Habitat Suitability Index Research Articles

전주천 상류부의 서식처 적합도 지수 및 생태유량 산정

In this study, WUA (Weighted Usable Area) based on the Instream Flow Incremental Methodology (IFIM) was calculated to determine ecological flow at JeonJu-Cheon by using River2D model. To calibrate River2D, simulation results for low flow conditions of River2D were compared with calibrated HEC-RAS simulation results and the optimum parameters were determined. The results were RMSE (0.18), NSE (0.71) and coefficient of determination (0.78) for velocity and RMSE (0.02), NSE (0.71), coefficient of determination (0.73) for water depth. The result shows that the model successfully simulates the water flows. A selected target fish species to build the habitat suitability index were composed of Zaccoplatypus and Coreoleuciscus splendidus. These species showed the highest occurrences over the past decade in f ish monitoring. Also, The WUA-Discharge curve was calculated with the suitability index in a medium flow conditions. From the result, WUA is changed according to flowrate. In the flowrate-WUA/A graph, ecological flow can be determined at 1.8~2.0 m/s for Zaccoplatypus 2.0 m/s and Coreoleuciscus splendidus 1.8 m/s at JeonJu-Cheon upstream. When compared with flow-duration analysis, it is demonstrative that simulation results fitted ecological flow considering quantity of available habitat for each fish species.

Estimation of optimal ecological flowrates for fish habitats in a nature-like fishway of a large river

Fishways are constructed to provide longitudinal connectivity of streams or rivers where their flow has been altered by in-stream structures such as dams or weirs. Nature-like fishways have an additional function of providing fish habitats. In the study, we estimated the role of a nature-like fishway (length: 700 m, slope: 1/100) for fish habitat by using two dominant species in the Sangju Weir, Nakdong River, to calculate the optimal ecological flow rate using Physical HABitat SIMulation (PHABSIM). To identify the dominant species that used the fishway, we conducted trap monitoring from August to November 2012 at the fishway exit. The dominant species were Zacco platypus and Opsariichthys uncirostric amurensis with a relative abundance of 62.1% and 35.9%, respectively. Optimal habitat suitability indices (HSIs) for Z. platypus and O. u. amurensis were calculated as 0.6-0.8 m/s (water velocity) and 0.2-0.4 m (water depth), and 0.5-0.7 m/s (water velocity) and 0.1-0.3 m (water depth), respectively. The optimal ecological flow rates (OEFs) for Z. platypus and O. u. amurensis were 1.6 and 1.7 cubic meter per second (CMS), respectively. The results of the study can be used in a management plan to increase the habitat function of nature-like fishways in the Sangju Weir. This methodology can be utilized as an appropriate tool that can determine the habitat function of all nature-like fishways.

Assessing Potential Habitat and Carrying Capacity for Reintroduction of Plains Bison (Bison bison bison) in Banff National Park.

Interest in bison (Bison bison, B. bonasus) conservation and restoration continues to grow globally. In Canada, plains bison (B. b. bison) are threatened, occupying less than 0.5% of their former range. The largest threat to their recovery is the lack of habitat in which they are considered compatible with current land uses. Fences and direct management make range expansion by most bison impossible. Reintroduction of bison into previously occupied areas that remain suitable, therefore, is critical for bison recovery in North America. Banff National Park is recognized as historical range of plains bison and has been identified as a potential site for reintroduction of a wild population. To evaluate habitat quality and assess if there is sufficient habitat for a breeding population, we developed a Habitat Suitability Index (HSI) model for the proposed reintroduction and surrounding areas in Banff National Park (Banff). We then synthesize previous studies on habitat relationships, forage availability, bison energetics and snowfall scenarios to estimate nutritional carrying capacity. Considering constraints on nutritional carrying capacity, the most realistic scenario that we evaluated resulted in an estimated maximum bison density of 0.48 bison/km2. This corresponds to sufficient habitat to support at least 600 to 1000 plains bison, which could be one of the largest 10 plains bison populations in North America. Within Banff, there is spatial variation in predicted bison habitat suitability and population size that suggests one potential reintroduction site as the most likely to be successful from a habitat perspective. The successful reintroduction of bison into Banff would represent a significant global step towards conserving this iconic species, and our approach provides a useful template for evaluating potential habitat for other endangered species reintroductions into their former range.

Modeling spatiotemporal variability of the bioclimate envelope of Homarus americanus in the coastal waters of Maine and New Hampshire

A bioclimate envelope model was developed to evaluate the potential impacts of climate variability on American lobster (Homarus americanus). Bioclimate envelopes were defined by season-, sex-, and stage- specific Habitat Suitability Indices (HSI) based on (1) bottom temperature, (2) bottom salinity, and (3) depth. The species’ association to each of these three environmental attributes was expressed using Suitability Indices (SIs) calibrated by standardized lobster abundance derived from 14 years of fishery independent survey. A regional ocean model (Finite-Volume Community Ocean Model) was integrated with the HSI to hindcast spatiotemporal variability of bioclimate envelopes for American lobster in coastal waters of Maine and New Hampshire from 1978 to 2013. The model predictions indicated higher habitat suitability in inshore waters for both adult and juvenile lobsters. A statistically significant increasing trend in habitat suitability was observed for both sexes and stages (juvenile and adult) during the spring (April–June), while no significant trend in habitat suitability was observed in the fall (September–November). This study provides a modeling framework to reconstruct climatically suitable lobster ranges that can be used to formulate climate-based hypotheses for future studies of this species.

Habitat quantity of Red-cockaded Woodpecker Picoides borealis (Aves: Piciformes: Picidae) in its former historic landscape near the Big Thicket National Preserve, Texas, USA

<p>We quantified pine-forested habitat suitable for Red-cockaded Woodpecker <em>Picoides borealis</em> in the former historic range of the species to assess the potential for possible re-colonization. We used a remotely-sensed image and geographic information systems (GIS) to create a land-use/land (LU/LC) binary cover map, from which we calculated the habitat suitability index (HSI) based on an estimated home range of 50ha. A sensitivity analysis revealed the necessity for more data to make an accurate estimate, but our analysis of landscape metrics indicates more than 930ha of suitable habitat patches. These patches are heavily fragmented and mostly located on private lands. They can be assessed for understory and herbaceous vegetation and can be restored for possible re-establishment of approximately 18 groups/colonies of Red-cockaded Woodpeckers.</p><div> </div>

Assessment of climate change impacts on river hydrology and habitat suitability of Oxynoemacheilus bergianus. Case study: Kordan River, Iran

Iran is located in a geographical location that is not immune from climate change effects. Therefore, it is necessary to assess the influence of climate change on water resources since this part of the ecosystem is the first component that will be affected by climate change. The main purpose of this study is to assess climate change impacts on environmental flows by using hydrological indicators in Kordan River, Iran. In this regard, at first, the future climate change in the region was projected by using HadCM3 general circulation model in three 30-year periods, 2011–2040, 2041–2070, and 2071–2099, considering the A2 and B1 emission scenarios. Afterwards, Kordan River streamflow was simulated by using the SWAT model for the baseline period (1985–2010) and the future and hydrological indicators, such as magnitude, duration, timing, and frequency of extreme flows, were analyzed. Results showed a reduction in discharge. Under the A2 scenario, discharge decreased from 3.31 to 2.66 m3/s, while under the B1 scenario, this reduction was up to 2.86 m3/s for 100 years into the future. In addition to reduction of discharge, the occurrence time of maximum and minimum flows is projected to change as well. This phenomenon will change the habitat suitability and introduce some risks for aquatic life. Finally, in order to analyze Kordan River habitat suitability, we chose Oxynoemacheilus bergianus, which can be a suitable index for the ecosystem. In this regard, Habitat Suitability Index (HSI) was used, which is obtained based on river characteristics such as water depth, velocity, and water temperature. According to the results, the percentage of time that HSI is at a rate between 0.4 and 0.6 is expected to decrease from 100–70% to 80–60% under both scenarios by 2071–2099.

A habitat suitability model for Chinese sturgeon determined using the generalized additive method

Summary The Chinese sturgeon is a type of large anadromous fish that migrates between the ocean and rivers. Because of the construction of dams, this sturgeon’s migration path has been cut off, and this species currently is on the verge of extinction. Simulating suitable environmental conditions for spawning followed by repairing or rebuilding its spawning grounds are effective ways to protect this species. Various habitat suitability models based on expert knowledge have been used to evaluate the suitability of spawning habitat. In this study, a two-dimensional hydraulic simulation is used to inform a habitat suitability model based on the generalized additive method (GAM). The GAM is based on real data. The values of water depth and velocity are calculated first via the hydrodynamic model and later applied in the GAM. The final habitat suitability model is validated using the catch per unit effort (CPUE d ) data of 1999 and 2003. The model results show that a velocity of 1.06–1.56 m/s and a depth of 13.33–20.33 m are highly suitable ranges for the Chinese sturgeon to spawn. The hydraulic habitat suitability indexes (HHSI) for seven discharges (4000; 9000; 12,000; 16,000; 20,000; 30,000; and 40,000 m 3 /s) are calculated to evaluate integrated habitat suitability. The results show that the integrated habitat suitability reaches its highest value at a discharge of 16,000 m 3 /s. This study is the first to apply a GAM to evaluate the suitability of spawning grounds for the Chinese sturgeon. The study provides a reference for the identification of potential spawning grounds in the entire basin.

基于栖息地指数的东太平洋黄鳍金枪鱼渔场预报

基于栖息地指数的东太平洋黄鳍金枪鱼渔场预报

Spatial Quantification of White-tailed Deer Habitat of a Wetland-dominated Landscape in Central Lower Michigan

ABSTRACT White-tailed deer (Odocoileus virginianus), can be a keystone herbivore that can greatly impact conditions in forest ecosystems. Results of previous deer herbivory research could cause biologists concern when managing wetlands as suitable habitat for migratory waterfowl because intense herbivory can negatively impact plant communities. Biologists at Shiawassee National Wildlife Refuge (SNWR), Saginaw, Michigan, observed obvious effects of white-tailed deer herbivory within wetland plant communities. Our objective was to evaluate white-tailed deer habitat suitability within a landscape dominated by wetland vegetation types used by deer during the 2011 and 2012 growing seasons to help inform deer and water bird habitat management decision making. We classified 1m x 1m aerial imagery data in ArcGIS v10.0 and developed a white-tailed deer habitat suitability index (HSI) model. Moist soil units, lakeplain prairie, and bottomland hardwood forests demonstrated high habitat suitability for white-tailed d...

Physical habitat simulation system (PHABSIM) 을 이용한 금강의 두드럭조개 (Lamprotula coreana) 서식지 평가

본 조사는 2013년 6월부터 8월까지 금강 상류에서 멸종위기야생생물 I급인 두드럭조개 (Lamprotula coreana)의 서식지를 조사하였다. 서식지 평가를 위하여 하천의 물리적 구조인 여울, 소 및 유수역이 모두 포함된 다양한 서식환경에서 서식상태를 조사하였으며, 하천단면, 수심, 유속, 하상재료 및 서식지 유형 등을 현장에서 측정 하였다. 서식 확인된 두드럭조개는 크기, 무게 및 연령을 기록하고 서식지에 재살포하였고, 서식지적합도지수 (Habitat suitability index, HSI)와 PHABSIM (physical habitat simulation system)에 의한 최적 생태유량 산정을 위하여, 각각의 채집 장소에서 수심, 유속 및 하상재료 등을 기록하였다. 서식지 평가는 수위, 유량 및 하천단면의 현장조사 결과와 두드럭조개의 HSI를 PHABSIM에 적용하여 가용서식지면적 (weighted usable area, WUA)과 유량의 관계 곡선을 작성하였다. 금강 상류에서 채집된 두드럭조개는 각장 <TEX>$73.1{\pm}18.4mm$</TEX> 및 전중 <TEX>$131.6{\pm}72.3g$</TEX> 이었으며, 연령은 2-7년생까지 서식하는 것으로 확인되었다. 두드럭조개의 HSI는 수심 0.4-0.5 m, 유속 0.3-0.5 m/s, 하상재료는 모래-호박돌로 나타났다. PHABSIM에 의해 모의된 최적유량은 2.1 cms였으며, WUA는 <TEX>$3,730m^2$</TEX>/1000 m로 나타났다. 두드럭조개의 서식지 평가 결과는 최근 각종 하천 공사 및 생태적 교란 등으로 서식 범위가 감소하고 있는 시점에서 서식지 복원 및 관리를 위한 기초자료로 활용될 수 있을 것이다. This study sampled endangered species, Lamprotula coreana, and surveyed its habitat at the Guem River with three times from June to August 2013. To assess the habitat, this study conducted field survey considering diverse physical conditions of stream, such as pool, run and riffle, and measured transect, water depth, water velocity, substrate structure, and habitat type. When L. coreana collected, length, weight and age were measured. Water velocity, water depth and substrate structure were recorded to develop HSI (habitat suitability index) and performed PHABSIM (physical habitat simulation) to estimate the optimum flow discharge. Water level, flow discharge and transect data were used for habitat assessment, and PHABSIM was applied to calculate WUA (weighed usable area). Shell length was <TEX>$73.1{\pm}18.4mm$</TEX> (28.5-102.0 mm), shell weight was <TEX>$131.6{\pm}72.3g$</TEX> (28.0-281.0 g) and age was two to seven years from L. coreana collected at the upstream of the Guem River. Developed HSI indicated that the optimal habitat for L. coreana was 0.4-0.5 m for water depth, 0.3-0.5 m/s for water velocity and sand to boulder for substrate structure. The optimum ecological flow discharge for L. coreana was 2.1 cms and WUA was <TEX>$3,730m^2$</TEX>/1000 m by the result of PHABSIM. Recently, river construction work and habitat disturbance have caused negative impact on the distribution of L. coreana. The result of this study would provide fundamental data for habitat restoration and management of L. coreana.

댐 하류 하천에서 하상변동 모델을 이용한 어류 물리서식처 변화 모의

This study investigated the impact of the morphological change on a physical fish habitat in the downstream reach of a dam using long-term mobile bed simulation. The quasi-steady model was used for hydraulic simulation and the habitat suitability index model was applied for physical habitat simulation. For simulating long-term morphological change of the stream bed, The Exner equation was used. Sorting of bed material was also considered. The results of simulation showed that erosion and armoring process occurred in a reach downstream of the dam and change of physical habitat for Zacco platypus followed. These results indicate that channel morphology and substrate conditions effected the physical habitat for considering long-term investigation.

Environmental flow in the River Ondas basin in Bahia, Brazilian Cerrado.

This paper aimed to estimate the environmental flow of a water basin located in the Brazilian Cerrado using the bidimensional model River2D. The study was carried out in a stretch of the lower portion of the River Ondas in the western part of the state of Bahia, Brazil. To carry out the ecohydrological modeling, the following were used: topobathymetry, hydraulic characterization, the streamflows with the probability of non-exceedances (Q50, Q60, Q70, Q80, Q90, and Q95), and the Habitat Suitability Index for species of the genus Hypostomus. In the River2D, the weighted usable areas (WUAs) pertaining to the streamflows associated with different non-exceedances were simulated for the later construction of optimization and identification matrices of the streamflows that maximize the habitat area throughout the year. For juvenile Hypostomus, WUA increased as streamflow increased, with higher values associated with Q50. For adult specimens, lower WUA values were observed associated with Q50, while higher values were associated with Q95, which shows a preference for lower streamflows. The environmental flows found for the stretch of the River Ondas varied over the course of the year. The lowest environmental flows were observed in September (30.31 m(3) s(-1)) and October (29.98 m(3) s(-1)), while the highest were observed in February (44.22 m(3) s(-1)) and March (43.16 m(3) s(-1)). The environmental flow regime obtained restricts the water availability in the basin, for the purpose of water capture, which shows the importance of ecohydrological studies in forming a basis for water resource management actions.

Application of the physical habitat simulation for fish species to assess environmental flows in an Atlantic Forest Stream in South-eastern Brazil

ABSTRACT The physical habitat simulation sub-routine of the Instream Flow Incremental Methodology (IFIM) uses hydraulic modeling and suitability indices of target fish species to predict how differences in-stream flows affect the microhabitat occupation by fish species. This habitat modelling approach was adopted to assess the ecological effects of running flows on three neotropical fish species of different orders (Bryconamericus ornaticeps , Ancistrus multispinis and Geophagus brasiliensis ).The study encompassed two reaches of an Atlantic Forest stream in Southeastern Brazil where topographic and hydraulic (depth, velocity and type of substrate) characteristics were measured to implement one-dimensional hydraulic simulation. Sub aquatic observation of fish was performed to collect data on microhabitat use and these data were used to develop habitat suitability curves that were used in the habitat simulation to obtain the habitat suitability index (HSI) and weighted usable area (WUA) versus flow curves. Upon these curves minimum and optimum environmental flows for the target fish species were proposed. Bryconamericus ornaticeps and A. multispinis selected microhabitats around 0.6 m depth, whereas G. brasiliensis showed a wider suitable range (0.35-0.9 m). All the three species were mainly observed in microhabitat with low flow velocity (0.1 m/s). Bryconamericus ornaticeps selected more frequently coarse substrate (e.g. boulders) but it appeared also over sandy substrate, whereas A. multispinis and G. brasiliensis selected preferably boulders. The range of 0.65-0.85 m3/s was found as the optimum to meet the needs of the three fish species. Our results agree with the necessary objective information to perform grounded management actions in the frame of a management program aiming at ecosystem conservation. Thereby it can be considered a successful pilot study in environmental flow assessment in an Atlantic Forest stream of Brazil.

Evaluating short‐ and long‐term impacts of fuels treatments and simulated wildfire on an old‐forest species

Fuels‐reduction treatments are commonly implemented in the western U.S. to reduce the risk of high‐severity fire, but they may have negative short‐term impacts on species associated with older forests. Therefore, we modeled the effects of a completed fuels‐reduction project on fire behavior and California Spotted Owl (Strix occidentalis occidentalis) habitat and demography in the Sierra Nevada to assess the potential short‐ and long‐term trade‐offs. We combined field‐collected vegetation data and LiDAR data to develop detailed maps of forest structure needed to parameterize our fire and forest‐growth models. We simulated wildfires under extreme weather conditions (both with and without fuels treatments), then simulated forest growth 30 years into the future under four combinations of treatment and fire: treated with fire, untreated with fire, treated without fire, and untreated without fire. We compared spotted owl habitat and population parameters under the four scenarios using a habitat suitability index developed from canopy cover and large‐tree measurements at nest sites and from previously derived statistical relationships between forest structure and fitness (λ) and equilibrium occupancy at the territory scale. Treatments had a positive effect on owl nesting habitat and demographic rates up to 30 years after simulated fire, but they had a persistently negative effect throughout the 30‐year period in the absence of fire. We conclude that fuels‐reduction treatments in the Sierra Nevada may provide long‐term benefits to spotted owls if fire occurs under extreme weather conditions, but can have long‐term negative effects on owls if fire does not occur. However, we only simulated one fire under the treated and untreated scenarios and therefore had no measures of variation and uncertainty. In addition, the net benefits of fuels treatments on spotted owl habitat and demography depends on the future probability that fire will occur under similar weather and ignition conditions, and such probabilities remain difficult to quantify. Therefore, we recommend a landscape approach that restricts timber harvest within territory core areas of use (~125 ha in size) that contain critical owl nesting and roosting habitat and locates fuels treatments in the surrounding areas to reduce the potential for high‐severity fire in territory core areas.

Temporal habitat suitability modeling of Caspian shad (Alosa spp.) in the southern Caspian Sea

&lt;p&gt;To comprehensively manage an ecosystem such as that of the Caspian Sea, the world’s largest lake, detailed knowledge of the habitat traits of the living organisms in the ecosystem is essential. The present study examined environmental variables and used the Habitat Suitability Index (HSI) model to determine the most preferred seasonal habitat and optimal environmental range of Caspian shad (&lt;em&gt;Alosa &lt;/em&gt;spp). The fish preferred deep waters with low levels of total organic matter and sea level anomaly in winter and productive areas with a high concentration of chlorophyll-a (Chl&lt;em&gt;a&lt;/em&gt;) and relatively high benthos biomass in spring. The number per unit area (NPUA)-based HSI model determined that the geometric mean model (GMM) was the optimal model for defining a suitable habitat in winter. For spring, the arithmetic mean model (or GMM) in the NPUA-based HSI model most accurately predicted preferred habitat for Caspian shad. The average NPUA in both seasons increased with the HSI; areas with an HSI of between 0.4 and 0.6 in spring and between 0.6 and 0.8 in winter had a high percentage of total catch. Areas with an HSI of more than 0.5 had over 91% and 63% of the total catch in spring and winter, respectively, demonstrating the reliability of the NPUA-based HSI model in predicting Caspian shad habitat. The present study shows that remotely sensed data plus depth are the most critical environmental variables in Caspian shad habitats and that Chl&lt;em&gt;a&lt;/em&gt; and SLA are the most critical remotely sensed parameters for near real-time prediction of Caspian shad habitat.&lt;/p&gt;

Modeling habitat suitability index for Chilean jack mackerel (Trachurus murphyi) in the South East Pacific

Habitat models, such as the habitat suitable index (HSI), have been extensively used to estimate the spatial distribution of fish species based on the quality of habitat. Fishery dependent data from commercial fishing vessels are an important or potentially the only source of scientific information available in these fisheries, especially for the highly migratory stocks in the high seas. In this study we use catch and effort data from the Chinese trawl fishery combined with remote sensing data including sea surface temperature (SST), sea surface height (SSH) and sea surface chlorophyll-a concentration (Chl-a) to define suitable index (SI) for jack mackerel (Trachurus murphyi) in the South East Pacific Ocean. Observed SI values were calculated based on the frequency distribution of fishing effort for each environmental variable, and parameters of the SI models were estimated using nonlinear regression. SI models for SST, SSH, and Chl-a were combined into two empirical HSI models, the arithmetic mean model (AMM) and the geometric mean model (GMM). Results indicate that the AMM performs better than the GMM model to quantify the scale of best available habitat for jack mackerel. Catch distribution fit well with the predicted high-quality habitat in 2013: 85.5%, 100.0% and 97.0% of total catch in fall, winter and spring respectively, were caught in areas predicted with better habitat. The seasonal variation of suitable habitat in latitude is consistent with that of the gravity centers of fishing effort and the 15°C isotherm. There is strong agreement between annual total catch by the international trawl fishery and mean suitable habitat area during the period 2001–2010, but an opposite tendency from 2011 to 2013. This may be related to the lowest biomass of jack mackerel and catch quota introduced by the South Pacific Regional Fisheries Management Organization since 2010.

Modeling and Validation of Environmental Suitability for Schistosomiasis Transmission Using Remote Sensing.

BackgroundSchistosomiasis is the most widespread water-based disease in sub-Saharan Africa. Transmission is governed by the spatial distribution of specific freshwater snails that act as intermediate hosts and human water contact patterns. Remote sensing data have been utilized for spatially explicit risk profiling of schistosomiasis. We investigated the potential of remote sensing to characterize habitat conditions of parasite and intermediate host snails and discuss the relevance for public health.MethodologyWe employed high-resolution remote sensing data, environmental field measurements, and ecological data to model environmental suitability for schistosomiasis-related parasite and snail species. The model was developed for Burkina Faso using a habitat suitability index (HSI). The plausibility of remote sensing habitat variables was validated using field measurements. The established model was transferred to different ecological settings in Côte d’Ivoire and validated against readily available survey data from school-aged children.Principal FindingsEnvironmental suitability for schistosomiasis transmission was spatially delineated and quantified by seven habitat variables derived from remote sensing data. The strengths and weaknesses highlighted by the plausibility analysis showed that temporal dynamic water and vegetation measures were particularly useful to model parasite and snail habitat suitability, whereas the measurement of water surface temperature and topographic variables did not perform appropriately. The transferability of the model showed significant relations between the HSI and infection prevalence in study sites of Côte d’Ivoire.Conclusions/SignificanceA predictive map of environmental suitability for schistosomiasis transmission can support measures to gain and sustain control. This is particularly relevant as emphasis is shifting from morbidity control to interrupting transmission. Further validation of our mechanistic model needs to be complemented by field data of parasite- and snail-related fitness. Our model provides a useful tool to monitor the development of new hotspots of potential schistosomiasis transmission based on regularly updated remote sensing data.

The Niche Limitation Method (NicheLim), a new algorithm for generating virtual species to study biogeography

Virtual species are simplified models of real species that codify the response of those species to the climatic conditions. Virtual species have been used to quantify the response of species to climatic changes, to predict potential shifts in species’ geographic ranges and to test the methods used to predict the geographic ranges of species (Ecological Niche Models). Today, there are different methods used to construct virtual species for biogeographic analysis. All of those methods combine partial suitabilities across variables (temperature, precipitation, etc.) to create one multi-variable habitat suitability index. The normal procedure for combining partial suitabilities is to sum or multiply the individual layers. However, this procedure might yield misleading results. In this paper, we run several analyses that indicate that those methods underestimate the role of the limitation factors (factors with unsuitable conditions that should decrease the habitat suitability index to zero). To solve this problem we programmed an algorithm—the Niche Limitation algorithm (NicheLim). NicheLim uses the same philosophy as the BIOCLIM model: species have independent physiological tolerances to the environmental variables. This means that we must first transform each continuous layer into a presence-absence variable, and then combine them. Here, we discuss the current framework for constructing virtual species in biogeography and its main drawbacks. We then explain the improvements of using NicheLim to create our virtual species and test biogeographic hypotheses.

Understanding the distribution of a threatened bird at multiple levels: A hierarchical analysis of the ecological niche of the Santa Marta Bush-Tyrant (Myiotheretes pernix)

ABSTRACT An understanding of the ecological factors determining bird species' distributions is essential for making informed conservation decisions. These data are especially important for range-restricted species, such as the Santa Marta Bush-Tyrant (Myiotheretes pernix), a threatened endemic of the Sierra Nevada de Santa Marta (SNSM) in Colombia. Here we adopt a novel hierarchical analysis to describe the bush-tyrant's ecological niche and infer the regional and local determinants of its limited distribution. We first describe habitat selection based on local habitat use and microhabitats used for foraging. We then use a geoprocessing modeling algorithm to combine habitat selection data with a climatic niche model. The resulting model produced an index of habitat suitability, which we converted into a predicted geographic distribution. Santa Marta Bush-Tyrants showed no clear habitat preferences, but favored forested and secondary growth habitats over open areas, at elevations between 2,100 and 3,300 m....

Hydrologic and water-quality rehabilitation of environments for suitable fish habitat

Summary Aquatic ecological rehabilitation is attracting increasing public and research attention, but without knowledge of the responses of aquatic species to their habitats the success of habitat restoration is uncertain. Thus efficient study of species response to habitat, through which to prioritize the habitat factors influencing aquatic ecosystems, is highly important. However many current models have too high requirement for assemblage information and have great bias in results due to consideration of only the species’ attribute of presence/absence, abundance or biomass, thus hindering the wider utility of these models. This paper, using fish as a case, presents a framework for identification of high-priority habitat factors based on the responses of aquatic species to their habitats, using presence/absence, abundance and biomass data. This framework consists of four newly developed sub-models aiming to determine weightings for the evaluation of species’ contributions to their communities, to quantitatively calculate an integrated habitat suitability index for multi-species based on habitat factors, to assess the suitable probability of habitat factors and to assess the rehabilitation priority of habitat factors. The framework closely links hydrologic, physical and chemical habitat factors to fish assemblage attributes drawn from monitoring datasets on hydrology, water quality and fish assemblages at a total of 144 sites, where 5084 fish were sampled and tested. Breakpoint identification techniques based on curvature in cumulated dominance along with a newly developed weighting calculation model based on theory of mass systems were used to help identify the dominant fish, based on which the presence and abundance of multiple fish were normalized to estimate the integrated habitat suitability index along gradients of various factors, based on their variation with principal habitat factors. Then, the appropriate probability of every principal habitat factor was estimated and graded, and the priority of habitat factors for rehabilitation was determined. Application of the model to Jinan City, a pilot city for the construction of a civilized and ecological city in China, proved effective, revealing that carbonate is the poorest habitat factor and has the highest priority for ecological rehabilitation. This was tested using two methods: alternative priority models and a dataset of all habitat factors in place of only the principal habitat factors. We also found that hydrological factors have higher priority than the water quality factors at the levels of both the whole city and its subordinate eco-regions and therefore that hydrological factors deserve special attention in the future ecosystem rehabilitation. Further, the current habitat state makes nearly half of the habitats in Jinan City undesirable for fish communities, largely due to long-term agricultural practices. Spatially, rivers in the mountainous region south of Jinan city and adjacent to the urban area and rivers in the agricultural region north of the city should be emphasized in future habitat rehabilitation. All of these findings have substantial ramifications for the rehabilitation of aquatic ecosystems in Jinan City as a reference for river ecological remediation in rivers with scarce ecological data worldwide.