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Revealing phylogeographic structure is important for accurate subspecies delineation and understanding a species’ evolutionary history. In leopards (Panthera pardus), there are currently nine subspecies recognized. On the African continent, only one subspecies occurs (P. p. pardus), although mitochondrial DNA from historical samples suggests the presence of three putative continental clades: (1) West Africa (WA), (2) Central Africa (CA), and (3) Southern Africa (SA). So far, whole genome data did not recover this phylogeographic structure, although leopards in the southern periphery of their distribution range in Africa have not yet been investigated in detail. The Mpumalanga province of South Africa is of particular interest, as here, the CA and the SA clade possibly meet. The aim of this study was to characterize the first mitogenomes of African leopards from Mpumalanga, to help clarifying how South African leopards fit into continental patterns of genetic differentiation. Complete mitogenomes from nine leopards, including a strawberry leopard, were assembled de novo and included in phylogenetic analysis, in combination with 32 publicly available mitogenomes. Bayesian inference and maximum likelihood analyses identified two deeply diverged putative clades within South Africa, which were more genetically distinct than two subspecies in Asia. The clades dated back to 0.76-0.86 million years ago, indicating that they originated during the climatically unstable Mid-Pleistocene, as seen in other large mammals. The Pleistocene refuge theory states that the maintenance of savanna refugia in East and Southern Africa promoted the divergence between populations. As such, leopards may reflect the unique climatic history of southern Africa, which has resulted in eminent and endemic genetic diversity., Revealing phylogeographic structure is important for accurate subspecies delineation and understanding a species' evolutionary history. In leopards (Panthera pardus), there are currently nine subspecies recognized. On the African continent, only one subspecies occurs (P. p. pardus), although mitochondrial DNA from historical samples suggests the presence of three putative continental clades: (1) West Africa (WA), (2) Central Africa (CA), and (3) Southern Africa (SA). So far, whole genome data did not recover this phylogeographic structure, although leopards in the southern periphery of their distribution range in Africa have not yet been investigated in detail. The Mpumalanga province of South Africa is of particular interest, as here, the CA and the SA clade possibly meet. The aim of this study was to characterize the first mitogenomes of African leopards from Mpumalanga, to help clarifying how South African leopards fit into continental patterns of genetic differentiation. Complete mitogenomes from nine leopards, including a strawberry leopard, were assembled de novo and included in phylogenetic analysis, in combination with 32 publicly available mitogenomes. Bayesian inference and maximum likelihood analyses identified two deeply diverged putative clades within South Africa, which were more genetically distinct than two subspecies in Asia. The clades dated back to 0.76-0.86 million years ago, indicating that they originated during the climatically unstable Mid-Pleistocene, as seen in other large mammals. The Pleistocene refuge theory states that the maintenance of savanna refugia in East and Southern Africa promoted the divergence between populations. As such, leopards may reflect the unique climatic history of southern Africa, which has resulted in eminent and endemic genetic diversity.

Estimation of survival rates is important for developing and evaluating conservation options for large carnivores. However, telemetry studies for large carnivores are often characterized by small sample sizes that limit meaningful conclusions. We used data from 10 published and 8 unpublished studies of leopards Panthera pardus in southern Africa to estimate survival rates and investigate causes of leopard mortality. Mean survival rates were significantly lower in non-protected (0.55 ± SE 0.08) compared to protected areas (0.88 ± 0.03). Inside protected areas juveniles had significantly lower survival (0.39 ± 0.10) compared to subadults (0.86 ± 0.07) and adults (0.88 ± 0.04). There was a greater difference in cause of death between protected and non-protected areas for females compared to males, with people being the dominant cause of mortality outside protected areas for both females and males. We suggest there is cause for concern regarding the sustainability of leopard populations in South Africa, as high female mortality may have severe demographic effects and a large proportion of suitable leopard habitat lies in non-protected areas. However, because a large proportion of deaths outside protected areas were attributed to deliberate killing by people, we suggest that management interventions may have the potential to increase leopard survival dramatically. We therefore stress the urgency to initiate actions, such as conflict mitigation programmes, to increase leopard survival in non-protected areas

Estimation of survival rates is important for developing and evaluating conservation options for large carnivores. However, telemetry studies for large carnivores are often characterized by small sample sizes that limit meaningful conclusions. We used data from 10 published and 8 unpublished studies of leopards Panthera pardus in southern Africa to estimate survival rates and investigate causes of leopard mortality. Mean survival rates were significantly lower in non-protected (0.55 ± SE 0.08) compared to protected areas (0.88 ± 0.03). Inside protected areas juveniles had significantly lower survival (0.39 ± 0.10) compared to subadults (0.86 ± 0.07) and adults (0.88 ± 0.04). There was a greater difference in cause of death between protected and non-protected areas for females compared to males, with people being the dominant cause of mortality outside protected areas for both females and males. We suggest there is cause for concern regarding the sustainability of leopard populations in South Africa, as high female mortality may have severe demographic effects and a large proportion of suitable leopard habitat lies in non-protected areas. However, because a large proportion of deaths outside protected areas were attributed to deliberate killing by people, we suggest that management interventions may have the potential to increase leopard survival dramatically. We therefore stress the urgency to initiate actions, such as conflict mitigation programmes, to increase leopard survival in non-protected areas