The sixth rhino: a taxonomic re-assessment of the critically endangered northern white rhinoceros

Ethical Analysis of the Application of Assisted Reproduction Technologies in Biodiversity Conservation and the Case of White Rhinoceros (Ceratotherium simum) Ovum Pick-Up Procedures

Originally applied on domestic and lab animals, assisted reproduction technologies (ARTs) have also found application in conservation breeding programs, where they can make the genetic management of populations more efficient, and increase the number of individuals per generation. However, their application in wildlife conservation opens up new ethical scenarios that have not yet been fully explored. This study presents a frame for the ethical analysis of the application of ART procedures in conservation based on the Ethical Matrix (EM), and discusses a specific case study—ovum pick-up (OPU) procedures performed in the current conservation efforts for the northern white rhinoceros (Ceratotherium simum cottoni)—providing a template for the assessment of ART procedures in projects involving other endangered species.

Naïve-like pluripotency to pave the way for saving the northern white rhinoceros from extinction

The northern white rhinoceros (NWR) is probably the earth's most endangered mammal. To rescue the functionally extinct species, we aim to employ induced pluripotent stem cells (iPSCs) to generate gametes and subsequently embryos in vitro. To elucidate the regulation of pluripotency and differentiation of NWR PSCs, we generated iPSCs from a deceased NWR female using episomal reprogramming, and observed surprising similarities to human PSCs. NWR iPSCs exhibit a broad differentiation potency into the three germ layers and trophoblast, and acquire a naïve-like state of pluripotency, which is pivotal to differentiate PSCs into primordial germ cells (PGCs). Naïve culturing conditions induced a similar expression profile of pluripotency related genes in NWR iPSCs and human ESCs. Furthermore, naïve-like NWR iPSCs displayed increased expression of naïve and PGC marker genes, and a higher integration propensity into developing mouse embryos. As the conversion process was aided by ectopic BCL2 expression, and we observed integration of reprogramming factors, the NWR iPSCs presented here are unsuitable for gamete production. However, the gained insights into the developmental potential of both primed and naïve-like NWR iPSCs are fundamental for in future PGC-specification in order to rescue the species from extinction using cryopreserved somatic cells.

Individuality, species-specific features, and female discrimination of male southern white rhinoceros courtship calls

Male vocalizations associated with courtship can play a key role in mate selection. They may help females obtain information about males' quality and identity and/or may contain species-specific properties that help prevent interspecies breeding. Despite vocalizations being a prominent part of the courtship of white rhinos, the role that they play in white rhino breeding behaviour has not been extensively studied. Both southern (SWR) and critically endangered northern white rhino (NWR) males intensively vocalize during courtship with hic calls. We examined these calls and found that call properties differed between NWR and SWR males. In addition, we found that individual SWR males could be identified with a high degree of accuracy using their hic calls and that the signature information capacity in hic calls would allow females to individually recognize about 11 adult males living in or moving through their home-ranges, which may help with mate selection. Then, we conducted playback experiments with wild anoestrus SWR females. The females discriminated between the NWR and SWR hic calls and between the SWR hic and SWR pant calls. However, we only found differences in the latency of observed behaviours, not in their duration or in the intensity of females' reaction. This might suggest that females which are not in oestrus are not highly responsive to a male's motivation (i.e., seeking contact or mating), but are more interested in assessing his dominance status or familiarity. Ultimately, our results indicate that courtship hic calls encode information which might help females choose mating partners.

Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros

Africa's black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa's Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.

A Model for Dental Age Verification Using Ultrastructural Imaging for Modern and Fossil Representatives of the Rhinocerotidae Family

The analyses were performed on a right third premolar (P₃) of a white rhinoceros female (Ceratotherium simum, Burchell 1817). The specimen was born in captivity at London Zoo (Zoological Society of London), then in the 1970s transferred to Kiev Zoo (Peremohy Avenue), Ukraine, and was kept there until it died at a documented chronological age of 48 years. The female died because of its age, which indicates it was kept in good conditions adequate to the requirements of this species. Photographs and micrographs with radiological documentation were taken on the said tooth. Its structural characteristics were determined, and on the occlusal surface areas and points of anatomical constitution of its crown were identified. The tooth was also histologically evaluated via sections taken horizontally in a mesial-distal plane through the crown, horizontally in a mesial-distal plane through the coronal portion of the root, and longitudinally in a lingual-buccal plane through the crown and the root. Preparations with ground sections were made and observed in white, polarized, and reflected light. In the subsequent stage X-ray and SEM imaging has also been used, for analysis of the distribution of annual growth layers of mineralized dental tissues of cement and dentine, counted from the root canal center to the buccal surface. An attempt was also made to confirm the annual season in which the animal died, based on cement growth lines. It was observed that the growth lines were visible in all the analyzed sections, in dentine and cement. In the cement, the lines were relatively few and did not represent the attested age of the animal. The analysis of the coloration of the cement lines indicated that the animal was regularly fed a diet that was not seasonally differentiated. From the X-ray examination comes a conclusion that the animal did not suffer from periodontal diseases. Visible growth lines were observed on the dentine. On the horizontal section through the crown growth lines in the dentine were few and unclear. On the longitudinal section, both on the caudal and rostral roots, these lines were clearly visible and much more numerous than expected considering the known age of the animal, as more than 50 were counted. On horizontal sections through the upper part of both roots, distinct growth lines were observed in the dentine, and their number-48 for both roots-corresponded precisely to the age of the animal. The results of our study indicate that this method has significant potential for application to verify the age at death for modern and fossil representatives of rhinoceros.

Rewinding Extinction in the Northern White Rhinoceros: Genetically Diverse Induced Pluripotent Stem Cell Bank for Genetic Rescue

Extinction rates are rising, and current conservation technologies may not be adequate for reducing species losses. Future conservation efforts may be aided by the generation of induced pluripotent stem cells (iPSCs) from highly endangered species. Generation of a set of iPSCs from multiple members of a species can capture some of the dwindling genetic diversity of a disappearing species. We generated iPSCs from fibroblasts cryopreserved in the Frozen Zoo^®: nine genetically diverse individuals of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni) and two from the closely related southern white rhinoceros (Ceratotherium simum simum). We used a nonintegrating Sendai virus reprogramming method and developed analyses to confirm the cells' pluripotency and differentiation potential. This work is the first step of a long-term interdisciplinary plan to apply assisted reproduction techniques to the conservation of this highly endangered species. Advances in iPSC differentiation may enable generation of gametes in vitro from deceased and nonreproductive individuals that could be used to repopulate the species.

An Ethical Assessment Tool (ETHAS) to Evaluate the Application of Assisted Reproductive Technologies in Mammals' Conservation: The Case of the Northern White Rhinoceros (Ceratotherium simum cottoni)

Assisted reproductive technologies (ARTs) can make a difference in biodiversity conservation. Their application, however, can create risks and raise ethical issues that need addressing. Unfortunately, there is a lack of attention to the topic in the scientific literature and, to our knowledge, there is no tool for the ethical assessment of ARTs in the context of conservation that has been described. This paper reports the first applications of the Ethical Assessment Tool (ETHAS) to trans-rectal ovum pick-up (OPU) and in vitro fertilization (IVF) procedures used in a northern white rhinoceros (Ceratotherium simum cottoni) conservation project. The ETHAS consists of two checklists, the Ethical Evaluation Sheet and the Ethical Risk Assessment, and is specifically customized for each ART procedure. It provides an integrated, multilevel and standardized self-assessment of the procedure under scrutiny, generating an ethical acceptability ranking (totally, partially, not acceptable) and a risk rank (low, medium, high), and, hence, allows for implementing measures to address or manage issues beforehand. The application of the ETHAS to the procedures performed on the northern white rhinoceros was effective in ensuring a high standard of procedures, contributing to the acceptability and improved communication among the project's partners. In turn, the tool itself was also refined through an iterative consultation process between experts and stakeholders.

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results.

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells

The critically endangered northern white rhinoceros is believed to be extinct in the wild, with the recent death of the last male leaving only two remaining individuals in captivity. Its extinction would appear inevitable, but the development of advanced cell and reproductive technologies such as cloning by nuclear transfer and the artificial production of gametes via stem cells differentiation offer a second chance for its survival. In this work, we analyzed genome-wide levels of genetic diversity, inbreeding, population history, and demography of the white rhinoceros sequenced from cryopreserved somatic cells, with the goal of informing how genetically valuable individuals could be used in future efforts toward the genetic rescue of the northern white rhinoceros. We present the first sequenced genomes of the northern white rhinoceros, which show relatively high levels of heterozygosity and an average genetic divergence of 0.1% compared with the southern subspecies. The two white rhinoceros subspecies appear to be closely related, with low genetic admixture and a divergent time <80,000 yr ago. Inbreeding, as measured by runs of homozygosity, appears slightly higher in the southern than the northern white rhinoceros. This work demonstrates the value of the northern white rhinoceros cryopreserved genetic material as a potential gene pool for saving this subspecies from extinction.

Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview

We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of 'orthodox' taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen-based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of 'utilizers' such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported 'taxonomic inflation' has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.

Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae

Background

Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus.

Methods

ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods.

Results

Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species.

Discussion

The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.

Rewinding the process of mammalian extinction

With only three living individuals left on this planet, the northern white rhinoceros (Ceratotherium simum cottoni) could be considered doomed for extinction. It might still be possible, however, to rescue the (sub)species by combining novel stem cell and assisted reproductive technologies. To discuss the various practical options available to us, we convened a multidisciplinary meeting under the name "Conservation by Cellular Technologies." The outcome of this meeting and the proposed road map that, if successfully implemented, would ultimately lead to a self-sustaining population of an extremely endangered species are outlined here. The ideas discussed here, while centered on the northern white rhinoceros, are equally applicable, after proper adjustments, to other mammals on the brink of extinction. Through implementation of these ideas we hope to establish the foundation for reversal of some of the effects of what has been termed the sixth mass extinction event in the history of Earth, and the first anthropogenic one. Zoo Biol. 35:280-292, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.

Sex and species recognition by wild male southern white rhinoceros using contact pant calls

Recognition of information from acoustic signals is crucial in many animals, and individuals are under selection pressure to discriminate between the signals of conspecifics and heterospecifics or males and females. Here, we first report that rhinos use information encoded in their calls to assess conspecifics and individuals of closely related species. The southern (Ceratotherium simum) and critically endangered northern (C. cottoni) white rhinos are the most social out of all the rhinoceros species and use a contact call pant. We found that southern white rhino pant calls provide reliable information about the caller's sex, age class and social situation. Playback experiments on wild territorial southern white rhinoceros males revealed that they responded more strongly to the pant calls of conspecific females compared to the calls of other territorial males. This suggests that pant calls are more important form of communication between males and females than between territorial males. Territorial southern males also discriminated between female and territorial male calls of northern species and reacted more intensively to the calls of northern than southern males. This might be caused by a novelty effect since both species naturally live in allopatry. We conclude that white rhinos can directly benefit from assessing individuals at long distances using vocal cues especially because their eyesight is poor. Pant calls thus likely play a significant role in their social relationships and spatial organization. In addition, better understanding of vocal communication in white rhinos might be helpful in conservation management particularly because of their low reproduction in captivity.

Discrimination of familiarity and sex from chemical cues in the dung by wild southern white rhinoceros

Communication in rhinos is primarily mediated by the vocal and olfactory signals as they have relatively poor eyesight. White rhinos are the most social of all the rhinoceros species, they defecate at common dungheaps and the adult bulls use dung and urine to mark their territory. Chemical communication may therefore be particularly important in the social interactions of white rhinos, and its knowledge could be very helpful in their management and conservation. However, no studies have investigated up until now the olfactory discrimination in any rhinoceros species in the wild. We have experimentally studied the reactions of the wild southern white rhinos (Ceratotherium simum) to the dung of familiar and unfamiliar adult females and adult territorial males. We registered the number of sniffing events, the duration of sniffing and the latency of the vigilance posture from the onset of sniffing. The dung of unfamiliar rhinos was sniffed longer than that of familiar rhinos. The rhinos showed a shorter latency of vigilance posture to the familiar dung of males than that of females. For unfamiliar dung, they displayed a shorter latency of vigilance posture to female than male dung. Our results indicate that the rhinos are able to discriminate the familiarity and sex of conspecifics from the smell of their dung. Olfactory cues could therefore play an important role in the social relationships and spatial organization of the southern white rhinoceros.

Contact calls of the northern and southern white rhinoceros allow for individual and species identification

Inter-individual relationships particularly in socially living mammals often require a well-developed communication system. Vocal and olfactory signals are the most important for the communication of rhinos, however, their vocal communication has been investigated to a very limited extent so far. White rhinos have the most developed social system out of all the rhinoceros species and vocal signals might therefore play an important role in their social interactions. We recorded repetitive contact pant calls from six captive northern white rhinos (Ceratotherium cottoni) and 14 captive and free-ranging southern white rhinos (Ceratotherium simum) and examined if they transmit information about individual identity, species, social context and age class. Discriminant analyses revealed that a high percentage of the pant calls of both species could be classified to a correct individual. We calculated signature information capacity of pant calls recorded from adult animals in isolation at 3.19 bits for the northern white rhinos and at 3.15 bits for the southern white rhinos, which can potentially allow for a vocal discrimination of nine individuals of both species. We found that pant calls varied by species. Northern white rhinos had longer calls and also differed from the southern white rhinos in several frequency parameters of their calls. We also analysed the pant calls of southern white rhinos for the differences between the age classes and between social contexts in which they were recorded. Our results show that pant calls carry information about individual, species, age class and context. The ability to recognize this information would allow rhinos, in addition to olfactory cues, to communicate with highly increased accuracy. A better understanding of communication of white rhinos has potential practical use in their management and conservation particularly because of the low breeding success of white rhinos in captivity.

Detecting inter-cusp and inter-tooth wear patterns in rhinocerotids

Extant rhinos are the largest extant herbivores exhibiting dietary specialisations for both browse and grass. However, the adaptive value of the wear-induced tooth morphology in rhinos has not been widely studied, and data on individual cusp and tooth positions have rarely been published. We evaluated upper cheek dentition of browsing Diceros bicornis and Rhinoceros sondaicus, mixed-feeding R. unicornis and grazing Ceratotherium simum using an extended mesowear method adapted for rhinos. We included single cusp scoring (EM(R)-S) to investigate inter-cusp and inter-tooth wear patterns. In accordance with previous reports, general mesowear patterns in D. bicornis and R. sondaicus were attrition-dominated and C. simum abrasion-dominated, reflecting their respective diets. Mesowear patterns for R. unicornis were more attrition-dominated than anticipated by the grass-dominated diet, which may indicate a low intake of environmental abrasives. EM(R)-S increased differentiation power compared to classical mesowear, with significant inter-cusp and inter-tooth differences detected. In D. bicornis, the anterior cusp was consistently more abrasion-dominated than the posterior. Wear differences in cusp position may relate to morphological adaptations to dietary regimes. Heterogeneous occlusal surfaces may facilitate the comminution of heterogeneous browse, whereas uniform, broad grinding surfaces may enhance the comminution of physically more homogeneous grass. A negative tooth wear gradient was found in D. bicornis, R. sondaicus and R. unicornis, with wear patterns becoming less abrasion-dominated from premolars to molars. No such gradients were evident in C. simum which displayed a uniform wear pattern. In browsers, premolars may be exposed to higher relative grit loads, which may result in the development of wear gradients. The second premolar may also have a role in food cropping. In grazers, high absolute amounts of ingested abrasives may override other signals, leading to a uniform wear pattern and dental function along the tooth row, which could relate to the observed evolution towards homodonty.

Genetics and the last stand of the Sumatran rhinoceros Dicerorhinus sumatrensis

The Sumatran rhinoceros Dicerorhinus sumatrensis is on the brink of extinction. Although habitat loss and poaching were the reasons of the decline, today's reproductive isolation is the main threat to the survival of the species. Genetic studies have played an important role in identifying conservation priorities, including for rhinoceroses. However, for a species such as the Sumatran rhinoceros, where time is of the essence in preventing extinction, to what extent should genetic and geographical distances be taken into account in deciding the most urgently needed conservation interventions? We propose that the populations of Sumatra and Borneo be considered as a single management unit.