Habitats as predictors in species distribution models: Shall we use continuous or binary data?

The representation of a land cover type (i.e. habitat) within an area is often used as an explanatory variable in species distribution models. However, it is possible that a simple binary presence/absence of the suitable habitat might be the most important determinant of the presence/absence of some species and, thus, be a better predictor of species occurrence than the continuous parameter (area). We hypothesize that the binary predictor is more suitable for relatively rare habitats (e.g. wetlands) while for common habitats (e.g. forests) the amount of the focal habitat is a better predictor. We used the Third Atlas of Breeding Birds in the Czech Republic as the source of species distribution data and CORINE Land Cover inventory as the source of the landcover information. To test our hypothesis, we fitted generalized linear models of 32 water and 32 forest bird species. Our results show that for water bird species, models using binary predictors (presence/absence of the habitat) performed better than models with continuous predictors (i.e. the amount of the habitat); for forest species, however, we observed the opposite. Thus, future studies using habitats as predictors of species occurrences should consider the prevalence of the habitat in the landscape, and the biological role of the habitat type in the particular species' life history. In addition, performing a preliminary comparison of the performance of the binary and continuous versions of habitat predictors (e.g. using information criteria) prior to modelling, during variable selection, can be beneficial. These are simple steps that will improve explanatory and predictive performance of models of species distributions in biogeography, community ecology, macroecology and ecological conservation

Landscape-level effects of forest on pollinators and fruit set of guava (<i>Psidium guajava</i> L.) in orchards across Southern Thailand

Pollination by wild pollinators is a key ecosystem service threatened by anthropogenic-induced land-use change. The proximity to natural habitat has previously been shown to positively affect pollinator communities and improve crop yield and quality but empirical evidence is limited from most parts of the World. Here, across six farms in Southern Thailand, we investigated the significance of landscape-level effects of natural habitat (proportion of and distance to evergreen forest) on both visitation rate and richness of pollinators as well as fruit set of guava (Psidium guajava L.), a local economically-important crop in the tropics. Overall, the most abundant pollinator was the Asian honey bee Apis cerana (39% of all visits) and different species of stingless bees (37%). We found that pollinator richness was unrelated to the proportion and distance to evergreen forest, however, the proportion of forest within a 1, 5 and 10 km radius had a significant positive impact on visitation rate of wild pollinators. Still, neither the various forest parameters nor pollinator visitation rate showed a significant impact on fruit set of guava, perhaps because guava self-pollinates. This illustrates that landscape-level degradation of natural habitat may negatively impact pollinator communities without diminishing the crop yield of the farmers

Use of response guilds of understory birds in threatened subtropical forest to monitor selective logging impact

Unplanned logging is one of the greatest current threats to native forests biodiversity. About 90% of the piedmont forest in the Southern Andean Yungas has been converted to other land-use types and the remaining forests fragments are being intensively logged without management plans. Bird species, especially understory birds, are good indicators of forest diversity and integrity. The aim of this study was to identify understory bird species associated with changes in the forest structure caused by selective logging and to explore whether it is possible to use these species as a monitoring tool. We observed that Sittasomus griseicapillus, Turdus rufiventris, Lepidocolaptes angustirostris, Casiornis rufus, Thraupis sayaca, and Tolmomyias sulphurescens were associated to unlogged sites with higher density of timber-yielding and standing dead trees. Thamnophilus caerulescens, Leptotila megalura, Synallaxis scutata, Poecilotriccus plumbeiceps, and Catharus ustulatus were favoured by logging activities and associated with understory visual obstruction. Mean cut-off abundance thresholds were 2.74 ind/ha for the avian guild associated with unlogged forest and 1.79 ind/ha for the guild associated with logged forest. Sustainable forest management schemes need to retain the understory visual obstruction at values similar to those of unlogged forest (43.75%), together with an adequate density (≥10 ind/ha) of standing dead trees with at least 19.5 cm in DBH, and a minimum of 210 ind/ha of timber tree species. Bird species identified in this study can be used in monitoring schemes to evaluate the implementation of these guidelines.Fil: Tallei, Ever Denis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Rivera, Luis Osvaldo. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Schaaf, Alejandro Alberto. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Vivanco, Constanza Guadalupe. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Politi, Natalia. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; Argentin

Modelling nonlinear responses of a desert rodent species to environmental change with hierarchical dynamic generalized additive models

Modelling abundance fluctuations of species is a crucial first step for understanding and forecasting system dynamics under future conditions. But, especially in multivariate response data, this can be hampered by characteristics of the study system such as unknown complexity, differently formed spatial and temporal dependency, non-linear relationships, and observation characteristics such as zero-inflation. This study aimed to explore how such challenges can be addressed by using hierarchical Dynamic Generalized Additive Models (DGAM) for multivariate count responses in a Bayesian framework while modelling multi-site monthly captures for the Desert Pocket Mouse (Chaetodipus penicillatus) over 23 years from a long-term study in Arizona, USA. By fitting models of increasing complexity and developing bespoke checking functions that captured targeted ecological aspects such as spatio-temporal dependence, we show how nonlinear dynamic models can be built to improve forecasts for multivariate count-valued time series.We found strong evidence that accounting for non-linear and time-lagged effects of as much as 12 months improved model fit and forecasting performance. Evaluation of models for other species in geographically different habits is essential for generalizing model strategies and insights into long-term abundance-environment relationships, while systematic comparisons will only be possible if multivariate modelling workflows account for the complexity of non-linear and lagged effects and potentially also other aspects such as biotic interactions

The global exposure of species ranges and protected areas to forest management

Aim Many vertebrate species globally are dependent on forests, most of which require active protection to safeguard global biodiversity. Forests, however, are increasingly either being disturbed, planted or managed in the form of timber or food plantations. Because of a lack of spatial data, forest management has commonly been ignored in previous conservation assessments. Location Global. Methods We combine a new global map of forest management types created solely from remote sensing imagery with spatially explicit information on the distribution of forest-associated vertebrate species and protected areas globally. Using Bayesian logistic regressions, we explore whether the amount of forested habitat available to a species as well as information on species-specific threats can explain differences in IUCN extinction risk categories. Results We show that disturbed and human-managed forests dominate the distributional ranges of most forest-associated species. Species considered as non-threatened had on average larger amounts of non-managed forests within their range. A greater amount of planted forests did not decrease the probability of species being threatened by extinction. Even more worrying, protected areas are increasingly being established in areas dominated by disturbed forests. Conclusion Our results imply that species extinction risk and habitat assessments might have been overly optimistic with forest management practices being largely ignored so far. With forest restoration being at the centre of climate and conservation policies in this decade, we caution that policy makers should explicitly consider forest management in global and regional assessments

Detecting ecological thresholds for biodiversity in tropical forests: Knowledge gaps and future directions

Protecting tropical forests and their biological diversity is a global priority. Understanding if thresholds of forest cover exist beyond which biodiversity displays non-linear declines is key to developing appropriate conservation strategies and policies, but uncertainty remains around the identification and characteristics of these thresholds. We performed a global systematic review of studies using forest cover gradient to identify an ecological threshold across tropical forest ecosystems. Our systematic review finds 68 ecological thresholds reported in 33 peer-reviewed publications. Three main conclusions emerged: first, we show clear geographical gaps in ecological thresholds studies, with 72% of reported thresholds found in South America, over half in Brazil; second, we see ecological threshold studies follow taxonomic biases in line with wider conservation research; and third, there is a lack of homogeneity and comparability in the metrics and sampling designs used to identify a threshold. This global review shows interest in ecological thresholds continues to grow, but further evidence is needed to understand their application in tropical forest management. We identify the main gaps in knowledge and provide guidance to focus research efforts on six key aspects to better understand their potential as a policy-making tool for tropical forest conservation

Avian communities and ecoacoustics in a tropical human-modified landscape

Large areas of the tropics have been cleared of forest and converted to agriculture. The consequent human-modified landscapes (HMLs) comprise a heterogenous mix of habitats; forest fragments and riparian strips are embedded in a matrix of cattle pasture, non-native timber plantations, and urban centres. These habitat changes can have dramatic consequences for wildlife, leading to range shifts and extirpations. In turn, this can influence the integrity of ecosystem services such as frugivory and seed dispersal. Understanding how habitat conversion affects natural ecosystems is critical to inform conservation interventions, but requires long-term biodiversity monitoring and detailed knowledge of species-level responses to HMLs. The research presented in this thesis was conducted in the Emparador HML, in central Republic of Panama. In Chapter 2, we show that the regional avian community is shaped by extent of forest cover across the landscape, and to a lesser degree, extent of forest fragmentation and distance to core forest. Effects of forest cover and fragmentation were examined at local (10 ha) and landscape (500 ha) scales. Species-level responses to these factors varied widely; while abundance of many species increased with greater local-scale forest cover, greater landscape-scale forest cover was often associated with declines. Generalist species that readily persist in HMLs still responded positively to local-scale forest cover, suggesting that even smaller forest fragments in these landscapes are important for maintaining diverse avian assemblages. Critically, we found that species’ responses were not associated with particular traits such as dietary composition or forest dependence, highlighting that species may often exhibit idiosyncratic responses to landscape structure. Chapters 3 and 4 address the wider issue of long-term monitoring, and the potential for data collection over large spatiotemporal scales using remote audio recorders. Ecoacoustics, the study of environmental sound is a relatively new discipline, and as such there is still considerable uncertainty surrounding best-practice for collecting and processing recordings. One of the most straightforward means of utilising audio recordings for environmental monitoring is via acoustic indices. These are objective measures of sound based on features such as pitch and amplitude. To date, attempts to use these indices have been hindered by inconsistent or inappropriate methodologies. In Chapter 3, we determine how many recordings are required to comprehensively capture a soundscape, the acoustic energy of a location. Furthermore, we demonstrate that there are habitat-specific patterns in acoustic indices values, suggesting that these indices reflect differences in vegetation structure and wildlife. We develop this further in Chapter 4, where we show that avian species richness and abundance are clearly linked to patterns in acoustic indices values. Critically, these patterns were coherent among habitat types emphasising their potential for monitoring. Acoustic indices sensitive to the frequencies occupied by bird song have the greatest potential for monitoring an avian community. The results from these two chapters suggest that acoustic indices can be effective tools for monitoring biodiversity, with values reflecting consistent differences across habitats, and among avian assemblages. Audio recordings are a source of permanent, verifiable evidence that can be collected at much greater spatiotemporal scales than traditional biodiversity monitoring data. As the use of audio recorders grows, it is important to compare their efficacy with standard methods of data collection. In Chapter 5, we contrast data derived from audio recordings with that gathered using standard point count methods, and consider whether recorders are a feasible means of surveying antbirds (Thamnophilidae), a disturbance-sensitive avian taxon. Both approaches revealed species’ responses to landscape structure, with qualitatively similar patterns in response to forest cover and vegetation quality. We show that common species can be readily monitored using audio recorders, with greater levels of detectability compared with point counts. However, rarer species were more likely to be detected using point counts. The work presented in this thesis helps to explain the patterns seen in avian responses to Neotropical HMLs. In particular we emphasise the importance of forest cover for maintaining bird assemblages in these landscapes. We demonstrate the utility of audio recorders for data collection, and highlight their potential for future biodiversity monitoring. In the face of human population growth, and ongoing habitat disturbance and agricultural intensification, conservation efforts are essential to avoid widespread species extinctions and ecosystem collapse. Interventions must take place in HMLs, to bolster ecosystem services, provide buffer zones for protected areas, and improve connectivity in the wider landscape

Improving the identification of priority areas for conserving neotropical biodiversity : assessing uncertainties in spatial conservation prioritization

Critical thresholds in habitat reduction besides multiple threats such as climate change are leading to a biodiversity decline (Newbold et al. 2016; Betts et al. 2017; Melo et al. 2018; Roque et al. 2018), consistently predicted in multiple scenarios (Jenkins 2003; Thomas et al. 2004; Pereira et al. 2010; Bellard et al. 2012). Accordingly, extinction rates of species are now 8 to 100 times higher than those previously known (Ceballos et al. 2015). This biodiversity crisis imposes new challenges on conservation planning for prioritizing locations and efforts to guarantee the persistence of species and ecosystems over time (Meir et al. 2004; Wilson et al. 2016; Reside et al. 2018). The most common initiatives in conservation planning for safeguarding biodiversity and counteract biodiversity decline continue to be the expansion of the protected areas (PAs) systems (Jenkins & Joppa 2009; Watson et al. 2014). However, in a world increasingly dominated by human transformation processes (Ellis & Ramankutty 2008; Ellis 2011) and with limited economic resources for conservation (Wilson et al. 2009; Waldron et al. 2013), it is critical to expand this view and integrate conservation practices in human-modified landscapes (Ellis 2013). The adequate allocation of the limited resources available for biodiversity conservation is crucial for achieving global, national, and sub-national conservation targets (Dobrovolski et al. 2014; Pouzols et al. 2014; Venter et al. 2014; Di Marco et al. 2016; Espirito-Santo et al. 2017). Consequently, a critical issue in spatial conservation prioritization should be to minimize the uncertainty about what and where to conserve, in order to maximize the success of conservation planning (Regan et al. 2009; Wilson et al. 2009). Thus, I tested in this thesis how robustness of the planning process may be increased by applying the three principles proposed in the systematic conservation planning framework, (1) representation, (2) persistence, and (3) cost-efficiency (Margules & Sarkar 2007), but also by highlighting the variability of the conservation prioritization process to diverse approaches using different information (Langford et al. 2011). I evaluated the impact of several approaches and analyzed the sensitivity of the identification of priority areas for conservation in the Neotropics, one of the most biodiverse regions in the world, and also one with the most urgent needs of identifying conservation priorities. I present a comprehensive spatial conservation prioritization that addressed the composition (8563 spp.), structure (663 ecosystems), and function (5382 ecological groups) of biodiversity, showing the regional variability of conservation priorities according to the biodiversity attribute represented (Chapter 1). Also, I applied different approaches of costs and factors associated with the persistence of Neotropical biodiversity, and framed them in the land-sharing/sparing model to propose possible conservation actions in the region (Chapter 2). Finally, I evaluated multiple variables related to the systematic conservation planning principles, representation, persistence, and cost-efficiency, to analyze what factors better guide conservation priorities in the Neotropics across regional and national levels (Chapter 3). My results showed that Aichi 11 target for conserving 17% of terrestrial biodiversity in the Neotropics cannot be fulfilled with the current PAs. The prioritized areas proposed, as well as PAs, meet on average 60% of conservation targets, but being 60% more efficient in the extent of area selected. I show that in the most threatened biodiversity hotspots, the effectiveness and representativeness of biodiversity depend strictly on the inclusion of new conservation areas. Comparing biodiversity attributes, I found a higher level of surrogacy using a compositional approach explained by the number of biodiversity features and their overlapping levels. However, conservation priorities vary regionally, suggesting that the use of a single biodiversity attribute, may lead to inaccurate selections of conservation priorities (Chapter 1). I also found that costs are more influential in the selection of conservation areas than persistence measures. Using the variability in the priority areas found, we identified regions where land acquisition would be most suitable for conservation and restoration (land-sparing), and areas where conservation agreements would be more appropriate to implement restoration or wildlife-friendly farming conservation strategies (land-sharing) (Chapter 2). Through a sensitivity analysis, we found that representativeness of biodiversity, and particularly the proportion of natural habitats guides conservation priorities at the regional level, while the factors associated with costs and persistence are more critical at the Neotropical level. In the Neotropics, conservation priorities responded to the spatial conservation prioritization model, favoring complementarity and reducing conservation costs (Chapter 3). However, conservation planning at the regional level should consider several mechanisms to guarantee the success of biodiversity protection over time (Chapters 1, 2 and 3). Finally, I concluded that there is no single approach or a combination of them, which cover the whole variability in spatial information on biodiversity, costs, and persistence to conservation. Regional differences in conservation areas selected influence conservation planning differently, consequently leading to identify distinct priorities and conservation actions related. The regional variability in conservation areas selection found indicates more different strategies that should be applied to conservation planning, since biodiversity attributes, and cost and persistence approaches guide the selection differently (Chapters 1 and 2). However, despite variability in conservation areas selection, we could identify priority areas where coincidences over multiple approaches occur (Chapters 1 and 2). In these areas, the uncertainty in defining priority areas is reduced, supporting the definition of more robust conservation priorities and actions by identifying those factors related to conservation areas selection (Chapter 3). These irreplaceable areas were located in critical and threatened global biodiversity hotspots, e.g., the Chaco, the Atlantic forest, the Pantanal, Cerrado, and Caatinga regions in Brazil, and the moist and dry forests of northern Andes (Chapters 1 and 2).Doctor en Estudios Ambientales y RuralesDoctoradohttps://orcid.org/0000-0001-6570-439Xhttps://scholar.google.com/citations?user=R89PYbAAAAAJ&hl=es&oi=aohttps://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=000123529

A review of threshold responses of birds to landscape changes across the world

Identifying the threshold of habitat cover beyond which species of birds are locally lost is useful for understanding the biological consequences of landscape changes. However, there is little consensus regarding the impact of landscape changes on the likelihood of species extinctions. We conducted a literature search using Scopus and ISI Web of Knowledge databases to identify studies where bird species were used to estimate threshold responses to landscape changes. We obtained a list of 31 papers published from 1994 to 2018, with 24 studies conducted at temperate latitudes and seven in tropical regions. Nineteen studies were based on species-level assessments, and investigators used a variety of response variables such as probability of detection and occurrence to detect threshold responses. Eight studies were based on communities, and species richness and abundance were primarily used to detect threshold responses. Four studies included both communities and species-level assessments. Methods used to identify threshold responses varied among studies, but most relied on either regression models to visually identify values from graphs or piecewise regression to estimate a specific threshold value. Although the limited number of studies and their variety of approaches and methods prevented a formal meta-analysis, we found that mean threshold responses in studies that reported either a range or a single threshold value were 27.9% at temperate latitudes (range = 1.3–90%; N = 11) and 33.6% at tropical latitudes (range = 20–50%; N = 7). Considering only studies where single threshold values were reported, the mean habitat cover threshold was 11% for studies conducted at temperate latitudes (N = 3) and 29.5% for studies in the tropics (N = 4). These crude estimates suggest that tropical species might be more susceptible to habitat loss than temperate species. Although application of the threshold concept is still controversial, the number of studies using this approach is increasing because the results of such studies may have direct application to conservation strategies and restoration of landscapes for bird conservation

Novel approaches to inform tropical bird conservation in human modified landscapes

In this thesis I utilise a combination of newly advanced methodological and statistical approaches to assess knowledge gaps concerning biodiversity in human-modified tropical landscapes. Specifically, I use cutting-edge LiDAR technology, occupancy modelling and soundscape analysis to document the responses of tropical birds to land-use change in Borneo. I first evaluate the contribution that riparian reserves - protected natural vegetation around waterways in production landscapes - have in supporting biodiversity. By assessing the avian community structure and richness of riparian reserves I demonstrate that these landscape features can offer significant biodiversity benefits, and support comparable levels of species diversity to logged riparian forests provided they are of sufficient size (>80 m in total width) and habitat quality (>75 tC ha-1 of tree biomass). I show that in oil palm estates riparian reserves would need to be >200 m in total width (i.e. 100 m from each riverbank) to preserve comparable numbers of forest specialist bird to logged riparian forest. I then examine whether responses of species and trait groups to habitat disruption follow linear trajectories or non-linear responses whereby abrupt changes to occupancy and diversity occur once thresholds of disturbance are exceeded. Habitat disruption across a land-cover gradient from intact forest to oil palm plantations was characterised via LiDAR metrics that quantify habitat structure in three dimensions. By scrutinising the individual responses of 171 bird species and 17 different multi-species trait groups to these metrics via hierarchical multi-species occupancy modelling, I show that the majority of species respond to habitat degradation in a non-linear fashion. I demonstrate that thresholds in species response scale up to abrupt changes in trait group richness, particularly those associated with important ecosystem functions such as pollination, seed dispersal and insectivory. I find trait groups exhibit highly varied thresholds from one another. I also highlight how exceeding particular thresholds of degradation in human modified tropical landscapes could result in abrupt changes to ecosystem functioning, thereby making human-modified tropical landscape less resilient to further perturbations. Last, I seek to test the application of recently developed acoustic approaches for monitoring biodiversity in human-modified tropical landscapes. I assess the performance of five commonly used 'soundscape' indices in corresponding to variation in observed or estimated bird diversity from field data. I find that sources of acoustic bias in production landscapes (including human produced noise and the sound of running), make broad application of acoustic monitoring technologies to heavily disturbed habitats such as intensive farmland challenging. I demonstrate that controlling for time-of-day, using noise-reduction algorithms and excluding certain habitat types, improves the capacity of acoustic indices to reflect both observed bird richness, and estimates of species numbers derived from occupancy models. Taken together, the three studies in this thesis reveal the biodiversity value of riparian areas, the potential for non-linear responses of species to habitat change, and the efficacy of novel monitoring techniques applied to biodiversity monitoring in human-modified tropical landscapes. I offer a number of recommendations and applications of these three sets of findings and explore their implication for biodiversity conservation in tropical regions. By addressing these three knowledge gaps using a combination of newly available innovations I demonstrate not only the importance of the findings themselves, but also highlight how innovations in technology, analytical technique and monitoring approach when used in conjunction can elucidate biodiversity patterns that were otherwise less well known