The ecology of otters in an urban environment

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the Degree of Doctor of Philosophy. Johannesburg, 2018Urban development has rapidly become the largest contributing factor of biodiversity decline across the planet. Regardless, certain species can survive these novel environments due to their opportunistic nature or occurrence in niche specific areas within urban areas. The aim of my study was to establish whether two otter species, the African clawless otter (Aonyx capensis) and the spotted-necked otter (Hydrictis maculicollis), in an urban environment showed similar ecological patterns in distribution (spatial arrangement), diet, and habitat use compared to conspecific individuals in areas with moderate to low levels of human disturbance. Firstly, I investigated the distribution and frequency of each species based on occurrence of signs (e.g. spraints and footprints) in relation to urban and peri-urban areas of central Gauteng, South Africa. Both species were present in central Gauteng, with a greater number of A. capensis signs found. No difference was observed between the number of signs found in urban and peri-urban areas for both species. Secondly, habitat variables measured near otter signs showed several differences in variables between urban and peri-urban areas. Otter movement through urban areas appeared to be associated with tall grass species, reed beds, and trees, which provided means of concealment for the animals, as well as avoidance of buildings to reduce human encounters. Thirdly, diet analysis based on prey remains in otter faecal samples resulted in lower than expected levels of crab and fish, and revealed higher than expected numbers of less common prey (e.g. birds and mammals) being consumed. Finally, the genetic diversity of individuals was measured using allele frequency to determine the level of reproductive success (ability to survive and produce viable offspring; Fisher, 1915) of A. capensis. Results showed a high level of genetic recombination between individuals in the population suggesting no movement restrictions are being experienced by otters, but genetic diversity was low. Otters are able to utilise resources available in this novel environment, which does not appear to be affecting movement, habitat utilisation or diet. A high genetic flow suggests successful use of urban areas, although there is concern about future genetic health in Gauteng based on the lower level of genetic variance.MT 201

Differentiation of two South African otter species (Aonyx capensis and Lutra maculicollis) from spraint based on partial CytB primer sets

AbstractAccurate species identification based on visual cues can be challenging due to morphological similarities and the cryptic nature of certain species. Thus a more conclusive method of identification is required, namely DNA barcoding. This is the case regarding two South African otter species, Cape Clawless otter (Aonyx capensis) and the spotted necked otter (Lutra maculicollis). Due to the cryptic nature of these animals faecal samples, known as spraints, are the easiest way of confirming the presence of the animal in an area. In this study, we compared results obtained for universal and partial CytB primer sets on collected spraint and tissue control samples. Universal CytB primers revealed a low percentage of amplified otter species from faecal samples (species specific amplification success of 10.9%) whereas, the partial CytB primer set resulted in successful amplification of 45 out of 55 (82%) samples. We were thus able to positively differentiate between the two otter species using the partial CytB primer set developed in this study. The ability to accurately identify species using partial DNA will be beneficial in understanding numerous aspects of the behaviour and ecological importance of animals in their environment

The bii4africa dataset of faunal and floral population intactness estimates across Africa’s major land uses

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species’ population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate ‘intactness scores’: the remaining proportion of an ‘intact’ reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region’s major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/ taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems

The bii4africa dataset of faunal and floral population intactness estimates across Africa’s major land uses

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species’ population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate ‘intactness scores’: the remaining proportion of an ‘intact’ reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region’s major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems

Genetic diversity of African clawless otters (Aonyx capensis) occurring in urbanised areas of Gauteng, South Africa

Genetic diversity is the basis of the evolutionary potential of species to respond to environmental changes. However, restricting the movement of species can result in populations becoming less connected which can reduce gene flow and can subsequently result in a loss of genetic diversity. Urban expansion can lead to the fragmentation of habitats which affects the ability of species to move freely between areas. In this study, the genetic diversity of the African clawless otter (Aonyx capensis) in Gauteng (South Africa) was assessed using non-invasive sampling techniques. DNA was extracted from spraint (faecal) samples collected along nine rivers and genotyped using 10 microsatellites to assess population structure and genetic diversity. Samples were grouped based on locality and by catchment to determine whether isolated subpopulations exist. Genetic diversity of A. capensis in Gauteng was found to be low (mean observed heterozygosity (Ho)=0.309). Analysis of genetic structure provides support for the otter populations being panmictic with high gene flow between populations from different rivers. Results from the study indicate that the movement of A. capensis is not affected by physical barriers in urbanised areas. However, because the genetic diversity of the species in the study area is low, these animals may not be able to cope with future environmental changes. Significance: Genetic structure analysis of the sampled Gauteng otter population indicates the population is panmictic; however, a low level of genetic diversity in this population has also been identified and may affect how the population copes with future environmental changes. Physical restrictions in urbanised areas do not appear to be affecting movement of the species