Occupancy

About: Occupancy is a research topic. Over the lifetime, 2757 publications have been published within this topic receiving 68288 citations.

Landscape context matters: local habitat and landscape effects on the abundance and patch occupancy of collared lizards in managed grasslands

Abstract: The distribution and abundance of a species may be simultaneously influenced by both local-scale habitat features and the broader patch and landscape contexts in which these populations occur. Different factors may influence patch occupancy (presence–absence) versus local abundance (number of individuals within patches), and at different scales, and thus ideally both occupancy and abundance should be investigated, especially in studies that seek to understand the consequences of land management on species persistence. Our study evaluated the relative influences of variables associated with the local habitat patch, hillside (patch context), and landscape context on patch occupancy and abundance of the collared lizard (Crotaphytus collaris) within tallgrass prairie managed under different fire and grazing regimes in the northern Flint Hills of Kansas, USA. Using a multi-model information-theoretic approach that accounted for detection bias, we found that collared lizard abundance and occupancy was influenced by factors measured at both the local habitat and landscape scales. At a local scale, collared lizard abundance was greatest on large rock ledges that had lots of crevices, high vegetation complexity, and were located higher up on the hillslope. At the landscape scale, collared lizard abundance and occupancy were both higher in watersheds that were burned frequently (1–2 year intervals). Interestingly, grazing only had a significant effect on occupancy and abundance within less frequently burned (4-year burn interval) watersheds. Our results suggest that, in addition to the obvious habitat needs of this species (availability of suitable rock habitat), land-management practices have the potential to influence collared lizard presence and abundance in the grasslands of the Flint Hills. Thus, mapping the availability of suitable habitat is unlikely to be sufficient for evaluating species distributions and persistence in such cases without consideration of landscape management and disturbance history.

Integrating occupancy models and structural equation models to understand species occurrence

Abstract: Understanding the drivers of species occrrece s a fundamenal goal in basic and applied ecology. Occupancy models have emerged as a popular approach for inferring species occurrence because they account for problems associated with imperfect detection in field surveys. Current models, however, are limited because they assume covariates are independent (i.e., indirect effects do not occur). Here, we combined structural equation and occupancy models to investigate complex influences on species occurrence while accounting for imperfect detection. These two methods are inherently compatible because they both provide means to make inference on latent or unobserved quantities based on observed data. Our models evaluated the direct and indirect roles of cattle grazing, water chemistry, vegetation, nonnative fishes, and pond permanence on the occurrence of six pond-breeding amphibians, two of which are threatened: the California tiger salamander (Ambysloma californiense) and the California red-legged frog (Rana draytonil). While cattle had strong effects on pond vegetation and water chemistry, their overall effects on amphibian occurrence were small compared to the consistently negative effects of nonnative fish. Fish strongly reduced occurrence probabilities for four of five native amphibians, including both species of conservation concern. These results could help to identify drivers of amphibian declines and to prioritize strategies for amphibian conservation. More generally, this approach facilitates a more mechanistic representation of ideas about the causes of species distributions in space and time. As shown here, occupancy modeling and structural equation modeling are readily combined, and bring rich sets of techniques that may provide unique theoretical and applied insights into basic ecological questions.

Efficient occupancy model-fitting for extensive citizen-science data.

Abstract: Appropriate large-scale citizen-science data present important new opportunities for biodiversity modelling, due in part to the wide spatial coverage of information. Recently proposed occupancy modelling approaches naturally incorporate random effects in order to account for annual variation in the composition of sites surveyed. In turn this leads to Bayesian analysis and model fitting, which are typically extremely time consuming. Motivated by presence-only records of occurrence from the UK Butterflies for the New Millennium data base, we present an alternative approach, in which site variation is described in a standard way through logistic regression on relevant environmental covariates. This allows efficient occupancy model-fitting using classical inference, which is easily achieved using standard computers. This is especially important when models need to be fitted each year, typically for many different species, as with British butterflies for example. Using both real and simulated data we demonstrate that the two approaches, with and without random effects, can result in similar conclusions regarding trends. There are many advantages to classical model-fitting, including the ability to compare a range of alternative models, identify appropriate covariates and assess model fit, using standard tools of maximum likelihood. In addition, modelling in terms of covariates provides opportunities for understanding the ecological processes that are in operation. We show that there is even greater potential; the classical approach allows us to construct regional indices simply, which indicate how changes in occupancy typically vary over a species’ range. In addition we are also able to construct dynamic occupancy maps, which provide a novel, modern tool for examining temporal changes in species distribution. These new developments may be applied to a wide range of taxa, and are valuable at a time of climate change. They also have the potential to motivate citizen scientists.

Differences in the umbrella effects of African amphibians and mammals based on two estimators of the area of occupancy

Abstract: Conservation organizations are collecting large-scale data regarding distribution and threats to vertebrate taxa. These data sets will enable planners to systematically identify large-scale conservation priorities; however, they will cover only a tiny proportion of living organisms. Therefore, it is essential to investigate to what extent the areas selected for conservation actions can provide protection for other species. We analyzed the umbrella effect between amphibians and mammals across mainland Africa. We built habitat suitability models within the geographic ranges of 1654 species, based on data collected in the framework of the World Conservation Union (IUCN) Global Amphibian Assessment and IUCN Global Mammal Assessment. We applied systematic reserve selection algorithms to two sets of estimators of the area of occupancy of amphibians and mammals (geographic ranges and estimated suitable areas) and thus selected four reserve systems. We then quantified the protection that each of the four systems provided for amphibians and mammals. Reserves selected for amphibians and mammals were comparable in area, with the former concentrated in the Afrotropical region and the latter more evenly dispersed. Mammal reserves left fewer gaps in species coverage among amphibians than the reverse, but amphibian reserves included a larger proportion of each mammal's area of occupancy than the reverse. For both taxa, setting reserves to include estimated suitable areas instead of ranges resulted in the clustering of reserves in the tropics. Furthermore, it efficiently protected hidden gaps (species with unsuitable portions of their range inside protected areas) in the other taxon and included a higher proportion of the area of occupancy of the other taxon. Overall, amphibians and mammals in Africa acted as an umbrella for a high proportion of species in the other taxon. Focusing on estimated suitable areas instead of ranges improved the umbrella effect of both taxa.