Linking models of animal behaviour and habitat management: Atlantic salmon parr and river discharge

Understanding preferences of animals is of fundamental importance for modelling habitat quality and quantity. Important theoretical developments, for example using ideal free and ideal despotic distributions (IDD), have enabled biologists to build conceptual frameworks for relating habitat preferences of individual animals to distributions and dynamics of populations. At the same time, managers of natural resources have established predictive empirical models as a basis for understanding habitat quality. For example, the Physical Habitat Simulation model (PHABSIM) has been widely applied for managing river flows. The aim of this study was to conduct experiments, using Atlantic salmon parr, to test whether observed population distributions could be predicted using simple behaviour theory and PHABSIM. We show that predictions from PHABSIM depend crucially on population density, discharge and the interaction between density and discharge at the time when the model is parameterized. These findings can, in part, be explained by consideration and application of the IDD. However, the results of the experiments also suggest that models derived from first behavioural principles may need to be unexpectedly complex and species‐specific if they are to capture the population response to variations in water discharge effectively.     

Familiarity confers anti‐predator and foraging advantages on juvenile brown trout

Understanding preferences of animals is of fundamental importance for modelling habitat quality and quantity. Important theoretical developments, for example using ideal free and ideal despotic distributions (IDD), have enabled biologists to build conceptual frameworks for relating habitat preferences of individual animals to distributions and dynamics of populations. At the same time, managers of natural resources have established predictive empirical models as a basis for understanding habitat quality. For example, the Physical Habitat Simulation model (PHABSIM) has been widely applied for managing river flows. The aim of this study was to conduct experiments, using Atlantic salmon parr, to test whether observed population distributions could be predicted using simple behaviour theory and PHABSIM. We show that predictions from PHABSIM depend crucially on population density, discharge and the interaction between density and discharge at the time when the model is parameterized. These findings can, in part, be explained by consideration and application of the IDD. However, the results of the experiments also suggest that models derived from first behavioural principles may need to be unexpectedly complex and species‐specific if they are to capture the population response to variations in water discharge effectively.     

Effects of habitat complexity on ant assemblages

We investigated responses of ant communities to habitat complexity, with the aim of assessing complexity as a useful surrogate for ant species diversity. We used pitfall traps to sample ants at twenty-eight sites, fourteen each of low and high habitat complexity, spread over ca 12 km in Sydney sandstone ridge-top woodland in Australia. Ant species richness was higher in low complexity areas, and negatively associated with ground herb cover, tree canopy cover, soil moisture and leaf litter. Ant community composition was affected by habitat complexity, with morphospecies from the genera Monomorium, Rhytidoponera and Meranoplus being the most significant contributors to compositional differences. Functional group responses to anthropogenic disturbance may be facilitated by local changes in habitat complexity. Habitat complexity, measured as a function of differences in multiple strata in forests, may be of great worth as a surrogate for the diversity of a range of arthropod groups including ants.     

Habitat selection in a large orb‐weaving spider: vegetational complexity determines site selection and distribution

1. The distribution of the large orb‐weaving spider Argiope trifasciata in old field habitats of North America and the habitat selection process this species used was studied for 2 years. 2. Because web spiders have limited dispersal abilities and an energetically costly prey capture device, they do not have the ability to sample potential foraging sites. Structural complexity of the vegetation to which the web must be attached is relatively easy to assess. The hypothesis that the structural complexity is a primary factor in determining initial web site selection was tested both by relating the natural distribution of the spiders across habitats to vegetational complexity and by manipulating the complexity of the habitats in a series of experiments. 3. Argiope trifasciata was not distributed evenly among three old field vegetation types. Habitat complexity was related to spider density in both years although no measure of insect activity, prey capture, or prey consumption was correlated with spider distribution. 4. Three experimental manipulations were conducted to test the impact of habitat structure on spider establishment: (1) the amount of natural vegetation was reduced, (2) structures were added to a simple habitat, and (3) the complexity of the structures added was varied. In each case, spiders were introduced and establishment of webs was monitored. In all manipulations, spider establishment was related to the complexity of the substrate available. 5. These results are important for understanding the cues that influence foraging site selection and therefore provide insight into the distribution of species with limited dispersal abilities and high site investment requirements.     

Habitat and hydrology condition indices for the upper Mississippi,Missouri, and Ohio rivers

Habitat and hydrology indices were developed to assess the conditions in reaches of the impounded Mississippi river, the Fort Peck and Garrison reaches of the upper Missouri river, the Missouri National Recreational river (MNRR), the channelized lower Missouri river, and the Ohio river. Data were obtained from field sampling, air photo interpretation, and U.S. Geological Survey (USGS) hydrologic records. Habitat and hydrology attributes were incorporated into four habitat indices (channel complexity, substrate quality, littoral cover, and riparian condition) and one hydrology index. Construction of habitat indices for these very large rivers was complicated by a lack of previous research demonstrating methods for choosing and weighting the metrics used to compose these indices. Many habitat metrics used to assess habitat quality in small rivers proved irrelevant or impractical for assessing habitat quality in the upper Mississippi, Missouri, and Ohio rivers. In addition, these very large rivers, unlike smaller streams, were subject to physical and hydrological alterations due to channelization, revetment, levees, and dams. Because of the lack of proven indicators of habitat condition in very large rivers, we began with a large number of measures of natural and anthropogenic stress, eliminating only those metrics that failed tests of range, redundancy, and correlation with longitudinal position along the river. The lock and low-head dam sequences on the impounded Mississippi and Ohio influenced both hydrological patterns and the resident fish community, with conditions recovering with increased distance below dams, until hydrology was once again altered by impoundment from a downriver dam. Channel complexity and hydrology indices displayed the highest correlations with a multimetric fish index, possibly because these indices integrated habitat condition over a larger scale than the transect- and site-scaled littoral cover and riparian indices. Data limitations prevented the calculation of a littoral cover and a channel complexity index for the upper Missouri and Ohio rivers, respectively.     

Habitat structural complexity and morphological diversity of fish assemblages in a Neotropical floodplain river

High species richness and evenness in structurally complex habitats has been hypothesized to be associated with niche partitioning. To test this idea, relationships between habitat structural complexity in river littoral-zone habitats and morphological diversity of tropical fishes were examined in the Cinaruco River, Venezuela. Six habitat attributes were quantified in 45 sites spanning a range of structural complexity. Fishes were collected during day and night to estimate species density and relative abundances at each site. Twenty-two morphological variables were measured for each species. Principal components analysis (PCA) of physical habitat data yielded two axes that modeled >80% of variation across sites. The first two axes from PCA of fish morphological variables modeled >70% of variation. Species density during both day and night was negatively associated with flow velocity and positively associated with habitat complexity. Similarity of day and night samples from the same site was significantly greater for sites with high habitat complexity and low flow. In general, mean local assemblage morphological PC scores were not significantly associated with habitat PC scores. Average, maximum, and standard deviation of morphological Euclidean distances of local assemblages revealed positive associations with structural complexity and negative associations with flow. These relationships held even when the positive relationship of species density was statistically removed from assemblage morphological patterns. Findings suggest that both species niche compression and assemblage niche space increase when habitat complexity is greater and flow velocity is lower in this tropical lowland river.Electronic Supplementary Material Supplementary material is available for this article at     

Estimating forest habitat complexity in relation to time since fire

Forest structure does not form an even distribution over forested landscapes; rather, it produces a mosaic or patchwork pattern. ‘Habitat complexity scores’ provide a method of describing changes in vegetation biomass and, when assessed at randomly located plots, a frequency distribution of habitat can be developed. The frequency distribution can be used to describe characteristics of the pattern of habitat complexity, such as the mean and heterogeneity of habitat over the whole forest. In the present paper, an historical sequence of habitat complexity scores collected from 99 sites over an 18‐year period was used. The frequency distribution of the habitat complexity scores was fitted using a binomial distribution and the parameters of the binomial distribution were modelled to provide a relationship between the frequency of different habitat environments across the landscape and the time since wildfire. In most cases, the binomial distributions fitted the observed data significantly. The relationship between the binomial parameters and the time since fire was found to be highly significant (P < 0.01). Habitat complexity scores were predicted from the model solely as a function of time since fire, allowing both retrospective and future predictions of the distribution of habitats to be undertaken.     

秦岭细鳞鲑栖息地环境特征研究

为研究秦岭细鳞鲑（Brachymystax lenok tsinlingensis）的栖息地环境选择偏好,对陕西陇县秦岭细鳞鲑国家级自然保护区和甘肃秦州珍稀水生野生动物国家级自然保护区内25个样点进行了鱼类采样和生境测量。共采集到130尾秦岭细鳞鲑样本,样点的平均分布密度为（0.10±0.07）尾/m,两个保护区内秦岭细鳞鲑的密度存在显著性差异（P < 0.05）。与秦岭细鳞鲑密度分布呈正相关的因子依次为坡度、跌水区密度、海拔、粗糙度、遮蔽度、底栖动物生物量和流速,与密度呈负相关的环境因子依次为河宽、水深和溶氧。冗余性分析（RDA）筛选了坡度、粗糙度、遮蔽度、海拔和跌水区5个关键环境因子。基于关键环境因子的实测值建立了栖息地适合度曲线,秦岭细鳞鲑分布的最适坡度范围为5%-10%,海拔分布范围为1500-2000 m,粗糙度范围0.3-0.4;跌水区密度范围12-18个/100 m,遮蔽度在0.5以上。     

Spatial Scaling of Environmental Variables Improves Species-Habitat Models of Fishes in a Small,Sand-Bed Lowland River

Habitat suitability and the distinct mobility of species depict fundamental keys for explaining and understanding the distribution of river fishes. In recent years, comprehensive data on river hydromorphology has been mapped at spatial scales down to 100 m, potentially serving high resolution species-habitat models, e.g., for fish. However, the relative importance of specific hydromorphological and in-stream habitat variables and their spatial scales of influence is poorly understood. Applying boosted regression trees, we developed species-habitat models for 13 fish species in a sand-bed lowland river based on river morphological and in-stream habitat data. First, we calculated mean values for the predictor variables in five distance classes (from the sampling site up to 4000 m up- and downstream) to identify the spatial scale that best predicts the presence of fish species. Second, we compared the suitability of measured variables and assessment scores related to natural reference conditions. Third, we identified variables which best explained the presence of fish species. The mean model quality (AUC = 0.78, area under the receiver operating characteristic curve) significantly increased when information on the habitat conditions up- and downstream of a sampling site (maximum AUC at 2500 m distance class, +0.049) and topological variables (e.g., stream order) were included (AUC = +0.014). Both measured and assessed variables were similarly well suited to predict species’ presence. Stream order variables and measured cross section features (e.g., width, depth, velocity) were best-suited predictors. In addition, measured channel-bed characteristics (e.g., substrate types) and assessed longitudinal channel features (e.g., naturalness of river planform) were also good predictors. These findings demonstrate (i) the applicability of high resolution river morphological and instream-habitat data (measured and assessed variables) to predict fish presence, (ii) the importance of considering habitat at spatial scales larger than the sampling site, and (iii) that the importance of (river morphological) habitat characteristics differs depending on the spatial scale.     

基于河流生境调查的东河河流生境评价

河流生境是河流生态系统的重要组成部分,是河流生物赖以生存的基础。以位于三峡库区腹心区域的典型山区河流东河为研究对象,采用河流生境调查(RHS)方法调查河流生境,选择河流生境质量评价指数(HQA)、河流生境退化指数(HMS)评估河流生境现状,分析生境质量和人为干扰的空间分布规律。结果表明,51个河段的HQA值介于24—66之间。29.4%河段的HQA为优,29.4%为良,23.5%为中,9.8%为较差,7.8%为差。从HMS看,7.8%的河段保持较自然状态,19.6%受到轻微的破坏,41.2%退化明显,27.5%退化严重,3.9%受到剧烈破坏。HQA与HMS存在显著的负相关关系。东河上、中、下游河段的HQA无明显差异,但HMS差异显著。从干扰来源看,东河上游和中游河流生境主要受引水式小水电、沿河公路、河道采砂影响。东河下游河流生境受高强度的土地开发(农业用地、建设用地),河道采砂,河堤、排污管、桥梁等水工构筑物的修建和三峡水库水位的波动影响。RHS评价结果能较直观地反映河流生境状况,以及导致河流生境质量衰退的原因。     

Long-term variation in the winter resident bird community of Guánica Forest, Puerto Rico: lessons for measuring and monitoring species richness

ABSTRACT.   Because the winter season is potentially limiting for migratory birds, understanding their nonbreeding distributional patterns is essential. At a given site, patterns of species occurrence and abundance may vary over time and, within a species, wintering strategies may vary with regard to the degree that individuals are site-faithful both within and between winters. We examined long-term patterns in the composition of a winter resident bird community to determine how long a site must be studied to understand the wintering community. Over a 34-yr period of constant-effort mist netting at a site in Guánica, Puerto Rico, we captured 21 species of winter resident birds, with mean total captures varying from 8.3 to 18.9 individuals per net line and 6–14 species captured per year. Species richness capture/recapture models generated numbers similar to actual capture rates. Capture and recapture data allowed us to categorize winter residents into three groups: sporadic winter residents (14 species), regular winter residents (four species captured nearly every year), and dominant winter residents (three species captured each year with high rates of recapture). Our results suggest that sampling for at least three consecutive winters is needed to accurately characterize the bird community at a site. However, sampling for 5 yr is better, and 10-yr samples generate patterns similar to those based on our entire 34-yr sample. A 1-yr sample provides minimal information about the composition and characteristics of a winter resident bird community.     

River channel habitat diversity (RCHD) and macroinvertebrate community

Correspondence of habitat and macroinvertebrate diversity was investigated in twenty Czech rivers. With regard to the importance of river characteristics (depth, current velocity and substratum) River Channel Habitat Diversity method was developed within this paper. The method is focused directly on the stream wetted channel and it assesses habitat diversity and richness computed as Shannon-Wiener’s index. Macroinvertebrate samples were taken by the national PERLA method at each study site, diversity index was also calculated and compared with habitat and substrate diversity. Habitat diversity was important for macroinvertebrate communities according to multivariate assessment, but contrary to the hypothesis it was not significantly correlated with macroinvertebrate diversity. Based on the results, broader rivers had lower habitat diversity than smaller streams, and were more influenced by human activities (lower habitat diversity, higher pollution). Results obtained by the RCHD and RHS methods were not significantly correlated.     

Characterising hydromorphological features of selected Italian rivers: a comparative application of environmental indices

The purpose of this study was to test the applicability of different methods of river habitat assessment and their respective indices in a series of sample sites in Italy. These investigations were carried out within the EU AQEM project with the aim of combining the macroinvertebrate information with that achieved by investigating the hydromorphological characteristics of the river ecosystem as well as the surrounding landscape features. The River Habitat Survey (including the derived indices Habitat Modification Score and Habitat Quality Assessment) from U.K., and three Italian indices (Index of Fluvial Functioning, Buffer Strip Index and Wild State Index) were applied at 33 AQEM sites distributed in three different Italian river types. The obtained results indicate the overall ability of the applied indices to detect the degradation gradient, including river morphology and habitat, in the studied riverine ecosystems. Index of Fluvial Functioning seems useful to promptly describe the ecological quality of rivers as suggested by the good correlation with the AQEM multimetric biotic index. The Buffer Strip Index, showing a clear affinity with the Habitat Quality Assessment, seems suitable to assess richness and quality of the physical structure of a riverine site. The Habitat Modification Score recorded efficiently the morphological impact where present (e.g., North Apennine river sites), while the Italian indices appear to be not appropriate for differentiating this impact type from the general degradation of rivers.     

Variability in spatial and temporal occurrence of presettlement and settlement‐stage fishes associated with shallow reefs

Presettlement and settlement‐stage fishes were studied in a large, log‐spiral bay in temperate South Africa. The aim was to describe the assemblage composition, density and distribution associated with four types of habitats common to the bay: high profile reef, low profile reef, reef‐associated sand and open sand spatially separated from reef. Samples were collected with both a plankton ring net and a light trap at each habitat type as part of a mixed‐method approach. A total of 4084 presettlement and settlement‐stage fishes belonging to 31 teleost families and 84 species were captured. Reef‐associated sand and open sand habitats yielded higher species richness and diversity than the high and low‐profile reef habitats. Engraulidae, Gobiidae, Clupeidae and Cynoglossidae were the dominant fish families captured with the ring net, while Engraulidae, Clupeidae, Carangidae and Clinidae were captured with the light trap. A temporal difference in the abundance of presettlement fishes occurred between the sampling periods with highest values recorded during the summer settlement period. Habitat type together with associated physico‐chemical variables played a pivotal role in determining presettlement fish species composition, density and distribution across habitat types.     

Suspension feeders transform massive amounts of seston in large northern rivers

The concentration and transport of faecal pellets (FPs) produced by blackfly (Diptera: Simuliidae) larvae were estimated in a large, free-flowing river in the north of Sweden during 1997–1999. FPs were abundant from May through August and FP loads in transport peaked at 429 t dry mass d−1 at a site in the lower part of the river in 1997. Daily transport at the same site, averaged over each study period (16 Jun.–18 Sep. 1997, 6 Apr.–10 Sep. 1998, and 21 Apr.–5 Aug. 1999), was estimated to be 93.7 t dry mass (3.7 t carbon), 47.5 t dry mass (1.9 t carbon and) and 69.2 t dry mass (2.7 t carbon), respectively. On a large scale, there was a downstream trend of increasing FP concentration and, during periods with greater discharge, sedimentation was reduced so that more material was exported from the river. Samples from six sites in a regulated river (into which our focal river flows) parallel to six sites in the unregulated tributary showed considerably lower FP concentrations in the regulated river, presumably because of much smaller blackfly populations as a consequence of habitat loss through damming. A survey of two other large, unregulated rivers in northern Sweden confirmed that these also carry large amounts of FPs. We conclude that the transformation of small suspended food particles into considerably larger FPs by huge populations of filter-feeding blackfly larvae is a major process in large northern rivers.     

Using drift nets to capture early life stages and monitor spawning of the Yangtze River Chinese sturgeon (Acipenser sinensis)

A sampling system for capturing sturgeon eggs using a D-shaped bottom anchored drift net was used to capture early life stages (ELS) of Chinese sturgeon, Acipenser sinensis , and monitor annual spawning success at Yichang on the Yangtze River, 1996–2004, before and just after the Three Gorges Dam began operation. Captured were 96 875 ELS (early life stages: eggs, yolk-sac larvae = eleuthero embryos, and larvae); most were eggs and only 2477 were yolk-sac larvae. Most ELS were captured in the main river channel and inside the bend at the Yichang spawning reach. Yolk-sac larvae were captured for a maximum of 3 days after hatching began, indicating quick dispersal downstream. The back-calculated day of egg fertilization over the eight years indicated a maximum spawning window of 23 days (20 October–10 November). Spawning in all years was restricted temporally, occurred mostly at night and during one or two spawning periods, each lasting several days. The brief temporal spawning window may reduce egg predation by opportunistic predators by flooding the river bottom with millions of eggs. During 1996–2002, the percentage of fertilized eggs in an annual 20-egg sample was between 63.5 to 94.1%; however, in 2003 the percentage fertilized was only 23.8%. This sudden decline may be related to the altered environmental conditions at Yichang caused by operation of the Three Gorges Dam. Further studies are needed to monitor spawning and changes in egg fertilization in this threatened population.     

Water-borne seed transport and seed deposition during flooding in a small river-valley in Northern Germany

Water-borne seed transport and seed deposition during flooding were studied in the Upper Eider river (N-Germany) by direct sampling of the rivers seed content with aquatic seed traps and by analysing the number of deposited seeds on sedimentation mats which were exposed near the river on the soil surface during a flooding period of approx. three weeks.The number of seeds which were transported at the surface of the river Eider was continuously analysed by four aquatic seed traps for a period of 20 weeks (July–December 2000). To test the capture rate of these traps, a recapture experiment with colour marked seeds of Helianthus annuus L. was carried out. During the investigation period approx. 9000 seeds of 76 species were captured by the four aquatic seed traps. The number of trapped seeds varied both spatially (across the river profile) and temporally. Considering this variation and the capture rate of the traps, the water-borne seed transport was estimated to be 3139 seeds per week and meter of the river profile.The seed deposition during a flood in early spring 2002 was analysed by using 20 sedimentation mats. To distinguish effects of seed dispersal into patches from outside from seed rearrangement within patches, the water-borne seed transport was excluded from one half of the mats by fencing them with a woven fabric which was permeable for water but not for floating seeds. Outside of the exclosures 152 viable seeds of 26 species were deposited on the sedimentation mats while only one single seedling was found on mats from which water-borne seed transport was excluded.The results demonstrate that hydrochorous dispersal processes might play an important role in connecting otherwise fragmented populations in periodically flooded habitats along rivers.     

Influence of dams and habitat condition on the distribution of redhorse (Moxostoma) species in the Grand River watershed, Ontario

Redhorse, Moxostoma spp., are considered to be negatively affected by dams although this assertion is untested for Canadian populations. One hundred and fifty-one sites in the Grand River watershed were sampled to identify factors influencing the distribution of redhorse species. Individual species of redhorse were captured from 3 to 32% of sites. The most widespread species were golden redhorse, M. erythrurum (30%) and greater redhorse, M. valenciennesi (32%), while river redhorse, M. carinatum, was only found along the lower Grand River. Redhorse were absent from the highly fragmented Speed River sub-watershed and upper reaches of the Conestogo River and the Grand River. Redhorse species richness was positively correlated to river fragment size and upstream drainage area. Generalized additive models (GAMs) were applied to evaluate the influence of river fragment length, connectivity and habitat on species distribution. Principal component analysis reduced habitat data to three axes representing: channel structure, substrate, and pool, riffle and run habitats (PC1); gradient and drainage area (PC2); and cover (PC3). GAMs indicate that PC2 was important for predicting black redhorse and greater redhorse site occupancy and PC1 was important for golden redhorse. River fragment length was important for predicting site occupancy for shorthead redhorse, but not other species.     

Habitat selection by two species of small mammals in the Atlantic Forest,Brazil: Comparing results from live trapping and spool-and-line tracking

Habitat selection by small mammals is usually evaluated using data from live trapping, which provides little information about the movements of individuals. Few studies used movement data or compared the results of different sampling methods to study habitat selection by these animals. We evaluated habitat selection by the rodent Nectomys squamipes and the marsupial Micoureus paraguayanus in the Atlantic Forest of Brazil using the spool-and-line technique. We also determined if percentage of captures reflected the amount of movements in each habitat. Habitat selection was determined comparing use and availability of five habitat types at two spatial scales (movement paths and movement areas) using compositional analysis, which allowed ranking of habitats according to their relative use by animals. The use of available habitat types was non-random for both species at both spatial scales. The two species had contrasting habitat affinities directly related to their particular habits, with N. squamipes using predominantly the stream habitat, and M. paraguayanus using mainly the restinga forest habitat. Patterns of habitat selection were similar at both spatial scales probably due to the small size of movement areas, which may not represent habitat use at a broader scale. For both species, live trapping and movement data provided the same ranking in habitat use, demonstrating that simple capture indices may be used to study habitat selection by these species across different habitat types.     

Helminths in Leuciscus cephalus from the river Adda, Lombardy, Northern Italy

Chubs (Leuciscus cephalus) were caught at various locations along the river Adda and from Lake of Como (Lombardy, Northern Italy) and endoparasitic helminths were studied in order to integrate the knowledge on distribution of helminth fauna of chubs in Lombardy and to investigate on the structure of its parasite infracommunities with respect to different habitat typologies. The following species of parasites were isolated: Pomphorynchus laevis, Allocreadium markewitschi, Parasymphylodora markewitschi, Raphidascaris acus, Hysterothylacium aduncum and Molnaria intestinalis. P laevis resulted the most common species (P = 56.52%). The mean abundances and the prevalence of helminths were different in chubs according to the sampling site. The mean abundances were lower in chubs sampled in the lake than those sampled in the river. Particularly, P. laevis showed the highest prevalences in fish captured in the river sites. The trematodes (P. markewitschi and A. markewitschi) seem to be more related with "lake" typology. These results are discussed and related to differences in life cycle of these parasites and to other factors like sampling period and the conditions of the aquatic sites that could influence the richness of parasite species.