Browsing by Author "McManus, Jeannine"

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    Low microsatellites used to investigate leopard genetic structure severely restricts the results by Ropiquet et al. (2015) to infer population structure for managers
    (Elsevier, 2016) McManus, Jeannine; Smuts, Bool
    Low microsatellites used to investigate leopard genetic structure severely restricts the results by Ropiquet et al. (2015) to infer population structure for managers.
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    Red, gold, and green: comparative genomics of polymorphic leopards from South Africa
    (Oxford University Press, 2025) McManus, Jeannine; Lagcher, Elina; Bosse, Mirte
    An important goal of comparative and functional genomics is to connect genetic polymorphisms to phenotypic variation. Leopards (Panthera pardus) from northern South Africa are particularly diverse, as here a unique color morph occurs, as well as two deeply diverged southern (SA) and central African (CA) mitochondrial clades, stemming from Pleistocene refugia. Here, we present the first whole genomes of a red leopard and a black (captive) leopard, and wildtypes belonging to the CA and SA mitochondrial clades, to evaluate genome-wide diversity, divergence, and high-impact mutations that may relate to their phenotype. In the black leopard, we found long runs of homozygosity (ROHs), low nucleotide diversity across the genome, and a large number of homozygous structural variants, likely resulting from inbreeding to maintain this color morph in captivity. In red leopards, runs of homozygosity were slightly longer compared to wildtype leopards, with potential deleterious mutations relating to its phenotype, including impaired vision. When assessing population structure, we found no divergence between CA and SA leopards and the rest of Africa, whether comparing single nucleotide or structural variants. This illustrates the homogenizing effect of introgression, and highlights that although leopards in northern South Africa may be phenotypically unique, they are not genetically different.
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    Wildlife- friendly livestock management promotes mammalian biodiversity recovery on a semi-arid Karoo farm in South Africa
    (Frontiers Media, 2021) Schurch, Mathew, P.E.; Goets, Stefan; McManus, Jeannine; Pardo, Lain, E.
    Agriculture is an essential production system used to feed the growing human population, but at the same time has become a major driver of biodiversity loss and environmental degradation. Employing production methods that restore degraded landscapes can have a positive impact on biodiversity, whilst improving food production. We assessed how mammalian biodiversity, specifically richness and their relative abundances varied on five Karoo farms in South Africa that had been amalgamated and subjected to a transition from traditional livestock grazing techniques (sporadic rotational grazing and lethal predator control) to wildlife-friendly non-lethal predator management, using human shepherding of livestock under a high-density short-duration grazing regime. We used camera trap data collected over a 4-year period, to measure mammalian species richness, distribution and relative abundance on the wildlife-friendly farm to investigate temporal changes throughout the conversion from traditional farming practices. In the last year of the study (2019) additional cameras were used to provide a spatial comparison of mammalian species on the wildlife-friendly farm to two neighboring farms, a traditional livestock farm using lethal predator controls, and a game farm. We found that mammalian species richness increased year on year resulting in a significant increase of 24% over the duration of the study. Herbivores showed an increase of 33% in the number of species detected over the years, while predator species increased by 8%. The relative abundance and distribution of most species also showed increases as the conversion process took place. For example, 73% of the herbivore species detected throughout the study increased in their relative abundance. Similarly, 67% of all species showed an increase in the number of sites occupied over the years. In the final year of the study the wildlife-friendly farm had more mammalian species compared to the game farm and traditional livestock farm, with the latter two sites having a similar number of species when compared to the commencement of the conversion of the wildlife-friendly site. These broad improvements in mammalian biodiversity demonstrate that livestock production can benefit local mammalian biodiversity through a combination of herder grazing management and wildlife-friendly farming.