Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

USE OF THE ZOOLOGICAL INFORMATION MANAGEMENT SYSTEM (ZIMS) DATABASE (2003-2023) FOR EVALUATION OF PRACTITIONER-SELECTED MELOXICAM DOSES AND THE RELATIONSHIP TO AVIAN TAXONOMY.

Meloxicam, a commonly used NSAID, has wide variation in pharmacokinetics between different avian species. The present study hypothesized that meloxicam dosage regimens were similar within, but differ between, groups of avian species with similar feeding habits, habitats, or migratory behaviors. Utilizing the international Zoological Information Management System (ZIMS), drug usage extracts were compiled for meloxicam across eleven major orders of birds. The orders were selected based on their prevalence in zoological collections, wildlife rehabilitation centers, the pet trade, and production environments. Each species with a record available in drug usage extracts was classified into broad categories of main habitat, diet, and migratory status. Significant patterns associated with habitat, diet, or migratory status were not identified statistically. An inverse relationship was identified statistically between the practitioner mg/kg dose and body weight in kg in birds that weigh approximately 20 kg or greater. This study includes practitioner-reported summary data of current doses used in the veterinary field to treat many different avian species. Adverse effects of meloxicam were recorded in <5% of individuals evaluated at the species level in this study.

GUT MICROBIOME DIVERSITY OF THREE RHINOCEROS SPECIES IN EUROPEAN ZOOS.

The wild rhinoceros populations have declined drastically in the past decades because the rhinoceros are heavily hunted for their horns. Zoological institutions aim to conserve rhinoceros populations in captivity, but one of the challenges of ex situ conservation is to provide food sources that resemble those available in the wild. Considering that the mammalian gut microbiota is a pivotal player in their host's health, the gut microbiota of rhinoceros may also play a role in the bioavailability of nutrients. Therefore, this study aims to characterize the fecal microbiome composition of grazing white rhinoceros (WR; Ceratotherium simum) and greater one-horned rhinoceros (GOHR; Rhinoceros unicornis) as well as the browsing black rhinoceros (BR; Diceros bicornis) kept in European zoos. Over the course of 1 yr, 166 fecal samples in total were collected from 9 BR (n = 39), 10 GOHR (n = 56), and 14 WR (n = 71) from 23 zoological institutions. The bacterial composition in the samples was determined using 16S rRNA gene Illumina sequencing. The fecal microbiomes of rhinoceros clustered by species, with BR clustering more distantly from GOHR and WR. Furthermore, the data report clustering of rhinoceros microbiota according to individual rhinoceros and institutional origin, showing that zoological institutions play a significant role in shaping the gut microbiome of rhinoceros species. In addition, BR exhibit a relatively higher microbial diversity than GOHR and WR. BR seem more susceptible to microbial gut changes and appear to have a more diverse microbiome composition among individuals than GOHR and WR. These data expand on the role of gut microbes and can provide baseline data for continued efforts in rhinoceros conservation and health status.

SARS-CoV-2 in lions, gorillas and zookeepers in the Rotterdam Zoo, the Netherlands, a One Health investigation, November 2021.

In November 2021, seven western lowland gorillas and four Asiatic lions were diagnosed with COVID-19 at Rotterdam Zoo. An outbreak investigation was undertaken to determine the source and extent of the outbreak and to identify possible transmission routes. Interviews were conducted with staff to identify human and animal contacts and cases, compliance with personal protective equipment (PPE) and potential transmission routes. Human and animal contacts and other animal species suspected to be susceptible to SARS-CoV-2 were tested for SARS-CoV-2 RNA. Positive samples were subjected to sequencing. All the gorillas and lions that could be tested (3/7 and 2/4, respectively) were RT-PCR positive between 12 November and 10 December 2021. No other animal species were SARS-CoV-2 RNA positive. Forty direct and indirect human contacts were identified. Two direct contacts tested RT-PCR positive 10 days after the first COVID-19 symptoms in animals. The zookeepers' viral genome sequences clustered with those of gorillas and lions. Personal protective equipment compliance was suboptimal at instances. Findings confirm transmission of SARS-CoV-2 among animals and between humans and animals but source and directionality could not be established. Zookeepers were the most likely source and should have periodic PPE training. Sick animals should promptly be tested and isolated/quarantined.

Serum 25(OH)D Analysis in Captive Pachyderms (Loxodonta africana, Elephas maximus, Diceros bicornis, Rhinoceros unicornis, Tapirus indicus) in Europe.

This study aimed to detect seasonal and species differences in serum 25-hydroxy vitamin D (25(OH)D) concentrations during summer and winter months in captive pachyderms in Europe. Both elephant species had low 25(OH)D while African elephants did not show a seasonal variation. Asian elephants had significantly higher 25(OH)D compared to their African counterparts but also did not show a seasonal difference. Both rhinoceros species investigated had higher 25(OH)D compared to both elephant species; the Indian rhinoceros had high circulating levels year-round, while the black rhinoceroses showed significantly lower 25(OH)D in winter. Malayan tapirs have very low 25(OH)D, comparable to horses. The higher 25(OH)D of elephants and rhinoceroses could indicate that elephants and rhinoceroses are capable of producing vitamin D. This might indicate that the Indian rhinoceroses are capable of producing enough endogenous vitamin D year-round at latitudes around 52° N, while both elephant species and the black rhinoceros are not. This study also showed that it is likely that both elephant species and rhinoceros species are capable of absorbing cholecalciferol from the digestive tract, according to the existing literature, while tapirs may not.

ONT read assembly of the black rhino genome.

OBJECTIVES: The black rhinoceros (Diceros bicornis) is an endangered mammal for which a captive breeding program is part of the conservation effort. Black rhinos in zoo's often suffer from chronic infections and heamochromatosis. Furthermore, breeding is hampered by low male fertility. To aid a research project studying these topics, we sequenced and assembled the genome of a captive male black rhino using ONT sequencing data only. DATA DESCRIPTION: This work produced over 100 Gb whole genome sequencing reads from whole blood. These were assembled into a 2.47 Gb draft genome consisting of 834 contigs with an N50 of 29.53 Mb. The genome annotation was lifted over from an available genome annotation for black rhino, which resulted in the retrieval of over 99% of gene features. This new genome assembly will be a valuable resource in for conservation genetic research in this species.