Drivers and facilitators of the illegal killing of elephants across 64 African sites.

Ivory poaching continues to threaten African elephants. We (1) used criminology theory and literature evidence to generate hypotheses about factors that may drive, facilitate or motivate poaching, (2) identified datasets representing these factors, and (3) tested those factors with strong hypotheses and sufficient data quality for empirical associations with poaching. We advance on previous analyses of correlates of elephant poaching by using additional poaching data and leveraging new datasets for previously untested explanatory variables. Using data on 10 286 illegally killed elephants detected at 64 sites in 30 African countries (2002-2020), we found strong evidence to support the hypotheses that the illegal killing of elephants is associated with poor national governance, low law enforcement capacity, low household wealth and health, and global elephant ivory prices. Forest elephant populations suffered higher rates of illegal killing than savannah elephants. We found only weak evidence that armed conflicts may increase the illegal killing of elephants, and no evidence for effects of site accessibility, vegetation density, elephant population density, precipitation or site area. Results suggest that addressing wider systemic challenges of human development, corruption and consumer demand would help reduce poaching, corroborating broader work highlighting these more ultimate drivers of the global illegal wildlife trade.

Plant richness, turnover, and evolutionary diversity track gradients of stability and ecological opportunity in a megadiversity center.

Research on global patterns of diversity has been dominated by studies seeking explanations for the equator-to-poles decline in richness of most groups of organisms, namely the latitudinal diversity gradient. A problem with this gradient is that it conflates two key explanations, namely biome stability (age and area) and productivity (ecological opportunity). Investigating longitudinal gradients in diversity can overcome this problem. Here we investigate a longitudinal gradient in plant diversity in the megadiverse Cape Floristic Region (CFR). We test predictions of the age and area and ecological opportunity hypotheses using metrics for both taxonomic and phylogenetic diversity and turnover. Our plant dataset includes modeled occurrences for 4,813 species and dated molecular phylogenies for 21 clades endemic to the CFR. Climate and biome stability were quantified over the past 140,000 y for testing the age and area hypothesis, and measures of topographic diversity, rainfall seasonality, and productivity were used to test the ecological opportunity hypothesis. Results from our spatial regression models showed biome stability, rainfall seasonality, and topographic heterogeneity were the strongest predictors of taxonomic diversity. Biome stability alone was the strongest predictor of all diversity metrics, and productivity played only a marginal role. We argue that age and area in conjunction with non-productivity-based measures of ecological opportunity explain the CFR's longitudinal diversity gradient. We suggest that this model may possibly be a general explanation for global diversity patterns, unconstrained as it is by the collinearities underpinning the latitudinal diversity gradient.

Finding rare species and estimating the probability that all occupied sites have been found.

Detecting occupied sites of rare species, and estimating the probability that all occupied sites are known within a given area, are desired outcomes for many ecological or conservation projects. Examples include managing all occupied sites of a threatened species or eradicating an emerging invader. Occupied sites may remain undetected because (1) sites where the species potentially occurs had not been searched, and (2) the species could have been overlooked in the searched sites. For rare species, available data are typically scant, making it difficult to predict sites where the species probably occurs or to estimate detection probability in the searched sites. Using the critically endangered Rose's mountain toadlet (Capensibufo rosei), known from only two localities, we outline an iterative process aimed at estimating the probability that any unknown occupied sites remain and maximizing the chance of finding them. This includes fitting a species distribution model to guide sampling effort, testing model accuracy and sampling efficacy using the occurrence of more common proxy species, and estimating detection probability using sites of known presence. The final estimate of the probability that all occupied sites were found incorporates the uncertainties of uneven distribution, relative area searched, and detection probability. Our results show that very few occupied sites of C. rosei are likely to remain undetected. We also show that the probability of an undetected occupied site remaining will always be high for large unsearched areas of potential occurrence, but can be low for smaller areas intended for targeted management interventions. Our approach is especially useful for assessing uncertainty in species occurrences, planning the required search effort needed to reduce probability of unknown occurrence to desired levels, and identifying priority areas for further searches or management interventions.

Does a trade-off between growth plasticity and resource conservatism mediate post-fire shrubland responses to rainfall seasonality?

Growth plasticity may allow fire-prone species to maximize their recovery rates during temporary, sporadic periods of rainfall availability in the post-fire environment. However, moisture-driven growth plasticity could be maladaptive in nutrient-limited environments that require tighter control of growth and resource use. We investigated whether a trade-off between plasticity and conservatism mediates growth responses to altered rainfall seasonality in neighbouring shrubland communities that occupy different soils. We monitored post-fire vegetation regrowth in two structurally similar, Mediterranean-type shrublands for 3 years. We investigated the effects of experimentally altered rainfall seasonality on post-fire species' growth rates. We found that moisture-driven growth plasticity was higher among species occupying the fertile soils of the renosterveld site relative to those occupying the nutrient-poor soils of the fynbos site. This resulted in higher overall responsiveness of post-fire recovery patterns in renosterveld to experimental shifts in rainfall seasonality. In post-fire shrubland communities, the trade-off between moisture-dependent growth plasticity and resource conservatism could be mediated by soil nutrient availability. Therefore, edaphic differences between structurally similar shrublands could lead to differences in their sensitivity to post-fire rainfall seasonality.

Are animals shrinking due to climate change? Temperature-mediated selection on body mass in mountain wagtails.

Climate change appears to affect body size of animals whose optimal size in part depends on temperature. However, attribution of observed body size changes to climate change requires an understanding of the selective pressures acting on body size under different temperatures. We examined the link between temperature and body mass in a population of mountain wagtails (Motacilla clara) in KwaZulu-Natal, South Africa, between 1976 and 1999, where temperature increased by 0.18 [Formula: see text]C. The wagtails became lighter by 0.035 g per year. Partitioning this trend, we found that only a small part of the effect (0.009 g/year) was due to individuals losing weight and a large part (0.027 g/year) was due to lighter individuals replacing heavier ones. Only the latter component was statistically significant. Apparently, the wagtails were reacting to selection for reduced weight. Examining survival, we found that selection was temperature-mediated, i.e., lighter individuals survived better under high temperatures, whereas heavier individuals survived better under low temperatures. Our results thus support the hypothesis that temperature drove the decline in body mass in this wagtail population and provides one of the first demonstrations of the selective forces underlying such trends.

Extreme Climate-Induced Life-History Plasticity in an Amphibian.

Age-specific survival and reproduction are closely linked to fitness and therefore subject to strong selection that typically limits their variability within species. Furthermore, adult survival rate in vertebrate populations is typically less variable over time than other life-history traits, such as fecundity or recruitment. Hence, adult survival is often conserved within a population over time, compared to the variation in survival found across taxa. In stark contrast to this general pattern, we report evidence of extreme short-term variation of adult survival in Rose's mountain toadlet (Capensibufo rosei), which is apparently climate induced. Over 7 years, annual survival rate varied between 0.04 and 0.92, and 94% of this variation was explained by variation in breeding-season rainfall. Preliminary results suggest that this variation reflects adaptive life-history plasticity to a degree thus far unrecorded for any vertebrate, rather than direct rainfall-induced mortality. In wet years, these toads appeared to achieve increased reproduction at the expense of their own survival, whereas in dry years, their survival increased at the expense of reproduction. Such environmentally induced plasticity may reflect a diversity of life-history strategies not previously appreciated among vertebrates.

Climate change leads to increasing population density and impacts of a key island invader.

The considerable threats of invasive rodents to island biodiversity are likely to be compounded by climate change. Forecasts for such interactions have been most pronounced for the Southern Ocean islands where ameliorating conditions are expected to decrease thermal and resource restrictions on rodents. Firm evidence for changing rodent populations in response to climate change, and demonstrations of associated impacts on the terrestrial environment, are nonetheless entirely absent for the region. Using data collected over three decades on sub-Antarctic Marion Island, we tested empirically whether mouse populations have changed through time and whether these changes can be associated significantly with changing abiotic conditions. Changes in invertebrate populations, which have previously been attributed to mouse predation, but with little explicit demographic analysis, were also examined to determine whether they can be associated with changing mouse populations. The total number of mice on the island at annual peak density increased by 430.0% between 1979-1980 and 2008-2011. This increase was due to an advanced breeding season, which was robustly related to the number of precipitation-free days during the non-breeding season. Mice directly reduced invertebrate densities, with biomass losses of up to two orders of magnitude in some habitats. Such invertebrate declines are expected to have significant consequences for ecosystem processes over the long term. Our results demonstrate that as climate change continues to create ameliorating conditions for invasive rodents on sub-Antarctic islands, the severity of their impacts will increase. They also emphasize the importance of rodent eradication for the restoration of invaded islands.

Dynamic occupancy models for explicit colonization processes.

The dynamic, multi-season occupancy model framework has become a popular tool for modeling open populations with occupancies that change over time through local colonizations and extinctions. However, few versions of the model relate these probabilities to the occupancies of neighboring sites or patches. We present a modeling framework that incorporates this information and is capable of describing a wide variety of spatiotemporal colonization and extinction processes. A key feature of the model is that it is based on a simple set of small-scale rules describing how the process evolves. The result is a dynamic process that can account for complicated large-scale features. In our model, a site is more likely to be colonized if more of its neighbors were previously occupied and if it provides more appealing environmental characteristics than its neighboring sites. Additionally, a site without occupied neighbors may also become colonized through the inclusion of a long-distance dispersal process. Although similar model specifications have been developed for epidemiological applications, ours formally accounts for detectability using the well-known occupancy modeling framework. After demonstrating the viability and potential of this new form of dynamic occupancy model in a simulation study, we use it to obtain inference for the ongoing Common Myna (Acridotheres tristis) invasion in South Africa. Our results suggest that the Common Myna continues to enlarge its distribution and its spread via short distance movement, rather than long-distance dispersal. Overall, this new modeling framework provides a powerful tool for managers examining the drivers of colonization including short- vs. long-distance dispersal, habitat quality, and distance from source populations.

Coupled range dynamics of brood parasites and their hosts responding to climate and vegetation changes.

As populations shift their ranges in response to global change, local species assemblages can change, setting the stage for new ecological interactions, community equilibria and evolutionary responses. Here, we focus on the range dynamics of four avian brood parasite species and their hosts in southern Africa, in a context of bush encroachment (increase in woody vegetation density in places previously occupied by savanna-grassland mosaics) favouring some species at the expense of others. We first tested whether hosts and parasites constrained each other's ability to expand or maintain their ranges. Secondly, we investigated whether range shifts represented an opportunity for new host-parasite and parasite-parasite interactions. We used multispecies dynamic occupancy models with interactions, fitted to citizen science data, to estimate the contribution of interspecific interactions to range shifts and to quantify the change in species co-occurrence probability over a 25-year period. Parasites were able to track their hosts' range shifts. We detected no deleterious effect of the parasites' presence on either the local population viability of host species or the hosts' ability to colonize newly suitable areas. In the recently diversified indigobird radiation (Vidua spp.), following bush encroachment, the new assemblages presented more potential opportunities for speciation via host switch, but also more potential for hybridization between extant lineages, also via host switch. Multispecies dynamic occupancy models with interactions brought new insights into the feedbacks between range shifts, biotic interactions and local demography: brood parasitism had little detected impact on extinction or colonization processes, but inversely the latter processes affected biotic interactions via the modification of co-occurrence patterns.

Twenty-five years of change in southern African passerine diversity: nonclimatic factors of change.

We analysed more than 25 years of change in passerine bird distribution in South Africa, Swaziland and Lesotho, to show that species distributions can be influenced by processes that are at least in part independent of the local strength and direction of climate change: land use and ecological succession. We used occupancy models that separate species' detection from species' occupancy probability, fitted to citizen science data from both phases of the Southern African Bird Atlas Project (1987-1996 and 2007-2013). Temporal trends in species' occupancy probability were interpreted in terms of local extinction/colonization, and temporal trends in detection probability were interpreted in terms of change in abundance. We found for the first time at this scale that, as predicted in the context of bush encroachment, closed-savannah specialists increased where open-savannah specialists decreased. In addition, the trend in the abundance of species a priori thought to be favoured by agricultural conversion was negatively correlated with human population density, which is in line with hypotheses explaining the decline in farmland birds in the Northern Hemisphere. In addition to climate, vegetation cover and the intensity and time since agricultural conversion constitute important predictors of biodiversity changes in the region. Their inclusion will improve the reliability of predictive models of species distribution.

Patterns of bird migration phenology in South Africa suggest northern hemisphere climate as the most consistent driver of change.

Current knowledge of phenological shifts in Palearctic bird migration is largely based on data collected on migrants at their breeding grounds; little is known about the phenology of these birds at their nonbreeding grounds, and even less about that of intra-African migrants. Because climate change patterns are not uniform across the globe, we can expect regional disparities in bird phenological responses. It is also likely that they vary across species, as species show differences in the strength of affinities they have with particular habitats and environments. Here, we examine the arrival and departure of nine Palearctic and seven intra-African migratory species in the central Highveld of South Africa, where the former spend their nonbreeding season and the latter their breeding season. Using novel analytical methods based on bird atlas data, we show phenological shifts in migration of five species - red-backed shrike, spotted flycatcher, common sandpiper, white-winged tern (Palearctic migrants), and diederik cuckoo (intra-African migrant) - between two atlas periods: 1987-1991 and 2007-2012. During this time period, Palearctic migrants advanced their departure from their South African nonbreeding grounds. This trend was mainly driven by waterbirds. No consistent changes were observed for intra-African migrants. Our results suggest that the most consistent drivers of migration phenological shifts act in the northern hemisphere, probably at the breeding grounds.

Bottom-up effects of a no-take zone on endangered penguin demographics.

Marine no-take zones can have positive impacts for target species and are increasingly important management tools. However, whether they indirectly benefit higher order predators remains unclear. The endangered African penguin (Spheniscus demersus) depends on commercially exploited forage fish. We examined how chick survival responded to an experimental 3-year fishery closure around Robben Island, South Africa, controlling for variation in prey biomass and fishery catches. Chick survival increased by 18% when the closure was initiated, which alone led to a predicted 27% higher population compared with continued fishing. However, the modelled population continued to decline, probably because of high adult mortality linked to poor prey availability over larger spatial scales. Our results illustrate that small no-take zones can have bottom-up benefits for highly mobile marine predators, but are only one component of holistic, ecosystem-based management regimes.

Fire-mediated disruptive selection can explain the reseeder-resprouter dichotomy in Mediterranean-type vegetation.

Crown fire is a key selective pressure in Mediterranean-type plant communities. Adaptive responses to fire regimes involve trade-offs between investment for persistence (fire survival and resprouting) and reproduction (fire mortality, fast growth to reproductive maturity, and reseeding) as investments that enhance adult survival lower growth and reproductive rates. Southern hemisphere Mediterranean-type ecosystems are dominated by species with either endogenous regeneration from adult resprouting or fire-triggered seedling recruitment. Specifically, on nutrient-poor soils, these are either resprouting or reseeding life histories, with few intermediate forms, despite the fact that the transition between strategies is evolutionarily labile. How did this strong dichotomy evolve? We address this question by developing a stochastic demographic model to assess determinants of relative fitness of reseeders, resprouters and hypothetical intermediate forms. The model was parameterised using published demographic data from South African protea species and run over various relevant fire regime parameters facets. At intermediate fire return intervals, trade-offs between investment in growth versus fire resilience can cause fitness to peak at either of the extremes of the reseeder-resprouter continuum, especially when assuming realistic non-linear shapes for these trade-offs. Under these circumstances, the fitness landscape exhibits a saddle which could lead to disruptive selection. The fitness gradient between the peaks was shallow, which may explain why this life-history trait is phylogenetically labile. Resprouters had maximum fitness at shorter fire-return intervals than reseeders. The model suggests that a strong dichotomy in fire survival strategy depends on a non-linear trade-off between growth and fire persistence traits.

Melanin-specific life-history strategies.

The maintenance of genetic variation is a long-standing issue because the adaptive value of life-history strategies associated with each genetic variant is usually unknown. However, evidence for the coexistence of alternative evolutionary fixed strategies at the population level remains scarce. Because in the tawny owl (Strix aluco) heritable melanin-based coloration shows different physiological and behavioral norms of reaction, we investigated whether coloration is associated with investment in maintenance and reproduction. Light melanic owls had lower adult survival compared to dark melanic conspecifics, and color variation was related to the trade-off between offspring number and quality. When we experimentally enlarged brood size, light melanic males produced more fledglings but in poorer condition, and they were less often recruited in the local breeding population than those of darker melanic conspecifics. Our results also suggest that dark melanic males allocate a constant effort to raise their brood independently of environmental conditions, whereas lighter melanic males finely adjust reproductive effort in relation to changes in environmental conditions. Color traits can therefore be associated with life-history strategies, and stochastic environmental perturbation can temporarily favor one phenotype over others. The existence of fixed strategies implies that some phenotypes can sometimes display a "maladapted" strategy. Long-term population monitoring is therefore vital for a full understanding of how different genotypes deal with trade-offs.

Spatial occupancy models applied to atlas data show Southern Ground Hornbills strongly depend on protected areas.

Determining the range of a species and exploring species--habitat associations are central questions in ecology and can be answered by analyzing presence--absence data. Often, both the sampling of sites and the desired area of inference involve neighboring sites; thus, positive spatial autocorrelation between these sites is expected. Using survey data for the Southern Ground Hornbill (Bucorvus leadbeateri) from the Southern African Bird Atlas Project, we compared advantages and disadvantages of three increasingly complex models for species occupancy: an occupancy model that accounted for nondetection but assumed all sites were independent, and two spatial occupancy models that accounted for both nondetection and spatial autocorrelation. We modeled the spatial autocorrelation with an intrinsic conditional autoregressive (ICAR) model and with a restricted spatial regression (RSR) model. Both spatial models can readily be applied to any other gridded, presence--absence data set using a newly introduced R package. The RSR model provided the best inference and was able to capture small-scale variation that the other models did not. It showed that ground hornbills are strongly dependent on protected areas in the north of their South African range, but less so further south. The ICAR models did not capture any spatial autocorrelation in the data, and they took an order, of magnitude longer than the RSR models to run. Thus, the RSR occupancy model appears to be an attractive choice for modeling occurrences at large spatial domains, while accounting for imperfect detection and spatial autocorrelation.

Climate, social factors and research disturbance influence population dynamics in a declining sociable weaver metapopulation.

Population trends are determined by gains through reproduction and immigration, and losses through mortality and emigration. These demographic quantities and resulting population dynamics are affected by different external and internal drivers. We examined how these demographic quantities were affected by weather, research-induced disturbance, local density, colony site and year in a metapopulation of 17 sociable weaver (Philetairus socius) colonies over 17 years of study (4 years for reproduction). Most colonies declined, but at different rates. The four demographic quantities were related to different drivers. Survival strongly varied among years and colonies and was positively related to rainfall and negatively related to extreme temperature (together explaining 30% of variation) and disturbance (measured as number of captures conducted at a colony; 7%). There was a trend for a positive relationship between reproduction and rainfall (50%). Movement was mainly related to local density: individuals were more likely to emigrate from small to large colonies and from colonies that were either well below or above their long-term mean. They were more likely to immigrate into colonies that were nearby, and below their mean size. We then quantified the effects of these relationships on metapopulation dynamics using a multi-site matrix projection model. Rainfall was potentially a strong driver of metapopulation dynamics. In addition, field-work disturbance might have contributed to the decline of this metapopulation but could not explain its full magnitude. Hence, through a combination of analytical methods we were able to obtain information on the main drivers affecting dynamics in a declining metapopulation.

How life history influences population dynamics in fluctuating environments.

A major question in ecology is how age-specific variation in demographic parameters influences population dynamics. Based on long-term studies of growing populations of birds and mammals, we analyze population dynamics by using fluctuations in the total reproductive value of the population. This enables us to account for random fluctuations in age distribution. The influence of demographic and environmental stochasticity on the population dynamics of a species decreased with generation time. Variation in age-specific contributions to total reproductive value and to stochastic components of population dynamics was correlated with the position of the species along the slow-fast continuum of life-history variation. Younger age classes relative to the generation time accounted for larger contributions to the total reproductive value and to demographic stochasticity in "slow" than in "fast" species, in which many age classes contributed more equally. In contrast, fluctuations in population growth rate attributable to stochastic environmental variation involved a larger proportion of all age classes independent of life history. Thus, changes in population growth rates can be surprisingly well explained by basic species-specific life-history characteristics.

Novel methods reveal shifts in migration phenology of barn swallows in South Africa.

Many migratory bird species, including the barn swallow (Hirundo rustica), have advanced their arrival date at Northern Hemisphere breeding grounds, showing a clear biotic response to recent climate change. Earlier arrival helps maintain their synchrony with earlier springs, but little is known about the associated changes in phenology at their non-breeding grounds. Here, we examine the phenology of barn swallows in South Africa, where a large proportion of the northern European breeding population spends its non-breeding season. Using novel analytical methods based on bird atlas data, we show that swallows first arrive in the northern parts of the country and gradually appear further south. On their north-bound journey, they leave South Africa rapidly, resulting in mean stopover durations of 140 days in the south and 180 days in the north. We found that swallows are now leaving northern parts of South Africa 8 days earlier than they did 20 years ago, and so shortened their stay in areas where they previously stayed the longest. By contrast, they did not shorten their stopover in other parts of South Africa, leading to a more synchronized departure across the country. Departure was related to environmental variability, measured through the Southern Oscillation Index. Our results suggest that these birds gain their extended breeding season in Europe partly by leaving South Africa earlier, and thus add to scarce evidence for phenology shifts in the Southern Hemisphere.

What can occupancy models gain from time-to-detection data?

The time taken to detect a species during site occupancy surveys contains information about the observation process. Accounting for the observation process leads to better inference about site occupancy. We explore the gain in efficiency that can be obtained from time-to-detection (TTD) data and show that this model type has a significant benefit for estimating the parameters related to detection intensity. However, for estimating occupancy probability parameters, the efficiency improvement is generally very minor. To explore whether TTD data could add valuable information when detection intensities vary between sites and surveys, we developed a mixed exponential TTD occupancy model. This new model can simultaneously estimate the detection intensity and aggregation parameters when the number of detectable individuals at the site follows a negative binomial distribution. We found that this model provided a much better description of the occupancy patterns than conventional detection/nondetection methods among 63 bird species data from the Karoo region of South Africa. Ignoring the heterogeneity of detection intensity in the TTD model generally yielded a negative bias in the estimated occupancy probability. Using simulations, we briefly explore study design trade offs between numbers of sites and surveys for different occupancy modeling strategies.

Generation time and temporal scaling of bird population dynamics.

Theoretical studies have shown that variation in density regulation strongly influences population dynamics, yet our understanding of factors influencing the strength of density dependence in natural populations still is limited. Consequently, few general hypotheses have been advanced to explain the large differences between species in the magnitude of population fluctuations. One reason for this is that the detection of density regulation in population time series is complicated by time lags induced by the life history of species that make it difficult to separate the relative contributions of intrinsic and extrinsic factors to the population dynamics. Here we use population time series for 23 bird species to estimate parameters of a stochastic density-dependent age-structured model. We show that both the strength of total density dependence in the life history and the magnitude of environmental stochasticity, including transient fluctuations in age structure, increase with generation time. These results indicate that the relationships between demographic and life-history traits in birds translate into distinct population dynamical patterns that are apparent only on a scale of generations.