共查询到20条相似文献,搜索用时 15 毫秒
1.
In this article, we describe ednaoccupancy , an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model‐selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species. 相似文献
2.
Luis Bedriñana‐Romano Rodrigo Hucke‐Gaete Francisco Alejandro Viddi Juan Morales Rob Williams Erin Ashe José Garcés‐Vargas Juan Pablo Torres‐Florez Jorge Ruiz 《Diversity & distributions》2018,24(7):991-1004
Aim
Species distribution models are useful tools for depicting important habitat, assessing abundance and orienting conservation efforts. For small populations in poorly studied ecosystems, available data are often scarce and patchy. To overcome this limitation, we aim to evaluate the use of different data types within a hierarchical Bayesian framework with the goal of modelling the abundance and distribution of a small and highly migratory population of blue whale (BW, Balaenoptera musculus) summering in Chilean Northern Patagonian (CNP).Location
CNP, Eastern South Pacific (ESP).Methods
We constructed a Bayesian hierarchical species distribution Model (HSDM), combining a binomial N‐mixture model used to model BW groups counts in line‐transect data (2009, 2012 and 2014) with a logistic regression for modelling presence‐availability data (2009–2016), allowing both models to share covariate parameters for borrowing strength in estimations.Results
Distance to areas of high chlorophyll‐a concentration during spring before summering season (AHCC‐s) was the most important and consistent explanatory variable for assessing BW abundance and distribution in CNP. Incorporating accessorial presence‐only data reduced uncertainty in parameters estimation when comparing with a model using only line‐transect data, although other covariates of secondary importance failed to be retained in this model.Main conclusions
Our results remark the capability of HSDM for integrating different data types providing a potential powerful tool when data are limited and heterogeneous. Results indicate that AHCC‐s, and possibly thermal fronts, could modulate BW abundance and distribution patterns in CNP. Preliminary model‐based delimitations of possible priority conservation areas for BW in CNP overlap with highly used vessel navigation routes and areas destined to aquaculture.3.
4.
Antoine Adde Marcel Darveau Nicole Barker Steven Cumming 《Diversity & distributions》2020,26(10):1248-1263
5.
Jacob B. Socolar Simon C. Mills Torbjrn Haugaasen James J. Gilroy David P. Edwards 《Ecology and evolution》2022,12(10)
Ecologists often seek to infer patterns of species occurrence or community structure from survey data. Hierarchical models, including multi‐species occupancy models (MSOMs), can improve inference by pooling information across multiple species via random effects. Originally developed for local‐scale survey data, MSOMs are increasingly applied to larger spatial scales that transcend major abiotic gradients and dispersal barriers. At biogeographic scales, the benefits of partial pooling in MSOMs trade off against the difficulty of incorporating sufficiently complex spatial effects to account for biogeographic variation in occupancy across multiple species simultaneously. We show how this challenge can be overcome by incorporating preexisting range information into MSOMs, yielding a “biogeographic multi‐species occupancy model” (bMSOM). We illustrate the bMSOM using two published datasets: Parulid warblers in the United States Breeding Bird Survey and entire avian communities in forests and pastures of Colombia''s West Andes. Compared with traditional MSOMs, the bMSOM provides dramatically better predictive performance at lower computational cost. The bMSOM avoids severe spatial biases in predictions of the traditional MSOM and provides principled species‐specific inference even for never‐observed species. Incorporating preexisting range data enables principled partial pooling of information across species in large‐scale MSOMs. Our biogeographic framework for multi‐species modeling should be broadly applicable in hierarchical models that predict species occurrences, whether or not false absences are modeled in an occupancy framework. 相似文献
6.
Haddock Melanogrammus aeglefinus in the North sea increased their distributional range when more abundant, but this density dependent habitat selection (DDHS) explained only a small part of the year‐on‐year variation in distribution patterns. The condition of haddock was examined at 24 sites in the North Sea in August and September 2004 and related to their abundance, to examine if the ideal free distribution theory (IFD), which assumes that organisms select habitats that maximize their rate of food intake, can be used to explain this variation in large scale distribution patterns. At a given temperature, condition (hepato‐somatic index, I H ) was better at stations where haddock were most abundant. Therefore, haddock were not distributed perfectly according to the IFD in 2004. The positive correlation between abundance and I H , however, indicated there was some habitat selection by haddock, as in the total absence of habitat selection no correlation between I H and abundance, and no spatial variation in abundance was expected. DDHS may only explain a small part of the yearly variation in the distribution because haddock did not equalize and maximize their fitness at the scale of the North Sea. In addition, stable isotope analysis of muscle samples showed that haddock did not avoid competition for food when at high abundance by feeding at a lower or wider range of trophic levels. 相似文献
7.
Distribution models are increasingly being used to understand how landscape and climatic changes are affecting the processes driving spatial and temporal distributions of plants and animals. However, many modeling efforts ignore the dynamic processes that drive distributional patterns at different scales, which may result in misleading inference about the factors influencing species distributions. Current occupancy models allow estimation of occupancy at different scales and, separately, estimation of immigration and emigration. However, joint estimation of local extinction, colonization, and occupancy within a multi‐scale model is currently unpublished. We extended multi‐scale models to account for the dynamic processes governing species distributions, while concurrently modeling local‐scale availability. We fit the model to data for lark buntings and chestnut‐collared longspurs in the Great Plains, USA, collected under the Integrated Monitoring in Bird Conservation Regions program. We investigate how the amount of grassland and shrubland and annual vegetation conditions affect bird occupancy dynamics and local vegetation structure affects fine‐scale occupancy. Buntings were prevalent and longspurs rare in our study area, but both species were locally prevalent when present. Buntings colonized sites with preferred habitat configurations, longspurs colonized a wider range of landscape conditions, and site persistence of both was higher at sites with greener vegetation. Turnover rates were high for both species, quantifying the nomadic behavior of the species. Our model allows researchers to jointly investigate temporal dynamics of species distributions and hierarchical habitat use. Our results indicate that grassland birds respond to different covariates at landscape and local scales suggesting different conservation goals at each scale. High turnover rates of these species highlight the need to account for the dynamics of nomadic species, and our model can help inform how to coordinate management efforts to provide appropriate habitat configurations at the landscape scale and provide habitat targets for local managers. 相似文献
8.
Yadav Ghimirey;Raju Acharya;Jeffrey Mintz; 《Ecology and evolution》2024,14(11):e70572
Species richness is an important metric used for undertaking conservation management decisions. However, species richness estimates are influenced by species detection probabilities, with potential to entirely overlook species during surveys. Occupancy models which account for imperfect detection provide unbiased estimates, ensuring accurate estimates of richness. We carried out a camera trap survey in the mountains of north-central Nepal during 2017 and documented a total of 21 mammal species. Here, we used multi-species occupancy models within a Bayesian hierarchical framework to reassess our initial species richness estimate and to understand the influence of environmental covariates on occupancy and species richness of mammals in the area. Our model estimated the mean species richness was ~26 species (95% CRI: 21–36 species), suggesting we might have missed ~5 species during the survey. The mean probability of occupancy and detection of mammal species were estimated to be 0.2895%CRI:0.08–0.46$$ 0.28 left(95%mathrm{CRI}:0.08hbox{--} 0.46right) $$ and 0.02 (95% CRI:0.01–0.03) respectively. Mammalian species richness of the area had an anticipated positive relationship with tree canopy cover β=1.908,95%CI=0.989–2.827,p=1.95e−04$$ left(beta =1.908,95%mathrm{CI}=0.989hbox{--} 2.827,p=1.95mathrm{e}-04right) $$ though its positive relationship with anthropogenic disturbance was surprising β=1.339,95%CI=0.334–2.344,p=0.012$$ left(beta =1.339,95%mathrm{CI}=0.334hbox{--} 2.344,p=0.012right) $$. Mammalian species richness had a quadratic relationship with elevation as is expected. This research contributes to baseline information of the mammal community ecology in north-central Nepal and supports the need for future multi-season surveys to understand the influence of temporal factors on mammalian community and species richness in the area. 相似文献
9.
10.
Sandra V. Flechas Andrea Paz Andrew J. Crawford Carolina Sarmiento Aldemar A. Acevedo Wilmar Bolívar‐García Claudia L. Echeverry‐Sandoval Rosmery Franco Cindy Mojica Amanda Muñoz Pablo Palacios‐Rodríguez Andrés M. Posso‐Terranova Paulina Quintero‐Marín Luis A. Rueda‐Solano Fernando Castro‐Herrera Adolfo Amézquita 《Biotropica》2017,49(5):685-694
Global amphibian declines have been attributed to several factors including the chytrid fungal pathogen, Batrachochytrium dendrobatidis (Bd), that infects hosts’ skin and causes death by inhibiting immune response and impairing osmoregulatory function. Here, we integrate extensive new field data with previously published locality records of Bd in Colombia, a megadiverse and environmentally heterogeneous country in northwestern South America, to determine the relative importance of environmental variables and reproductive mode for predicting the risk of Bd infection in amphibians. We surveyed 81 localities across Colombia and sampled 2876 individual amphibians belonging to 14 taxonomic families. Through a combination of end‐point PCR and real‐time PCR analyses, Bd was detected in 338 individuals (12%) representing 43 localities (53%) distributed from sea level to 3200 m. We found that annual mean temperature and variables related with seasonality in precipitation and temperature appeared to define the most suitable areas for the establishment of the pathogen. In addition, prevalence of infection appeared to be higher in species with a terrestrial reproductive mode. Our study provides the first large‐scale study of the current and potential distribution of Bd in the biodiversity hotspot centered on Colombia. We hope the newly provided information on the extent of the distribution of the pathogen and the potential areas where Bd may impact the amphibian fauna will inform decision making by environmental authorities and future conservation action. 相似文献
11.
Thomas J. Rodhouse Sara Rose Trent Hawkins Rogelio M. Rodriguez 《Conservation Science and Practice》2021,3(7):e435
Bat conservation has been impeded by a lack of basic information about species' distributions and abundances. Public participation in closing this gap via citizen (community) science has been limited, but bat species that produce low-frequency calls audible to the unaided human ear provide an overlooked opportunity for collaborative citizen science surveys. Audible bats are rare in regional faunas but occur globally and can be under-surveyed by traditional methods. During 2019–2020, we were joined by community members to conduct aural surveys and expand our knowledge of rare audible desert bats in western North America through a structured survey design broadly adaptable for practitioners across the globe where audible bats occur. Our study was integrated into a statistically robust but flexible master sample in use by the North American Bat Monitoring Program (NABat), ensuring representativeness of data contributions. We used survey results to update a Bayesian species distribution model for the rare spotted bat, Euderma maculatum, accounting for imperfect detection and including land cover occupancy predictors. Detection probability was estimated ~0.7 ± 0.1. Informative priors from a previous attempt to model E. maculatum were leveraged with the new citizen science data to support spatial predictions of occurrence previously impeded by data sparsity and which reinforced the biogeographic importance of arid cliffs and canyons. Our results are preliminary but encouraging, and future surveys can scale up through the NABat design structure and Bayesian modeling framework. We encourage future surveys to use recording devices to obtain voucher calls and double-observer methods to address false-positive detection errors that arise with inexperienced volunteers. Our design and model supported approach to integrating citizen science surveys into bat conservation programs can strengthen both the scientific understanding of rare species and public engagement in conservation practices. 相似文献
12.
Guilherme H. S. Freitas Lílian M. Costa Pedro H. V. B. P. Silva Anderson V. Chaves Leonardo C. Ribeiro Marcos Rodrigues 《Journal of Field Ornithology》2019,90(2):128-142
Birds in the genus Cinclodes are habitat specialists, with most restricted to the highlands of South America. The recently described Cipo Cinclodes (C. espinhacensis) is isolated in the southern Espinhaço Range of Brazil and is considered Endangered in Brazil and Near Threatened by the IUCN, but as a subspecies of Long‐tailed Cinclodes (C. pabsti). We examined the population and spatial ecology of Cipo Cinclodes at two geographic scales to improve our understanding of their basic biology and conservation status. We monitored 30 birds at Serra do Breu and found relatively large home ranges (mean = 9.3 ha), a density of paired adults of 0.09/ha, a male‐skewed adult sex ratio (males/total adults = 0.57) due to territories occupied by unpaired males, and long‐term site fidelity. Cipo Cinclodes used all habitat types available in our study area, including rocky outcrops, grasslands, and riparian areas, but habitat selection analyses revealed the importance of riparian areas for foraging and rocky outcrops for nesting. At the species distribution scale, we compiled known and novel recorded occurrence points and used them to calculate the extent of occurrence (EOO) and the area of occupancy (AOO). We used a Maxent species distribution model to generate a binary map to estimate upper limits for EOO (EOO around the model predicted area) and AOO (comprised by the model predicted area within the EOO). We obtained 41 locations, resulting in an EOO of 890.7 km2 (up to 1748.7 km2) and an AOO of 100 km2 (up to 327.5 km2). The global population is estimated to be between 880 and 2882 birds, which is concerning because small populations are at risk of extinction due to demographic stochasticity, genetic drift, and the interaction of these factors. As such, our results support the designation of Cipo Cinclodes as Endangered on the Brazilian red list. 相似文献
13.
Habitat loss is a primary cause of species decline, and predicting the distribution of quality habitats across broad scales is needed for conservation of rare species. Secretive marsh birds are a group of emergent-wetland specialists that include multiple threatened and endangered species whose populations have been impacted by wetland loss and modification. Habitat suitability for marsh birds is poorly mapped, and predictions of habitat quality over broad scales are primarily generated via expert judgment. We developed data-driven models to predict fine-resolution habitat quality for 13 marsh bird species across their ranges within the U.S. We demonstrate how these models are useful for conservation by quantifying range contraction, assessing the usefulness of existing protected areas, and assessing the vulnerability of habitats to global change for rare species. These tools provide a quantitative foundation for broad-scale conservation, research, and monitoring efforts, and a starting point for adaptive conservation of marsh bird breeding habitat over broad spatial extents. 相似文献
14.
Sara Snell Taylor James Umbanhowar Allen H. Hurlbert 《Global Ecology and Biogeography》2020,29(4):736-747
15.
Understanding habitat selection by breeding birds and their newly fledged young can be an essential aspect of the conservation of vulnerable species. During 2015–2017, we examined nest site selection of Worthington's marsh wren (Cistothorus palustris griseus) and MacGillivray's seaside sparrow (Ammospiza maritima macgillivraii), and fledgling habitat use by Worthington's marsh wren, 2 imperiled species in northeast Florida, USA. We compared vegetation at unused points to vegetation at nests of both subspecies and at locations used by radio-tagged marsh wren fledglings. Vegetation was taller and stem counts were greater at nest sites compared to unused points. Worthington's marsh wrens also used nest sites with a greater proportion of tall-form smooth cordgrass (Spartina alterniflora) than was observed at unused points. Worthington's marsh wren fledglings also used locations with taller, denser vegetation, but vegetation use changed with fledgling age and tidal stage; older fledglings more frequently used areas with short-form smooth cordgrass and bare ground (and more so during low tides). In contrast, so few nests and nestlings were in black needlerush (Juncus roemerianus) that we could not consider it in our analysis despite its prevalence within our study sites. Our results indicate that tall, dense cordgrass is an important habitat component for these subspecies during the nesting and fledgling life stages in southeastern Atlantic salt marshes. 相似文献
16.
Density-dependent habitat selection in migratory passerines during stopover: what causes the deviation from IFD? 总被引:2,自引:0,他引:2
We studied the distribution of migratory warblers (genus: Sylvia) in poor and high quality habitat patches at a stopover site in the northern Negev, Israel. The purpose of our study was to test predictions based on the ideal free distribution (IFD) model by using a natural ecosystem which has a high turnover of individuals moving between unfamiliar foraging patches. We trapped birds in two groves of Pistacia atlantica embedded within a coniferous forest. The fruit-density ratio between these groves was 45:1. We compared bird density, body condition and habitat matching (the ratio between bird density and resource density) at the two sites. To analyse the data we integrated two approaches to density-dependent habitat selection: the isodar method and the habitat matching rule. As predicted by the IFD model, we found that habitat suitability decreased with bird density with a high correlation between warbler densities in the two habitat patches. Contrary to IFD predictions, warbler density in the poor patch was higher than expected by the habitat-matching rule. This habitat under-matching, had a cost: in the rich habitat the average energy gain per individual bird was higher than in the poor habitat. Further analysis suggests that the apparent habitat under-matching is not due to interference or differences in warbler competitive abilities. Therefore, we suggest that this migratory bird community is not at equilibrium because the birds possess imperfect knowledge of resource distribution. We propose that this lack of knowledge leads to free, but not ideal distributions of migrant birds in unfamiliar stop over sites. 相似文献
17.
Pattern in the distribution of Britain's upland breeding birds 总被引:1,自引:0,他引:1
We use a quantitative approach to identify fifty-eight species of birds which breed in association with the British uplands. Similarities and differences between this list of 'upland birds' and previous more subjective lists are discussed. We then study pattern in the distribution of these species throughout the uplands. A high degree of regionalization is found, and interpreted in terms of the habitat composition of different regions, and known bird–habitat associations. Different regions differ widely, not only with respect to their bird species composition, but also in the number and conservation importance of their upland bird assemblages. In particular, we contrast the uplands of Wales and England with those of Scotland. The Welsh and English uplands contain a relatively low number of upland bird assemblages and are divided into a few large regions, each dominated by a single assemblage type. In comparison, the Scottish uplands are more varied, both in terms of the total number of assemblages, and the range of assemblages found at a small scale. The study provides a means of viewing any upland region within the national context. 相似文献
18.
19.
Asuncin Semper-Pascual Cole Burton Matthias Baumann Julieta Decarre Gregorio Gavier-Pizarro Bibiana Gmez-Valencia Leandro Macchi Matías E. Mastrangelo Florian Ptzschner Patricia V. Zelaya Tobias Kuemmerle 《Proceedings. Biological sciences / The Royal Society》2021,288(1942)
Land-use change is a root cause of the extinction crisis, but links between habitat change and biodiversity loss are not fully understood. While there is evidence that habitat loss is an important extinction driver, the relevance of habitat fragmentation remains debated. Moreover, while time delays of biodiversity responses to habitat transformation are well-documented, time-delayed effects have been ignored in the habitat loss versus fragmentation debate. Here, using a hierarchical Bayesian multi-species occupancy framework, we systematically tested for time-delayed responses of bird and mammal communities to habitat loss and to habitat fragmentation. We focused on the Argentine Chaco, where deforestation has been widespread recently. We used an extensive field dataset on birds and mammals, along with a time series of annual woodland maps from 1985 to 2016 covering recent and historical habitat transformations. Contemporary habitat amount explained bird and mammal occupancy better than past habitat amount. However, occupancy was affected more by the past rather than recent fragmentation, indicating a time-delayed response to fragmentation. Considering past landscape patterns is therefore crucial for understanding current biodiversity patterns. Not accounting for land-use history ignores the possibility of extinction debt and can thus obscure impacts of fragmentation, potentially explaining contrasting findings of habitat loss versus fragmentation studies. 相似文献
20.
CHRISTOPHER WINCHESTER STEVEN B. CASTLEBERRY MICHAEL T. MENGAK 《The Journal of wildlife management》2009,73(3):374-379
ABSTRACT We examined a suite of models in an information theoretic framework to identify factors restricting presence of the endangered Key Largo woodrat (Neotoma floridana smalli) throughout its remaining habitat. Models containing variables related to availability of nest sites and mammalian predator abundances were supported by our data. Abundance of natural (large overstory trees) and artificial (rock and debris piles) nest substrate were the most important predictor variables, followed by indices of feral cat and raccoon (Procyon lotor) abundance. We recommend increasing abundance of nest substrate in the short term through addition of artificial nest substrate and in the long term through continued protection of remaining forest habitat. 相似文献