Are chest marks unique to Asiatic black bear individuals?

Development of Genetic Markers for Sex and Individual Identification of the Japanese Giant Flying Squirrel (Petaurista leucogenys) by an Efficient Method Using High-Throughput DNA Sequencing

DNA markers that detect differences in the number of microsatellite repeats can be highly effective for genotyping individuals that lack differences in external morphology. However, isolation of sequences with different microsatellite repeat numbers between individuals has been a time-consuming process in the development of DNA markers. Individual identification of Japanese giant flying squirrels (Petaurista leucogenys) has been challenging because this species is arboreal and nocturnal and exhibits little to no morphological variation between individuals. In this study, we developed DNA markers for sex and individual identification of this species by an efficient method using high-throughput DNA sequence data. Paired-end 5 Gb (2 × 250 bp) and 15 Gb (2 × 150 bp) genome sequences were determined from a female and a male Japanese giant flying squirrel, respectively. We searched SRY and XIST genes located on Y and X chromosomes, respectively, from high-throughput sequence data and designed primers to amplify these genes. Using these primer sets, we succeeded to identify the sex of individuals. In addition, we selected 12 loci containing microsatellites with different numbers of repeats between two individuals from the same data set, and designed primers to amplify these sequences. Twenty individuals from nine different locations were discriminated using these primer sets. Furthermore, both sex and microsatellite markers were amplified from DNA extracted non-invasively from single fecal pellet samples. Based on our results for flying squirrels, we expect our efficient method for developing non-invasive high-resolution individual- and sex-specific genotyping to be applicable to a diversity of mammalian species.

Multispecies facial detection for individual identification of wildlife: a case study across ursids

To address biodiversity decline in the era of big data, replicable methods of data processing are needed. Automated methods of individual identification (ID) via computer vision are valuable in conservation research and wildlife management. Rapid and systematic methods of image processing and analysis are fundamental to an ever-growing need for effective conservation research and practice. Bears (ursids) are an interesting test system for examining computer vision techniques for wildlife, as they have variable facial morphology, variable presence of individual markings, and are challenging to research and monitor. We leveraged existing imagery of bears living under human care to develop a multispecies bear face detector, a critical part of individual ID pipelines. We compared its performance across species and on a pre-existing wild brown bear Ursus arctos dataset (BearID), to examine the robustness of convolutional neural networks trained on animals under human care. Using the multispecies bear face detector and retrained sub-applications of BearID, we prototyped an end-to-end individual ID pipeline for the declining Andean bear Tremarctos ornatus. Our multispecies face detector had an average precision of 0.91-1.00 across all eight bear species, was transferable to images of wild brown bears (AP = 0.93), and correctly identified individual Andean bears in 86% of test images. These preliminary results indicate that a multispecies-trained network can detect faces of a single species sufficiently to achieve high-performance individual classification, which could speed-up the transferability and application of automated individual ID to a wider range of taxa.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42991-021-00168-5.

Steyaert S, Tochigi K, Inagaki A, Myojo H, Yamazaki K, Koike S. Animal-borne video systems provide insight into the reproductive behavior of the Asian black bear

Previous studies on the mating system of the Asian black bear (Ursus thibetanus) have been limited to observations of captive populations and estimations of multiple paternities. Hence, the mating system of wild bears remains poorly understood. Animal-borne camera systems (i.e., cameras mounted on animals) provide novel tools to study the behavior of elusive animals. Here, we used an animal-borne video system to record the activities of wild bears during the mating season. Video camera collars were attached to four adult Asian black bears (male "A" and "B," and female "A" and "B") captured in Tokyo, central Japan, in May and June 2018. The collars were retrieved in July 2018, after which the video data were downloaded and analyzed in terms of bear activity and mating behavior. All the bears were found to interact with other uniquely identifiable bears for some of the time (range 9-22 days) during the deployment period (range 36-45 days), and multiple mating in males was documented. Both males and females exhibited different behaviors on social days (i.e., days when the bear interacted with conspecifics) compared with solitary days (i.e., days with no observed interactions with conspecifics). Compared with solitary days, the bears spent a lower proportion of time on foraging activities and higher proportion of time on resting activities on social days. Our results suggest that Asian black bears have a polygamous mating system, as both sexes consort and potentially mate with multiple partners during a given mating season. Furthermore, bears appeared to reduce their foraging activities on social days and engaged more in social interactions.

Spot on: using camera traps to individually monitor one of the world’s largest lizards

Abstract ContextEstimating animal abundance often relies on being able to identify individuals; however, this can be challenging, especially when applied to large animals that are difficult to trap and handle. Camera traps have provided a non-invasive alternative by using natural markings to individually identify animals within image data. Although camera traps have been used to individually identify mammals, they are yet to be widely applied to other taxa, such as reptiles. AimsWe assessed the capacity of camera traps to provide images that allow for individual identification of the world’s fourth-largest lizard species, the perentie (Varanus giganteus), and demonstrate other basic morphological and behavioural data that can be gleaned from camera-trap images. MethodsVertically orientated cameras were deployed at 115 sites across a 10000km2 area in north-western Australia for an average of 216 days. We used spot patterning located on the dorsal surface of perenties to identify individuals from camera-trap imagery, with the assistance of freely available spot ID software. We also measured snout-to-vent length (SVL) by using image-analysis software, and collected image time-stamp data to analyse temporal activity patterns. ResultsNinety-two individuals were identified, and individuals were recorded moving distances of up to 1975m. Confidence in identification accuracy was generally high (91%), and estimated SVL measurements varied by an average of 6.7% (min=1.8%, max=21.3%) of individual SVL averages. Larger perenties (SVL of >45cm) were detected mostly between dawn and noon, and in the late afternoon and early evening, whereas small perenties (SVL of <30cm) were rarely recorded in the evening. ConclusionsCamera traps can be used to individually identify large reptiles with unique markings, and can also provide data on movement, morphology and temporal activity. Accounting for uneven substrates under cameras could improve the accuracy of morphological estimates. Given that camera traps struggle to detect small, nocturnal reptiles, further research is required to examine whether cameras miss smaller individuals in the late afternoon and evening. ImplicationsCamera traps are increasingly being used to monitor reptile species. The ability to individually identify animals provides another tool for herpetological research worldwide.

Reproductive parameters and cub survival of brown bears in the Rusha area of the Shiretoko Peninsula, Hokkaido, Japan

Knowing the reproductive characteristics of a species is essential for the appropriate conservation and management of wildlife. In this study, we investigated the demographic parameters, including age of primiparity, litter size, inter-birth interval, reproductive rate, and cub survival rate, of Hokkaido brown bears (Ursus arctos yesoensis) in the Rusha area on the Shiretoko Peninsula, Hokkaido, Japan, based on a long-term, individual-based monitoring survey. A total of 15 philopatric females were observed nearly every year from 2006 to 2016, and these observations were used to estimate reproductive parameters. The mean age of primiparity was 5.3 ± 0.2 (SE) years (n = 7, 95% CI = 5.0-5.6). We observed 81 cubs in 46 litters from 15 bears. Litter size ranged from one to three cubs, and averaged 1.76 ± 0.08 (SE) cubs/litter (95% CI = 1.61-1.91). Inter-birth intervals ranged from 1 to 4 years, and the mean value was estimated as 2.43 (95% CI = 2.16-2.76) and 2.53 (95% CI = 2.26-2.85) years in all litters and in litters that survived at least their first year, respectively. The reproductive rate was estimated from 0.70 to 0.76 young born/year/reproductive adult female, depending on the method of calculation. The cub survival rate between 0.5 and 1.5 years ranged from 60 to 73%. Most cub disappearances occurred in July and August, suggesting that cub mortality is mainly due to poor nutrition in the summer. All reproductive parameters observed in the Rusha area on the Shiretoko Peninsula fell within the range reported in Europe and North America, and were among the lowest or shortest age of primiparity, litter size, and inter-birth intervals, and ranked at a high level for reproductive rate.

Photos provide information on age, but not kinship, of Andean bear

Using photos of captive Andean bears of known age and pedigree, and photos of wild Andean bear cubs <6 months old, we evaluated the degree to which visual information may be used to estimate bears' ages and assess their kinship. We demonstrate that the ages of Andean bear cubs ≤6 months old may be estimated from their size relative to their mothers with an average error of <0.01 ± 13.2 days (SD; n = 14), and that ages of adults ≥10 years old may be estimated from the proportion of their nose that is pink with an average error of <0.01 ± 3.5 years (n = 41). We also show that similarity among the bears' natural markings, as perceived by humans, is not associated with pedigree kinship among the bears (R (2) < 0.001, N = 1,043, p = 0.499). Thus, researchers may use photos of wild Andean bears to estimate the ages of young cubs and older adults, but not to infer their kinship. Given that camera trap photos are one of the most readily available sources of information on large cryptic mammals, we suggest that similar methods be tested for use in other poorly understood species.