Browsing by Author "Altwegg, Res"

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    Behavioural, microhabitat, and phylogenetic dimensions of intrasexual contest competition in combatant monkey beetles (Scarabaeidae: Hopliini)
    (2021) Rink, Ariella N; Altwegg, Res; Colville, Jonathan F; Bowie, Rauri C K
    The importance of sexual selection as a driver of evolution, from microevolution to speciation, has overwhelmingly been studied in the context of female choice, but there is evidence that male-male competition can also drive evolution. Recent reviews of the intrasexual competition literature have developed several hypotheses of weapon divergence in both allopatry and sympatry and have suggested means by which weapon divergence may cause reproductive isolation and speciation, both alone and together with mate choice and ecological selection. Here, I assess the role of sexual selection, in the context of environmental variation at the level of the contest substrate and the developmental environment, in contributing to microevolution within the monkey beetles (Coleoptera: Scarabaeidae: Hopliini), a taxonomically and phenotypically diverse group of pollinating insects in the Greater Cape Floristic Region (GCFR) that shows a high degree of sexual dimorphism and mating behaviour driven by male-male competition. I build on previous observations of hind leg use in intrasexual male-male contest for reproductive access to females by showing that, in Heterochelus chiragricus, contests occur in the context of a significantly maleskewed sex-ratio and consist of vigorous wrestling and pushing between two males on the flower heads occupied by embedded, feeding females, who apparently exert no mate choice. Contest outcomes are influenced by hind femur size and residency effects, and I apply hypotheses informed by evolutionary game theory to assess how males make decisions regarding persistence versus retreat. I proceed to assess the evidence for the ‘divergent fighting contexts' hypothesis which predicts weapon divergence driven by intrasexual contest competition in the context of variation in the contest substrate. I find that hind leg size in another combatant monkey beetle, the species complex Scelophysa trimeni, varies across gradients of flower size among several spatially distributed populations, suggesting that variation in flower size (the contest substrate) mediates selection for weapon morphologies that maximise performance under different fighting styles necessitated by differences in the contest substrate. I also find that male elytral colour varies both across gradients in the developmental environment and with variation in flower colour, suggesting that this trait may function as an honest signal of male fitness, but also that it may be under selection to maximise signal transmission against variable backgrounds of contest substrates. Finally, I quantify the extent to which integration, modularity, multivariate allometry, and phylogenetic effects influence the evolutionary lability of male monkey beetle's hind legs, and so mediate the pace of their evolutionary diversification in response to these varying contest substrates. My findings support a two-module pattern of modularity at both static and evolutionary levels, and I find that allometric scaling relationships are conserved within S. trimeni. These findings indicate that monkey beetle weapons are relatively unconstrained in their evolutionary diversification across divergent fighting substrates. I conclude by discussing these findings within the broader field of sexual selection and monkey beetle ecology and suggest directions for further work. The findings presented here support a role for sexual selection, interacting with variation in the flower contest substrate, as being an important driver of the diversification of monkey beetles in the GCFR.
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    Bird's response to seasonality: investigating the range dynamics of birds through dynamic occupancy models
    (2025) Kani, Luvuyo; Altwegg, Res; Maphisa, David
    Birds can respond to seasonal environmental fluctuations through migration. Among different migratory species and populations, there is varying sensitivity to different seasonal environmental cues, thus leading to different seasonal range dynamics and migration strategies. In this study, I used dynamic occupancy models on the South African Bird Atlas Project 2 (SABAP 2) data to investigate the seasonal range dynamics of a selection of five migratory and six nomadic bird species in western South Africa. In the context of this study, seasonal range dynamics are defined as when a species arrives and departs a given area. I used dynamic occupancy models to estimate monthly changes in occupancy between 2014 and 2018. I modelled local extinction (departure) and colonisation (arrival) as a function of changes and anomalies in average monthly rainfall, temperature and vegetation. Among the obligate migrants, the best performing models indicated that colonization and extinction parameters were mostly driven by seasonal changes in average rainfall, temperature and vegetation. In nomadic species, colonization was driven by seasonal changes in average rainfall, temperature and vegetation, while extinction was driven by anomalies in rainfall, temperature and vegetation. The models successfully captured the generally known seasonal pattern in occupancy (arrival and departure) of all five obligate migrants, while no regular seasonal fluctuation in occupancy was evident among the nomadic species. Over the four-year period, no species showed a strong shift in seasonal range dynamics in both groups. However, I do suspect that the same methodology done at a finer spatial and temporal scale may reveal changes in seasonal range dynamics of some species. This study demonstrates that dynamic occupancy modelling using citizen science data is a viable methodology for investigating seasonal range dynamics.
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    Calling ecology of micro frogs (Microbatrachella capensis): a case study using acoustic spatial capture recapture
    (2020) Gedert, Jennifer; Measey, John; Altwegg, Res
    Amphibians worldwide are declining, increasing the demand for monitoring populations of many threatened amphibians, including the South African Critically Endangered micro frog (Microbatrachella capensis). I attempted to improve ongoing monitoring efforts by determining the calling ecology of the micro frog population on the Cape Flats. I used acoustic spatial capture recapture to calculate call density and identify the main factors that determine periods of maximum frog calls. Increased calling behaviour was found early in the season and in response to rainfall. In addition, micro frogs were found to call more at night than during the day. This suggests that future monitoring of this species should occur at night, after rain, and early in the winter breeding season. From the call density estimates, I calculated the size of the micro frog population on the Cape Flats to be about 200 adult frogs when an equal sex ratio of adult males and females is assumed. Future monitoring and conservation efforts should take into consideration this baseline population estimate and keep track of any demographic trends in the population.
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    Citizen science reveals complex changes in barn swallow phenology in South Africa over three decades
    (2016) Burman, Marc Sebastian; Underhill, Leslie G; Altwegg, Res; Erni, Birgit; Remisiewicz, Magdalena
    Palearctic migrants, including barn swallows Hirundo rustica, responded to climate change in Europe from the mid to late 1900s with phenological changes, mostly showing earlier arrival and start of breeding. During this period, barn swallows in the Palearctic exhibited variable patterns of change in the timing of their arrival, breeding and departure from the breeding grounds. At the South African non-breeding grounds, the timing of migration shifted between the 1980s and 2000s, again with geographic variability. To explain these changes further, I examined geographic and temporal variability in the timing of flight feather ('primary') moult, and trends in body weight, in barn swallows ringed in South Africa between 1986 and 2012. Citizen science bird ringing, started in South Africa in 1948, generated all the data used in this project. All data were obtained from the South African Bird Ringing Unit (SAFRING).
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    Demographic and genetic variability in Cape Dwarf Chameleons, Bradypodion pumilum, withink a fragmented, urban habitat
    (2012) Katz, Eric Michael; Tolley, Krystal A; Bishop, Jacqueline M; Altwegg, Res
    Habitat fragmentation is recognized as a primary cause of biodiversity loss. To maximize biodiversity maintenance, researchers in the field of conservation biology often investigate population demography and genetic variability for species inhabiting fragmented landscapes. Findings from such work enable effective conservation management, maximizing viability for potentially imperiled populations. Previous research has relied predominately on spatial analysis when investigating population demography and genetic variability; however, temporal analysis is also important to species conservation. As of 2006, reptiles and amphibians had the highest threat status among small, terrestrial vertebrates, warranting continual investigation of herpetofaunal species inhabiting fragmented landscapes. Of the two, reptiles are the more poorly studied, though are suggested to be equally or more threatened than amphibians. The Cape Dwarf Chameleon, Bradypodion pumilum, exemplifies one potentially threatened reptile species which has suffered habitat loss, due to urbanization, inducing fragmentation and transformation among much of its habitat. As a result, many B. pumilum populations currently exist as a collection of isolated groups inhabiting critically endangered ecosystems.
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    Departures from the energy-biodiversity relationship in south african passerines: are the legacies of past climates mediated by behavioral constraints on dispersal?
    (Public Library of Science, 2015) Péron, Guillaume; Altwegg, Res
    Legacies of paleoclimates in contemporary biodiversity patterns have mostly been investigated with global datasets, or with weakly dispersive organisms, and as a consequence been interpreted in terms of geographical or physical constraints. If paleoclimatic legacies also occurred at the regional scale in the distributions of vagile organisms within biomes, they would rather suggest behavioral constraints on dispersal, i.e., philopatric syndromes. We examined 1) the residuals of the regression between contemporary energy and passerine species richness in South African biomes and 2) phylogenetic dispersion of passerine assemblages, using occupancy models and quarter-degree resolution citizen science data. We found a northeast to southwest gradient within mesic biomes congruent with the location of Quaternary mesic refugia, overall suggesting that as distance from refugia increased, more clades were lacking from local assemblages. A similar but weaker pattern was detected in the arid Karoo Biomes. In mobile organisms such as birds, behavioral constraints on dispersal appear strong enough to influence species distributions thousands of years after historical range contractions.
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    Does seasonality drive spatial patterns in demography? Variation in survival in African reed warblers Acrocephalus baeticatus across southern Africa does not reflect global patterns
    (John Wiley & Sons Ltd., 2014) Jansen, Dorine Y.M.; Abadi, Fitsum; Harebottle, Doug; Altwegg, Res
    Among birds, northern temperate species generally have larger clutches, shorter development periods and lower adult survival than similarly-sized southern and tropical species. Even though this global pattern is well accepted, the driving mechanism is still not fully understood. The main theories are founded on the differing environmental seasonality of these zones (higher seasonality in the North). These patterns arise in cross-species comparisons, but we hypothesized that the same patterns should arise among populations within a species if different types of seasonality select for different life histories. Few studies have examined this. We estimated survival of an azonal habitat specialist, the African reed warbler, across the environmentally diverse African subcontinent, and related survival to latitude and to the seasonality of the different environments of their breeding habitats. Data (1998–2010) collected through a public ringing scheme were analyzed with hierarchical capture-mark-recapture models to determine resident adult survival and its spatial variance across sixteen vegetation units spread across four biomes. The models were defined as state-space multi-state models to account for transience and implemented in a Bayesian framework. We did not find a latitudinal trend in survival or a clear link between seasonality and survival. Spatial variation in survival was substantial across the sixteen sites (spatial standard deviation of the logit mean survival: 0.70, 95% credible interval (CRI): 0.33–1.27). Mean site survival ranged from 0.49 (95% CRI: 0.18–0.80) to 0.83 (95% CRI: 0.62–0.97) with an overall mean of 0.67 (95% CRI: 0.47–0.85). A hierarchical modeling approach enabled us to estimate spatial variation in survival of the African reed warbler across the African subcontinent from sparse data. Although we could not confirm the global pattern of higher survival in less seasonal environments, our findings from a poorly studied region contribute to the study of life-history strategies.
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    Drivers of bird species richness within moist high-altitude grasslands in eastern South Africa
    (Public Library of Science, 2016) Maphisa, David H; Smit-Robinson, Hanneline; Underhill, Les G; Altwegg, Res
    Moist high-altitude grasslands in South Africa are renowned for high avifaunal diversity and are priority areas for conservation. Conservation management of these areas conflicts with management for other uses, such as intensive livestock agriculture, which requires annual burning and leads to heavy grazing. Recently the area has become target for water storage schemes and renewable electricity energy projects. There is therefore an urgent need to investigate environmental factors and habitat factors that affect bird species richness in order to optimise management of those areas set aside for conservation. A particularly good opportunity to study these issues arose at Ingula in the eastern South African high-altitude grasslands. An area that had been subject to intense grazing was bought by the national power utility that constructed a pumped storage scheme on part of the land and set aside the rest for bird conservation. Since the new management took over in 2005 the area has been mostly annually burned with relatively little grazing. The new management seeks scientific advice on how to maintain avian species richness of the study area. We collected bird occurrence and vegetation data along random transects between 2006 and 2010 to monitor the impact of the new management, and to study the effect of the habitat changes on bird species richness. To achieve these, we convert bird transect data to presence only data to investigate how bird species richness were related to key transect vegetation attributes under this new grassland management. First we used generalised linear mixed models, to examine changes in vegetation grass height and cover and between burned and unburned habitats. Secondly, we examined how total bird species richness varied across seasons and years. And finally we investigated which habitat vegetation attributes were correlated with species richness of a group of grassland depended bird species only. Transects that were burned showed a larger decrease in vegetation cover compared to transects that were not burned. Grass height increased over time. Bird species richness was highest in summer compared to other seasons and increased over time. Overall bird species richness increased over the three summer surveys but species richness of birds that prefer heavily grazed habitat showed little change over the three years. Changes in bird species richness were best explained by the model with grass height for combined species richness of grassland depended birds but also for birds that prefer heavy grazing when treated alone. On one hand birds that prefer moderate grazing were best explained by a null model. However, overall bird species richness was better positively correlated to grass height than grass cover or dead grass. We conclude that frequent burning alone with relatively reduced grazing led to higher but less dense grass, which benefited some species and disadvantaged others. We suggest that management of this grassland use combination of fire and grazing and leave some areas unburned to accommodates birds of various habitat needs.
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    Effects of protected areas and climate change on the occupancy dynamics of common bird species in South Africa
    (2018) Duckworth, Greg; Altwegg, Res
    Protected areas are tracts of land set aside primarily for the conservation of biodiversity and natural habitats. They are intended to mitigate biodiversity loss caused by land-use change worldwide. Climate change has been shown to disrupt species' natural distributions and patterns, and poses a significant threat to global biodiversity. The goals of this thesis are to address these important issues, and understand how protected areas and climate change affect the range dynamics of common, resident bird species in South Africa. Common species were used because they have been shown to drive important ecosystem patterns, and a decline in abundance and diversity of common species can indicate drastic declines in ecosystem integrity. This thesis comprises four data chapters; in the first three I model the occupancy dynamics of 200 common, resident bird species in South Africa to gain an understanding of how the proportion of protected areas within a landscape affects common species. For the last data chapter, I examined the effects of protected areas and a changing climate on the range dynamics of Cape Rock-jumper (Chaetops frenatus), a species endemic to the southwestern part of South Africa and whose population is declining rapidly in response to climate change. I modelled its occupancy dynamics in relation to climate, vegetation, and protected area. Overall, my key findings show bird abundances vary widely as a function of protected areas, but on average, bird abundances are higher in regions with a higher proportion of protected areas, compared to regions with a lower proportion. I found that the conservation ability of protected areas was influenced by the type of land-use found in the surrounding landscape. For example, the extent of agricultural land in proximity to a protected area significantly increased the mean abundance of birds in that protected area, whilst the average abundance of most species was not affected by the extent of urban area near protected area. On average, species preferentially colonized and persisted within landscapes with a higher proportion of protected area, compared to landscapes with a lower proportion of protected area. However, protected areas were not able to slow the extinction rate for all species, and the average extinction rate for some groups of species actually increased as the extend of protected areas within a landscape increased. Furthermore, Cape Rock-jumper also preferentially occupied regions with higher proportions of protected area. Despite this, Cape Rock-jumper’s range is predicted to shrink considerably in response to a hotter and mildly drier climate forecast for the region. As a result, Cape Rock-jumper will likely be of conservation concern as the climate over its range continues to change. I conclude that, in general, protected areas are effective at conserving common bird species over a heterogeneous landscape in South Africa, and should be prioritised as key conservation strategies in the future. I further conclude that climate change will be a concern to an endemic species, and to biodiversity in general. This will likely place extra stress on the importance of protected areas to mitigate responses of species to climate change.
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    Efficient Bayesian analysis of occupancy models with logit link functions
    (2018) Clark, Allan E; Altwegg, Res
    Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coef‐ ficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We de‐ velop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub (https://github.com/AllanClark/Rcppocc).
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    An experimental approach to assess the role of nest predation in the population dynamics of the sociable weaver (Philetairus socius)
    (2016) Lloyd, Kyle; Altwegg, Res; Covas, Rita; Doutrelant, Claire; Maciejewski, Kristi
    Predation is a widespread population process that has been shown to affect the distribution, abundance and dynamics of populations in ecosystems. This is the first study that used an experimental approach to assess the effect of nest predation on the population dynamics of the sociable weaver (Philetairus socius), a keystone species in the semi-arid savannas of the Kalahari and Namib regions. Snakes were excluded from five colonies for five breeding seasons and two colonies for three breeding seasons, with another eight colonies acting as the controls. Reproductive output, colony size, dispersal events and several environmental variables were measured between 2010 and 2015. This was done to determine (1) what effect nest predator exclusion had on reproductive output; (2) how this related to colony and population size trends by using a matrix-projection metapopulation model; (3) how protected colonies influence movement patterns; and (4) if nest predation had a compensatory or positive effect by reducing the intraspecific competition of a colony. The fourth aim was investigated by tracking the foraging paths of eight colonies of varying sizes, with foraging distance acting as a proxy for intraspecific competition. Colonies that were protected from snake predation produced, on average, more than double the number of fledglings per female per breeding season that were produced in unprotected colonies. However, the magnitude of this effect decreased with increasing colony size of protected colonies, most likely due to the negative effects that large colony sizes have on reproductive output. Increasing aridity was found to have a negative effect on reproductive output and warmer winter minimum temperatures were found to have a positive effect. My results suggested that protecting a subset of colonies in the metapopulation may be sufficient in preventing population declines under climate change conditions. The protected colonies played an important role in structuring and connecting the movement network of the metapopulation, whilst colony size explained the migration rates of colonies. However, predation was not found to have a compensatory effect in reducing the intraspecific competition (measured as foraging distance) of a colony. Instead, foraging distance was probably determined by the ability to thermoregulate under hot and humid conditions. To fully understand the effects of nest predation on sociable weaver population dynamics, future studies need to investigate the response of snake predators to sociable weaver behaviour and environmental conditions.
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    Fishery, population dynamics and stock assessment of geelbek (Atractoscion aequidens), a commercially important migrant fish species off the coast of South Africa
    (2018) Boyd, Danielle Winona; Altwegg, Res; Winker, Henning; Kerwath, Sven E
    Geelbek (Atractoscion aequidens) is an important fish species in South Africa's linefishery, a fishing sector defined by its fishing gear of rod and reel or handline. Distributed from Cape Point (34°21'S, 18°29'E) on the south west coast to Kosi Bay (26°51'S, 32°53'E) on the east coast, they are targeted throughout their range by the commercial linefishery, recreational anglers and small-scale fishers. The majority of geelbek are caught on the Agulhas Bank during austral summer. Due to current minimum size limits of 600 mm (total length, TL), well below the 50% size-at-maturity (950 mm TL), the majority of the catches are comprised of immature fish, making the stock vulnerable to growth overfishing. Adults (>5 years) migrate seasonally to spawn off KwaZulu-Natal and congregate in offshore shoals at night. These spawning aggregations allow fishermen to catch large numbers of fish, making geelbek also vulnerable to recruitment overfishing. This study aims to improve understanding of the fishery and population dynamics of geelbek to help inform natural resource management of the geelbek linefishery. A stock assessment of South African geelbek was undertaken to fulfil this aim. For this purpose, spatially and seasonally explicit equilibrium per-recruit and dynamic age-structured operating models were developed for geelbek to account for the dynamic in stock structure as a result of the intra-annual coastal migration and differences in the vulnerability of life history stages to varying fishing pressure along South Africa's coastline. These models were developed using statistical programming environment R. The models were parameterised and calibrated using length and catch data from the National Marine Linefish System (NMLS) and life history parameters sourced from peer-reviewed literature. Per-recruit analyses were performed to estimate current stock-specific fisheries mortality rates and the spawner biomass depletion. These estimates were used as input into the stochastic age-structured simulation model and calibrated using available commercial catch data (1987 - 2011). The stochastic operating model was used to predict the probability of stock recovery and long-term sustainability under eleven alternative fisheries management strategies. The current stock status was estimated at 9.9% (approximately 10%) of the pristine spawner biomass (SB₀) using per-recruit analysis. This was compared to the stock depletion estimates of ~5 and 7% SB₀ from prior assessments conducted in the late 1990s and 1980s. This study indicated that there was a ~50 to 100% increase in spawner biomass over the past twenty years. However, this level of stock depletion is still considered critically low with respect to the previous limit management goal of increasing spawner biomass depletion rates above 25% SB₀, the collapsed limit reference level, advised by Griffiths in 1997. Eleven management strategies were simulated, examining the effects of decreases in harvest rates, closed seasons and areas and changes in minimum size limits, initiated in 2020, and tested over the medium (ten years) to long (twenty years) term. The least efficient management strategy was continuing at the status quo, with a minimum size limit of 600 mm (TL), which predicted only 1% and 2% increase in SB by 2030 and 2040, respectively. The most efficient in terms of a rapid recovery was a full fishery closure 'control scenario' (moratorium), which predicted a recovery to the threshold reference level for sustainable fishing at 40% SB₀ by 2025, and approaching pristine levels by 2040. Increasing the minimum size limit to the size-at-50%-maturity, 950 mm TL, had the second highest recovery rate, reaching 25% SB₀ by 2027, and nearing 40% SB₀ by 2035, at which point its trajectory is asymptotic to 40% SB₀. Decreasing the harvest rate by 50% across all regions and seasons had the third highest recovery rate, reaching 25% SB₀ by 2035, but levelling off thereafter. All the other management strategies resulted in slight stock recoveries, but with all stock trajectories remaining below 14% SB₀ in the long term. Additionally, the impact of various strategies, such as increasing the minimum size limit to the size-at-50%-maturity, 950 mm TL, were unequal, with the east coast experiencing increasingly higher catches over time, whereas the catches for the south south west coast declined drastically throughout the year, and did not improve with time. Such unequal distribution of the impact of management intervention is a consequence of the migratory life history of the geelbek stock. These results provide comprehensive insights into the population dynamics and current impacts on the geelbek stock, suggesting that this species remain severely depleted at ~10% SB₀. Rebuilding the stock to sustainable levels would require serious management intervention.
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    Foraging efficiencies and species' distributions : an explanation of the Hadeda ibis (Bostrychia hagedash) in relation to soil moisture
    (2008) Duckworth, Greg; Underhill, Leslie G; Altwegg, Res
    The influence of soil moisture on the foraging time needed to meet BMR (foraging efficiency) in hadedas was explored in Cape Town, South Africa. This was done by monitoring hadedas foraging and recording the prey items eaten successfully per minute on soils of different moisture. BMR was calculated using a published method and diet calorimetry was used to determine the amount of energy in their diet. Results indicate that hadedas are able to forage most efficiently at intermediate soil moistures (0.40 -0.80 cm³.cm-³) whilst at either low or high soil moisture they are less efficient.
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    From both sides: dire demographic consequences of carnivorous mice and longlining for the critical endangered Tristan albatrosses on Gough Island
    (2009) Wanless, Ross M; Ryan, Peter G; Altwegg, Res; Angel, Andrea; Cooper, John; Cuthbert, Richard; Hilton, Geoff M
    The IUCN recently uplisted the Tristan albatross (Diomedea dabbenena) to Critically Endangered. Here we present new data indicating negative population trends on Gough Island arising from low adult survival (∼91%, ascribed to accidental mortality on fishing gear) and low breeding success (averaging 32%, due to mouse predation). Fledgling production from 1979 to 2007 and numbers of incubating adults from 1956 to 2007 have both decreased by ∼1% p.a. Consecutive annual counts of incubating adults and a population model permit the first reliable estimates of the Tristan albatross population, presently 5400 breeding adults and 11,300 birds in all age- and stage-classes. Population models explore scenarios of likely demographic trends using combinations of hypothetical best-case estimates vs. observed estimates for two key parameters: adult survival and breeding success. These scenarios highlight the relative benefits to the species of eradicating mice or mitigating bycatch. The model scenario using observed estimates predicts annual growth rate at −2.85%. Adult survival rates have probably decreased in recent years, concomitant with increased longline fishing effort, which might explain the discrepancy between counts and modelled trends. Negative trends cannot be reversed by improving breeding success alone, and adult survival must exceed an improbable 97% to balance the current chick production. A worst-case scenario including a fixed number of adult deaths annually predicted a catastrophic 4.2% p.a. decrease and extinction in ∼30 years. Population growth was most sensitive to adult survival, but even using an adult survival estimate without fishery mortality, current breeding success is insufficient to maintain the population. These findings do not support the ‘compensatory mitigation of bycatch’ model (offsetting bycatch impacts by eradicating invasive species), and the impacts of both fishery mortality and mouse predation must be addressed to improve the conservation status of the Critically Endangered Tristan albatross.
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    Geographic range dynamics of South Africa's bird species
    (2014) Loftie-Eaton, Megan; Underhill, Les; Altwegg, Res
    A key issue in species conservation is a knowledge of the geographic ranges of species, and how these are changing through time. For birds there is a special opportunity to undertake studies of range changes, making use of the data collected by the First and Second Southern African Bird Atlas Projects (SABAP1 and SABAP2), which are separated in time by about two decades. In this thesis, I first describe the strengths and the weaknesses of the databases collected by these two citizen science projects, and therefore discuss the limitations placed on the analyses. We then undertake two sets of analyses, one focused on species, and one focused on areas. I show that, across all species, the Family to which the species belongs is an explanatory variable which explains approximately 45% of range expansion or contraction of a species. Diet and mass are also significant explanatory variables. For the analyses by areas, we demonstrate that the general encroachment of shrubs and trees in the savanna biome appears to have had a profound impact on the occurrence and abundance of a large suit of bird species, with the small insectivores and frugivores showing the largest increases.
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    Martial eagles and the national power grid in South Africa: the implications of pylon-nesting for conservation management
    (2015) Berndt, Jessie; Jenkins, Andrew R; Altwegg, Res; Amar, Arjun
    Many large, sparsely distributed raptors are threatened by a host of anthropogenic factors, while a minority may actually benefit from some aspects of development and environmental change. Clarity on the size and trajectory of such populations is essential for effective conservation management, but can be difficult to achieve. One solution is to use multivariate habitat association models to derive critical estimates of distribution and abundance. The South African population of Martial Eagle Polemaetus bellicosus is currently estimated at < 800 adult birds , with the bulk of the known population believed to be residing in the larger protected areas. However, Martial Eagles also build nests on pylons that support high voltage transmission lines running through the largely treeless, semiarid landscapes of the Karoo. The main aim of this study was to develop a better understanding of the environmental factors that influence Martial Eagle territory densities and locations along South African transmission lines, and thereby estimate the size of this population and its relative importance to the national conservation status of this globally threatened species. I used habitat association models to d escribe Martial Eagle territory density in relation to eight environmental covariates. Models were first fitted to eagle territory data for the central Karoo regions, collected and pooled over the period 2002 - 2006, and then applied to predict the number of pairs present on each of three adjacent sections of unsurveyed line (northern, southern and eastern lines) . Once these model predictions were verified by a series of aerial and ground surveys, I fitted the models to all the known Martial Eagle territory records for the transmission network and extrapolated from these back to the rest of the network using the fitted relationships. Ultimately, the models predicted 52 additional Martial Eagle territories on the remaining transmission network with a confidence interval ranging from 38 to 67 (based on models that explained up to 39 % of the total variance in terms of only two explanatory terms – rainfall and the proportion of cultivated land). I then examined the role of territoriality and social structure in the eagle population in determining the location and dispersion of pylon nests. To do this I used the location of active nests from the original central Karoo data and a similar number of randomly selected points. I then asked whether I could predict the nest locations from each of the eight environmental covariates and distance to its nearest conspecific active nest or its nearest nest of any other large eagle species. Using a logistic generalised linear model with regression splines for distance to nearest other nest, I found that Martial Eagles strongly avoid proximity to conspecific nests (mean distance to conspecific nest = 28.2 km, range 2.5 - 167.1 km, n = 306). This result shows that minimum spacing should be considered in predicting the distribution of eagles on unsurveyed transmission lines. Lastly, I further investigated the geographical extent of pylon nesting in South African Martial Eagles, with particular focus on variation in the frequency of this behaviour in relation to biome - scale variation in the availability of trees as natural nest sites. To do this, I related Martial Eagle reporting rates generated by citizen - science bird atlas data to the density of transmission lines and biome types across South Africa. While these analyses yielded some suggestive results, such as significant positive and negative relationships between reporting rates and line density in the Desert (P = 0.02) versus the Savanna (P < 0.001) biomes respectively, data sparseness in arid areas and a generally low detection probability limited the conclusiveness of these results. The refined habitat association models developed in this study predict that the South African transmission grid supports 130 - 159 breeding pairs of Martial Eagle. This figure has never been estimated or calculated before, and suggests that 36 % of the national breeding population could reside largely in the commercial ranchland and nest on man - made structures. This result, which is at odds with the generally held belief that the Martial Eagle is increasingly confined to large protected areas, has significant implications for the thinking around the conservation management of this globally threatened species.
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    Modelling the range-wide density patterns of the Arthroleptella lightfooti using acoustic monitoring data
    (2019) Poongavanan, Jenicca; Altwegg, Res; Durbach, Ian; Measev, John
    Species distributions are often limited by environmental factors and according to the abundant—centre hypothesis, abundance should be highest Where the environment is most favourable for the species. So, do the same environmental factors determine occurrence and abundance patterns inside the range? I examined this question using Arthroleptella lightfooti, a species of frog from the family of Pyxicephalidae, endemic to the mountains of the Cape peninsula. South Africa. I used density estimates obtained from acoustic Spatially Explicit Capture Recapture (aSCR) methods and data from an acoustic survey using an array of 6 microphones to construct the first Peninsula wide population-density surface for this visually cryptic but acoustically active species. The analysis consisted of three stages. The first involved creating two sets of data from the original: one shows whether the species is present or not and the other indicates the density when the species is present. The second stage consisted of fitting a Hurdle Model to the data where the presence data is modelled using logistic regression and the density data is separately modelled using ordinary linear regression. The third stage involved combining the two models to estimate the expected density of the species. Confidence intervals were built using non-parametric bootstrapping. It was found that covariates explaining variation in occurrence were not the same as those explaining variation in density, suggesting that processes determining occurrence were not always those determining density. Of the environmental conditions examined, although predictive of occurrence, were generally poor predictors of A. lightfooti density. Presence of the Lightfoot’s moss frog was largely explained by topographic features and availability of water. In contrast. predictions of density were only weakly related to these same environmental factors and in some cases contradicting one another. The second part of this study produces the first Peninsula wide population density surface of A. 11'ghtfo0t1'. At the same time, it assesses the ability of using opportunistically collected presence-only records in combination with the higher quality density data to improve the estimation of expected population-density surface of A. Iightfooti. The presence-only records were constructed into a habitat suitability map using an ensemble of species distribution models. The habitat suitability map was then integrated in the modelling framework as a covariate in order to improve the estimation of expected population—(lensity surface of A. liglitfooti. However, the habitat suitability covariate resulted as being uninformative.
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    Movement of the Cape dwarf chameleon (Bradypodion pumilum): are they vulnerable to habitat fragmentation?
    (2014) Rebelo, Alexander Douglas; Tolley, Krystal A; Altwegg, Res
    Habitat fragmentation threatens the persistence of natural populations globally. Dispersal between populations can mitigate the negative impacts of habitat fragmentation. The Cape dwarf chameleon (Bradypodion pumilum) occupies heavily fragmented habitat and yet few studies have investigated their ability to disperse and thus persist. In this study I monitored chameleon movements and habitat use in the semi-transformed Noordhoek Wetlands, South Africa. Radio-telemetry was used to track adult chameleons (N=11) over 10 days during March 2010 and April 2014. Data were analysed using linear mixed effects models including relevant predictor variables. The chameleon habitat use, such as perch height, thickness and vegetation cover, including their GPS positions, was recorded hourly during the day. The increase in area used by chameleons over time increased at a relatively constant rate. Male and females showed similar areas of utilisation and daily displacement. However, males perched in higher, in less dense vegetation and on relatively thicker stems than females, although the latter two were not statistically supported. Additionally, chameleon vegetation use varied between day and night, but not between early morning, midday and late afternoon, where chameleons perched in higher and less dense vegetation at night than during the day. Habitats surrounded by wide spaces devoid of vegetation could isolate populations of Cape dwarf chameleons. However, the chameleon movement is unhindered by constraints of territory and by connecting habitat fragments together with corridors of suitable vegetation, the effects of fragmentation could be mitigated.
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    Phenological changes in the Southern Hemisphere
    (Public Library of Science, 2013) Chambers, Lynda E; Altwegg, Res; Barbraud, Christophe; Barnard, Phoebe; Beaumont, Linda J; Crawford, Robert J M; Durant, Joel M; Hughes, Lesley; Keatley, Marie R; Low, Matt
    Current evidence of phenological responses to recent climate change is substantially biased towards northern hemisphere temperate regions. Given regional differences in climate change, shifts in phenology will not be uniform across the globe, and conclusions drawn from temperate systems in the northern hemisphere might not be applicable to other regions on the planet. We conduct the largest meta-analysis to date of phenological drivers and trends among southern hemisphere species, assessing 1208 long-term datasets from 89 studies on 347 species. Data were mostly from Australasia (Australia and New Zealand), South America and the Antarctic/subantarctic, and focused primarily on plants and birds. This meta-analysis shows an advance in the timing of spring events (with a strong Australian data bias), although substantial differences in trends were apparent among taxonomic groups and regions. When only statistically significant trends were considered, 82% of terrestrial datasets and 42% of marine datasets demonstrated an advance in phenology. Temperature was most frequently identified as the primary driver of phenological changes; however, in many studies it was the only climate variable considered. When precipitation was examined, it often played a key role but, in contrast with temperature, the direction of phenological shifts in response to precipitation variation was difficult to predict a priori . We discuss how phenological information can inform the adaptive capacity of species, their resilience, and constraints on autonomous adaptation. We also highlight serious weaknesses in past and current data collection and analyses at large regional scales (with very few studies in the tropics or from Africa) and dramatic taxonomic biases. If accurate predictions regarding the general effects of climate change on the biology of organisms are to be made, data collection policies focussing on targeting data-deficient regions and taxa need to be financially and logistically supported.