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Species distribution models (SDMs) are statistical tools used to develop continuous predictions of species occurrence. 'Integrated SDMs' (ISDMs) are an elaboration of this approach with potential advantages that allow for the dual use of opportunistically collected presence-only data and site-occupancy data from planned surveys. These models also account for survey bias and imperfect detection through the use of a hierarchical modelling framework that separately estimates the species-environment response and detection process. This is particularly helpful for conservation applications and predictions for rare species, where data are often limited and prediction errors may have significant management consequences. Despite this potential importance, ISDMs remain largely untested under a variety of scenarios. We performed an exploration of key modelling decisions and assumptions on an ISDM using the endangered Baird's tapir (Tapirus bairdii) as a test species. We found that site area had the strongest effect on the magnitude of population estimates and underlying intensity surface and was driven by estimates of model intercepts. Selecting a site area that accounted for the individual movements of the species within an average home range led to population estimates that coincided with expert estimates. ISDMs that do not account for the individual movements of species will likely lead to less accurate estimates of species intensity (number of individuals per unit area) and thus overall population estimates. This bias could be severe and highly detrimental to conservation actions if uninformed ISDMs are used to estimate global populations of threatened and data-deficient species, particularly those that lack natural history and movement information. However, the ISDM was consistently the most accurate model compared to other approaches, which demonstrates the importance of this new modelling framework and the ability to combine opportunistic data with systematic survey data. Thus, we recommend researchers use ISDMs with conservative movement information when estimating population sizes of rare and data-deficient species. ISDMs could be improved by using a similar parameterization to spatial capture-recapture models that explicitly incorporate animal movement as a model parameter, which would further remove the need for spatial subsampling prior to implementation. © 2019 Foundation for Environmental Conservation. Department of Geography and the Environment, University of Texas at Austin, Austin, TX 78712, United States, Global Wildlife Conservation, Austin, TX, United States Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, United States Kelly, M.J., Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, United States Department of Ecology and Evolutionary Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada El Colegio de la Frontera sur, Departamento de Conservacion de la Biodiversidad, Lerma, Campeche, Mexico, Fundación Yaguara-Panama, Ciudad del Saber, Panama Global Wildlife Conservation, Austin, TX, United States, Panthera, New York, NY, United States, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States Proyecto de Conservación de Aguas y Tierras, ProCAT Colombia/Internacional, Bogotá, Colombia Instituto Internacional en Conservación y Manejo de Vida Silvestre, Universidad Nacional, Heredia, 3000-1350, Costa Rica Instituto Internacional en Conservación y Manejo de Vida Silvestre, Universidad Nacional, Heredia, 3000-1350, Costa Rica Instituto Internacional en Conservación y Manejo de Vida Silvestre

Although many large mammals currently face significant threats that could lead to their extinction, resources for conservation are often scarce, resulting in the need to develop efficient plans to prioritize conservation actions. We combined several methods in spatial ecology to identify the distribution of the endangered Baird's tapir across its range from southern Mexico to northern Colombia. Twenty-eight habitat patches covering 23% of the study area were identified, harboring potentially 62% or more of the total population for this flagship species. Roughly half of the total area is under some form of protection, while most of the remaining habitat (~70%) occurs in indigenous/local communities. The network with maximum connectivity created from these patches contains at least one complete break (in Mexico between Selva El Ocote and Selva Lacandona) even when considering the most generous dispersal scenario. The connectivity analysis also highlighted a probable break at the Panama Canal and high habitat fragmentation in Honduras. In light of these findings, we recommend the following actions to facilitate the conservation of Baird's tapir: 1) protect existing habitat by strengthening enforcement in areas already under protection, 2) work with indigenous territories to preserve and enforce their land rights, and help local communities maintain traditional practices; 3) re-establish connections between habitat patches that will allow for connectivity across the species' distribution; 4) conduct additional noninvasive surveys in patches with little or no species data; and 5) collect more telemetry and genetic data on the species to estimate home range size, dispersal capabilities, and meta-population structure. Universidad Nacional, Costa Rica North Carolina State University, United States University of Texas at Austin, United States Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Colombia Universidad de Antioquia, Colombia Universidad Nacional Autónoma de México, México Universidad Nacional Autónoma de Honduras, Honduras Universidad Técnica Nacional, Costa Rica Universidad Michoacana de San Nicolás de Hidalgo, México Instituto Internacional en Conservación y Manejo de Vida Silvestre

Aim We test a new species distribution modelling (SDM) framework, while comparing results to more common distribution modelling techniques. This framework allows for the combination of presence-only (PO) and presence-absence (PA) data and accounts for imperfect detection and spatial bias in presence data. The new framework tested here is based on a Poisson point process model, which allows for predictions of population size. We compared these estimates to those provided by experts on the species. Species and Location Presence data on Baird's tapir (Tapirus bairdii) throughout its range from southern Mexico to northern Colombia were used in this research, primarily from the years 2000 to 2016. Methods Four SDM frameworks are compared as follows: (1) Maxent, (2) a presence-only (PO) SDM based on a Poisson point process model (PPM), (3) a presence-absence (PA) SDM also based on a PPM and (4) an Integrated framework which combines the previous two models. Model averaging was used to produce a single set of coefficient estimates and predictive maps for each model framework. A hotspot analysis (Gi*) was used to identify habitat cores from the predicted intensity of the Integrated model framework. Results Important variables to model the distribution of Baird's tapir included land cover, human pressure and topography. Accounting for spatial bias in the presence data affected which variables were important in the model. Maxent and the Integrated model produced predictive maps with similar patterns and were considered to be more in agreement with expert knowledge compared to the PO and PA models. Main conclusions Total abundance as predicted by the model was higher than expert opinion on the species, but local density estimates from our model were similar to available independent assessments. We suggest that these results warrant further validation and testing through collection of independent test data, development of more precise predictor layers and improvements to the model framework.

Cryptic function loss occurs when the ecological function of an animal population is significantly altered as a result of disturbance, even though the species is still present in the ecosystem. We reviewed the evidence for cryptic function loss to be widespread among seed disperser populations that persist under disturbed conditions. We found overwhelming support for the seed dispersal effectiveness of animals to be negatively impacted by all forms of disturbance (population decline, changes in community assemblages, habitat change, and climate change). However, seed dispersal was positively affected in some examples, particularly when extirpation of an interacting frugivore or predator enhanced fruit consumption. It is essential that we improve our understanding of the mechanisms by which seed dispersal is lost, even though the disperser's population remains viable, as there are many unanswered questions that hinder an objective understanding of this threat. We need to consider how seed dispersal effectiveness is determined by species population size and small changes in phenotypes. In addition, we must increase our understanding of behavioral impacts on seed dispersal and how it might be regulated by disturbance. The complexity and flexibility of seed dispersal interactions could mean that communities are adaptable to many changes; alternatively, ecosystems might be severely threatened by cryptic function loss because of the myriad ways in which multiple frugivore populations can be simultaneously affected and the fact that early signs of function loss can be hidden by stable population sizes.

Group living among ungulates has evolved mainly in species living in open habitats, such as grasslands and savannas, whereas in the forest, few ungulate species form groups and these tend to be small. Therefore, the white-lipped peccary (Tayassu pecari), a Neotropical ungulate listed as Vulnerable by the IUCN, represents an almost unique social occurrence as it lives in large and cohesive groups, yet it inhabits dense tropical forests. Large variations in group sizes have been observed throughout the species range, with reports of herds with less than 10 to around 300 individuals. We examined factors that might cause variation in group size in white-lipped peccary, including ecological and anthropogenic variables. We conducted an extensive literature review and used our original data to compile information on white-lipped peccary's group size across its range. We built models to quantitate generalizations for group sizes distinguishing data from areas with high human influence, and areas that have not been significantly disturbed by humans for at least the last 20 years. We found that white-lipped peccary's group size for all sites was most strongly predicted by a combination of the distances to the nearest human settlement and rainfall and its seasonality. Results from the undisturbed sites indicated that group size is positively influenced by rainfall. Our results contribute to understand why group size varies in different environments that are subjected to different ecological and human conditions. Information on these relationships is a key to advance our understanding of the socio-ecological strategies of animal species living in groups. Resumen La vida en grupos en ungulados ha evolucionado principalmente en especies que viven en areas abiertas, tales como sabanas y pastizales, mientras que solamente algunas especies de ungulados que viven en bosques forman grupos, y estos tienden a ser pequenos. Por esta razon, el pecari de labios blancos (Tayassu pecari), un ungulado Neotropical clasificado como Vulnerable por la UICN, representa una fenomeno social unico, ya que vive en grandes grupos cohesivos, a pesar de habitar bosques tropicales densos. Se han observado grandes variaciones en los tamanos de grupo en su distribucion, con reportes de manadas que varian de menos de 10 a mas de 300 individuos. En este estudio examinamos los factores que pueden estar causando esta variacion, incluyendo variables ecologicas y antropogenicas. Hicimos una revision exhaustiva de la literatura y usamos nuestros datos originales para compilar informacion de tamanos de grupo a lo largo de su rango. Construimos modelos estadisticos para cuantificar generalizaciones para tamanos de grupos distinguiendo datos de areas con alta presion humana (i.e. caceria) y areas que no han recibido presion humana importante en por al menos 20 anos. Encontramos que los tamanos de grupos son afectados por una combinacion de la distancia al asentamiento humano mas cercano y la cantidad de lluvia y su estacionalidad. Los resultados de los sitios con poca presion humana indican que los grupos mas grandes se encuentran en areas con mayor precipitacion. Nuestros resultados contribuyen a entender porque los tamanos de grupo varian en diferentes ambientes que estan sujetos a diferentes condiciones ecologicas y humanas. La informacion de estas relaciones es clave para avanzar en nuestro conocimiento de las estrategias socio-ecologicas de especies que viven en grupos.

The essential functional roles performed by animal species are lost when they become locally extinct, and ecosystems are critically threatened by this decline in functional diversity. Theory that links function, diversity, and ecosystem stability exists but fails to assess function loss that occurs in species with persistent populations. The entire functional role of a species, or a critical component of it, can be lost following large population declines (functional extinction), following population increase, or after behavioural adaptations to changes in the population, community, habitat, or climate. Here, we provide a framework that identifies the scenarios under which 'cryptic' function loss can occur in persistent populations. Cryptic function loss is potentially widespread and critically threatens ecosystem stability across the globe.

In 1975, wildlife managers reintroduced desert bighorn sheep (Ovis canadensis mexicana) to Tiburon Island, Mexico, where endemic mule deer (Odocoileus hemionus sheldoni) occur. We predicted that these species would use both mountain and plains habitats, but would have different diets, minimizing negative interspecific effects. By censusing pellet groups, we found that both ungulates occurred in both habitats, but bighorn sheep were more abundant in mountains and mule deer were more abundant in plains. Microhistological analyses determined that diets of both species consisted of the same 39 plant species, of which 13 plant species each composed ≥4% of the diet and together composed 70–80% of the total diet. Plants in low abundance represented 26–32% of diets in the mountains and 45–56% of diets in the plains. Overall diet overlap was 68% and overlap did not differ between mountains or plains, but did differ among seasons. Overlap in habitat agreed with predictions, but diet overlap was contrary to our predictions. Our results differ from studies on the mainland, which found overlap in habitat use, but not in diet. Overlap in resource use coupled with the rapid increase in abundance of bighorn sheep since their reintroduction to Tiburon may have an impact on mule deer. Additional research is needed to determine whether abundance of mule deer has changed in response to the reintroduction of bighorn sheep.

Tapirs are one of the last extant megafauna species that survived the Pleistocene extinctions. Given their size and digestive system characteristics, tapirs might be the last potential seed disperser of plant species that were previously dispersed by other large mammal species that are now extinct. We compiled evidence from 39 published scientific studies showing that tapirs have a key role as seed dispersers and seed predators. Tapirs play an important role either through seed predation or by facilitating the recruitment of seeds over long distances, therefore influencing the diversity of plant species in the ecosystem. Neotropical tapirs might have a unique role as long-distance seed dispersers of large seeds (

Even though the full process of seed dispersal is the combination of movement mode and distance, deposition, successful germination and survival (Nathan 2006, Westcott et al. 2005), relatively few studies have documented the role of mammals as facilitators of germination and survival (Paine & Harms 2009). In particular, the effectiveness of large terrestrial mammals (>50 kg) as effective dispersers of large seeds is poorly known, but has been linked to the treatment of the seeds in their digestive system, the deposition of viable seeds in nutrient-rich environments (faeces) and favourable sites. Other aspects related to long-distance movements, defecation patterns and home-range size are frequently cited as factors that favour the deposition of seeds far from parent trees, which is expected to reduce predation and intraspecific competition, and enhance fitness (Schupp et al. 2002). We addressed these issues through a large-scale field experiment.

The distribution and dynamics of plant populations depend on the recruitment of young individuals, which is influenced by seed production, animal seed dispersal, dispersal distance, and the deposition of seeds in favourable places for seed germination/establishment and seedling survival. In particular, seeds dispersed over long distances will likely encounter new environmental conditions that occur at large spatial scales, with seed and seedling survival influenced by the adaptation of plant populations to soil and climate conditions. In this paper, it is hypothesized that seed germination and seedling survival probabilities depend on seed origin and deposition sites. A reciprocal seed and seedling transplant experiment was carried out with zapote seeds (Manilkara zapota) to determine the effect of origin and deposition sites on seed germination and seedling survival over a year in the Greater Calakmul Region of Mexico. Two origin and two deposition sites were selected that show different soil moisture levels within the habitat of the Baird's tapir, a major seed disperser of M. zapota seeds. The results show that sites of origin and deposition influenced seed germination and seedling survival probabilities. This suggests that the displacement of seeds far from parent trees, while potentially reducing intraspecific competition, does not ensure their survival, and that seeds need to be deposited in microsites within their environmental tolerance for dispersal to be successful. Furthermore, this paper emphasizes the importance of field experiments to provide strong inference about the effects of environmental conditions on recruitment and distribution of plant species.

The Yucatan Peninsula contains some of the largest tracts of tropical forest in Mexico. These forests host six species of ungulates, including the largest and last survivor of the Neotropical megafauna, the Central American Tapir; one of the rarest ungulate species in Mexico, the White-lipped Peccary; and one endemic species of deer, the Gray Brocket. The Yucatan Peninsula is also home to another peccary species, two more deer species, five felid species, including the jaguar and the puma, and three species of primates. Most of these species face serious conservation threats, as their habitat is increasingly fragmented and because they are among the preferred targets of subsistence hunters. Some of these species require large areas of habitat in good conservation status to fulfill their basic needs for survival. Several research projects undertaken in the past years, and some currently being carried out, have addressed a lack of basic ecological information in this region. Among the ungulates, ecological research has focused on tapir, white-lipped peccary and the three deer species. For felids, scientific attention has been focused on the two largest species, the jaguar and puma; and all three primate species have received scientific attention recently, although more studies have focused on the black howler monkey. This chapter is an attempt to summarize what is currently known about these, the largest mammal species of the Yucatan Peninsula, and to point out gaps in the existing information. Such information is absolutely necessary to design conservation and management plans for these highly interesting and endangered species.

Landscape connectivity is considered a priority for ecosystem conservation because it may mitigate the synergistic effects of climate change and habitat loss. Climate change predictions suggest changes in precipitation regimes, which will affect the availability of water resources, with potential consequences for landscape connectivity. The Greater Calakmul Region of the Yucatan Peninsula (Mexico) has experienced a 16% decrease in precipitation over the last 50 years, which we hypothesise has affected water resource connectivity. We used a network model of connectivity, for three large endangered species (Baird’s tapir, white-lipped peccary and jaguar), to assess the effect of drought on waterhole availability and connectivity in a forested landscape inside and adjacent to the Calakmul Biosphere Reserve. We used reported travel distances and home ranges for our species to establish movement distances in our model. Specifically, we compared the effects of 10 drought scenarios on the number of waterholes (nodes) and the subsequent changes in network structure and node importance. Our analysis revealed that drought dramatically influenced spatial structure and potential connectivity of the network. Our results show that waterhole connectivity and suitable habitat (area surrounding waterholes) is lost faster inside than outside the reserve for all three study species, an outcome that may drive them outside the reserve boundaries. These results emphasize the need to assess how the variability in the availability of seasonal water resource may affect the viability of animal populations under current climate change inside and outside protected areas.