Identification,characterization, validation and cross-species amplification of genic-SSRs in Indian Mustard (<Emphasis Type="Italic">Brassica juncea</Emphasis>)

Brassica juncea is an economically important oilseed crop worldwide. It has limited genomic resources at present. We generated 47,962,057 expressed sequence reads which were assembled into 45,280 unigenes. A total of 4108 SSR loci (≥10 bp) were identified in these unigenes. Trinucleotide was the most frequent repeat unit (59.91 %) followed by di- (38.66 %), tetra - (0.71 %), hexa - (0.49 %) and pentanucleotide repeats (0.24 %). Primers were designed for 2863 SSR loci among which 460 were selected for primer synthesis. A total of 339 loci amplified successfully of which 134 (39.5 %) exhibited polymorphism among six B. juncea genotypes with PIC values ranging from 0.18 to 0.81. Further, 25 polymorphic SSRs were used for analysis of genetic variability in 25 genotypes of Brassicas and their wild relatives. Two to five alleles with PIC values 0.22–0.66 were detected at these loci. The dendrogram grouped the genotypes according to their known pedigree/systematic position.     

Recent observations of intraspecific predation and cannibalism among polar bears in the southern Beaufort Sea

Intraspecific killing has been reported among polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus). Although cannibalism is one motivation for such killings, the ecological factors mediating such events are poorly understood. Between 24 January and 10 April 2004, we confirmed three instances of intraspecific predation and cannibalism in the Beaufort Sea. One of these, the first of this type ever reported for polar bears, was a parturient female killed at her maternal den. The predating bear was hunting in a known maternal denning area and apparently discovered the den by scent. A second predation event involved an adult female and cub recently emerged from their den, and the third involved a yearling male. During 24 years of research on polar bears in the southern Beaufort Sea region of northern Alaska and 34 years in northwestern Canada, we have not seen other incidents of polar bears stalking, killing, and eating other polar bears. We hypothesize that nutritional stresses related to the longer ice-free seasons that have occurred in the Beaufort Sea in recent years may have led to the cannibalism incidents we observed in 2004.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Behavioral development of a polar bear cub (Ursus maritimus) in captivity

The difficulty of observing polar bears (Ursus maritimus) in the wild has prohibited the gathering of behavioral data necessary to develop a baseline set of milestones for monitoring cub development. This study describes and quantifies previously undocumented trends in behavior observed in a captive cub–information that will be useful both in future comparative studies and in the implementation of husbandry improvements. Nearly 400 hr of behavioral data were collected, 100 hr of which were video recordings from the maternity den during the first 3 months of life. Den videos were scored to determine activity budgets and levels of maternal contact. For the remainder of the first year, mother and cub were observed in the outdoor enclosure. The onset and relative frequency of 40 discrete cub behaviors were tracked, as were patterns of mother–cub contact, including nursing and weaning. This study revealed that environmental conditions, habitat enrichment, and conditioning procedures influenced the patterns of developmental behavior exhibited by a polar bear cub. Both climatic and developmental factors had significant effects on the time the bears spent swimming. Management practices, such as environmental enrichment, and a conditioning procedure involving separation of mother and cub caused transient changes in several tracked behaviors. As the cub aged, the longest time between consecutive maternal contacts increased. Nursing bouts recorded per hour of observation decreased, and the duration of individual nursing bouts and pre‐nurse begging periods increased. Zoo Biol 22:507–514, 2003. © 2003 Wiley‐Liss, Inc.     

Relationship type affects the reliability of dispersal distance estimated using pedigree inferences in partially sampled populations: A case study involving invasive American mink in Scotland

Estimating dispersal—a key parameter for population ecology and management—is notoriously difficult. The use of pedigree assignments, aided by likelihood‐based software, has become popular to estimate dispersal rate and distance. However, the partial sampling of populations may produce false assignments. Further, it is unknown how the accuracy of assignment is affected by the genealogical relationships of individuals and is reflected by software‐derived assignment probabilities. Inspired by a project managing invasive American mink (Neovison vison), we estimated individual dispersal distances using inferred pairwise relationships of culled individuals. Additionally, we simulated scenarios to investigate the accuracy of pairwise inferences. Estimates of dispersal distance varied greatly when derived from different inferred pairwise relationships, with mother–offspring relationship being the shortest (average = 21 km) and the most accurate. Pairs assigned as maternal half‐siblings were inaccurate, with 64%–97% falsely assigned, implying that estimates for these relationships in the wild population were unreliable. The false assignment rate was unrelated to the software‐derived assignment probabilities at high dispersal rates. Assignments were more accurate when the inferred parents were older and immigrants and when dispersal rates between subpopulations were low (1% and 2%). Using 30 instead of 15 loci increased pairwise reliability, but half‐sibling assignments were still inaccurate (>59% falsely assigned). The most reliable approach when using inferred pairwise relationships in polygamous species would be not to use half‐sibling relationship types. Our simulation approach provides guidance for the application of pedigree inferences under partial sampling and is applicable to other systems where pedigree assignments are used for ecological inference.     

Eisbärenzucht (Ursus maritimus Phipps, 1774) im Zoo am Meer Bremerhaven – Fortsetzung einer langen Tradition

Breeding polar bears has a long tradition in the Zoo am Meer, the “Zoo at the Sea” in Bremerhaven. In the years between 1935 and 1974 three female bears gave birth to 32 cubs and 19 of them were successfully raised. In the following years many attempts to tie in with this tradition failed. Bad constructional conditions and disadvantageous animal pairings were the main reasons for the missing breeding success. After completely reconstructing the polar bear enclosure in the year 2002, as well as extending the breeding area with an additional smaller breeding cave in 2012 and pairing male Lloyd and female Valeska in 2013 a new polar bear birth and upbringing could be experienced after 40 years. Offspring Lale is the 35^th cub in Bremerhaven Zoo.     

应用微卫星分型进行小熊猫亲子鉴定

小熊猫栖息于喜马拉雅与横断山脉,是亚洲濒危物种。中国的小熊猫谱系已登记圈养小熊猫个体９６８ 只,现有存活个体３５５ 只（２０１３ 年）,然而,现有谱系中存在部分信息不明确的问题。为此,我们选择１９ 对小熊猫特异性引物对４１ 只圈养小熊猫进行微卫星扩增,并分析其亲缘关系。将获取的亲子鉴定结果,结合种群原始记录信息,利用Pedigraph 软件构建福州圈养小熊猫的种群遗传谱系图。结果表明：在母子关系确实的情况下,１９个基因座位的联合父权排除概率为０. ９９９９９９６８;利用６ 个已知双亲的后代检验１９ 个基因座位的可信度,后代与双亲的基因型完全符合孟德尔遗传定律,表明１９个基因座位能有效确认小熊猫的亲权关系。应用１９ 个微卫星标记成功地为１５ 个后代找到了生物学父亲。尽管一些雌性个体在繁殖期有多重交配的行为,亲子鉴定的结果显示同一窝小熊猫均来自单一父权。基因型比对结果表明７ 对双胞胎均属于异卵双生子。福州种群的后代中除＃９２０和＃９２１ 外,其余均源于＃４８７ 或＃８９８ 两只雄性,表明不同个体参与繁殖的机会不均等。因此,利用现代繁殖技术,加强濒危野动物种群管理,科学制定繁殖计划具有积极的现实意义。     

Grizzly bear population vital rates and trend in the Northern Continental Divide Ecosystem,Montana

We estimated grizzly bear (Ursus arctos) population vital rates and trend for the Northern Continental Divide Ecosystem (NCDE), Montana, between 2004 and 2009 by following radio-collared females and observing their fate and reproductive performance. Our estimates of dependent cub and yearling survival were 0.612 (95% CI = 0.300–0.818) and 0.682 (95% CI = 0.258–0.898). Our estimates of subadult and adult female survival were 0.852 (95% CI = 0.628–0.951) and 0.952 (95% CI = 0.892–0.980). From visual observations, we estimated a mean litter size of 2.00 cubs/litter. Accounting for cub mortality prior to the first observations of litters in spring, our adjusted mean litter size was 2.27 cubs/litter. We estimated the probabilities of females transitioning from one reproductive state to another between years. Using the stable state probability of 0.322 (95% CI = 0.262–0.382) for females with cub litters, our adjusted fecundity estimate (m_x) was 0.367 (95% CI = 0.273–0.461). Using our derived rates, we estimated that the population grew at a mean annual rate of approximately 3% (λ = 1.0306, 95% CI = 0.928–1.102), and 71.5% of 10,000 Monte Carlo simulations produced estimates of λ > 1.0. Our results indicate an increasing population trend of grizzly bears in the NCDE. Coupled with concurrent studies of population size, we estimate that over 1,000 grizzly bears reside in and adjacent to this recovery area. We suggest that monitoring of population trend and other vital rates using radioed females be continued. © 2011 The Wildlife Society.     

Growth rate of 21 captive-born,mother-raised cheetah cubs

This paper presents the growth rate of 21 clinically normal, mother-raised. captive cheetah cubs from birth through 45 days of age. The development of a growth curve for healthy, mother-raised cheetah cubs provides a diagnostic tool for individuals involved in cheetah propagation. Use of the curve may alert caretakers to problems early and thus help reduce the high neonatal mortality rate seen in captive-born cheetah cubs. The growth curve was constructed using 21 (11 males and 10 females) captiveborn cheetah cubs from six litters (offspring of three unrelated adult males and three unrelated adult females) born at the Columbus Zoo from September 1985 through December 1989. Each cub was weighed to the nearest gram the morning after birth and approximately the same time every consecutive morning for 45 days. The mean weight the morning after birth was 463 g (range 385–542 g). The average litter size was 3.5 (range 2–4, n = 6). The daily weight gain was 40–50 g/cub/day.     

Body composition of three polar bear (Ursus maritimus) cubs found dead at Svalbard

We determined the body composition from the carcasses of three 3- to 4-months-old polar bear cubs found dead at Svalbard, Norway. Two of the cubs were killed by a male bear at the den and one cub died from starvation. These three carcasses weighed 70-77% of total body mass of cubs. The ash and protein content of the three carcasses were similar but the starving cub had higher water content and lower fat content than the two killed cubs. The fat content varied from 1.3% (starving cub) to 12.9% while the content of water and fat was similar (about 76%) in the three cubs. More data on the body composition of polar bear cubs at time of emergence from the den are needed to understand the breeding ecology and reproductive energetics of female polar bears.     

Consequences of long-distance swimming and travel over deep-water pack ice for a female polar bear during a year of extreme sea ice retreat

Polar bears (Ursus maritimus) prefer to live on Arctic sea ice but may swim between ice floes or between sea ice and land. Although anecdotal observations suggest that polar bears are capable of swimming long distances, no data have been available to describe in detail long distance swimming events or the physiological and reproductive consequences of such behavior. Between an initial capture in late August and a recapture in late October 2008, a radio-collared adult female polar bear in the Beaufort Sea made a continuous swim of 687 km over 9 days and then intermittently swam and walked on the sea ice surface an additional 1,800 km. Measures of movement rate, hourly activity, and subcutaneous and external temperature revealed distinct profiles of swimming and walking. Between captures, this polar bear lost 22% of her body mass and her yearling cub. The extraordinary long distance swimming ability of polar bears, which we confirm here, may help them cope with reduced Arctic sea ice. Our observation, however, indicates that long distance swimming in Arctic waters, and travel over deep water pack ice, may result in high energetic costs and compromise reproductive fitness.     

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single‐nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine‐scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine‐scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine‐scale population delineation in polar bears.     

Families in space: relatedness in the Barents Sea population of polar bears (Ursus maritimus)

The kin structure and dispersal pattern of polar bears ( Ursus maritimus ) of the Barents Sea was investigated during the spring mating season using two complementary approaches. First, individual genotypes based on the analyses of 27 microsatellite loci of 583 polar bears were related to field information gathered from 1146 bears in order to reconstruct the animals' pedigrees and to infer geographical distances between adult bears of different relatedness categories. According to the data, the median natal dispersal distance of the male animals was 52 km while that of the females was 93 km. Second, the relatedness of pairs of adult bears was estimated and correlated to the geographical distance between them. The female dyads had a much stronger kin structure than the male dyads. The 'pedigree approach' revealed a male kin structure which could not be detected using the 'relatedness approach'. This suggests that, on a broader scale, effective dispersal is slightly male biased. Despite fidelity to natal areas, male-mediated gene flow may nevertheless prevent genetic differentiation. Males might occasionally shift their home range which could therefore lead to a male-biased breeding dispersal. Our results showed that a nonterritorial species such as the polar bear that has a high dispersal potential, lives in a highly unstable environment and migrates seasonally is still able to exhibit a distinct kin structure during the mating season.     

Identifying marker typing incompatibilities in linkage analysis.

A common problem encountered in linkage analyses is that execution of the computer program is halted because of genotypes in the data that are inconsistent with Mendelian inheritance. Such inconsistencies may arise because of pedigree errors or errors in typing. In some cases, the source of the inconsistencies is easily identified by examining the pedigree. In others, the error is not obvious, and substantial time and effort are required to identify the responsible genotypes. We have developed two methods for automatically identifying those individuals whose genotypes are most likely the cause of the inconsistencies. First, we calculate the posterior probability of genotyping error for each member of the pedigree, given the marker data on all pedigree members and allowing anyone in the pedigree to have an error. Second, we identify those individuals whose genotypes could be solely responsible for the inconsistency in the pedigree. We illustrate these methods with two examples: one a pedigree error, the second a genotyping error. These methods have been implemented as a module of the pedigree analysis program package MENDEL.     

Heritability of body size in the polar bears of Western Hudson Bay

Among polar bears (Ursus maritimus), fitness is dependent on body size through males’ abilities to win mates, females’ abilities to provide for their young and all bears’ abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449‐individual pedigree and an array of 5,433 single nucleotide polymorphisms (SNPs) to provide the first quantitative genetic study of polar bears. We used animal models to estimate heritability (h²) among polar bears handled between 1966 and 2011, obtaining h² estimates of 0.34–0.48 for strictly skeletal traits and 0.18 for axillary girth (which is also dependent on fatness). We genotyped 859 individuals with the SNP array to test for marker–trait association and combined p‐values over genetic pathways using gene‐set analysis. Variation in all traits appeared to be polygenic, but we detected one region of moderately large effect size in body length near a putative noncoding RNA in an unannotated region of the genome. Gene‐set analysis suggested that variation in body length was associated with genes in the regulatory cascade of cyclin expression, which has previously been associated with body size in mice. A greater understanding of the genetic architecture of body size variation will be valuable in understanding the potential for adaptation in polar bear populations challenged by climate change.     

Genetic analysis reveals promiscuity among female cheetahs

Cheetahs (Acinonyx jubatus) have a combination of ranging patterns and social system that is unique in mammals, whereby male coalitions occupy small territories less than 10% of the home range of solitary females. This study uses non-invasive genetic sampling of a long-term study population of cheetah in the Serengeti National Park in Tanzania to infer the mating system. Individual cheetah genotypes at up to 13 microsatellite loci were obtained from 171 faecal samples. A statistical method was adapted to partition the cubs within each litter (n=47) into full-sibling clusters and to infer the father of each cluster using these loci. Our data showed a high rate of multiple paternity in the population; 43% of litters with more than one cub were fathered by more than one male. The results also demonstrated that female fidelity was low, and provided some evidence that females chose to mate with unrelated males within an oestrus cycle. The low rate of paternity assignments indicated that males living outside the study area contributed substantially to the reproduction of the cheetah population.     

Assessment of genotyping accuracy in a non-invasive DNA-based population survey of Asiatic black bears (Ursus thibetanus): lessons from a large-scale pilot study in Iwate prefecture,northern Japan

Non-invasive DNA genotyping using hair samples has become a common method in population surveys of Asiatic black bears (Ursus thibetanus) in Japan; however, the accuracy of the genotyping data has rarely been discussed in empirical studies. Therefore, we conducted a large-scale pilot study to examine genotyping accuracy and sought an efficient way of error-checking hair-trapping data. We collected 2,067 hair samples, successfully determined the genotypes of 1,245 samples, and identified 295 individuals. The genotyping data were further divided into 3 subsets of data according to the number of hairs used for DNA extraction in each sample (1–4, 5–9, and ≥10 hairs), and the error rates of allelic dropout and false alleles were estimated for each subset using a maximum likelihood method. The genotyping error rates in the samples with ≥10 hairs were found to be lower than those in the samples with 1–4 and 5–9 hairs. The presence of erroneous genotypes among the identified individuals was further checked using a post hoc goodness-of-fit test that determined the match between the expected and observed frequencies of individual homozygotes at 0–6 loci. The results indicated the presence of erroneous genotypes, possibly as a result of allelic dropout, in the samples. Therefore, for improved accuracy, it is recommended that samples containing ≥10 hairs should be used for genotyping and a post hoc goodness-of-fit test should be performed to exclude erroneous genotypes before proceeding with downstream analysis such as capture-mark-recapture estimation.     

Genetic monitoring of a founder population of brown bears (Ursus arctos) in central Austria

The small population of brown bears in central Austria originated from a single migrant bear that had settled in the area in 1972 and three bears that were released in the years 1989–1993. Subsequently, the population has been monitored by radio-tracking and collecting data on bear signs and observations. In 2000 we started a genetic monitoring program of the population with the aim to obtain data on population size, sex ratio, relationships as well as movements of individuals. We present results from six years of genetic monitoring, which were combined with field observations. During this time 1,005 hair and faecal samples were gathered in an area of >3,000 km2, most of them in the core area of <1,000 km². Furthermore we analysed blood samples from captured individuals. Eight microsatellite and two sex determination loci were employed for DNA profiling. The number of detected individuals is surprisingly low, ranging from 5–8 per year. Concerning relationships the analysis reveals that all genotyped individuals are descendants of the founder individuals indicating that no immigration took place. Only one male and three females (mother and 2 daughters) took part in reproduction. Considering the fact that 28 bears were born in this region since 1991 the question arises where the bears disappear to. Our results suggest that subadult bears migrate from the core area. However, indices of bear occurrence outside the core area are rare and migration could be proved only for two young males. Other explanations, such as increased natural mortality and illegal hunting are discussed.     

Serum corticosteroid binding globulin expression is modulated by fasting in polar bears (Ursus maritimus)

Polar bears (Ursus maritimus) from several subpopulations undergo extended fasting during the ice-free season. However, the animals appear to conserve protein despite the prolonged fasting, though the mechanisms involved are poorly understood. We hypothesized that elevated concentrations of corticosteroid binding globulin (CBG), the primary cortisol binding protein in circulation, lead to cortisol resistance and provide a mechanism for protein conservation during extended fasting. The metabolic state (feeding vs. fasting) of 16 field sampled male polar bears was determined based on their serum urea to creatinine ratio (>25 for feeding vs. <5 for fasting). There were no significant differences in serum cortisol levels between all male and female polar bears sampled. Serum CBG expression was greater in lactating females relative to non-lactating females and males. CBG expression was significantly higher in fasting males when compared to non-fasting males. This leads us to suggest that CBG expression may serve as a mechanism to conserve protein during extended fasting in polar bears by reducing systemic free cortisol concentrations. This was further supported by a lower serum glucose concentration in the fasting bears. As well, a lack of an enhanced adrenocortical response to acute capture stress supports our hypothesis that chronic hunger is not a stressor in this species. Overall, our results suggest that elevated serum CBG expression may be an important adaptation to spare proteins by limiting cortisol bioavailability during extended fasting in polar bears.