Hierarchy theory reveals multiscale predictors of Arkansas darter (Etheostoma cragini) abundance in a Great Plains riverscape

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Linking microhabitat availability and local density of rainbow trout in low-gradient Japanese streams

Quantification of reach-based microhabitat availability for rainbow trout (Oncorhynchus mykiss), considering their microhabitat requirements in two low-gradient streams, northern Japan, was attempted to test for habitat space limitation of local trout density. Underwater observations revealed that fish selected microhabitats of moderate current velocity, relatively greater depth and shorter distance to overhead cover in both streams, although habitat features used and available differed slightly between the streams. Habitat space for fish potentially available in the channel environment was evaluated using principal component analysis (PCA) of both available and used microhabitat. A close relationship was evident in both streams between reach-based microhabitat availability and fish density, which was assessed by a three-pass removal method. Direct estimates of fish microhabitat availability using PCA can contribute to accurate predictions of local fish density and provide insight into the mechanisms responsible for fish–habitat relationships in streams.     

Trophic ecology of the emerald notothen <Emphasis Type="Italic">Trematomus bernacchii</Emphasis> (Pisces,Nototheniidae) from Terra Nova Bay,Ross Sea,Antarctica

The trophic ecology of the emerald notothen Trematomus bernacchii was investigated using a sample of 284 specimens collected in the coastal waters of Terra Nova Bay (Ross Sea) during the summer season 1990–1991. The stomach-content analysis provided data on feeding habits and trophic niche breadth. Overall, 72 taxa of food items were identified; the most important as prey were infaunal and epifaunal polychaetes, amphipods and molluscs. Food of secondary importance comprised isopods, pycnogonids, fish and fish eggs. Several other taxa, such as euphausiids, mysids, decapods, echinoids, holothurians, priapulids and thaliaceans constituted food eaten in very small amounts and only occasionally. On the basis of their diet, T. bernacchii can be considered generalized feeders, with a wide niche breadth composed almost exclusively of benthic organisms. A cluster analysis was conducted to compare stomach-content data of subsamples selected on the basis of fish size and sampling depth, aiming to determine diet diversity and niche breadth, as well as factors involved in reducing intraspecific competition for food resources. Diet was different for fish sampled in shallow (90 m depth) and deeper waters (>90 m depth): while the first group fed mostly on bivalves (Adamussium colbecki) and amphipods, the latter preferred infaunal-epifaunal polychaetes. Conversely, fish size did not contribute significantly to diet diversification. According to our data and published data on feeding behaviour and sensory ecology, we conclude that in this species the intraspecific competition for food is reduced, either through habitat heterogeneity or different foraging strategies.     

Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen,a critically endangered Asian salmonid

For field ecologists, detecting a target species in the wild is a severe bottleneck to understanding its distribution and population status. Recently, environmental DNA (eDNA) techniques have been developed as a noninvasive monitoring tool for aquatic organisms. While applications of eDNA techniques for biomass estimation have been proposed, little is known about an applicable size range of the organisms, which might affect relationships between biomass and eDNA concentration. Here, we investigated eDNA from Sakhalin taimen (Parahucho perryi), a giant salmonid species of northern Japan. This species is critically endangered and difficult to detect in the wild by conventional sampling methods. Using quantitative real-time PCR, we tested correlations between eDNA concentration and fish density using fish with a wide range of ages and body sizes in aquarium experiments. We found that our new primers and probe were truly species-specific, and that the eDNA concentration was significantly correlated with fish density and body size (p < 0.001). Furthermore, based on our calculation, the eDNA concentrations were rather constant among aquaria with fish in different age and size groups when their total weight was adjusted. These results suggest that eDNA concentrations can be an indicator of biomass of Sakhalin taimen, although further research is needed for its application in natural environments.     

A note on a possible influence of traps on assessment of the diet of Jasus lalandii (H. Milne-Edwards)

Dietary analyses are important components of ecological studies. However, some methods of collecting organisms may expose them to exceptionally high densities of prey items, leading to inaccurate dietary assessments. These methods include the use of baited traps. We hypothesised that such a "trap effect" occurred during work on the diet of the rock lobster Jasus lalandii, because baited traps attracted isopods, which were then eaten opportunistically by trapped J. lalandii. To test this hypothesis, rock lobsters were collected at two sites using both baited-traps and Scuba diving. Results showed that large numbers of isopods were attracted to, and consumed, the trap-bait. Analyses of the stomach contents of trap-caught J. lalandii from both localities reflected a larger occurrence and significantly greater abundance of isopods in stomach samples from trap- rather than Scuba-caught rock lobsters. For probably similar reasons, small fish were significantly over-represented in the gut contents of trap-caught rock lobsters, although the evidence is less clear-cut and there may be other explanations for the high proportions of fish in the diet. Although isopods and fish may be naturally consumed at a low rate, predation on them is greatly inflated in traps, and the dietary analyses of trap-caught J. lalandii. All assessments of the diets of animals traditionally caught with traps should consider and account for such "trap effects", by calibrating the data for trap-caught animals against an alternative sampling method.     

Cross-scale Habitat Structure Drives Fish Body Size Distributions on Coral Reefs

Despite a large number of studies focusing on the complexity of coral reef habitats and the characteristics of associated fish assemblages, the relationship between reef structure and fish assemblages remains unclear. The textural discontinuity hypothesis, which proposes that multi-modal body size distributions of organisms are driven by discontinuous habitat structure, provides a theoretical basis that may explain the influence of habitat availability on associated organisms. In this study we use fractal techniques to characterize patterns of cross-scale habitat complexity, and examine how this relates to body-depth abundance distributions of associated fish assemblages over corresponding spatial scales. Our study demonstrates that: (1) Reefs formed from different underlying substrata exhibit distinct patterns of cross-scale habitat complexity; (2) The availability of potential refuges at different scales correlates with patterns in fish body depth distributions, but habitat structure is more strongly related to the relative abundance of fish in the body depth modes, rather than to the number of modes; (3) As reefs change from coral- to algal-dominated states, the complexity of the underlying reef substratum may change, presenting a more homogenous environment to associated assemblages; (4) Individual fish body depth distributions may be multi-modal, however, these distributions are not static characteristics of the fish assemblage and may change to uni-modal forms in response to changing habitat condition. In light of predicted anthropogenic changes, there is a clear need to improve our understanding of the scale of ecological relationships to anticipate future changes and vulnerabilities.     

An offshore buoy as a small artificial island and a fish-aggregating device (FAD) in the Mediterranean

The ODAS Italia 1 oceanographic buoy is moored in the Ligurian Sea, 37 nm from Genoa, along the Genoa-Cape Corse transect (43° 48.90 N–09° 06.80 E), over a 1270 m deep sea bottom. The underwater portion of the buoy is 37 m long and 0.60 m in diameter, acting as a small island for colonization of fouling organisms and as a fish-aggregating device (FAD). The role of the buoy in attracting and maintaining fish assemblages was investigated by visual censuses in different seasons at depths of 0–40 m. Fish from seven families, comprising 12 species, of which three are benthic, were recorded with maximum abundance in summer. Fouling was studied from samples collected on the buoy and on immersed panels. The fouling community of the buoy consisted of 34 algae and 100 animal species, including three fish. The settlement processes of the fouling community on the panels, in particular on those exposed for over 70 months at 12 m and 33 m depth, are described based on counts of settled organisms, the covering index of each taxa and biomass assessments. On the panels, 63 species were identified. The fouling biomass, on the panel submerged for 70 months, assessed as wet weight, reached 2.8 kg/m² at 12 m depth and 4.8 kg/m² at 33 m depth.Observations of benthic organisms settled directly on the buoy were made between 1988 and 1989 and when the buoy was retrieved and brought back to shore on April 15, 1991 after 52 months at sea. At this time, the fouling community along the full 37 m length of the buoy was sampled, and 91 taxa, including 83 species, were identified. Several of the species present on the buoy are shallow, coastal species, some with a very short larval period. Possible ways of colonization by such species are discussed. Despite seasonal changes, the pelagic fish community was more stable over the period of 11 years of study than the benthic community settled on the buoy (that is still developing).     

Reconstructing community relationships: the impact of sampling error, ordination approach, and gradient length

Effectively summarizing complex community relationships is an important feature in studies such as biodiversity, global change, and invasion ecology. The reliability of such community summaries depends on the degree of sampling variability that is present in the data, the structure of the data, and the choice of ordination method, but the relative importance of these factors is not understood. We compared the validity of results from different ordination methods by applying five levels of sampling error to a simulated coenoplane model at two gradient lengths using two types of data (abundance and presence–absence). The multivariate methods we compared were correspondence analysis (CA), detrended correspondence analysis (DCA), non-metric multidimensional scaling (NMDS), principal component analysis (PCA) and principal coordinates analysis (PCoA). Our results showed CA and PCA using presence–absence data were the most successful methods regardless of sampling error and gradient length, closely followed by the other methods using presence–absence data. With abundance data, PCA and CA were the most successful approaches with the short and long gradients, respectively. Approaches based on PCoA and NMDS using abundance data did not perform well regardless of the choice of distance measure used in the analysis. Both of these methods, along with the PCA using abundance data, were strongly affected by the longer gradient, leading to more distorted results.     

Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae)

A major challenge facing biodiversity conservation and management is that a significant portion of species diversity remains undiscovered or undescribed. This is particularly evident in subterranean animals in which species delimitation based on morphology is difficult because differentiation is often obscured by phenotypic convergence. Multilocus genetic data constitute a valuable source of information for species delimitation in such organisms, but until recently, few methods were available to objectively test species delimitation hypotheses using genetic data. Here, we use recently developed methods for discovering and testing species boundaries and relationships using a multilocus dataset in a widely distributed subterranean teleost fish, Typhlichthys subterraneus, endemic to Eastern North America. We provide evidence that species diversity in T. subterraneus is currently underestimated and that the picture of a single, widely distributed species is not supported. Rather, several morphologically cryptic lineages comprise the diversity in this clade, including support for the recognition of T. eigenmanni. The high number of cryptic species in Typhlichthys highlights the utility of multilocus genetic data in delimiting species, particularly in lineages that exhibit slight morphological disparity, such as subterranean organisms. However, results depend on sampling of individuals and loci; this issue needs further study.     

Linkages among physical and biological properties in tidepools on the Maine Coast

Tidepools experience significant gradients in ecologically relevant physical variables along the transition from ocean to terrestrial habitat (vertical axis) and from open coast to inner bays (horizontal axis). Associations amongst physical and biological variables, divided into algal, invertebrate and vertebrate (fish) groups, were examined in a tidepool survey dataset. Physical variables and the three biological groups were submitted separately to a principal component analysis (PCA). PCA scores were evaluated with Pearson correlation coefficients across the sampling units (tidepools) to identify significant correlations. Initially little structure in the data and no correlation amongst variables was present. At the onset of summer, correlations were confined amongst physical variables and algal and invertebrate components, followed in the late summer with correlations between invertebrate and fish components. By the fall, correlations were confined to fish and algal/invertebrate components. Species relationships followed a seasonal cycle with a succession from little to no structure, the forming of low trophic level relationships in the early summer to high trophic level relationships in late summer-fall, and deconstruction of structure with the onset of fall-winter storms and ice scour. The seasonal pattern, and well established vertical gradient, has nested within it species composition changes along a horizontal wave energy gradient. The horizontal gradient results in a shift from species which are physiologically adapted to extreme salinities and temperatures to those which are physically adapted to high wave-energy environments.     

Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative partitioning schemes, based on Bayesian and maximum likelihood (ML) criteria, is shown here to produce an optimal number of partitions. We tested this method using sequence data of 10 nuclear genes collected from 52 ray-finned fish (Actinopterygii) and four tetrapods. The concatenated sequences included 7995 nucleotide sites maximally split into 30 partitions defined a priori based on gene and codon position. Our results show that a model based on only 10 partitions defined by cluster analysis performed better than partitioning by both gene and codon position. Alternative data partitioning schemes also are shown to affect the topologies resulting from phylogenetic analysis, especially when Bayesian methods are used, suggesting that overpartitioning may be of major concern. The phylogenetic relationships among the major clades of ray-finned fish were assessed using the best data-partitioning schemes under ML and Bayesian methods. Some significant results include the monophyly of "Holostei" (Amia and Lepisosteus), the sister-group relationships between (1) esociforms and salmoniforms and (2) osmeriforms and stomiiforms, the polyphyly of Perciformes, and a close relationship of cichlids and atherinomorphs.     

东海大陆架鱼类群落的空间结构

根据1997～2000年东海大陆架水深30～200米海域4个航次的底拖网调查资料,运用多元分析(聚类分析和非度量多维标度(NMDS))、SIMPER以及BIO-ENV方法分析了东海鱼类群落的空间格局以及与非生物环境因子之间的关系。结果表明,东海大陆架海域鱼类群落在空间上可分为3个群落类型,分别为东海近海群落、东海大陆架外缘群落以及这两个群落之间的东海大陆架混合群落。东海大陆架鱼类群落的种类组成沿着水深梯度的变化明显,每种鱼类均有一定的水深范围。不同的流系具有不同的温盐特征,影响了鱼类的分布及其洄游,从而控制了不同鱼类群落类型的种类组成。东海大陆架鱼类群落类型中,大陆架外缘群落类型各调查季节在空间分布和种类组成上相对稳定,而东海近海群落类型和东海大陆架混合群落类型在夏季融合在一起,其它季节保持各自的空间结构。同时东海陆架区只在一种群落类型中出现的鱼类相对较少,多数鱼类同时出现在两个群落类型中或3个群落类型中,但是它们相对较集中的区域明显不同,在不同群落类型中的生物量和出现频率有很大的差异,这些鱼类在其不同的生长发育阶段由于对海洋环境的不同需求,它们根据繁殖或摄食需求而在东海陆架区范围内洄游以寻找最适的海洋环境,因此对3个群落类型定义是相对的,很难严格确定一个永久的鱼类群落地理区域,以形成相互隔离的鱼类群落,而且鱼类群落之间的边界随着季节不同发生变化。     

The influence of biomanipulations (fish removal) on the structure of lake foodwebs, case studies using the LakeWeb-model

This paper presents results on how intensive fishing (fish removal) islikely to influence the structure of lake foodwebs. The work is based on acomprehensive dynamic lake ecosystem model, LakeWeb, which accounts forproduction, biomasses, predation and abiotic/biotic interactions of nine keyfunctional groups of organisms: phytoplankton, bacterioplankton, two types ofzooplankton (herbivorous and predatory), two types of fish (prey and predatory),zoobenthos, macrophytes and benthic algae. The model uses ordinary differentialequations, the ecosystem scale and gives seasonal variations (the calculationtime is 1 week). It is designed to account for all fundamental abiotic/bioticinteractions and feedbacks for lakes in general for the nine target groups. TheLakeWeb-model has been calibrated and critically tested using empirical data andregressions based on data from many lakes. It has been shown that the model canclosely capture typical functional and structural patterns in lakes, whichshould give credibility to the results presented in this work. Obtaining suchresults using traditional methods, i.e., extensive field studies in one or a fewlakes, would be very demanding (in terms of money, persons involved and time).In this paper, results are presented for two lakes, one Swedish and oneBelarussian. The intensive fishing operations carried out in LakeBlacksåstjärn, Sweden, to reduce Hg-concentrations in fish did notsucceed. A typical cost of an intensive fishing is about 10,000–30,000 USDper lake of this size ( 0.25 km²). The costs toremove fish would be about 40–120 USD per kg ww fish removed! Intensivefishing simulated for Lake Batorino, Belarus, to reduce the fish biomass willlikely increase the prey fish biomass as long as the predation pressure on preyfish is lower than during the prefishing stage. The biomass of predatory fishwill recover only slowly. However, this operation is not likely to succeed inlowering the algal volume in lakes with a high biomass of predatory zooplankton.This is easy to state qualitatively and the LakeWeb-model offers a practicallyuseful tool to quantify such changes and identify lakes where biomanipulationsare likely to fail or succeed.     

Net cages enhance golden mussel (Limnoperna fortunei) larval density and condition factor

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Fish Sound Production in the Presence of Harmful Algal Blooms in the Eastern Gulf of Mexico

This paper presents the first known research to examine sound production by fishes during harmful algal blooms (HABs). Most fish sound production is species-specific and repetitive, enabling passive acoustic monitoring to identify the distribution and behavior of soniferous species. Autonomous gliders that collect passive acoustic data and environmental data concurrently can be used to establish the oceanographic conditions surrounding sound-producing organisms. Three passive acoustic glider missions were conducted off west-central Florida in October 2011, and September and October 2012. The deployment period for two missions was dictated by the presence of red tide events with the glider path specifically set to encounter toxic Karenia brevis blooms (a.k.a red tides). Oceanographic conditions measured by the glider were significantly correlated to the variation in sounds from six known or suspected species of fish across the three missions with depth consistently being the most significant factor. At the time and space scales of this study, there was no detectable effect of red tide on sound production. Sounds were still recorded within red tide-affected waters from species with overlapping depth ranges. These results suggest that the fishes studied here did not alter their sound production nor migrate out of red tide-affected areas. Although these results are preliminary because of the limited measurements, the data and methods presented here provide a proof of principle and could serve as protocol for future studies on the effects of algal blooms on the behavior of soniferous fishes. To fully capture the effects of episodic events, we suggest that stationary or vertically profiling acoustic recorders and environmental sampling be used as a complement to glider measurements.     

黄海中南部不同断面鱼类群落结构及其多样性

基于2006年9月和12月、2007年3月和5月对黄海中南部不同断面的底拖网调查数据,对黄海中南部不同断面的鱼类群落结构、多样性、单位时间的渔获量分布及其与环境因子的关系进行了分析。结果表明,调查中共捕获鱼类109种,其中鲈形目种类最多(45种,占40.18%),其次是鲉形目(12种,占10.71%)、鲱形目(10种,占8.93%)和鲽形目(10种,占8.93%),主要由暖温种和暖水种组成,并且暖水种和暖温种在各断面渔获量中所占的比例随时间不同而有所差异。各断面主要鱼种除小黄鱼Larimichthys polyactis、带鱼Trichiurus lepturus、银鲳Pampus argenteus等种类外,以小型中上层鱼类(鳀Engraulis japonicus、黄鲫Setipinna taty等)和底层经济价值较低的鱼类(黄鮟鱇Lophius litulon、细纹狮子鱼Liparis tanakai等)为主,各断面优势种渔获量均占其总渔获量的50%以上,主要鱼种渔获量均占其总渔获量85%以上。渔获物的营养级主要分布在4.2—4.5、3.0—3.3和3.6—3.9,各营养级渔获量随时间和断面的不同有所变化。鱼类长度谱主要集中在3—24 cm,由南向北长度谱逐渐增大。各断面鱼类群落多样性指数差异不大,与底层温度和深度关系密切。     

Depth-dependent indicators of algal turf herbivory throughout the Main Hawaiian Islands

Herbivorous fish are key to maintaining a balance between coral and algae on reefs, where reefs with greater herbivore biomass often show lower algal cover. For reefs worldwide, algal turf cover is expanding and is increasingly used as an indicator of disturbance. Water depth affects reef fish composition; thus, it may be expected that herbivory could also differ by depth. We examined relationships between algal turf cover and biomass (g m⁻²), density (# m⁻²) and size (cm) of herbivore groups (grazers, browsers and scrapers) across shallow (< 6 m), mid (6–18 m) and deep (18–30 m) coral reefs in the Main Hawaiian Islands. We find that across all depth classes, algal turf cover decreased with increasing grazer and scraper density, with steeper relationships observed at mid and deep reefs than in shallow reefs. In contrast, algal turf cover slightly increased with increasing grazer and browser biomass at deep reefs. Considering fish size, algal turf cover increased with larger grazer and scrapers at mid and deep reefs. The results indicate that herbivorous fish density, rather than biomass, is a better indicator of reductions in algal turf cover and resulting coral-algal balance on Hawaiian reefs, where smaller fish exert greater top-down control on cover than larger fish. Despite significant differences in herbivorous fish compositions, length-frequency distributions and fishing intensities across depth, algal turf cover remains similar across depths. Increases in fishing would have a disproportionately negative impact in deep than shallow reefs due to a lower overall fish density, where grazing functions in deep reefs are maintained by significantly fewer and smaller grazers and browsers, and larger scrapers, than in shallow reefs. Developing an understanding of patterns of algal turf herbivory by depth is important to understanding the spatial scale at which herbivory and regime shifts operate.

     

Distribution of cichlid fishes in the littoral of Lake Bacalar, Yucatan Peninsula

The distribution of cichlids in Lake Bacalar was assessed from January to September 1996, in eight shallow-water (< 2 m) stations, using a 20 m long seine net. Temperature, salinity/conductivity and dissolved oxygen were sensor-obtained; depth, submerged vegetation and bottom type were determined by visual inspection. Affinities between stations, based on fish abundance and environmental parameters, were analyzed by multivariate methods. Littoral of Bacalar town was the site with highest richness, diversity and abundance, probably promoted by the additional urban waste of organic matter. PCA defined two station-groups, one associated with muddy substrates, the other one with rocky/sandy bottoms. Cichlids are more abundant over muddy bottoms with abundant submerged vegetation, probably because of the abundance of prey and shelter.     

Imperfect detection and the determination of environmental flows for fish: challenges,implications and solutions

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Phytoclasts in palynofacies definition: the example of Rhaetian sedimentary organic matter in SE France

The aim of this paper is to calibrate palynofacies with eight classes of phytoclasts using statistical methods in order to construct a reference. Seven categories of palynomorphs are compared to the phytoclast reference. Principal components analysis (PCA) were performed, firstly using separated phytoclast and palynomorph parameters and, secondly, the two grouped describers on samples from two Rhaetian sections that outcrop in SE France. Factor plots of phytoclast data show an arrangement that we assume to be relevant to a crescent buoyant phytoclast order previously described by literature. This arrangement is associated with palynomorph describers (abundance of spores and acritarchs Micrhystridium and pollen Ovalipollis). Some lithological observations are antinomic with an interpretation of these groupings in terms of depositional energy but are presumably coherent with the water depth. Testing all the parameters simultaneously, we define six types of palynofacies ordered on a hypothesized water depth gradient, sustained by an inferred “buoyant factorial plan”. A low water depth palynofacies is associated with lagoons, beaches and marine-shelves. The phytoclasts present are the most buoyant particles on the palynomaceral arrangement. Bays, lagoons, foreshores, beaches, restricted-marine and marine-shelves produce the highest water depth palynofacies. The phytoclasts present are the poorest buoyant particles on the palynomaceral arrangement. Although the exact nature of the relations between energy, water depth and phytoclasts are unknown, the definition of palynofacies by PCA is an objective method for investigating and correlating sedimentary sections.