Habitat-based Model Research Articles

The need to step-up monitoring of Asian bears

Many wildlife species are threatened in Asia, including the five species of terrestrial bears (Asiatic black, Ursus thibetanus; brown, U. arctos; sloth, Melursus ursinus; sun, Helarctos malayanus; giant panda, Ailuropoda melanoleuca): many populations of these bears are thought to be declining or imperiled by small population size. Here our aim is to document how population assessments have been conducted for bears in Asia. We searched the literature and identified 102 studies published during 1999–2021 that investigated the status of an Asian bear population; these occurred in 24 of the 32 bear range countries in Asia. At the most basic level, 11% of studies verified presence of bears in places where they were not known to exist. The most common objective (53% of papers) was a distribution map, often derived from presence locations in a habitat-based model. Occupancy studies (15%) used temporal (time stamps on images from cameras) or spatial (transect segments) replicates, but tended to focus on “use”, so detector spacing was sometimes not appropriate for occupancy. Purported population indices, such as sign density or camera trap encounter rates, were reported in 16% of studies. One third of studies provided a population estimate, but only 10 studies in two decades used a rigorous method (e.g., mark–recapture). Sign surveys and interviews were the most common methods for determining bear presence, and local interviews were heavily relied upon for assessing population trend. Camera trapping has become increasingly prevalent, but only one study obtained a population estimate using photographs to distinguish natural individual markings. Only three studies used hair traps to obtain DNA-based population estimates, and three other studies obtained population estimates from DNA in scats. Just three studies quantitatively measured change in population size or occupancy over time, and none of these showed a decline. Unique rangewide sign surveys of giant pandas showed significant geographic expansion. The opinions of experts and local people, now heavily relied upon for population assessments, are not reliable or sensitive enough for monitoring. Quantitative population assessments are desirable to direct conservation actions toward the most perilous situations, and provide a means to gauge the effectiveness of conservation actions. This paper demonstrates the paucity of rigorous monitoring of Asian bears, and leads off a series of papers that propose improved methods for assessing distribution, occupancy, and density.

Catch per unit effort (CPUE) standardization of Argentine shortfin squid (Illex argentinus) in the Southwest Atlantic Ocean using a habitat-based model

ABSTRACT The Argentine shortfin squid (Illex argentinus) in the Southwest Atlantic Ocean is an economically important cephalopod. Catch per unit effort (CPUE) of species, a critical proxy for fish abundance, affected by many factors, including environmental variables. Given the importance and less considering of multiple environmental factors in the CPUE standardization for I. argentinus, this study provided an accurate standardized CPUE based on the habitat-based model incorporating the effect of environmental variables including sea surface temperature (SST), sea surface height (SSH), and chlorophyll a concentration (Chl-a). The results showed that the trends of yearly and monthly nominal CPUE were consistent with the standardized CPUE. As the highly concentrated fishing operations, the effective fishing effort was always lower than nominal fishing effort, subsequently, the standardized CPUE was found to be higher than nominal CPUE. Among the environmental factors, SSH and Chl-a are the primary environmental variables when standardizing I. argentinus CPUE revealed by habitat-based model. The precision of CPUE standardization could be improved by our methods. The findings will help to grasp the dynamics in the abundance and provide a basic information for the I. argentines stock assessment in the Southwest Atlantic Ocean.

Satellite-detected forest disturbance forecasts American marten population decline: The case for supportive space-based monitoring

Limited monitoring resources often constrain rigorous monitoring practices to species or populations of conservation concern. Insufficient monitoring can induce a tautology as lack of monitoring resources makes it difficult to determine whether a species or population deserves additional monitoring resources. When in-situ monitoring resources are limited, remote habitat monitoring could be a useful supplementary tool, as linking parameterized species distribution models to spatially explicit time-series of environmental correlates allows iterative prediction of population change. Yet the performance of predictive forecasts or hindcasts has been difficult to evaluate. We paired contemporary field data, historic population estimates, and a remotely-sensed archive of landscape change to evaluate predictions of American marten (Martes americana) population decline owing to habitat loss in Maine, USA. We estimated contemporary spatial patterns in marten density relative to landscape disturbance with spatial capture-recapture models. We compared current density estimates to historical density calculations to evaluate population decline, and compared historical calculations to habitat-based model predictions to evaluate the efficacy of habitat monitoring as a proxy for direct monitoring. Marten density was negatively associated with the proportion of surrounding regenerating forest, and point estimates within focal townships were 50–80% lower than historical calculations. Habitat-based hindcasts of marten density across our entire focal area interest suggested a smaller population decline (roughly 50%) within our focal area. Thus, although habitat-based predictions underpredicted marten decline, they provided correct directional inference. Habitat monitoring and predictions from species distribution models may provide useful inference about population changes given trends in habitat at limited expense when in-situ information is lacking.

Spatiotemporal trends in Canadian domestic wild boar production and habitat predict wild pig distribution

Understanding source dynamics of invasive species is crucial to their management. Free-ranging wild pigs (Sus scrofa) have caused considerable ecological and agricultural damage throughout their global range, including Canada. Objectives were to assess the spatial and temporal patterns in domestic wild boar and test the propagule pressure hypothesis to improve predictive ability of an existing habitat-based model of wild pigs. We reviewed spatiotemporal patterns in domestic wild boar production across ten Canadian provinces during 1991–2011 and evaluated the ability of wild boar farm distribution to improve predictive models of wild pig occurrence using a resource selection probability function for wild pigs in Saskatchewan. Domestic wild boar production in Canada increased from 1991 to 2001 followed by sharp declines in all provinces. The distribution of domestic wild boar farms in 2006 improved the fit and predictive ability of the habitat-based model, and the number of boar farms in adjacent rural municipalities had a relative variable importance of 0.84. Our results support the propagule pressure hypothesis, which states that establishment success is linked to source dynamics. Although eradication of wild pigs is rarely feasible after establishment over large areas, effective management will depend on strengthening regulations and enforcement of containment practices for Canadian domestic wild boar farms. Initiation of coordinated provincial and federal efforts to implement population control procedures for established wild pig populations are urgently needed to limit the spread of wild pigs and their impacts, and should focus on areas with existing or historic domestic wild boar farms.

Distribution, Abundance, and Habitat Associations of a Large Bivalve (Panopea generosa) in a Eutrophic Fjord Estuary

ABSTRACT Marine bivalves are important ecosystem constituents and frequently support valuable fisheries. In many nearshore areas, human disturbance—including declining habitat and water quality—can affect the distribution and abundance of bivalve populations, and complicate ecosystem and fishery management assessments. Infaunal bivalves, in particular, are frequently cryptic and difficult to detect; thus, assessing potential impacts on their populations requires suitable, scalable methods for estimating abundance and distribution. In this study, population size of a common benthic bivalve (the geoduck Panopea generosa) is estimated with a Bayesian habitat-based model fit to scuba and tethered camera data in Hood Canal, a fjord basin in Washington state. Densities declined more than two orders of magnitude along a north—south gradient, concomitant with patterns of deepwater dissolved oxygen, and intensity and duration of seasonal hypoxia. Across the basin, geoducks were most abundant in loose, unconsolidat...

Using Spatial Models to Target Conservation Efforts for the Endangered American Burying Beetle

Numerous studies have demonstrated that using ecological models is beneficial in recovering species listed un- der the Endangered Species Act (ESA). In addition, many federal agencies and environmental organizations have recom- mended using strategic approaches to conservation. One rare species in need of conservation is the American burying bee- tle (ABB, Nicrophorus americanus). The ABB was listed as endangered in 1989 and conservation efforts need to be tar- geted and improved to be successful in achieving de-listing. We combined presence/absence ABB surveys (1979- 2011), with habitat-based model projections, to identify specific habitats where the ABB is likely to occur. Our habitat based range for the ABB was 96.9% accurate in identifying positive ABB surveys (n=485) from 1979 to 2011. Previously, po- tential ABB habitat was identified using political or county boundaries and was not precise and also included areas that were unsuitable for ABB habitat. Using spatial data, known locations, and model projections, we reduced the potential habitat range by over 4.5 million acres (1.8 million hectares) from the county delineation, resulting in greater precision for conservation of the ABB, more targeted conservation efforts, and reduced costs to other federal agencies and industry that are required to have minimal impact to this endangered species under the ESA. Our approach will be useful to other agen- cies and other states that need to target conservation and recovery efforts for rare invertebrates.

Habitat and prey availability attributes associated with juvenile and early adult pallid sturgeon occurrence in the Missouri River, USA

The pallid sturgeon Scaphirhynchus albus is a federally endangered species native to the Missouri and lower Mississippi Rivers, USA. As part of recovery efforts, over 360 000 pallid sturgeon have been stocked into the Missouri River since 1994, and a standardized, long-term monitoring program was initiated in 2003. Understanding the distribution and habitat require- ments of juvenile and early adult pallid sturgeon (fork length <720 mm, age <10 yr) is an impor- tant goal of the monitoring and recovery programs. In this study, we collected information on habi- tat characteristics and prey availability from the upper Missouri River along the Nebraska-South Dakota border and compared these attributes between capture (present) and non-capture (absent) locations (N = 59). To evaluate the relative influence of habitat and prey availability on pallid sturgeon occurrence, we examined several candidate models using an information- theoretic approach. A prey availability model had the most support and included site-specific information on Diptera and Ephemeroptera abundance. A habitat-based model showed that juve- niles and early adults were found in relatively deeper water and avoided areas where bottom velocities were greater than 1.2 m s �1 . Although not as well supported as the prey-effects model (evidence ratio = 6.4), habitat features also provided a plausible model for predicting occurrence. The models developed here could be used to evaluate pallid sturgeon habitat potential in the Mis- souri River basin and help guide future monitoring and conservation management of this endan- gered species.

Standardizing CPUE of yellowfin tuna (Thunnus albacares) longline fishery in the tropical waters of the northwestern Indian Ocean using a deterministic habitat-based model

Data collected from a longline fishery in the Indian Ocean were used to evaluate the performance of a deterministic habitat-based standardization (detHBS) method for catch per unit effort (CPUE) standardization. The habitat preference indices of the yellowfin tuna (Thunnus albacares) were estimated for different depth, temperature, and dissolved oxygen (DO) classes. The detHBS was applied for standardizing the yellowfin tuna CPUE based on the habitat preference indices of the yellowfin tuna. Nominal CPUE and normalized nominal CPUE were compared with the standardized CPUE and normalized standardized CPUE, respectively, using Wilcoxon tests. The results showed that (1) there was significant difference between nominal CPUE and standardized CPUEs (p 0.01). This study suggests that detHBS effectively improved the precision of CPUE standardization, and the depth data set was the optimum data set in standardizing CPUE.

Linking local ecological knowledge and habitat modelling to predict absolute species abundance on large scales

Assessing the spatial structure of abundance of a species is a basic requirement to carry out adequate conservation strategies. However, existing attempts to predict species abundance, particularly in absolute units and on large scales, are scarce and have led to weak results. In this work we present a scheme to obtain, in an affordable way, a predictive model of absolute animal abundance on large scales based on the modelling of data obtained from local ecological knowledge (LEK) and its calibration. To exemplify this scheme, we build and validate a predictive absolute abundance model of the endangered terrestrial tortoise Testudo graeca in Southeast Iberian Peninsula. For that purpose, we collected distribution and relative abundance data of T. graeca using a low cost methodology, such as LEK, by means of interviewing shepherds. The information from LEK was employed to build a predictive habitat-based model of relative abundance. The relative abundance model was transformed into an absolute abundance model by means of calibration with a classical absolute abundance sampling method such as distance sampling. The obtained absolute abundance model predicted the observed absolute abundances values well in independent locations when compared with other works (R2 = 36%) and thus can offer a cost-effective predictive ability. Our results show that reliable habitat-based predictive maps of absolute species abundance on regional scales can be obtained starting from low cost sampling methods of relative abundance, such as LEK, and its calibration.

A habitat-based model for the spread of hantavirus between reservoir and spillover species

New habitat-based models for spread of hantavirus are developed which account for interspecies interaction. Existing habitat-based models do not consider interspecies pathogen transmission, a primary route for emergence of new infectious diseases and reservoirs in wildlife and man. The modeling of interspecies transmission has the potential to provide more accurate predictions of disease persistence and emergence dynamics. The new models are motivated by our recent work on hantavirus in rodent communities in Paraguay. Our Paraguayan data illustrate the spatial and temporal overlaps among rodent species, one of which is the reservoir species for Jabora virus and others which are spillover species. Disease transmission occurs when their habitats overlap. Two mathematical models, a system of ordinary differential equations (ODE) and a continuous-time Markov chain (CTMC) model, are developed for spread of hantavirus between a reservoir and a spillover species. Analysis of a special case of the ODE model provides an explicit expression for the basic reproduction number, R 0 , such that if R 0 < 1 , then the pathogen does not persist in either population but if R 0 > 1 , pathogen outbreaks or persistence may occur. Numerical simulations of the CTMC model display sporadic disease incidence, a new behavior of our habitat-based model, not present in other models, but which is a prominent feature of the seroprevalence data from Paraguay. Environmental changes that result in greater habitat overlap result in more encounters among various species that may lead to pathogen outbreaks and pathogen establishment in a new host.

Evolution of Coloniality in Birds: A Test of Hypotheses With the Red-Necked Grebe (Podiceps Grisegena)

Abstract Group breeding is perplexing, because individuals incur density-dependent fitness costs to breed in groups, yet no universal benefit appears to explain its evolution. Coloniality in birds, defined as dense nesting within limited territories, is a striking example of group breeding. Adaptive explanations for coloniality are diverse, and several research approaches have emerged. Here, we test models for the evolution of coloniality with a population of Red-necked Grebes (Podiceps grisegena). We distinguish habitat models from conspecific models for explaining the adaptive evolution of coloniality. Habitat models propose that the fitness benefits of colonial breeding are gained through the characteristics or location of the colony site, whereas conspecific models posit that the benefits of colonial breeding are gained solely from nesting near conspecifics. Red-necked Grebes are waterbirds that typically nest in a dispersed fashion, only rarely nesting in colonies. Both dispersed and colonial nesting co-occurred in the study population, and aquatic nests were found in three distinct habitat types. We gathered detailed demographic data and used analyses of covariance to test whether variation in habitat type or conspecific aggregation best explained differences in breeding success across the population. We further used fitness, genetic, and spatial data to test whether kin selection, sexual selection, or conspecific reproductive-success cueing may drive colony formation. The data provided strong support for a habitat-based model and inconsistently supported conspecific models. Our results suggest that colonial individuals of this population gain selfish benefits from relatively rare, high-quality habitat rather than from proximity of conspecifics. Evolución de la Colonialidad en las Aves: Una Evaluación de las Hipótesis en Podiceps grisegena

Incorporating spatial autocorrelation into the general linear model with an application to the yellowfin tuna (Thunnus albacares) longline CPUE data

Catch-per-unit-effort (CPUE) data have often been used to obtain a relative index of the abundance of a fish stock by standardizing nominal CPUE using various statistical methods. The theory underlying most of these methods assumes the independence of the observed CPUEs. This assumption is invalid for a fish population because of their spatial autocorrelation. To overcome this problem, we incorporated spatial autocorrelation into the standard general linear model (GLM). We also incorporated into it a habitat-based model (HBM), to reflect, more effectively, the vertical distributions of tuna. As a case study, we fitted both the standard-GLM and spatial-GLM (with or without HBM) to the yellowfin tuna CPUE data of the Japanese longline fisheries in the Indian Ocean. Four distance models (Gaussian, exponential, linear and spherical) were examined for spatial autocorrelation. We found that the spatial-GLMs always produced the best goodness-of-fit to the data and gave more realistic estimates of the variances of the parameters, and that HBM-based GLMs always produced better goodness-of-fit to the data than those without. Of the four distance models, the Gaussian model performed the best. The point estimates of the relative indices of the abundance of yellowfin tuna differed slightly between standard and spatial GLMs, while their 95% confidence intervals from the spatial-GLMs were larger than those from the standard-GLM. Therefore, spatial-GLMs yield more robust estimates of the relative indices of the abundance of yellowfin tuna, especially when the nominal CPUEs are strongly spatially autocorrelated.

Stock assessment of blue marlin (Makaira nigricans) in the Pacific using MULTIFAN-CL

In the Pacific, blue marlin are an incidental catch of longline fisheries and an important resource for big game recreational fishing. Over the past two decades, blue marlin assessments by different techniques have yielded results ranging from an indication of declining stock to a state of sustained yield at approximately the maximum average level. Longline fishing practices have changed over the years since the 1950s in response to changes in principal target species and to gear developments. Despite increasingly sophisticated attempts to standardize fishing effort with changing fishing practices, the stock assessments to date are likely confounded to a greater or lesser degree by changes in catchability for blue marlin. Yet, only data from commercial longline fisheries targeting tuna provide sufficient spatial and temporal coverage to allow assessment of this resource. To re-assess the blue marlin stocks in the Pacific and also to assess the efficacy of a habitat-based standardization of longline effort, a collaborative analysis was conducted involving scientists at the National Research Institute of Far Seas Fisheries, Shimizu, Japan, the Inter-American Tropical Tuna Commission, La Jolla, California, and the NOAA Fisheries Honolulu Laboratory, Honolulu, Hawaii. Using MULTIFAN-CL as an assessment tool, there was considerable uncertainty in quantifying the fishing effort levels that would produce a maximum sustainable yield. However, it was found that, at worst, blue marlin in the Pacific are close to a fully exploited state, that is the population and the fishery are somewhere near the top of the yield curve. Furthermore, it was found that effort standardization using a habitat-based model allowed estimation of parameters within reasonable bounds and with reduced confidence intervals about those values.

Population viability of coho salmon, &lt;I&gt;Oncorhynchus kisutch&lt;/I&gt;, in Oregon coastal basins: application of a habitat-based life cycle model

Population viability of coho salmon, &lt;I&gt;Oncorhynchus kisutch&lt;/I&gt;, in Oregon coastal basins: application of a habitat-based life cycle model

Path analysis of collective properties and habitat relationships of fish assemblages in coastal plain streams

Collective properties of fish assemblages at 44 sites in low-gradient streams (orders 1–3) on the upper coastal plain of South Carolina, U.S.A., were highly variable among sites: richness, 2–17 species per site; density, 0.2–9.5 individuals∙m−2; mean individual mass, 0.4–22.2 g per individual; and biomass, 0.1–42.1 g∙m−2. Principal components analysis reduced 15 habitat parameters to four interpretable components that were used as orthogonal predictive variables in path analysis. Path analysis, with a directional model containing intermediate steps and multiple dependent variables, was used as an alternative to multiple regression. Two principal components, associated with velocity (and its covariates) and depth (and its covariates), were the primary correlates of biomass (R2 = 49%), richness (44%), mean size (36%), and density (20%), with cover variables contributing relatively little to any R2value. Velocity effects were negative and depth effects positive for all collective properties. Habitat effects on biomass were mediated by effects on individual fish size rather than numbers. Correlations of collective properties at sites sampled in 2 years were similar to those from the single year, habitat-based path model, implying that the path model was adequate and inclusive, and accurately reflected collective properties of these communities.

Fish community structure of Oklahoma gulf coastal plains

We collected the common fish species in all available aquatic habitats (streams, oxbow lakes, swamps) in bottomlands of McCurtain County, Oklahoma. Abundance and distribution of fishes, and environmental data were analyzed by a multivariate approach and examined for fit to a hierarchical model. The variables maximum depth, substrate, and presence of flow were the most important variables predicting fish community structure. Our multivariate analyses demonstrate that environmental factors can explain much variation in presence and abundance of the common fish species. Kolasa's hierarchical model relates species to each other by comparing ranges. This habitat-based model explained the relationships of our species ranges.

Patterns of the Abundance of Species: A Comparison of Two Hierarchical Models

We compare two hierarchical, predictive models that explain the log-series pattern of distribution of species abundances. The Sequential Breakage Model (SBM) is based on the appropriation of fragments from the community niche volume, while the Habitat-Based Model (HBM) assumes a contemporary use of environmental volume by species acting in different scales. A detailed analysis of assumptions of the SBM indicates that its predictions rely on the establishment of a link between the niche overlap and abundance of species. We show that this link is inadequate and may be incorrect. The agreement between the abundances predicted by the SBM and the abundances observed in assemblages composed of three species cannot be thus considered as validation of this model. We conclude, however, that such an agreement supports the Habitat-Based Model. The predictions of the HBM are generated from a realistic combination of commonly observed ecological phenomena (habitat heterogeneity and patchiness), species properties (differentiated degrees of specialization), and the assumed relation between them. The latter model is sensitive to habitat heterogeneity. This difference may be used in testing both models under different ecological conditions and at various scales.