Genetic diversity and spatial genetic structure of African wild dogs (Lycaon pictus) in the Greater Limpopo transfrontier conservation area

Spatial genetic patterns in African wild dogs reveal signs of effective dispersal across southern Africa

Across much of Africa, decades of civil war, land reforms, and persecution by humans have decimated wildlife populations. African wild dogs (Lycaon pictus) have declined dramatically during the past decades, but have shown recent natural recolonisation of some areas. In Angola, they were rediscovered after almost five decades when no surveys were being conducted, and they have recolonised areas in southern Zimbabwe and northern South Africa. Wild dogs were also reintroduced to Mozambique, where only few individuals remained. Against this backdrop, understanding genetic structure and effective dispersal between fragmented populations is essential to ensure the best conservation approaches for the long-term survival of the species. Our study investigated population genetic diversity, differentiation and gene flow of wild dogs across southern Africa, to include areas where they have recently been rediscovered, reestablished or reintroduced. Our results point to four weakly differentiated genetic clusters, representing the lowveld of Zimbabwe/Limpopo, Kruger NP, Angola/KAZA-TFCA, and the managed metapopulation, counterbalanced by moderate levels of effective dispersal on a southern African scale. Our results suggest that if the human footprint and impact can be significantly minimized, natural dispersal of wild dogs could lead to the demographic recovery of the species in southern Africa.

African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity

African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species to adapt to environmental changes considering the low genomic diversity in this population.

Genetic Diversity and Relatedness among Captive African Painted Dogs in North America

African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for reintroductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate the development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.

African wild dogs (Lycaon pictus) show differences in diet composition across landscape types in Kruger National Park, South Africa

The Kruger National Park (KNP) is home to the last genetically viable, minimally managed population of African wild dogs (Lycaon pictus, wild dogs) in South Africa. Until 2004, this population remained stable, but since has been declining. In this study, we aimed to improve our understanding of the ecology of KNP wild dogs by estimating the relative contribution of different prey types to their diet across landscape types. Based on a Bayesian mixing model, we assessed wild dog diet and foraging preferences using stable isotope analysis. We sampled 73 individuals from 40 packs found in six different landscape types. In thickets, packs predominantly prey on small browsing and mixed-feeding species (accounting for ~73% of their diet), but occasionally hunt large grazers (~24%) and large browsers (~3%). In open landscape types where lions (Panthera leo) are more or less absent, such as in the Lowveld sour bushveld, wild dogs prey on large browsers and large grazers (~67%). Our results demonstrate that KNP wild dogs occupy a broader ecological niche than previously thought, with small browsers forming an integral part of their diet. We also present the first data describing differences in wild dog diet–tissue discrimination factors for tail hair and whiskers compared to respective stable nitrogen (δ15N) and carbon (δ13C) values obtained from feces of captive wild dogs, as well as from those of South Africa’s broader managed metapopulation. While these data should be considered preliminary, we suggest that until wild dog diet–tissue discrimination factors are calculated through a controlled feeding study, the discrimination factors calculated for the gray wolf (Canis lupus) should be used for wild dog-related isotope studies, rather than the often cited values for red foxes (Vulpes vulpes).

Phylogeography and niche modelling: reciprocal enlightenment

Phylogeography examines the spatial genetic structure of species. Environmental niche modelling (or ecological niche modelling; ENM) examines the environmental limits of a species’ ecological niche. These two fields have great potential to be used together. ENM can shed light on how phylogeographical patterns develop and help identify possible drivers of spatial structure that need to be further investigated. Specifically, ENM can be used to test for niche differentiation among clades, identify factors limiting individual clades and identify barriers and contact zones. It can also be used to test hypotheses regarding the effects of historical and future climate change on spatial genetic patterns by projecting niches using palaeoclimate or future climate data. Conversely, phylogeographical information can populate ENM with within-species genetic diversity. Where adaptive variation exists among clades within a species, modelling their niches separately can improve predictions of historical distribution patterns and future responses to climate change. Awareness of patterns of genetic diversity in niche modelling can also alert conservationists to the potential loss of genetically diverse areas in a species’ range. Here, we provide a simplistic overview of both fields, and focus on their potential for integration, encouraging researchers on both sides to take advantage of the opportunities available.

Why are demographic Allee effects so rarely seen in social animals?

Allee effects in group-living species are common, but little is known about the way in which Allee effects at the group-level scale up to influence population dynamics. Most notably, it remains unclear whether component Allee effects within groups (where some component of fitness in small groups decreases with decreasing group size) will translate into a population-level demographic Allee effect (where per capita fitness in small populations decreases with decreasing overall population size). The African wild dog (Lycaon pictus) is an obligate cooperative breeder that lives in packs and has a multitude of group-level component Allee effects. With the African wild dog as a case study, we use models to determine the effect that group structure has on the population dynamics of social animals and, specifically, whether Allee effects operating at the group level lead to a demographic Allee effect at the population level. We developed a suite of models to analyse the population dynamics of group-living species, as well as comparable "packless" models lacking group structure. By comparing these models, we can identify how Allee effects within groups influence population-level dynamics. Our results show that group structure buffers populations against a demographic Allee effect, because mechanisms affecting birth and mortality are more strongly influenced by group size than population size. We find that interactions between groups are vital in determining the relationship between density dependence within groups and density dependence at the population level. As sufficiently large groups provide protection against positive density dependence, even at low overall population sizes, our results have conservation implications for group-living species, as they suggest group size is a necessary population feature to consider in efforts to manage population size. Furthermore, we provide novel insight regarding the role that dispersal and pack size variation play in the buffering nature of social structure in groups subject to Allee effects.

The genetic tale of a recovering lion population (Panthera leo) in the Savé Valley region (Zimbabwe): A better understanding of the history and managing the future

The rapid decline of the African lion (Panthera leo) has raised conservation concerns. In the Savé Valley Conservancy (SVC), in the Lowveld of Zimbabwe, lions were presumably reduced to approximately 5 to 10 individuals. After ten lions were reintroduced in 2005, the population has recovered to over 200 lions in 2016. Although the increase of lions in the SVC seems promising, a question remains whether the population is genetically viable, considering their small founding population. In this study, we document the genetic diversity in the SVC lion population using both mitochondrial and nuclear genetic markers, and compare our results to literature from other lion populations across Africa. We also tested whether genetic diversity is spatially structured between lion populations residing on several reserves in the Lowveld of Zimbabwe. A total of 42 lions were genotyped successfully for 11 microsatellite loci. We confirmed that the loss of allelic richness (probably resulting from genetic drift and small number of founders) has resulted in low genetic diversity and inbreeding. The SVC lion population was also found to be genetically differentiated from surrounding population, as a result of genetic drift and restricted natural dispersal due to anthropogenic barriers. From a conservation perspective, it is important to avoid further loss of genetic variability in the SVC lion population and maintain evolutionary potential required for future survival. Genetic restoration through the introduction of unrelated individuals is recommended, as this will increase genetic heterozygosity and improve survival and reproductive fitness in populations.

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 African 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 1,000,000 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.