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.

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.

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.

Mechanistic reconciliation of community and invasion ecology.

Community and invasion ecology have mostly grown independently. There is substantial overlap in the processes captured by different models in the two fields, and various frameworks have been developed to reduce this redundancy and synthesize information content. Despite broad recognition that community and invasion ecology are interconnected, a process-based framework synthesizing models across these two fields is lacking. Here we review 65 representative community and invasion models and propose a common framework articulated around six processes (dispersal, drift, abiotic interactions, within-guild interactions, cross-guild interactions, and genetic changes). The framework is designed to synthesize the content of the two fields, provide a general perspective on their development, and enable their comparison. The application of this framework and of a novel method based on network theory reveals some lack of coherence between the two fields, despite some historical similarities. Community ecology models are characterized by combinations of multiple processes, likely reflecting the search for an overarching theory to explain community assembly and structure, drawing predominantly on interaction processes, but also accounting largely for the other processes. In contrast, most models in invasion ecology invoke fewer processes and focus more on interactions between introduced species and their novel biotic and abiotic environment. The historical dominance of interaction processes and their independent developments in the two fields is also reflected in the lower level of coherence for models involving interactions, compared to models involving dispersal, drift, and genetic changes. It appears that community ecology, with a longer history than invasion ecology, has transitioned from the search for single explanations for patterns observed in nature to investigate how processes may interact mechanistically, thereby generating and testing hypotheses. Our framework paves the way for a similar transition in invasion ecology, to better capture the dynamics of multiple alien species introduced in complex communities. Reciprocally, applying insights from invasion to community ecology will help us understand and predict the future of ecological communities in the Anthropocene, in which human activities are weakening species' natural boundaries. Ultimately, the successful integration of the two fields could advance a predictive ecology that is urgently required in a rapidly changing world.

Why a landscape view is important: nearby urban and agricultural land affects bird abundances in protected areas.

Protected areas are one of the primary conservation tools used worldwide. However, they are often embedded in a landscape that is intensely used by people, such as for agriculture or urban development. The proximity of these land-use types to protected areas can potentially affect the ecological effectiveness (or conservation effectiveness) of protected areas. In this article, we examine to what degree adjacent agricultural and urban land uses affect the ecological effectiveness of protected areas over the greater Gauteng region of South Africa. We selected 198 common, resident bird species, and analysed detection/non-detection data for these species collected over regular grid cells (approximately 61 km2 in area). For each species, we estimated abundance per grid cell with the Royle-Nichols model in relation to the proportion of protected area as a covariate. Our study focused on how this relationship between proportion of protected area and abundance (which we term the 'protection-abundance relationship') changed as a function of other land-use types in the grid cell. Specifically, we examined the interaction effects between protected area and both urban and agricultural land-use type per grid cell on bird abundance. We assigned each species to one of seven guilds, namely: frugivores, gleaners, granivores, ground-feeders, hawkers, predators and vegivores, and examined how the protection-abundance relationship varied across guilds in relation to agriculture and urban area. As urban area within a grid cell increased, the protection-abundance relationship became more positive for 58% of all species. At the level of guilds, the protection-abundance relationship became more positive for two guilds (granivores and ground-feeders), more negative for frugivores, and remained unchanged for the other four guilds (gleaners, hawkers, predators and vegivores). As agricultural area within a grid cell increased, the protection-abundance relationship became more positive for 49% of all species. At the guild level, the protection-abundance relationship became more positive for six guilds (frugivores, gleaners, ground-feeders, hawkers, predators and vegivores) and remained unchanged for the granivores. Our results show land-use type near protected areas modified the effect protected areas had on bird abundances, and hence the ecological effectiveness of protected areas. Our results suggest that protected areas should be viewed as constituents within the landscape, rather than islands of protection.

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.

Allometric relationships shape foreleg evolution of long-legged oil bees (Melittidae: Rediviva).

Exaggerated traits of pollinators have fascinated biologists for centuries. To understand their evolution, and their role in coevolutionary relationships, an essential first step is to understand how traits scale allometrically with body size, which may reveal underlying developmental constraints. Few pollination studies have examined how traits can adaptively diverge despite allometric constraints. Here, we present a comparative study of narrow-sense static and evolutionary allometry on foreleg length and body size of oil-collecting bees. Concurrently, we assess the relationship between scaling parameters and spur lengths of oil-secreting host flowers. Across species and populations, we found low variation in static slopes (nearly all <1), possibly related to stabilizing selection, but the static intercept varied substantially generating an evolutionary allometry steeper than static allometry. Variation in static intercepts was explained by changes in body size (∼28% species; ∼68% populations) and spur length (remaining variance: ∼36% species; ∼94% populations). The intercept-spur length relationship on the arithmetic scale was positive but forelegs did not track spur length perfectly in a one-to-one relationship. Overall, our study provides new insights on how phenotypic evolution in the forelegs of oil-collecting bees is related to the variability of the allometric intercept and adaptation to host plants.

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.

Nest boxes buffer the effects of climate on breeding performance in an African urban raptor.

As the world's human population increases, transformation of natural landscapes into urban habitats continues to increase. In Africa, rates of human population growth and urbanisation are among the highest in the world, but the impacts of these processes on the continent's biodiversity remain largely unexplored. Furthermore, the effects of ongoing anthropogenic climate change are likely to be severe and to interact with urbanisation. Some organisms appear resilient to urbanisation, and even proliferate in human-modified environments. One such species is the peregrine falcon Falco peregrinus in Cape Town, South Africa. Using a long-term data set (1989-2014), we investigate the relationship between breeding attempts, timing of breeding and breeding performance under varying weather conditions. Exploring these issues along an urbanisation gradient, we focus on the role of artificially provided nest boxes, and their capacity to buffer against extreme weather events. Pairs in more urbanised areas, and particularly those in nest boxes, were more likely to breed and to commence breeding earlier. Additionally, pairs using nest boxes were more likely to breed in years with higher rainfall. Warm and dry weather conditions generally advanced the timing of breeding, although this relationship with weather was not seen for urban pairs using nest boxes. Furthermore, weather did not impact breeding performance directly (breeding success and fledged brood size), but timing of breeding did, with earlier breeders producing more fledglings. Our study shows that falcons breeding in specially provided nest boxes were less sensitive to local weather dynamics than pairs using more natural nest sites. This has important implications as it suggests that the managed provision of such nesting sites can help this key urban species to cope with extreme weather events, which are predicted to increase with climate change.

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.

Efficient Bayesian analysis of occupancy models with logit link functions.

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 coefficient 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 develop 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).

Dynamic multi-species occupancy models reveal individualistic habitat preferences in a high-altitude grassland bird community.

Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass height and grass cover through burning and grazing to make habitat suitable for birds. However, different species have individual habitat preferences, which further vary through the season. We used a dynamic multi-species occupancy model to examine the seasonal occupancy dynamics of 12 common grassland bird species and their habitat preferences. We estimated monthly occupancy, colonisation and persistence in relation to grass height and grass cover throughout the summer breeding season of 2011/12. For majority of these species, at the beginning of the season occupancy increased with increasing grass height and decreased with increasing grass cover. Persistence and colonisation decreased with increasing grass height and cover. However, the 12 species varied considerably in their responses to grass height and cover. Our results suggest that management should aim to provide plots which vary in grass height and cover to maximise bird diversity. We also conclude that the decreasing occupancy with increasing grass cover and low colonisation with increasing grass height and cover is a results of little grazing on our study site. We further conclude that some of the 12 selected species are good indicators of habitat suitability more generally because they represent a range of habitat needs and are relatively easy to monitor.

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.

Effectiveness of protected areas for bird conservation depends on guild.

AIM: Protected areas are key conservation tools intended to increase biodiversity and reduce extinction risks of species and populations. However, the degree to which protected areas achieve their conservation goals is generally unknown for many protected areas worldwide. We assess the effect of protected areas on the abundance of 196 common, resident bird species. If protected areas were beneficial to avian biodiversity, we expect landscapes with a higher proportion of protected areas will have higher densities of species compared to landscapes with no protection. LOCATION: Greater Gauteng region, South Africa. METHODS: We analysed bird survey data collected over regular grid cells across the study area. We estimated bird abundance in relation to the proportion of a grid cell that was protected with the Royle-Nichols model and fitted the model once for each of the species. We examined variation in estimated abundance as a function of avian guild (defined by the type of food a species preferentially ate and its foraging mode) with a regression tree analysis. RESULTS: Abundance was significantly positively related to the proportion of protected areas in grid cells for 26% of the species, significantly negatively related in 15%, and not significantly related in 59% species. We found three distinct guild groups which differed in their average abundance, after accounting for associated variance. Group 1 consisted of guilds frugivores, ground-feeders, hawkers, predators, and vegivores and average abundance was strongly positively related to the proportion of protected areas. Group 2 included granivores, and average abundance was strongly negatively related to proportion of protected areas. Group 3 included gleaners only, and average abundance was not related to proportion of protected areas. MAIN CONCLUSION: We conclude that the network of protected areas within the greater Gauteng region sustained relatively higher abundances of common birds and thus perform an important conservation role.

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.

The second Southern African Bird Atlas Project: Causes and consequences of geographical sampling bias.

Using the Southern African Bird Atlas Project (SABAP2) as a case study, we examine the possible determinants of spatial bias in volunteer sampling effort and how well such biased data represent environmental gradients across the area covered by the atlas. For each province in South Africa, we used generalized linear mixed models to determine the combination of variables that explain spatial variation in sampling effort (number of visits per 5' × 5' grid cell, or "pentad"). The explanatory variables were distance to major road and exceptional birding locations or "sampling hubs," percentage cover of protected, urban, and cultivated area, and the climate variables mean annual precipitation, winter temperatures, and summer temperatures. Further, we used the climate variables and plant biomes to define subsets of pentads representing environmental zones across South Africa, Lesotho, and Swaziland. For each environmental zone, we quantified sampling intensity, and we assessed sampling completeness with species accumulation curves fitted to the asymptotic Lomolino model. Sampling effort was highest close to sampling hubs, major roads, urban areas, and protected areas. Cultivated area and the climate variables were less important. Further, environmental zones were not evenly represented by current data and the zones varied in the amount of sampling required representing the species that are present. SABAP2 volunteers' preferences in birding locations cause spatial bias in the dataset that should be taken into account when analyzing these data. Large parts of South Africa remain underrepresented, which may restrict the kind of ecological questions that may be addressed. However, sampling bias may be improved by directing volunteers toward undersampled regions while taking into account volunteer preferences.

Learning from single extreme events.

Extreme climatic events (ECEs) have a disproportionate effect on ecosystems. Yet much of what we know about the ecological impact of ECEs is based on observing the effects of single extreme events. We examined what characteristics affect the strength of inference that can be drawn from single-event studies, which broadly fell into three categories: opportunistic observational studies initiated after an ECE, long-term observational studies with data before and after an ECE and experiments. Because extreme events occur rarely, inference from such single-event studies cannot easily be made under the usual statistical paradigm that relies on replication and control. However, single-event studies can yield important information for theory development and can contribute to meta-analyses. Adaptive management approaches can be used to learn from single, or a few, extreme events. We identify a number of factors that can make observations of single events more informative. These include providing robust estimates of the magnitude of ecological responses and some measure of climatic extremeness, collecting ancillary data that can inform on mechanisms, continuing to observe the biological system after the ECE and combining observational data with experiments and models. Well-designed single-event studies are an important contribution to our understanding of biological effects of ECEs.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'.

Drivers of Bird Species Richness within Moist High-Altitude Grasslands in Eastern South Africa.

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.

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.

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.