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Abstract Introduction: The Wood Thrush is a migratory bird that has experienced dramatic declines in its populations in recent decades. This species overwinters in forest fragments with intermediate levels of habitat modification in Central America. However, more studies detailing the use of remnant forests through time are needed to elucidate the threats this species faces in the wintering grounds. Objective: To understand the effects of environmental and forest structure variables on the occupancy of Wood Thrush in Northern Costa Rica. Methods: The study area was the Área de Conservación Guanacaste (ACG), located in Northern Costa Rica, in December 2016, and during the 2018-2019 migration season. We estimated Wood Thrush occupancy and detection probability in four locations of ACG (dry forest, cloud forest, and two locations in the wet forest) using single-season occupancy models. We also estimated Wood Thrush occupancy and probability of persistence in different months in three vegetation types (open area, secondary forest, and old-growth forest) in the wet forest of ACG using a multi-season occupancy model approach. Results: Wood Thrush occupancy was best described by precipitation in the four locations of the ACG; the probability of occupancy increased with precipitation. The average occupancy of Wood Thrushes varied with vegetation type: open area with shrubs and forest edge (0.69 ± 0.09), secondary forest (0.46 ± 0.1), and old-growth forest (0.61 ± 0.1). Wood Thrush probability of persistence responded partially to changes in precipitation, with an unexpected increase in persistence when the rainfall continued decreasing in the season. Conclusion: Wood Thrush occupancy was best predicted by changes in precipitation considering a larger spatial scale. Its probability of persistence partially varied with precipitation. An increase in persistence closer to Spring migration might be explained by the start of the breeding season of resident birds, potentially reducing territorial conflicts and conserving energy before migration. The long-term protection of wet forests in Northern Costa Rica is of paramount importance for the conservation of Wood Thrushes in their wintering grounds.

Resumen Introducción: El Zorzal del Bosque es un ave migratoria que ha experimentado caídas dramáticas en sus poblaciones en las últimas décadas. Esta especie pasa el invierno en fragmentos de bosque con niveles intermedios de modificación de hábitat en Centroamérica. Sin embargo, se necesitan más estudios que detallen el uso de los bosques remanentes a lo largo del tiempo para dilucidar las amenazas que enfrenta esta especie en las zonas de invernada. Objetivo: Comprender los efectos de variables ambientales y de estructura del bosque en la ocurrencia del Zorzal del Bosque en el Norte de Costa Rica. Métodos: El área de estudio fue el Área de Conservación Guanacaste (ACG), ubicada en el Norte de Costa Rica, en diciembre de 2016, y en la temporada migratoria 2018-2019. Estimamos la ocurrencia y la probabilidad de detección del Zorzal del Bosque en cuatro ubicaciones de ACG (bosque seco, bosque nuboso y dos ubicaciones en el bosque húmedo) utilizando modelos de ocurrencia de una sola temporada. También estimamos la ocurrencia del Zorzal del Bosque y la probabilidad de persistencia en diferentes meses en tres tipos de vegetación (área abierta, bosque secundario y bosque primario) en el bosque húmedo de ACG utilizando un enfoque de modelo de ocurrencia multi-estacional. Resultados: La ocurrencia del Zorzal del Bosque estuvo mejor descrita por la precipitación en las cuatro localidades del ACG; la probabilidad de ocurrencia aumentó con las precipitaciones. La ocurrencia media de zorzales varió con el tipo de vegetación: área abierta con arbustos y borde de bosque (0.69 ± 0.09), bosque secundario (0.46 ± 0.1) y bosque primario (0.61 ± 0.1). La probabilidad de persistencia del zorzal respondió parcialmente a cambios en la precipitación, con un aumento inesperado en la persistencia cuando las precipitaciones continuaron disminuyendo en la temporada. Conclusión: La ocurrecia del Zorzal del Bosque varió con la precipitación considerando una escala espacial mayor. Su probabilidad de persistencia varió parcialmente con la precipitación. Un aumento en la persistencia más cerca de la migración de primavera podría explicarse por el inicio de la temporada de reproducción de las aves residentes, lo que podría reducir los conflictos territoriales y conservar energía antes de la migración. La protección a largo plazo de los bosques húmedos en el norte de Costa Rica es de suma importancia para la conservación de los Zorzales del Bosque en sus zonas de invernada.

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Although considered an evolutionary force responsible for shaping ecosystems and biodiversity, fires' natural cycle is being altered by human activities, increasing the odds of destructive megafire events. Here, we show that forest type modulates the responses of terrestrial mammals, from species to assemblage level, to a catastrophic megafire in the Brazilian Pantanal. We unraveled that mammalian richness was higher 1 year after fire passage compared to a pre-fire condition, which can be attributed to habitat modification caused by wildfires, attracting herbivores and open-area tolerant species. We observed changes in assemblage composition between burned/unburned sites, but no difference in mammalian richness or relative abundance. However, by partitioning the effects of burned area proportion per forest type (monospecific vs. polyspecific), we detected differential responses of mammals at several levels of organization, with pronounced declines in species richness and relative abundance in monospecific forests. Eighty-six percent of the species presented moderate to strong negative effects on their relative abundance, with an overall strong negative effect for the entire assemblage. Wildfires are predicted to be more frequent with climate and land use change, and if events analogous to Pantanal-2020 become recurrent, they might trigger regional beta diversity change, benefitting open-area tolerant species.

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Areas used for livestock production and dominated by native grasses represent a unique opportunity to reconcile biodiversity conservation and livestock production. However, limited knowledge of individual species' responses to rangeland management restricts our capacity to design grazing practices that favor endangered species and other priority birds. In this work, we applied Hierarchical Modelling of Species Communities (HMSC) to study individual species responses, as well as the influence of traits on such responses, to variables related to rangeland management using birds of the Rio de la Plata Grasslands as a case study. Based on presence-absence data collected in 454 paddocks across 46 ranches we inferred the response of 69 species considering imperfect detection. This degree of detail fills a major gap in rangeland management, as species-level responses can be used to achieve targeted conservation goals other than maximizing richness or abundance. We found that artificial pastures had an overall negative impact on many bird species, whereas the presence of tussocks had a positive effect, including all threatened species. Grassland specialists were in general sensitive to grass height and tended to respond positively to tussocks but negatively to tree cover. Controlling grass height via adjustments in stocking rate can be a useful tool to favor grassland specialists. To favor a wide range of bird species in ranches, a mosaic of short and tall native grasslands with patches of tussocks and trees is desirable. We also found that species-specific responses were modulated by their traits: small-sized birds responded positively to tussocks and tree cover while large species responded negatively to increasing grass height. Ground foragers preferred short grass while birds that scarcely use this stratum were not affected by grass height. Results on the influence of traits on bird responses are an important novelty in relation to previous work in rangelands and potentially increase our predicting capacity and model transferability across grassland regions.

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Although the species-area relationship is well known, it may interact with and be augmented or cancelled out by other factors, such as local human disturbance. We used data on site occupancy of the Endangered blonde capuchin monkey (Sapajus flavius) based primarily on a standardized program of local interviews to model the influence of past human disturbance on the occurrence of this species across remaining forest patches of northeastern Brazil within the Atlantic Forest and Caatinga biomes. To do so, we assessed environmental covariates that best represent the history of human impacts. We then used single-species occupancy models to assess site occupancy, while controlling for detection error during sampling. Surprisingly, we obtained a higher occupancy rate in the more arid Caatinga remnants than in the more mesic Atlantic Forest. Habitat patch size, history of site protection, and annual precipitation were the best predictors of local occupancy. Historical human disturbance, including subsistence hunting, has exerted considerable impact on the modern distribution of the blonde capuchin, whose geographic range largely spans a region historically lacking any wildlife protection. Matrix vegetation structure across the Caatinga, which so far has averted large-scale mechanized agriculture, also creates a benign landscape that likely benefits contemporary capuchin occupancy. Local extinctions of this endangered primate will most likely continue unabated unless a ban on hunting in remaining Atlantic Forest and Caatinga fragments can be enforced.

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Several studies in European and North American agroecosystems conclude that organic farming benefits birds compared to conventional farming. Nevertheless, there are some biases toward these geographic regions and farm size. Argentinian agroecosystems are particularly homogeneous with large arable fields and sparse uncultivated field margins (i.e. large-scale homogenous cropping systems). In Argentina only 0.55% of the total farmland is under organic farming. Thus, our aims were to assess differences in bird occupancy between organic versus conventional farming regimes, and whether bird occupancy varied in relation to annual crop proportion in both farming regimes in central Argentina agroecosystems. We surveyed 156 points in farms under conventional and 154 in organic farming regimes during two bird-breeding seasons. We used multi-species occupancy models with a Bayesian approach to estimate bird occupancy. We observed that the type of farming regime (organic in relation to conventional) had a weak effect on avian occupancy, varying by species and groups. Probability of occupancy was higher for a few insectivorous and omnivorous species but lower for carnivores in organic farms in relation to conventional ones. The proportion of annual crops was positively correlated with occupancy of an insectivore aerial forager, some insectivore foliage gleaners, a granivore, and some omnivorous species in organic farms, but not conventional farms. This work contributes to reducing geographic and small-scale heterogeneous cropping system biases in the avian agroecological literature. Our results, together with future studies needed to assess landscape configuration and composition, and resource availability for birds in each farming regime, will allow the evaluation of organic farming as a tool for the conservation of bird species in large-scale homogeneous cropping systems in temperate regions.

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The Pampas fox (Lycalopex gymnocercus) has suffered from hunting and human persecution for decades, both for fur trade or due to conflicts with livestock. However, studies assessing the effects of hunting pressure on this canid population ecology are lacking. In this work, we assessed the influence of several hunting-related variables on the daily activity patterns and habitat use of the Pampas fox. In private farms of central Argentina, we performed two camera-trapping surveys: one during the non-hunting season and other during the hunting season, distinguishing between sites with or without access by hunters. The habitat use of Pampas foxes did not vary between seasons, but their detectability was lower during the hunting season in habitats that allow humans to see foxes easily (i.e., habitats with high visibility). Pampas foxes selected dusk and night-time, increasing their activity at dusk hours on sites with hunting and showed differences in activity patterns related with the level of visibility of the habitat and to season. Hunting pressure may interact with anthropogenic habitat modifications and create ecological traps for the Pampas fox in agroecosystems.

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The responses of organisms to organic farming depend on the taxonomic group and landscape complexity. Following the intermediate landscape complexity hypothesis, organic farming can compensate for the lack of complexity in simple landscapes. Argentinian farmlands are simple with large fields and scarce linear habitat array, and conventional agriculture is almost the only agriculture practice. We hypothesize that there is an interaction effect of landscape complexity and farming practices on occupancy and species richness of small mammals in farmland of central Argentina. We selected circular landscapes under organic farming and low- and high-intensity conventional farming and quantified heterogeneity in each landscape considering different cover types (crops, resting plots, fallow land, border habitats, grasslands and man-made structures). We used multi-species occupancy models accounting for multiple seasons with a Bayesian approach to make the estimates. Landscapes under organic farms had the highest level of landscape heterogeneity. In simple Argentinian farmlands, organic farming benefited species richness and occupancy of all small mammal species. Some management strategies used in organic farming (wide and vegetated border habitats, diversity in types of production, winter cover crops, natural or semi-natural patches) should be taken into account to increase landscape complexity in conventional farming.

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Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980’s and phytoplankton communities in the water column since the early-1990’s. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.

El material genético que liberan los organismos en los componentes no vivos del ecosistema (aire, suelo, agua y sedimentos) recibe el nombre de ADN ambiental (ADNa) (eDNA, por su nombre en inglés). Este ADN previamente definido como ADN particulado ha sido utilizado desde mediados de la década de los ochenta y principios de los noventas para describir la composición de las comunidades microbianas en sedimentos marinos y de comunidades microbianas y fitoplanctónicas en la columna de agua. Recientemente el ADNa es utilizado principalmente para la detección y monitoreo de especies invasoras y en peligro. No obstante, existen múltiples áreas en las que este método puede ser utilizado como por ejemplo en ciencias forenses, ecología de poblaciones y comunidades, y taxonomía. Esta revisión proporciona información sobre esta nueva herramienta molecular, sus actuales y futuras aplicaciones, historia, principales consideraciones metodológicas y áreas emergentes para su uso en ecología y conservación de ambientes marinos y de agua dulce.

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Habitat characteristics and human activities are known to play a major role in the occupancy of jaguars Panthera onca across their range, however the key variables influencing jaguar distribution in Tortuguero National Park, Costa Rica, have yet to be identified. This study evaluated jaguar occupancy in Tortuguero National Park and the surrounding area. Jaguar detection/non-detection data was collected using digital camera traps distributed within the boundaries of the protected area. Local community members were also interviewed to determine jaguar occurrence in the Park’s buffer zone. Occupancy models were then applied to identify the habitat characteristics that may better explain jaguar distribution across the study area. From June 2012 to June 2013, a total of 4 339 camera trap days were used to identify 18 individual jaguars inside the protected area; 17 of these jaguars were exclusively detected within the coastal habitat, whilst the remaining individual was detected solely within the interior of the Park. Interviewees reported 61 occasions of jaguar presence inside the buffer zone, between 1995 and 2013, with 80% of these described by the communities of Lomas de Sierpe, Barra de Parismina and La Aurora. These communities also reported the highest levels of livestock predation by jaguars (85% of attacks). In the study area, jaguar occurrence was positively correlated with the seasonal presence of nesting green turtles Chelonia mydas, and negatively correlated with distance to the Park boundary. Our findings suggested that the current occupancy of the jaguar in the study area may be a response to: 1) the vast availability of prey (marine turtles) on Tortuguero beach, 2) the decline of its primary prey species as a result of illegal hunting inside the Park, and 3) the increase in anthropogenic pressures in the Park boundaries. Rev. Biol. Trop. 62 (4): 1449-1458. Epub 2014 December 01.

Las características del hábitat y las actividades humanas juegan un papel importante en la presencia del jaguar Panthera onca en toda su área de distribución, sin embargo, las variables clave que influyen en la distribución del jaguar en el Parque Nacional Tortuguero, Costa Rica, aún no se han identificado. Por lo tanto se evaluó la presencia del jaguar Panthera onca en este parque nacional y su área de amortiguamiento. Se recolectaron datos de detección/no detección del jaguar mediante cámaras trampa ubicadas dentro del parque, y se realizaron encuestas en las comunidades del área de amortiguamiento. Posteriormente, se emplearon modelos de ocupación para identificar los atributos del hábitat que mejor explicaban la presencia del felino en el área. Se identificaron 18 jaguares dentro del parque, de los cuales 17 estuvieron exclusivamente en el hábitat costero. En el área de amortiguamiento, las comunidades con una mayor presencia del felino (Lomas de Sierpe, Barra de Parismina y La Aurora) coincidieron con las zonas más conflictivas, en relación a la cacería y la depredación de jaguar sobre el ganado. La probabilidad de ocupación del jaguar se incrementa a medida que aumenta la presencia de la tortuga verde Chelonia mydas, y disminuye conforme la distancia al límite del parque se incrementa. Nuestros resultados indican que la actual presencia del jaguar se debe a: 1) la alta disponibilidad de presas (tortugas marinas) en el hábitat costero, 2) la disminución de las principales especies presa como resultado de la cacería y 3) al incremento de las actividades humanas en el área de amortiguamiento del parque.

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1. In recent years, there has been a fast development of models that adjust for imperfect detection. These models have revolutionized the analysis of field data, and their use has repeatedly demonstrated the importance of sampling design and data quality. There are, however, several practical limitations associated with the use of detectability models which restrict their relevance to tropical conservation science. 2. We outline the main advantages of detectability models, before examining their limitations associated with their applicability to the analysis of tropical communities, rare species and large-scale data sets. Finally, we discuss whether detection probability needs to be controlled before and/or after data collection. 3. Models that adjust for imperfect detection allow ecologists to assess data quality by estimating uncertainty and to obtain adjusted ecological estimates of populations and communities. Importantly, these models have allowed informed decisions to be made about the conservation and management of target species. 4. Data requirements for obtaining unadjusted estimates are substantially lower than for detectability-adjusted estimates, which require relatively high detection/recapture probabilities and a number of repeated surveys at each location. These requirements can be difficult to meet in large-scale environmental studies where high levels of spatial replication are needed, or in the tropics where communities are composed of many naturally rare species. However, while imperfect detection can only be adjusted statistically, covariates of detection probability can also be controlled through study design. Using three study cases where we controlled for covariates of detection probability through sampling design, we show that the variation in unadjusted ecological estimates from nearly 100 species was qualitatively the same as that obtained from adjusted estimates. Finally, we discuss that the decision as to whether one should control for covariates of detection probability through study design or statistical analyses should be dependent on study objectives. 5.Synthesis and applications. Models that adjust for imperfect detection are an important part of an ecologist's toolkit, but they should not be uniformly adopted in all studies. Ecologists should never let the constraints of models dictate which questions should be pursued or how the data should be analysed, and detectability models are no exception. We argue for pluralism in scientific methods, particularly where cost-effective applied ecological science is needed to inform conservation policy at a range of different scales and in many different systems.

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Forest degradation is arguably the greatest threat to biodiversity, ecosystem services, and rural livelihoods. Therefore, increasing understanding of how organisms respond to degradation is essential for management and conservation planning. We were motivated by the need for rapid and practical analytical tools to assess the influence of management and degradation on biodiversity and system state in areas subject to rapid environmental change. We compared bird community composition and size in managed (ejido, i.e., communally owned lands) and unmanaged (national park) forests in the Sierra Tarahumara region, Mexico, using multispecies occupancy models and data from a 2-year breeding bird survey. Unmanaged sites had on average higher species occupancy and richness than managed sites. Most species were present in low numbers as indicated by lower values of detection and occupancy associated with logging-induced degradation. Less than 10% of species had occupancy probabilities >0.5, and degradation had no positive effects on occupancy. The estimated metacommunity size of 125 exceeded previous estimates for the region, and sites with mature trees and uneven-aged forest stand characteristics contained the highest species richness. Higher estimation uncertainty and decreases in richness and occupancy for all species, including habitat generalists, were associated with degraded young, even-aged stands. Our findings show that multispecies occupancy methods provide tractable measures of biodiversity and system state and valuable decision support for landholders and managers. These techniques can be used to rapidly address gaps in biodiversity information, threats to biodiversity, and vulnerabilities of species of interest on a landscape level, even in degraded or fast-changing environments. Moreover, such tools may be particularly relevant in the assessment of species richness and distribution in a wide array of habitats.

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