth estimates for each region in the SIBER Bayesian model framework in R. Isotopic data from serially sectioned hair consistently produced larger estimates of isotopic dietary niche breadth than isotope data from whole hair samples. Serial sampling captures finer-scale changes in diet and when cumulatively used to estimate isotopic niche breadth, the serially sampled isotope data more fully captures dietary variability and true isotopic niche breadth.

Free-roaming dogs limit habitat use of giant pandas in nature reserves.

Giant pandas (Ailuropoda melanoleuca) were historically hunted using dogs and are currently threatened by free-roaming dogs and their associated diseases. To better understand the spatial magnitude of this threat, we used a GIS approach to investigate edge effects of dogs on giant panda habitat. We first examined two nature reserves with contrasting free-roaming dog populations: Liziping, with many dogs (~0.44/km2), and Daxiangling, with few dogs (~0.14/km2). Spatial analysis indicated that giant pandas at Liziping (but not Daxiangling) showed a shift in habitat use away from populated areas consistent with a risk response to the foray distance of free-roaming dogs (10.9 km path-distance). Most giant panda locations (86%) from the 2014 census in Liziping were clustered around remote "dog-free zones." Expanding this analysis across the entire giant panda range revealed that 40% of panda habitat is within the foray distance of dogs. Our assessment will inform dog control programs including monitoring, education, veterinary care, and other measures. We recommend that reserves designated for the release of translocated pandas receive priority consideration for dog control efforts. Only by understanding and managing complex interactions between humans, domestic animals, and wild animals can we sustain natural systems in a world increasingly dominated by humans.

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

Trends 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.

Giant panda protection: challenges and hopes.

In this paper, we discussed some major issues that hinder giant panda protection, such as diverse and mixed threats, habitat fragmentation, as well as the survey method to be improved, and some new protection actions appeared, such as the pilot program for the giant panda national park system and the administration of the giant panda national park was established. These information could provide important information for giant panda protection.

Evaluating giant panda as a surrogate species for conservation co-occurring species in the Baishuijiang National Nature Reserve.

The establishment of nature reserves is a key approach for biodiversity conservation worldwide. However, the effectiveness of nature reserves established by protecting the habitat needs of surrogate species is questioned. In this study, the Baishuijiang National Nature Reserve (Baishuijiang NNR), located in the Minshan Mountains, China, which is established mainly for the conservation of giant panda (a surrogate for the conservation of other endangered species) was selected. We quantitatively evaluated the conservation effectiveness of the reserve for giant panda and co-occurring species (here, seven protected species) using a maximum entropy model (Maxent), and analyzed spatial congruence between giant panda and other seven species. Results shown that the habitat of giant panda generally included the habitat of other seven protected species, suggesting that conservation of giant panda habitat also allows the conservation for the habitat of almost co-occurring species. Hence, the natural reserve established for giant panda as a surrogate species has a relatively high effectiveness. A high proportion of the suitable habitat for six species is inside the core zone, but a high proportion of the suitable habitat for two species is located in the experimental and buffer zones. Thus, the two species are affected by human activities. To improve the conservation effectiveness of the nature reserve, the management zones need to be amended. The result of the study will be beneficial for future conservation and management of the reserve. This study provides an effective method for evaluating the conservation effectiveness of nature reserves in other area of the worldwide.

Does hard mast production affect patterns of cementum annuli formation in premolar teeth of Asian black bears (Ursus thibetanus)?

Cementum annuli widths in mammals are is influenced by the nutrition of mammals. Reproductive stress has been is suggested to reduce the width of lead to narrower cementum annuli widths in female Asian black bears (Ursus thibetanus); however, food availability in autumn strongly impacts bear nutrition and likely impacts cementum widths as well. This study aimed to test how cementum annuli widths and the formation of false annuli were influenced by hard mast production. We established two hypotheses: (1) cementum annuli widths become narrower in poor mast years owing to inadequate nutritional conditions and (2) false annuli occur more frequently in poor mast years. We used teeth samples from male bears to avoid reproductive influences and separated width data into "adult" and "subadult" groups. We calculated the proportional width index (PWI) and used linear mixed models to estimate the masting effects on PWI. Generalized linear mixed models estimated the masting effects on false annuli frequency. True annuli widths and false annuli formation showed no significant relationship with mast production in adults. In subadults, poor mast production weak negative influence on false annuli formation. These new data resolve previous questions, allowing us to deduce that cementum annuli widths are a reliable index of reproductive success in female bears.

Palaeohistology and life history evolution in cave bears, Ursus spelaeus sensu lato.

The abundance of skeletal remains of cave bears in Pleistocene deposits can offer crucial information on the biology and life history of this megafaunal element. The histological study of 62 femora from 23 different European localities and comparisons with specimens of five extant ursid species revealed novel data on tissue types and growth patterns. Cave bear's femoral bone microstructure is characterized by a fibrolamellar complex with increasing amounts of parallel-fibered and lamellar bone towards the outer cortex. Remodelling of the primary bone tissue initially occurs close to the perimedullary margin of the bone cortex around the linea aspera. Although similar histological traits can be observed in many extant bear species, the composition of the fibrolamellar complex can vary greatly. Cave bears reached skeletal maturity between the ages of 10 and 14, which is late compared to other bear species. There is a significant correlation between altitude and growth, which reflects the different body sizes of cave bears from different altitudes.

A Bayesian state-space model using age-at-harvest data for estimating the population of black bears (Ursus americanus) in Wisconsin.

Population estimation is essential for the conservation and management of fish and wildlife, but accurate estimates are often difficult or expensive to obtain for cryptic species across large geographical scales. Accurate statistical models with manageable financial costs and field efforts are needed for hunted populations and using age-at-harvest data may be the most practical foundation for these models. Several rigorous statistical approaches that use age-at-harvest and other data to accurately estimate populations have recently been developed, but these are often dependent on (a) accurate prior knowledge about demographic parameters of the population, (b) auxiliary data, and (c) initial population size. We developed a two-stage state-space Bayesian model for a black bear (Ursus americanus) population with age-at-harvest data, but little demographic data and no auxiliary data available, to create a statewide population estimate and test the sensitivity of the model to bias in the prior distributions of parameters and initial population size. The posterior abundance estimate from our model was similar to an independent capture-recapture estimate from tetracycline sampling and the population trend was similar to the catch-per-unit-effort for the state. Our model was also robust to bias in the prior distributions for all parameters, including initial population size, except for reporting rate. Our state-space model created a precise estimate of the black bear population in Wisconsin based on age-at-harvest data and potentially improves on previous models by using little demographic data, no auxiliary data, and not being sensitive to initial population size.

Frequency of appearance of transverse (Harris) lines reflects living conditions of the Pleistocene bear-Ursus ingressus-(Sudety Mts., Poland).

Transverse lines, called Harris Lines (HL), osteological markers of recovery from growth arrest episodes, are visible in radiograms of recent and Pleistocene fossil bones. Since on the one hand they mark stressful episodes in life, and on the other are mainly used to trace health fluctuations in prehistoric human communities, I used a cave bear population to check if the processes that could affect the specie' condition were in any way reflected in the bone structure. 392 bear bones from Bear Cave in Kletno (collection: Department of Palaeozoology, University of Wroclaw), dated as 32 100 ±1300 to >49 000 years BP, were radiologically examined. The bones were found in a non-anatomical position; morphological analysis indicated that they belonged to different individuals. HL shadows were observed on 9 tibiae and 3 radii: 8.8% out of the 59 tibiae and 77 radii and 3.1% of all the bones. At least 3 transverse lines were recognised in those cases; the specimens were histologically examined. The bear individuals in question experienced regular malnutrition periods during their ontogeny. Starvation resulting in growth inhibition involved young individuals, aged 1 to 4 years. Juveniles aged 6 months, i.e. before weaning, or younger, showed no signs of nutritional stress. Starvation periods associated with seasonal food deficit were not long or common and had no significant effect on the development and welfare of the species. This is the first description of the occurrence of transverse lines in the Pleistocene bear.

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose.

The giant panda feeds almost exclusively on bamboo, a diet highly enriched in lignin and cellulose, but is characterized by a digestive tract similar to carnivores. It is still large unknown if and how the giant panda gut microbiota contributes to lignin and cellulose degradation. Here we show the giant pandas' gut microbiota does not significantly contribute to cellulose and lignin degradation. We found that no operational taxonomic unit had a nearest neighbor identified as a cellulolytic species or strain with a significant higher abundance in juvenile than cubs, a very low abundance of putative lignin and cellulose genes existed in part of analyzing samples but a significant higher abundance of genes involved in starch and hemicellulose degradation in juveniles than cubs. Moreover, a significant lower abundance of putative cellulolytic genes and a significant higher abundance of putative α-amylase and hemicellulase gene families were present in giant pandas than in omnivores or herbivores.

Role of nature reserves in giant panda protection.

Giant panda (Ailuropoda melanoleuca) is a flagship species in nature conservation of the world; to protect this species, 67 nature reserves have been established in China. To evaluate the protection effect of giant panda nature reserves, we analyzed the variation of giant panda number and habitat area of 23 giant panda nature reserves of Sichuan province based on the national survey data released by State Forestry Administration and Sichuan Forestry Department. Results showed that from the third national survey to the fourth, giant panda number and habitat area of 23 giant panda nature reserves of Sichuan province failed to realize the significant increase. Furthermore, we found that the total population growth rate of 23 nature reserves in the last 12 years was lower than those of the province total of Sichuan and the national total of China, and the total habitat area of the 23 nature reserves was decreasing in the last 12 years, but the province total and national total were all increasing. We propose that giant panda protection should pay more attention to how to improve the protective effects of nature reserves.

Sexual Maturity and Life Stage Influences Toxic Metal Accumulation in Croatian Brown Bears.

The influence of reproductive and (early) life stages on toxic metal levels was investigated in the brown bear (Ursus arctos), the largest mammalian predator species in Croatia. The purpose was to examine critical clusters in a population that might be at a higher risk of adverse health effects caused by metals as environmental contaminants. Levels of cadmium, mercury and lead in muscle, liver and kidney cortex of 325 male and 139 female bears, quantified by inductively coupled plasma mass spectrometry, were analysed according to distinct bear life stages (young: cub, yearling, subadult; mature: adult). Metal levels did not differ among sexes in young animals (< 4 years), except for mercury in muscles (higher in females), and adult females had higher cadmium and mercury. A trend of renal cadmium accumulation with age in immature male animals disappeared once they reached maturity, whereas for females this trend has only slowly declined in mature compared to immature bears. In early life stage (< 1 year), bear cubs had lower cadmium, comparable mercury, and higher lead in the kidneys than the bears of the following age category (yearlings). Due to a higher proportion of renal lead transfer from the mother to the cub compared with cadmium, it may be that the high burden of cadmium found in kidneys of older females has lower toxicological concern for their cubs than the lead content. Sex, reproductive, and life stages of bears were confirmed as important in assessing toxic metal burden.

Humans and climate change drove the Holocene decline of the brown bear.

The current debate about megafaunal extinctions during the Quaternary focuses on the extent to which they were driven by humans, climate change, or both. These two factors may have interacted in a complex and unexpected manner, leaving the exact pathways to prehistoric extinctions unresolved. Here we quantify, with unprecedented detail, the contribution of humans and climate change to the Holocene decline of the largest living terrestrial carnivore, the brown bear (Ursus arctos), on a continental scale. We inform a spatially explicit metapopulation model for the species by combining life-history data and an extensive archaeofaunal record from excavations across Europe with reconstructed climate and land-use data reaching back 12,000 years. The model reveals that, despite the broad climatic niche of the brown bear, increasing winter temperatures contributed substantially to its Holocene decline - both directly by reducing the species' reproductive rate and indirectly by facilitating human land use. The first local extinctions occurred during the Mid-Holocene warming period, but the rise of the Roman Empire 2,000 years ago marked the onset of large-scale extinctions, followed by increasingly rapid range loss and fragmentation. These findings strongly support the hypothesis that complex interactions between climate and humans may have accelerated megafaunal extinctions.

Consequences of severe habitat fragmentation on density, genetics, and spatial capture-recapture analysis of a small bear population.

Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the degree of contemporary habitat fragmentation and investigate the consequences of habitat fragmentation on population density and genetics of the HGS. Remaining natural habitats sustaining the HGS were significantly more fragmented and patchier than those supporting Florida's largest black bear subpopulation. Genetic diversity was low (AR = 3.57; HE = 0.49) and effective population size was small (NE = 25 bears), both of which remained unchanged over a period spanning one bear generation despite evidence of some immigration. Subpopulation density (0.054 bear/km2) was among the lowest reported for black bears, was significantly female-biased, and corresponded to a subpopulation size of 98 bears in available habitat. Conserving remaining natural habitats in the area occupied by the small, genetically depauperate HGS, possibly through conservation easements and government land acquisition, is likely the most important immediate step to ensuring continued persistence of bears in this area. Our study also provides evidence that preferentially placing detectors (e.g., hair traps or cameras) primarily in quality habitat across fragmented landscapes poses a challenge to estimating density-habitat covariate relationships using spatial capture-recapture models. Because habitat fragmentation and loss are likely to increase in severity globally, further investigation of the influence of habitat fragmentation and detector placement on estimation of this relationship is warranted.

Relationships between POPs, biometrics and circulating steroids in male polar bears (Ursus maritimus) from Svalbard.

The aim of this study was to determine the effects of persistent organic pollutants (POPs) and biometric variables on circulating levels of steroid hormones (androgens, estrogens and progestagens) in male polar bears (Ursus maritimus) from Svalbard, Norway (n = 23). Levels of pregnenolone (PRE), progesterone (PRO), androstenedione (AN), dehydroepiandrosterone (DHEA), testosterone (TS), dihydrotestosterone (DHT), estrone (E1), 17α-estradiol (αE2) and 17ß-estradiol (ßE2) were quantified in polar bear serum by gas chromatography tandem mass spectrometry (GC-MS/MS), while POPs were measured in plasma. Subsequently, associations between hormone concentrations (9 steroids), POPs (21 polychlorinated biphenyls (PCBs), 8 OH-PCBs, 8 organochlorine pesticides (OCPs) and OCP metabolites, and 2 polybrominated diphenyl ethers (PBDEs)) and biological variables (age, head length, body mass, girth, body condition index), capture date, location (latitude and longitude), lipid content and cholesterol levels were examined using principal component analysis (PCA) and orthogonal projections to latent structures (OPLS) modelling. Average concentrations of androgens, estrogens and progestagens were in the range of 0.57-83.7 (0.57-12.4 for subadults, 1.02-83.7 for adults), 0.09-2.69 and 0.57-2.44 nmol/L, respectively. The steroid profiles suggest that sex steroids were mainly synthesized through the Δ-4 pathway in male polar bears. The ratio between androgens and estrogens significantly depended on sexual maturity with androgen/estrogen ratios being approximately 60 times higher in adult males than in subadult males. PCA plots and OPLS models indicated that TS was positively related to biometrics, such as body condition index in male polar bears. A negative relationship was also observed between POPs and DHT. Consequently, POPs and body condition may potentially affect the endocrinological function of steroids, including development of reproductive tissues and sex organs and the general condition of male polar bears.