The Future of Artificial Intelligence in Monitoring Animal Identification, Health, and Behaviour.

With many advancements, technologies are now capable of recording non-human animals' location, heart rate, and movement, often using a device that is physically attached to the monitored animals. However, to our knowledge, there is currently no technology that is able to do this unobtrusively and non-invasively. Here, we review the history of technology for use with animals, recent technological advancements, current limitations, and a brief introduction to our proposed novel software. Canadian tech mogul EAIGLE Inc. has developed an artificial intelligence (AI) software solution capable of determining where people and assets are within public places or attractions for operational intelligence, security, and health and safety applications. The solution also monitors individual temperatures to reduce the potential spread of COVID-19. This technology has been adapted for use at the Toronto Zoo, initiated with a focus on Sumatran orangutans (Pongo abelii) given the close physical similarity between orangutans and humans as great ape species. This technology will be capable of mass data collection, individual identification, pose estimation, behaviour monitoring and tracking orangutans' locations, in real time on a 24/7 basis, benefitting both zookeepers and researchers looking to review this information.

The Adrenal Cortisol Response to Increasing Ambient Temperature in Polar Bears (Ursus maritimus).

Our objective was to identify the upper ambient temperature threshold that triggers an increase in cortisol in response to increased thermoregulatory demands in polar bears. The results reported here include endocrine data collected over two years from 25 polar bears housed in 11 accredited zoological institutions across North America. The effects of ambient temperature, sex, age group (juvenile, adult, elderly), breeding season and humidity on fecal cortisol metabolite (FCM) concentrations (N = 8439 samples) were evaluated using linear mixed models. Ambient temperatures were placed into five different categories: <5 °C, 6−10 °C, 11−15 °C, 16−20 °C, and >20 °C. Ambient temperature and humidity had a significant (p < 0.05) effect on FCM concentrations with significant (p < 0.05) interactions of sex, age and breeding season. Once biotic factors were accounted for, there was a significant (p < 0.05) increase in FCM concentrations associated with ambient temperatures above 20 °C in adult polar bears. The implications of these findings for the management of both zoo and wild polar bears are discussed.

Luteal phase length, endometrial edema, and behavior differentiate post-ovulatory events in a giant panda (Ailuropoda melanoleuca).

Despite decades of reproductive research on the giant panda (Ailuropoda melanoleuca), the post-ovulatory phase continues to confound zoologists in conservation and breeding centers around the world, often resulting in significant investments of time and resources without reproductive success. The purpose of this project was to document and compare post-ovulatory characteristics during a non-productive and productive breeding in the same individual in consecutive years. A multidisciplinary approach was used to monitor the visiting female giant panda at the Toronto Zoo through the luteal phase of her first two full reproductive cycles in 2014 and 2015. Monitoring occurred via urine-endocrine analysis, weekly ultrasound examinations, and continuous behavioral observations. The 2014 reproductive cycle consisted of a pseudopregnancy, characterized by an extended luteal phase (241 days), the identification of endometrial edema and folding during ultrasound examinations, and a lack of strong association between behavior patterns and urinary progestagen secretion. The 2015 reproductive cycle included increased feeding time through the primary progestagen rise compared to the previous year, followed by simultaneous decrease in appetite and increases in inactivity, resting, sitting upright, and pre-partum-associated behaviors. These changes began 25 days before the birth of twins on Day 153 post-ovulation. Both fetuses were detected via ultrasound 15 days pre-partum. These results suggest that an absence of pre-partum behaviors, ultrasound evidence of endometrial edema without a fetus, and an extended luteal phase may be indicative of pseudopregnancy in giant pandas. Simultaneous monitoring of morphology, behavior, and urinary-endocrine profiles showed clear differences between successful and unsuccessful reproductive years.

Urethral catheterization as an alternative method for collecting sperm in the black-footed ferret (Mustela nigripes).

The endangered black-footed ferret (BFF; Mustela nigripes) is an important example of the benefits of assisted reproduction in species conservation with both semen evaluation and artificial insemination using fresh and frozen sperm being successfully incorporated into the breeding program. Currently, electroejaculation (EE) is routinely utilized for semen collection in BFFs, a technique that requires custom equipment and experienced operators, and does not consistently yield viable samples in this species. In this case study, we evaluated the feasibility of urethral catheterization (UC) for semen collection, a method predominately tested in domestic and non-domestic felids, on four occasions (three BFF males). After general anesthesia with a combination of ketamine, midazolam and α2-agonist dexmedetomidine (thought to promote semen release into the urethra), a lightly lubricated, flexible feeding tube was passed into the urethral opening and advanced ~7-8 cm into the urethra. A syringe attached to the feeding tube was used to apply mild negative pressure to collect sperm. Semen samples were successfully collected on all four attempts. Sperm characteristics ranged as follows: 10.5-26.0 × 106 sperm/ml concentration, 50-90% motility and 36-61% normal sperm morphology. This is the first report of the use of UC as a potential alternative to EE in the BFF, a more field-friendly technique that is less invasive and more consistent for obtaining samples free of urine contamination.

The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis.

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.

De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis).

The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 ×) and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon-gene models derived from 9805 full-length open reading frames (FL-ORFs) constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology.