Genome sequence, population history, and pelage genetics of the endangered African wild dog (Lycaon pictus)

BACKGROUND: The African wild dog (Lycaon pictus) is an endangered sub-Saharan canid threatened by severe habitat fragmentation, human-wildlife conflict, and infectious disease. A highly specialized carnivore, it is distinguished by its social structure, dental morphology, absence of dewclaws, and colorful pelage. RESULTS: We sequenced the genomes of two individuals from populations representing two distinct ecological histories (Laikipia County, Kenya and KwaZulu-Natal Province, South Africa). We reconstructed population demographic histories for the two individuals and scanned the genomes for evidence of selection. CONCLUSIONS: We show that the African wild dog has undergone at least two effective population size reductions in the last one million years. We found evidence of Lycaon individual-specific regions of low diversity, suggestive of inbreeding or population-specific selection. Further research is needed to clarify whether these population reductions and low diversity regions are characteristic of the species as a whole. We documented positive selection on the Lycaon mitochondrial genome. Finally, we identified several candidate genes (ASIP, MITF, MLPH, PMEL) that may play a role in the characteristic Lycaon pelage

Space use of African wild dogs in relation to other large carnivores

Interaction among species through competition is a principle process structuring ecological communities, affecting behavior, distribution, and ultimately the population dynamics of species. High competition among large African carnivores, associated with extensive diet overlap, manifests in interactions between subordinate African wild dogs (Lycaon pictus) and dominant lions (Panthera leo) and spotted hyenas (Crocuta crocuta). Using locations of large carnivores in Hluhluwe-iMfolozi Park, South Africa, we found different responses from wild dogs to their two main competitors. Wild dogs avoided lions, particularly during denning, through a combination of spatial and temporal avoidance. However, wild dogs did not exhibit spatial or temporal avoidance of spotted hyenas, likely because wild dog pack sizes were large enough to adequately defend their kills. Understanding that larger carnivores affect the movements and space use of other carnivores is important for managing current small and fragmented carnivore populations, especially as reintroductions and translocations are essential tools used for the survival of endangered species, as with African wild dogs.The Smithsonian Institution Undersecretary for Science Endowment Funds, the American Zoo and Aquarium Association Conservation Endowment Fund, and Humboldt State University Sponsored Program Foundation (MSG); University of Pretoria, The Green Trust (WWFSA), and Bateleurs and Wildlife Conservation Trust (KZN) (MS); NRF, NSF, University of KwaZulu-Natal, Walt Disney Foundation and MGM, Wild about Cats, and Hluhluwe Tourism Association (RS); and THRIP (N. Ferguson) and Grand Hotel grants (C. Packer).http://www.plosone.orgam201

The curse of observer experience: Error in noninvasive genetic sampling.

Noninvasive genetic sampling (NGS) is commonly used to study elusive or rare species where direct observation or capture is difficult. Little attention has been paid to the potential effects of observer bias while collecting noninvasive genetic samples in the field, however. Over a period of 7 years, we examined whether different observers (n = 58) and observer experience influenced detection, amplification rates, and correct species identification of 4,836 gray wolf (Canis lupus) fecal samples collected in Idaho and Yellowstone National Park, USA and southwestern Alberta, Canada (2008-2014). We compared new observers (n = 33) to experienced observers (n = 25) and hypothesized experience level would increase the overall success of using NGS techniques in the wild. In contrast to our hypothesis, we found that new individuals were better than experienced observers at detecting and collecting wolf scats and correctly identifying wolf scats from other sympatric carnivores present in the study areas. While adequate training of new observers is crucial for the successful use of NGS techniques, attention should also be directed to experienced observers. Observer experience could be a curse because of their potential effects on NGS data quality arising from fatigue, boredom or other factors. The ultimate benefit of an observer to a project is a combination of factors (i.e., field savvy, local knowledge), but project investigators should be aware of the potential negative effects of experience on NGS sampling

An infectious disease and mortality survey in a population of free-ranging African wild dogs and sympatric domestic dogs

Disease can cause declines in wildlife populations and significantly threaten their survival. Recent expansion of human and domestic animal populations has made wildlife more susceptible to transmission of pathogens from domestic animal hosts. We conducted a pathogen surveillance and mortality survey for the population of African wild dogs (Lycaon pictus) in KwaZulu-Natal (KZN), South Africa, from January 2006–February 2007. Samples were obtained from 24 wild dogs for canine distemper virus (CDV) and canine parvovirus (CPV) serological testing. Data were collected on the presence of CDV, CPV, and rabies virus in the KZN domestic dog (Canis familiaris) population from 2004–06. The presence of these pathogens was confirmed in domestic dogs throughout KZN. Wild dogs exhibited 0% and 4.2% prevalence for CDV and CPV antibodies, respectively. In 2006 the largest wild dog pack in KZN was reduced from 26 individuals to a single animal; disease due to rabies virus was considered the most probable cause. This study provides evidence that CDV, CPV and rabies are potential threats to African wild dog conservation in KZN. The most economical and practical way to protect wild dogs from canine pathogens may be via vaccination of sympatric domestic dogs; however, such programmes are currently limited

Inbreeding, heterozygosity and fitness in a reintroduced population of endangered African wild dogs (Lycaon pictus)

It is crucial to understand the genetic health and implications of inbreeding in wildlife populations, especially of vulnerable species. Using extensive demographic and genetic data, we investigated the relationships among pedigree inbreeding coefficients, metrics of molecular heterozygosity and fitness for a large population of endangered African wild dogs (Lycaon pictus) in South Africa. Molecular metrics based on 19 microsatellite loci were significantly, but modestly correlated to inbreeding coefficients in this population. Inbred wild dogs with inbreeding coefficients of C0.25 and subordinate individuals had shorter lifespans than outbred and dominant contemporaries, suggesting some deleterious effects of inbreeding. However, this trend was confounded by packspecific effects as many inbred individuals originated from a single large pack. Despite wild dogs being endangered and existing in small populations, findings within our sample population indicated that molecular metrics were not robust predictors in models of fitness based on breeding pack formation, dominance, reproductive success or lifespan of individuals. Nonetheless, our approach has generated a vital database for future comparative studies to examine these relationships over longer periods of time. Such detailed assessments are essential given knowledge that wild canids can be highly vulnerable to inbreeding effects over a few short generations.This research was supported by the Smithsonian Institution Undersecretary for Science Endowment Fund, the University of Pretoria, Rotterdam Zoo Thandiza Fund, Humboldt State University Sponsored Program Foundation, Conservation Endowment Fund of the Association of Zoos and Aquariums, Disney Wildlife Conservation Fund, Knowsley Safari Park, DST-NRF Centre of Excellence for Invasion Biology, Khaki Fever Work Wear, Pittsburgh Zoo Conservation Fund and the Morris Animal Foundation. International travel was provided by British Airways

A survey of internal parasites in free-ranging African wild dogs (Lycaon pictus) from KwaZulu-Natal, South Africa

A study was undertaken between 1 January 2006 and 16 February 2007 to identify haemoparasites and gastrointestinal parasites infecting African wild dogs (Lycaon pictus) in KwaZulu-Natal (KZN) province, South Africa. Blood and faecal samples were opportunistically collected from wild dogs immobilized for collaring or translocation purposes (n = 24). Three common domestic canine gastrointestinal parasites, Toxocara canis, Dipylidium caninum and Ancylostoma spp., and two genera of canid protozoan GI parasites, Sarcocystis and Isospora, were identified in 12 fresh faecal samples. The seroprevalence of Ehrlichia canis from 24 individual serum samples analysed was 83%. However, only 21% of the 14 whole-blood smears evaluated for the presence of E. canis morulae within monocytes were positive. Twelve whole-blood smears were evaluated for the presence of Babesia canis trophozoites within erythrocytes and revealed 0% prevalence. Although there is currently no evidence of direct parasite-related mortality in the KZN population, the presence of internal parasites may be more detrimental to the overall health status of African wild dogs with immunosuppression as a result of other disease conditions, translocation stress, or inbreeding depression

Space Use of African Wild Dogs in Relation to Other Large Carnivores

<div><p>Interaction among species through competition is a principle process structuring ecological communities, affecting behavior, distribution, and ultimately the population dynamics of species. High competition among large African carnivores, associated with extensive diet overlap, manifests in interactions between subordinate African wild dogs (<i>Lycaon pictus</i>) and dominant lions (<i>Panthera leo</i>) and spotted hyenas (<i>Crocuta crocuta</i>). Using locations of large carnivores in Hluhluwe-iMfolozi Park, South Africa, we found different responses from wild dogs to their two main competitors. Wild dogs avoided lions, particularly during denning, through a combination of spatial and temporal avoidance. However, wild dogs did not exhibit spatial or temporal avoidance of spotted hyenas, likely because wild dog pack sizes were large enough to adequately defend their kills. Understanding that larger carnivores affect the movements and space use of other carnivores is important for managing current small and fragmented carnivore populations, especially as reintroductions and translocations are essential tools used for the survival of endangered species, as with African wild dogs.</p></div

Home ranges of African wild dogs, lions, and spotted hyenas during the (a) denning period, (b) post-denning period, and (c) non-denning period in 2004 in Hluhluwe-iMfolozi Park, South Africa.

<p>Home ranges of African wild dogs, lions, and spotted hyenas during the (a) denning period, (b) post-denning period, and (c) non-denning period in 2004 in Hluhluwe-iMfolozi Park, South Africa.</p

Mean percentage overlap (± SE) of (a) home ranges, (b) core use areas and (c) and volume of intersection (3-dimensional overlap) of home ranges of wild dogs with lions (n = 9) and spotted hyenas (n = 5) between periods in Hluhluwe-iMfolozi Park, South Africa, 2002–2004.

<p>Mean percentage overlap (± SE) of (a) home ranges, (b) core use areas and (c) and volume of intersection (3-dimensional overlap) of home ranges of wild dogs with lions (n = 9) and spotted hyenas (n = 5) between periods in Hluhluwe-iMfolozi Park, South Africa, 2002–2004.</p