Environmental DNA analysis for estimating the abundance and biomass of stream fish

相似文献   

Approaches to estimating fish biomass and potential yield in Lake Tanganyika

The annual fish yield of 73 000 tonnes (22.5 kg/ha) from Lake Tanganyika consists primarily of two planktivorous clupeids Stolothrissa tanganicae (Stdr.) and Limnothrissa miodon (Blgr.) and their centropomid predators, three Lates species (Nile perch) and Luciolates stappersii (Blgr.). At the north and south ends of the lake, the Lates spp. have been fished-up by purse-seines, and the clupeids and young L. stappersii predominate there. Estimates of pelagic fish biomass may employ (i) catch and fishing effort data (ii) abiotic variables (iii) echo-sounding surveys (iv) tropho-dynamic relationships.     

Rotenone calibration of fish density and biomass in a tropical stream sampled by two removal methods

A catch-depletion method was applied using two sampling gears in three sites of a small tributary of the Corumba River (Goiás State, Brazil) in two seasons. The gears were: a double stick net (DSN) in one site and electric fishing (EF) in two sites. The calibration of both gears was performed using rotenone. EF was almost sufficient to establish a complete local species list, but DSN was not. Underestimation of calculated density (N) and biomass (B) values for DSN and EF amounted to 62 and 29%, respectively. The results of N and B obtained by EF were too imprecise to calculate secondary fish production to be applied in a field bioenergetics model. We could not conclusively prove that mean body weight of sampled populations was significantly lower for fish caught by EF, although all of these means were higher for fish collected by rotenone, at each site and on two sampling occasions.     

Evaluation of methods for estimating macroinvertebrate species richness using individual stones in tropical streams

1. The most straightforward way to assess diversity in a site is the species count. However, a relatively large sample is needed for a reliable result because of the presence of many rare species in rich assemblages. The use of richness estimation methods is suggested by many authors as a solution for this problem in many cases.
2. We examined the performance of 13 methods for estimating richness of stream macroinvertebrates inhabiting riffles both at local (stream) and regional (catchment) scales. The evaluation was based on (1) the smallest sub-sample size needed to estimate total richness in the sample, (2) constancy of this size, (3) lack of erratic behaviour in curve shape and (4) similarity in curve shape through different data sets. Samples were from three single stream sites (local) and three from several streams within the same catchment basin (regional). All collections were made from protected forest areas in south-east Brazil.
3. All estimation methods were dependent on sub-sample size, producing higher estimates when using larger sub-sample sizes. The Stout and Vandermeer method estimated total richness in the samples with the smallest sub-sample size, but showed some erratic behaviour at small sub-sample sizes, and the estimated curves were not similar among the six samples. The Bootstrap method was the best estimator in relation to constancy of sub-sample sizes, but needed an unacceptably large sub-sample to estimate total richness in the samples. The second order Jackknife method was the second best estimator both for minimum sub-sample size and constancy of this size and we suggest its use in future studies of diversity in tropical streams. Despite the inferior performance of several other methods, some produced acceptable results. Comments are made on the utility of using these estimators for predicting species richness in an area and for comparative purposes in diversity studies.     

Relating fish biomass to habitat and chemistry in headwater streams of the northeastern United States

Stream pH and stream habitat have both been identified as important environmental features influencing total fish biomass in streams, but few studies have evaluated the relative influence of habitat and pH together. We measured total fish biomass, stream habitat, and stream pH in sixteen sites from three tributary systems in the northeastern United States. The habitat metrics included total pool area, a cover score, large wood frequency, and stream temperature. We created and compared nine linear models relating total fish biomass in summer to stream pH and stream habitat using Akaike’s Information Criterion (AIC) analysis. The best (most parsimonious) models included pool area and stream pH. These results and a separate comparison of three regressions (low-flow pH, pool area, and these two metrics together versus total fish biomass) suggest that both habitat and stream buffering capacity affect the total biomass of fish in northeastern US headwater streams. When stream pH is adequate (low-flow pH greater than at least 5.7), physical habitat is likely to be more important, but under lower pH conditions, habitat is likely to be less effective in accounting for the total biomass of fish in these streams. This work demonstrates the continued effects of stream acidification in the northeastern US and more generally, it illustrates the importance of considering both physical and chemical conditions of a stream when evaluating the factors influencing fish communities.     

Strong correspondence between gillnet catch per unit effort and hydroacoustically derived fish biomass in stratified lakes

1. Sampling of lake fish assemblages is a challenging task in fish science, and the information obtained strongly depends on the choice of sampling gear. The use of more than one sampling technique is generally preferred in order to achieve a comprehensive view on fish assemblage structure. Therefore, the knowledge of whether catches between fishing gears are comparable is crucial. 2. We compared catches in benthic multi‐mesh gillnets with fish biomass estimates obtained by vertical hydroacoustics in 18 European lakes strongly varying in morphometry and trophic status. Separate analyses were conducted for different depth strata and for several fish length thresholds to account for depth‐ and size‐selective gillnet catches. 3. Gillnet catches and hydroacoustically obtained fish biomass estimates were significantly correlated. The strength of correlations was independent of the fish length thresholds applied, but varied across different depth strata of the lakes, with the strongest correlations occurring in the shallow strata. 4. The results support the applicability of vertical hydroacoustics for the quantification of fish biomass in stratified lakes. Survey designs combining hydroacoustics with limited gillnetting at sampling dates shortly one after the other, the latter for the purpose of inventory sampling only, are a cost‐effective strategy for sampling fish assemblages in lakes. However, gillnet sampling does not provide reliable fish density estimates in very deep lakes with separate, pelagic‐dwelling fish assemblages.     

A comparison of alternative methods for estimating population density of the fiddler crab Uca annulipes at Saco Mangrove, Inhaca Island (Mozambique)

Visual counts of surface-active crabs both by binocular and burrow counting methods have been used in many studies to estimate population density. However, their reliability has not yet been assessed comparatively. Three methods for estimating the abundance of fiddler crabs Uca annulipes in a mangrove forest (Inhaca Island, Mozambique) were compared from three different sub-areas: two sub-areas inundated only during spring tides and one sub-area inundated in both spring and neap tides. Burrow, binocular and direct (excavation) counting methods were performed by plotting ten 0.25 m² quadrats in each sub-area over the four moon phases. Overall densities (per 0.25 m²) differed according to method, sub-area and lunar phase. Burrow count overestimated crab density by up to 20%, while binocular count underestimated density by up to 41%. Correlation coefficient estimated for both counting methods showed that burrow count gives better density estimates than binocular count (0.91 and 0.56, respectively). Sex ratios were also investigated within the three sub-areas and at the moon phases. Males are dominant throughout the studied period except during new moon and first quarter, indicating that when the number of gravid females is low, sex ratio bias for binocular count is minimal.     

Comparison of methods for estimating density of forest songbirds from point counts

New analytical methods have been promoted for estimating the probability of detection and density of birds from count data but few studies have compared these methods using real data. We compared estimates of detection probability and density from distance and time-removal models and survey protocols based on 5- or 10-min counts and outer radii of 50 or 100 m. We surveyed singing male Acadian flycatchers (Empidonax virescens), cerulean warblers (Dendroica cerulea), Kentucky warblers (Oporornis formosus), Louisiana waterthrushes (Parkesia motacilla), wood thrushes (Hylocichla mustelina), and worm-eating warblers (Helmitheros vermivorum) in bottomland and upland forest across 5 states in the Central Hardwoods Bird Conservation Region during the breeding season in 2007 and 2008. Detection probabilities differed between distance and time-removal models and species detectabilities were affected differently by year, forest type, and state. Density estimates from distance models were generally higher than from time-removal models, resulting from lower detection probabilities estimated by distance models. We found support for individual heterogeneity (modeled as a finite mixture model) in the time-removal models and that 50-m radius counts generated density estimates approximately twice as high as 100-m radius counts. Users should be aware that in addition to estimating different components of detectability, density estimates derived from distance and time-removal models can be affected by survey protocol because some count durations and plot radii may better meet model assumptions than others. The choice of a method may not affect the use of estimates for relative comparisons (e.g., when comparing habitats) but could affect conclusions when used to estimate population size. We recommend careful consideration of assumptions when deciding on point-count protocol and selection of analysis methods. © 2011 The Wildlife Society.     

A review of methods for estimating mortality due to parasites in wild fish populations

Six methods are described for detecting mortality due to parasitic infections in natural fish populations. They are: (a) through autopsies; (b) by determining the frequency of infections known to be eventually lethal; (c) by observing a decrease in the prevalence of a long-lived parasite (or permanent scar from a parasite) with host age; (d) by observing a decrease in the variance/mean ratio for the parasites with host age; (e) by comparing the observed frequency of a combination of two independent events with the calculated probability of their occurrence; and finally (f) by comparing the observed frequency distribution of the parasite, with a projected frequency based on data from lightly infected fish. In this technique, negative binomials are fitted to the data and truncated at various points. Some advantages and disadvantages of the different methods are given, together with examples. The methods do not necessarily provide definitive answers, but they are indicative of whether or not significant parasite-related mortality may be occurring, and in some cases provide an estimate of its probable magnitude in terms of the total host mortality rate.     

Formal analysis and evaluation of allometric methods for estimating above‐ground biomass of eelgrass

Eelgrass (Zostera marina) populations supply substantial amounts of organic materials to food webs in shallow coastal environments, provide habitat for many fishes and their larvae and abate erosion. The characterisation of eelgrass biomass dynamics is an important input for the assessment of the function and values for this important seagrass species. We here present original allometric methods for the non‐destructive estimation of above‐ground biomass of eelgrass. These assessments are based on measurements of lengths and areas of leaves and sheaths and mathematical models that can be identified by means of standard regression procedures. The models were validated by using data obtained from Z. marina meadows in the Punta Banda estuary B.C., Mexico, and in Jindong Bay, Korea. Using available data and concordance correlation index criteria we show that the values projected thorough the presented allometric paradigm reproduces observed values in a consistent way. The annual average value for observed above‐ground biomass was 1.46 ± 0.15 g shoot^?1, while the corresponding calculated value was 1.40 ± 0.13 g shoot^?1. We suggest that our method can be applied to other studies in which the architecture and growth form of leaves and sheaths are similar to those of eelgrass. This would provide reliable and simplified estimations of biomass while eliminating tedious laboratory processing and avoiding destructive sampling.     

Comparison of methods for estimating the biomass of three food-borne fungi with different growth patterns.

To evaluate the effectiveness of steps taken to reduce the growth of molds in food and feed, methods that can accurately quantify the degree of fungal contamination of solid substrates are needed. In this study, the ergosterol assay has been evaluated by comparing the results of this assay with spore counts and hyphal length measurements made with a microscope and with CFU counts. Three fungi with different growth patterns during cultivation on a synthetic agar substrate were used in these experiments. For the nonsporulating Fusarium culmorum, there was good agreement between changes in hyphal length, CFU, and ergosterol content. Penicillium rugulosum and Rhizopus stolonifer produced many spores, and the production of spores coincided with large increases in CFU but not with increases in hyphal length or ergosterol content. Spores constituted between 3 and 5% of the total fungal mass. Changes in ergosterol level were closely related to changes in hyphal length. It was concluded that ergosterol level is a suitable marker for use in quantitatively monitoring fungal growth in solid substrates.     

Comparison of visual survey and seining methods for estimating abundance of an endangered,benthic stream fish

We compared visual survey and seining methods for estimating abundance of endangered Okaloosa darters, Etheostoma okaloosae, in 12 replicate stream reaches during August 2001. For each 20-m stream reach, two divers systematically located and marked the position of darters and then a second crew of three to five people came through with a small-mesh seine and exhaustively sampled the same area. Visual surveys required little extra time to complete. Visual counts (24.2 ± 12.0; mean ± one SD) considerably exceeded seine captures (7.4 ± 4.8), and counts from the two methods were uncorrelated. Visual surveys, but not seines, detected the presence of Okaloosa darters at one site with low population densities. In 2003, we performed a depletion removal study in 10 replicate stream reaches to assess the accuracy of the visual survey method. Visual surveys detected 59% of Okaloosa darters present, and visual counts and removal estimates were positively correlated. Taken together, our comparisons indicate that visual surveys more accurately and precisely estimate abundance of Okaloosa darters than seining and more reliably detect presence at low population densities. We recommend evaluation of visual survey methods when designing programs to monitor abundance of benthic fishes in clear streams, especially for threatened and endangered species that may be sensitive to handling and habitat disturbance.     

Food web pathways for fish communities in small tropical streams

1. It is often assumed that invertebrate consumers in small tropical streams are dependent on allochthonous sources, although recent studies indicate that algae can form the base of food webs in tropical streams. Fish in tropical streams can feed across several trophic levels and the origin and path of energy and nutrient flow is uncertain for many species.
2. We collected fish, insects, periphyton, and leaf litter from 20 streams across four Atlantic Forest catchments. We analysed stomach contents of fish to define trophic guild and fish dietary trophic position. We also analysed stable isotopes of carbon and nitrogen of fish and their resources to identify the main basal resources of the food web and to estimate trophic positions and identify the path of energy flow.
3. We found that autochthonous sources were the primary resource base for fish communities. Trophic positions estimated from diet and isotopes were similar and correlated for insectivore and algivore–insectivore fish, but not for algivore–detritivore or omnivore fish. Using path analysis, fish classified as algivore–detritivores appear to have derived their biomass through a diet of primary consumer insects and periphytic algae and thus, are more likely to play a trophic role as algivore–insectivores in these streams. However, omnivores probably derived much of their biomass from aquatic insects.
4. Our findings support other studies of tropical systems in which the main basal resource is autochthonous, even in small streams. We also show that the assignment to a specific trophic guild for some fish species, based on gut contents, does not reflect what they assimilate into their bodies. In some species, food sources that are uncommon can make a disproportionately important contribution to their biomass.
5. This study affirms the important role of inconspicuous algal resources in aquatic food webs, even in small forested streams, and demonstrates the effectiveness of taking a combined approach of diet analysis, isotopic tracing, and modelling to resolve food web pathways where the level of omnivory is high.

     

Selection of line-transect methods for estimating the density of group-living animals: lessons from the primates

We review the four major contemporary methods for estimating density of group-living animals from line-transect sampling: perpendicular modelling of group centers, perpendicular modelling of center of measurable individuals, strip transects and animal-observer distance. The efficacy of each method is evaluated to produce a simple selection guide. We review the literature and use field data from the Udzungwa Mountains, Tanzania. The review is relevant to all group-living animals; however, examples are drawn from the primates. Perpendicular methods have better mathematical justification than non-perpendicular methods. For perpendicular methods using detection function models, it is preferable to measure group location using center of measurable individuals, as group centers are hard to estimate. The assumptions of detection function models are often broken in poor visibility habitats or with unhabituated animals. Alternatively strip transects may be used where there are reliable data on group spread and/or visibility. Strip transects are also the most practical, along with the animal-observer method; however, the latter lacks mathematical justification. We conclude that there are arguments for continued use of all four methods. In certain situations the use of raw encounter rates may also be considered. The appropriate method is determined by minimizing bias and considering time, resources and field conditions.     

Genetic sampling for estimating density of common species

Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult‐to‐capture species, genetic surveys from noninvasive collection of hair or scat has proved cost‐efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single‐session NGS sampling of hares. We compared spatial capture–recapture population estimates from live trapping to estimates derived from NGS, and assessed NGS costs. NGS provided population estimates similar to those derived from live trapping, but a higher density of sampling plots was required for NGS. The optimal NGS protocol for our study entailed deploying 160 sampling plots for 4 days and genotyping one pellet per plot. NGS laboratory costs ranged from approximately $670 to $3000 USD per field site. While live trapping does not incur laboratory costs, its field costs can be considerably higher than for NGS, especially when study sites are difficult to access. We conclude that NGS can work for common species, but that it will require field and laboratory pilot testing to develop cost‐effective sampling protocols.     

Identification of key microhabitats for fish assemblages in tropical Brazilian savanna streams

The habitat use by stream fish can provide an understanding of this important component of species niches, and the changes in the availability of certain structures of instream habitats have a strong influence on the occurrence and abundance of fish species. In this study, we identified the interaction networks between fish and microhabitats in 19 streams of three watersheds from the Brazilian savanna, known as the “Cerrado”. We also investigated whether the connectance between fish species and microhabitats depends on either the species abundance or availability of microhabitats and verified whether the use of stream microhabitats vary among watersheds. The data for the fish were obtained using standardized fish collections and underwater (snorkeling) observations to record the association of fish species with 11 stream microhabitats. We used the incidence data to calculate the connectance of species with different microhabitats, a Spearman correlation analysis to test the dependence of the connectance to the species abundance and microhabitat availability, and an Analysis of Similarity to test whether the use of stream microhabitats by fish can vary among watersheds. In all of the watersheds, the tetras of the family Characidae used the largest number of microhabitats. The most‐used microhabitats by the fish watersheds were the lateral surface, column surface, and unconsolidated substrate, which were differentially used by the fish in each watershed, indicating the variable importance of microhabitats. Despite this observation, the fish occurred more frequently in the lateral microhabitats. When the data for all of the streams were combined, the species connectance was correlated with the species abundance. We also discuss the consequences of the elimination of certain bottom structures in the context of siltation, which is the main issue in the studied region. The results of our study allowed the detection of key microhabitat structures and can be used for the aquatic ecosystems restoration. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Benthic algal biomass and productivity in high subarctic streams,Alaska

Year-round measurements of the standing crop of epilithic algae (as chlorophyll a concentration) in two streams — one second and one fourth order (map scale 1:63 360) — in interior Alaska (64°–65° N) were only about one tenth that reported from streams of temperate North America. Cell densities in these streams, however, were similar to those in comparable temperate streams. Year-round domination of the benthic flora by very tiny diatoms (Achnanthes spp.) may explain the apparent disparity between low chlorophyll a content and nearly average cell densities. Chlorophyll a standing crop in a more alkaline groundwater-fed stream, however, was higher and within the range of similarly sized temperate streams. Maximum chlorophyll a standing crop varied positively with alkalinity in 5 clear-water streams where standing crop was measured on natural or artificial substrates. Seasonal mean concentrations of sestonic chlorophyll a (used as estimates of benthic algal chlorophyll a standing crop) varied directly and significantly with alkalinity among ten clear-water streams; and, with total phosphorus among 8 of 10 clear-water and 5 brown-water streams studied. During the summer, when there is little darkness, gross primary productivity (as estimated by the diurnal dissolved-oxygen method) was similar to that of northern temperate streams. Gross primary productivity was also seen to vary directly with alkalinity in 5 clear-water streams of this region.U.S. Fish and Wildlife Service     

Life-history traits of invasive fish in small Mediterranean streams

We compared the life-history traits of native and invasive fish species from Catalan streams in order to identify the characters of successful invasive fish species. Most of the exotic fish species were characterized by large size, long longevity, late maturity, high fecundity, few spawnings per year, and short reproductive span, whereas Iberian native species exhibited predominantly the opposite suite of traits. Species native to the southeastern Pyrenees watershed were also significantly different from species native to the rest of the Iberian Peninsula but not native to this watershed. Iberian exotic species come predominantly from large river basins, whereas Catalan streams (and other small, coastal river basins) correspond to basins and streams of a smaller size and different hydrology, with differences in species composition and life-history traits of fish. The occurrence and spread of invasive species was not significantly related to life-history traits but to introduction date. The successful prediction of future invasive species is limited due to small differences in life-history and ecological traits between native and exotic species. Fecundity, age at maturity, water quality flexibility, tolerance to pollution and habitat seem the most discriminating life-history variables. This revised version was published online in July 2006 with corrections to the Cover Date.