Neotropical mammal responses to megafires in the Brazilian Pantanal

The increasing frequency and severity of human-caused fires likely have deleterious effects on species distribution and persistence. In 2020, megafires in the Brazilian Pantanal burned 43% of the biome's unburned area and resulted in mass mortality of wildlife. We investigated changes in habitat use or occupancy for an assemblage of eight mammal species in Serra do Amolar, Brazil, following the 2020 fires using a pre- and post-fire camera trap dataset. Additionally, we estimated the density for two naturally marked species, jaguars Panthera onca and ocelots Leopardus pardalis. Of the eight species, six (ocelots, collared peccaries Dicotyles tajacu, giant armadillos Priodontes maximus, Azara's agouti Dasyprocta azarae, red brocket deer Mazama americana, and tapirs Tapirus terrestris) had declining occupancy following fires, and one had stable habitat use (pumas Puma concolor). Giant armadillo experienced the most precipitous decline in occupancy from 0.431 ± 0.171 to 0.077 ± 0.044 after the fires. Jaguars were the only species with increasing habitat use, from 0.393 ± 0.127 to 0.753 ± 0.085. Jaguar density remained stable across years (2.8 ± 1.3, 3.7 ± 1.3, 2.6 ± 0.85/100 km2), while ocelot density increased from 13.9 ± 3.2 to 16.1 ± 5.2/100 km2. However, the low number of both jaguars and ocelots recaptured after the fire period suggests that immigration may have sustained the population. Our results indicate that the megafires will have significant consequences for species occupancy and fitness in fire-affected areas. The scale of megafires may inhibit successful recolonization, thus wider studies are needed to investigate population trends.

The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves

Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.

Overcoming racism in the twin spheres of conservation science and practice

It is time to acknowledge and overcome conservation's deep-seated systemic racism, which has historically marginalized Black, Indigenous and people of colour (BIPOC) communities and continues to do so. We describe how the mutually reinforcing ‘twin spheres’ of conservation science and conservation practice perpetuate this systemic racism. We trace how institutional structures in conservation science (e.g. degree programmes, support and advancement opportunities, course syllabuses) can systematically produce conservation graduates with partial and problematic conceptions of conservation's history and contemporary purposes. Many of these graduates go on to work in conservation practice, reproducing conservation's colonial history by contributing to programmes based on outmoded conservation models that disproportionately harm rural BIPOC communities and further restrict access and inclusion for BIPOC conservationists. We provide practical, actionable proposals for breaking vicious cycles of racism in the system of conservation we have with virtuous cycles of inclusion, equality, equity and participation in the system of conservation we want.

Effects of publication bias on conservation planning

Conservation planners need reliable information on spatial patterns of biodiversity. However, existing data sets are skewed because some ecosystems, taxa, and locations are underrepresented. We determined how many articles have been published in recent decades on the biodiversity of different countries and their constituent provinces. We searched the Web of Science catalogues Science Citation Index (SCI) and Social Science Citation Index (SSCI) for biodiversity-related articles published from 1993 to 2016 that included country and province names. We combined data on research publication frequency with other provincial-scale factors hypothesized to affect the likelihood of research activity (i.e., economic development, human presence, infrastructure, and remoteness). Areas that appeared understudied relative to the biodiversity expected based on site climate likely have been inaccessible to researchers for reasons, notably armed conflict. Geographic publication bias is of most concern in the most remote areas of sub-Saharan Africa and South America. Our provincial-scale model may help compensate for publication biases in conservation planning by revealing the spatial extent of research needs and the low cost of redoing this analysis annually.

Foraging ecology of African wolves (Canis lupaster) and its implications for the conservation of Ethiopian wolves (Canis simensis)

African wolves (AWs) are sympatric with endangered Ethiopian wolves (EWs) in parts of their range. Scat analyses have suggested a dietary overlap between AWs and EWs, raising the potential for exploitative competition, and a possible conservation threat to EWs. However, in contrast to that of the well-studied EW, the foraging ecology of AWs remains poorly characterized. Accordingly, we studied the foraging ecology of radio-collared AWs (n = 11 individuals) at two localities with varying levels of anthropogenic disturbance in the Ethiopian Highlands, the Guassa-Menz Community Conservation Area (GMCCA) and Borena-Saynt National Park (BSNP), accumulating 845 h of focal observation across 2952 feeding events. We also monitored rodent abundance and rodent trapping activity by local farmers who experience conflict with AWs. The AW diet consisted largely of rodents (22.0%), insects (24.8%), and goats and sheep (24.3%). Of the total rodents captured by farmers using local traps during peak barley production (July to November) in GMCCA, averaging 24.7 ± 8.5 rodents/hectare/day, 81% (N = 3009) were scavenged by AWs. Further, of all the rodents consumed by AWs, most (74%) were carcasses. These results reveal complex interactions between AWs and local farmers, and highlight the scavenging niche occupied by AWs in anthropogenically altered landscapes in contrast to the active hunting exhibited by EWs in more intact habitats. While AWs cause economic damage to local farmers through livestock predation, they appear to play an important role in scavenging pest rodents among farmlands, a pattern of behaviour which likely mitigates direct and indirect competition with EWs. We suggest two routes to promote the coexistence of AWs and EWs in the Ethiopian highlands: local education efforts highlighting the complex role AWs play in highland ecosystems to reduce their persecution, and enforced protection of intact habitats to preserve habitat preferred by EWs.

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads

Background

A high-quality reference genome assembly is a valuable tool for the study of non-model organisms. Genomic techniques can provide important insights about past population sizes and local adaptation and can aid in the development of breeding management plans. This information is important for fields such as conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets.

Findings

Here, we report the generation of high-quality reference genomes for the African wild dog (Lycaon pictus) at a low cost (<$3000), thereby facilitating future studies of this endangered canid. We generated assemblies for three individuals using the linked-read 10x Genomics Chromium system. The most continuous assembly had a scaffold and contig N50 of 21 Mb and 83 Kb, respectively, and completely reconstructed 95% of a set of conserved mammalian genes. Additionally, we estimate the heterozygosity and demographic history of African wild dogs, revealing that although they have historically low effective population sizes, heterozygosity remains high.

Conclusions

We show that 10x Genomics Chromium data can be used to effectively generate high-quality genomes from Illumina short-read data of intermediate coverage (∼25x–50x). Interestingly, the wild dog shows higher heterozygosity than other species of conservation concern, possibly due to its behavioral ecology. The availability of reference genomes for non-model organisms will facilitate better genetic monitoring of threatened species such as the African wild dog and help conservationists to better understand the ecology and adaptability of those species in a changing environment.

Rabies and Distemper Outbreaks in Smallest Ethiopian Wolf Population

Widespread deaths recently devastated the smallest known population of Ethiopian wolves. Of 7 carcasses found, all 3 tested were positive for rabies. Two wolves were subsequently vaccinated for rabies; 1 of these later died from canine distemper. Only 2 of a known population of 13 wolves survived.

Competition between sympatric wolf taxa: an example involving African and Ethiopian wolves

Carnivore populations are declining globally due to range contraction, persecution and prey depletion. One consequence of these patterns is increased range and niche overlap with other carnivores, and thus an elevated potential for competitive exclusion. Here, we document competition between an endangered canid, the Ethiopian wolf (EW), and the newly discovered African wolf (AW) in central Ethiopia. The diet of the ecological specialist EW was dominated by rodents, whereas the AW consumed a more diverse diet also including insects and non-rodent mammals. EWs used predominantly intact habitat, whereas AWs used mostly areas disturbed by humans and their livestock. We observed 82 encounters between the two species, of which 94% were agonistic. The outcomes of agonistic encounters followed a territory-specific dominance pattern, with EWs dominating in intact habitat and AWs in human-disturbed areas. For AWs, the likelihood of winning encounters also increased with group size. Rodent species consumed by EWs were also available in the human-disturbed areas, suggesting that these areas could be suitable habitat for EWs if AWs were not present. Increasing human encroachment not only affects the prey base of EWs, but also may impact their survival by intensifying competition with sympatric AWs.

An interdisciplinary review of current and future approaches to improving human-predator relations

In a world of shrinking habitats and increasing competition for natural resources, potentially dangerous predators bring the challenges of coexisting with wildlife sharply into focus. Through interdisciplinary collaboration among authors trained in the humanities, social sciences, and natural sciences, we reviewed current approaches to mitigating adverse human-predator encounters and devised a vision for future approaches to understanding and mitigating such encounters. Limitations to current approaches to mitigation include too much focus on negative impacts; oversimplified equating of levels of damage with levels of conflict; and unsuccessful technical fixes resulting from failure to engage locals, address hidden costs, or understand cultural (nonscientific) explanations of the causality of attacks. An emerging interdisciplinary literature suggests that to better frame and successfully mitigate negative human-predator relations conservation professionals need to consider dispensing with conflict as the dominant framework for thinking about human-predator encounters; work out what conflicts are really about (they may be human-human conflicts); unravel the historical contexts of particular conflicts; and explore different cultural ways of thinking about animals. The idea of cosmopolitan natures may help conservation professionals think more clearly about human-predator relations in both local and global context. These new perspectives for future research practice include a recommendation for focused interdisciplinary research and the use of new approaches, including human-animal geography, multispecies ethnography, and approaches from the environmental humanities notably environmental history. Managers should think carefully about how they engage with local cultural beliefs about wildlife, work with all parties to agree on what constitutes good evidence, develop processes and methods to mitigate conflicts, and decide how to monitor and evaluate these. Demand for immediate solutions that benefit both conservation and development favors dispute resolution and technical fixes, which obscures important underlying drivers of conflicts. If these drivers are not considered, well-intentioned efforts focused on human-wildlife conflicts will fail.

Phylogenetic evidence for the ancient Himalayan wolf: towards a clarification of its taxonomic status based on genetic sampling from western Nepal

Wolves in the Himalayan region form a monophyletic lineage distinct from the present-day Holarctic grey wolf Canis lupus spp. (Linnaeus 1758) found across Eurasia and North America. Here, we analyse phylogenetic relationships and the geographic distribution of mitochondrial DNA haplotypes of the contemporary Himalayan wolf (proposed in previous studies as Canis himalayensis) found in Central Asia. We combine genetic data from a living Himalayan wolf population collected in northwestern Nepal in this study with already published genetic data, and confirm the Himalayan wolf lineage based on mitochondrial genomic data (508 bp cytochrome b and 242 bp D-loop), and X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences. We then compare the genetic profile of the Himalayan wolf lineage found in northwestern Nepal with canid reference sequences from around the globe with maximum likelihood and Bayesian phylogeny building methods to demonstrate that the Himalayan wolf forms a distinct monophyletic clade supported by posterior probabilities/bootstrap for D-loop of greater than 0.92/85 and cytochrome b greater than 0.99/93. The Himalayan wolf shows a unique Y-chromosome (ZFY) haplotype, and shares an X-chromosome haplotype (ZFX) with the newly postulated African wolf. Our results imply that the Himalayan wolf distribution range extends from the Himalayan range north across the Tibetan Plateau up to the Qinghai Lakes region in Qinghai Province in the People's Republic of China. Based on its phylogenetic distinction and its older age of divergence relative to the Holarctic grey wolf, the Himalayan wolf merits formal classification as a distinct taxon of special conservation concern.

Ecological role of the giant root-rat (Tachyoryctes macrocephalus) in the Afroalpine ecosystem

Rodents with prevailing subterranean activity usually play an important role in the ecosystems of which they are a part due to the combined effect of herbivory and soil perturbation. This is the case for the giant root-rat Tachyoryctes macrocephalus endemic to the Afroalpine ecosystem of the Bale Mountains, Ethiopia. We studied the impact of root-rats on various ecosystem features within a 3.5-ha study locality dominated by Alchemilla pasture, which represents an optimal habitat for this species, in 2 periods of a year. The root-rats altered plant species composition, reducing the dominant forb, Alchemilla abyssinica, while enhancing Salvia merjame and a few other species, and reduced vegetation cover, but not the fresh plant biomass. Where burrows were abandoned by root-rats, other rodents took them over and A. abyssinica increased again. Root-rat burrowing created small-scale heterogeneity in soil compactness due to the backfilling of some unused burrow segments. Less compacted soil tended to be rich in nutrients, including carbon, nitrogen and phosphorus, which likely affected the plant growth on sites where the vegetation has been reduced as a result of root-rat foraging and burrowing.

Feasibility and efficacy of oral rabies vaccine SAG2 in endangered Ethiopian wolves

Diseases are a major cause of population declines in endangered populations of several canid species. Parenteral vaccination efforts to protect Ethiopian wolves (Canis simensis) from rabies have targeted the domestic dog reservoir, or the wolves themselves in response to confirmed outbreaks. Oral vaccination offers a more cost-efficient, safe and proactive approach to protect Ethiopian wolves and other threatened canids from rabies. Field trials of the oral vaccine Rabigen® SAG2Dog were undertaken in the Bale Mountains of southeastern Ethiopia. Four different bait types and three delivery methods were tested in twelve Ethiopian wolf packs, and the oral vaccine (using the preferred bait) was trialled in three packs. Vaccine uptake and immunization rates were measured through direct observations and in live-trapped animals through the assessment of biomarker levels and serological status. Commercial baits were never taken by wolves; goat meat baits had the highest uptake, compared to rodent and intestine baits. Targeted delivery from horseback and nocturnal delivery within a pack's territory performed favourably compared to random bait distribution. Bait uptake by non-target species was lowest during the nocturnal blind distribution. Of 21 wolves trapped after vaccination, 14 were positive for the biomarker iophenoxic acid (i.e. ingested the bait and most likely pierced the sachet with the vaccine). Of these, 86% (n=12/14) had levels considered sufficient to provide protective immunity to wildlife (⩾0.20IU/ml), and 50% (n=7/14) demonstrated antibody titres above the universally recognised threshold (⩾0.5IU/ml) -the baseline average was 0.09IU/ml (n=12 wolves). All but one of the wolves vaccinated in 2014 were alive 14months later. Our trials confirm the potential for SAG2, delivered in a goat meat bait, to effectively protect Ethiopian wolves against rabies, supporting the initiative for a more efficient and proactive approach to manage and eventually eliminate rabies in Ethiopian wolf populations.

Spatial organization of the pale fox in the Termit Massif of east Niger

Pale foxes ( Vulpes pallida ) have a widespread distribution across the Saharan-Sahel in northern Africa, but little is known about their ecology and natural history. Here, we provide the 1st ecological information on the species. We captured and radio-collared 10 pale foxes in the Termit & Tin Toumma National Nature and Cultural Reserve of east Niger. The adult body mass (1.20 ± SD 0.18kg, n = 6) was about half of what was previously reported, confirming this species as one of the smallest canids in the world. Body measurements were relatively similar between sexes, suggesting little if any sexual dimorphism. Mean ± SD home range size ( n = 6) was 6.79±3.58 km 2 using 100% minimum convex polygon and 5.62±3.11 km 2 using 95% fixed kernel density estimator. Overlap between adjacent pale fox ranges was generally low (mean overlap index = 0.11±0.22), with nearly exclusive core areas (mean overlap index = 0.02±0.06), suggesting pale foxes are territorial. Overall, the spatial ecology of pale foxes showed similar characteristics to other Vulpes species, especially those inhabiting arid and semiarid environments.

Canine distemper in endangered Ethiopian wolves

Investigation into mortalities within endangered species can direct conservation efforts.

The Ethiopian wolf (Canis simensis) is the world’s rarest canid; ≈500 wolves remain. The largest population is found within the Bale Mountains National Park (BMNP) in southeastern Ethiopia, where conservation efforts have demonstrated the negative effect of rabies virus on wolf populations. We describe previously unreported infections with canine distemper virus (CDV) among these wolves during 2005–2006 and 2010. Death rates ranged from 43% to 68% in affected subpopulations and were higher for subadult than adult wolves (83%–87% vs. 34%–39%). The 2010 CDV outbreak started 20 months after a rabies outbreak, before the population had fully recovered, and led to the eradication of several focal packs in BMNP’s Web Valley. The combined effect of rabies and CDV increases the chance of pack extinction, exacerbating the typically slow recovery of wolf populations, and represents a key extinction threat to populations of this highly endangered carnivore.

The physiology of cooperative breeding in a rare social canid; sex, suppression and pseudopregnancy in female Ethiopian wolves

Ethiopian wolves, Canis simensis, differ from other cooperatively breeding canids in that they combine intense sociality with solitary foraging, making them a suitable species in which to study the physiology of cooperative breeding. The reproductive physiology of twenty wild female Ethiopian wolves (eleven dominant and nine subordinate) in Ethiopia's Bale Mountains National Park was studied non-invasively through the extraction and assaying of estradiol, progesterone and glucocorticoids in collected fecal samples using enzyme and radioimmunoassays. All dominant females showed increased estradiol concentrations and/or mating behavior during the annual mating season. In contrast, none of the subordinate females showed increased estradiol concentrations or mating behavior during the mating season. However, two subordinate females came into estrus outside of the mating season. Both dominant and subordinate females had higher average progesterone concentrations during the dominant female's pregnancy than at other times of the year, and two subordinate females allosuckled the dominant female's pups. No statistically significant differences in glucocorticoid concentrations were found between dominant and subordinate females. These results suggest that subordinate females are reproductively suppressed during the annual mating season, but may ovulate outside of the mating season and become pseudopregnant. No evidence was found to suggest that reproductive suppression in subordinate females was regulated through aggressive behaviors, and no relationship was found between fecal glucocorticoids and dominance status.

Sex, stress and social status: patterns in fecal testosterone and glucocorticoid metabolites in male Ethiopian wolves

Ethiopian wolves, Canis simensis, live in large multi-male family packs, where males are philopatric and do not disperse. Within a pack, mating and breeding is largely monopolized by the dominant male and female, although extra-pack copulations are common, and subordinate males may sire pups in neighboring packs. Regardless of paternity, all males in a pack help rear the pups. We non-invasively studied patterns in fecal testosterone and glucocorticoid metabolite concentrations using radioimmunoassays of fecal samples collected from nine wild male Ethiopian wolves between August 2007 and February 2008. We tested the predictions of the Challenge Hypothesis, namely that fecal testosterone metabolite concentrations would be higher during the annual mating season, which is the portion of the reproductive cycle when mating and increased aggression typically occur, and lower when there were pups in the pack for which to care. Contrary to the predictions of the Challenge Hypothesis, we did not detect patterns in fecal testosterone metabolite concentrations associated with reproductive stage during our study period. Similarly, we found no patterns associated with reproductive stage in male fecal glucocorticoid metabolite concentrations. Dominant males had higher average fecal testosterone and glucocorticoid metabolite concentrations than did subordinates, which may be related to higher rates of aggression and mate guarding in dominant males of group-living canids, a pattern also reported in African wild dogs, Lycaon pictus.

Major histocompatibility complex diversity in the endangered Ethiopian wolf (Canis simensis)

The major histocompatibility complex (MHC) influences immune response to infection and vaccination. In most species, MHC genes are highly polymorphic, but few wild canid populations have been investigated. In Ethiopian wolves, we identified four DLA (dog leucocyte antigen)-DRB1, two DLA-DQA1 and five DQB1 alleles. Ethiopian wolves, the world's rarest canids with fewer than 500 animals worldwide, are further endangered and threatened by rabies. Major rabies outbreaks in the Bale Mountains of southern Ethiopia (where over half of the Ethiopian wolf population is located) have killed over 75% of wolves in the affected sub-populations. In 2004, following a rabies outbreak, 77 wolves were vaccinated, and 19 were subsequently recaptured to monitor the effectiveness of the intervention. Pre- and post-vaccination rabies antibody titres were available for 18 animals, and all of the animals sero-converted after vaccination. We compared the haplotype frequencies of this group of 18 with the post-vaccination antibody titre, and showed that one haplotype was associated with a lower response (uncorrected P < 0.03). In general, Ethiopian wolves probably have an adequate amount of MHC variation to ensure the survival of the species. However, we sampled only the largest Ethiopian wolf population in Bale, and did not take the smaller populations further north into consideration.

The cryptic African wolf: Canis aureus lupaster is not a golden jackal and is not endemic to Egypt

The Egyptian jackal (Canis aureus lupaster) has hitherto been considered a large, rare subspecies of the golden jackal (C. aureus). It has maintained its taxonomical status to date, despite studies demonstrating morphological similarities to the grey wolf (C. lupus). We have analyzed 2055 bp of mitochondrial DNA from C. a. lupaster and investigated the similarity to C. aureus and C. lupus. Through phylogenetic comparison with all wild wolf-like canids (based on 726 bp of the Cytochrome b gene) we conclusively (100% bootstrap support) place the Egyptian jackal within the grey wolf species complex, together with the Holarctic wolf, the Indian wolf and the Himalayan wolf. Like the two latter taxa, C. a. lupaster seems to represent an ancient wolf lineage which most likely colonized Africa prior to the northern hemisphere radiation. We thus refer to C. a. lupaster as the African wolf. Furthermore, we have detected C. a. lupaster individuals at two localities in the Ethiopian highlands, extending the distribution by at least 2,500 km southeast. The only grey wolf species to inhabit the African continent is a cryptic species for which the conservation status urgently needs assessment.

The impact of conservation on the status of the world's vertebrates

Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

Low-coverage vaccination strategies for the conservation of endangered species

The conventional objective of vaccination programmes is to eliminate infection by reducing the reproduction number of an infectious agent to less than one, which generally requires vaccination of the majority of individuals. In populations of endangered wildlife, the intervention required to deliver such coverage can be undesirable and impractical; however, endangered populations are increasingly threatened by outbreaks of infectious disease for which effective vaccines exist. As an alternative, wildlife epidemiologists could adopt a vaccination strategy that protects a population from the consequences of only the largest outbreaks of disease. Here we provide a successful example of this strategy in the Ethiopian wolf, the world's rarest canid, which persists in small subpopulations threatened by repeated outbreaks of rabies introduced by domestic dogs. On the basis of data from past outbreaks, we propose an approach that controls the spread of disease through habitat corridors between subpopulations and that requires only low vaccination coverage. This approach reduces the extent of rabies outbreaks and should significantly enhance the long-term persistence of the population. Our study shows that vaccination used to enhance metapopulation persistence through elimination of the largest outbreaks of disease requires lower coverage than the conventional objective of reducing the reproduction number of an infectious agent to less than one.