Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo).

BACKGROUND: Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. RESULTS: In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. CONCLUSIONS: The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Wild versus domestic prey in the diet of reintroduced tigers (Panthera tigris) in the livestock-dominated multiple-use forests of Panna Tiger Reserve, India.

Grazing livestock in openly accessible areas is a common practice in the multiple-use forests of India; however, its compatibility with the reintroduction of tigers to these areas requires examination. Here, we investigated the diet of tigers in a livestock-dominated multiple-use buffer zone of the Panna Tiger Reserve, India. We hypothesised that the presence of feral cattle, along with open-access grazing practices in multiple-use forests, would increase the incidence of predation on livestock by tigers, even when wild prey are available. We used generalised linear models to test whether predation of livestock versus wild animals was influenced by (1) the sex and age class of tigers, (2) season, and (3) the distance of prey from the core-zone boundary of the reserve. Overall, sub-adult tigers and male tigers killed more livestock than wild prey, even when wild prey was available. In the winter and rainy seasons livestock were killed in higher numbers in the buffer zone than in summers, this may be because of the seasonally changing livestock herding patterns in the area. Further, with increasing distance from the core-zone boundary, all tigers killed more livestock, possibly because livestock were more easily accessible than wild prey. Our results show that open-access and unregulated livestock grazing is not currently compatible with large carnivore conservation in the same landscape. Such practices will lead to an increase in negative tiger-human-livestock interactions. In conclusion, we suggest the need to encourage locals to corral valuable cattle, leaving feral/unwanted livestock for tigers. This simple strategy would benefit both local inhabitants and tiger conservation in the multiple-use forests of India.

Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo).

Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.