Spatial predictors of fish species composition in European lowland lakes

Composition of animal communities can be shaped by both local and regional processes. Among others, dispersal of organisms links local and regional patterns and determines the similarity of communities at increasing spatial distances. Unique and shared spatial and environmental contributions to fish community composition were calculated for watercourse distances between 49 hydrologically connected lakes in the German lowland area. Variation partitioning indicated a dominant unique effect of spatial predictors on fish community composition, whereas the effects of lake morphometry and productivity were weaker. The spatial effect was attributable to an uneven occurrence of small, littoral fish species found even at the small spatial extension covered here (maximum spatial distance ?550 km). Distance decay of community similarity was moderate, but significant, if all 31 fish species were considered, but the slope of the decay function became steeper if only 11 small‐sized, primarily littoral species were included. These results suggest that fish in European lowland lakes can be considered a metacommunity with limited dispersal along watercourse connections in particular for small‐sized species. The analysis supports that for an appropriate evaluation of spatial effects on fish community similarity, reliable estimates of local richness are required which include in particular also rare, small‐sized species occurring primarily in littoral areas. Furthermore, watercourse distance is a more reliable approximation than Euclidean distance to the real spatial dimension of fish dispersal.     

Five Hundred Sixty-Five Triples of Chicken,Human, and Mouse Candidate Orthologs

The Human Genome Project has provided abundant gene sequence information on human and important model organisms. The chicken is well positioned from an evolutionary standpoint to serve as a link between higher and lower organisms, particularly mammals, and amphibia and fish. In this study we used stringent criteria to select 565 triples of chicken, human, and mouse candidate orthologs. We analyze the sequences with respect to nucleotide and amino acid similarities. This analysis also allows measurement of evolutionary distances of different proteins. We found that chicken-human and chicken-mouse sequence identities are highly correlated; similarly for chicken-human and chicken-mouse evolutionary distances. With chicken as the out-group, we found that mouse has a higher substitution rate than human, supporting the generation-time effect hypothesis. We also described the transversion bias, which is the preference for some transversions than others in nucleotide substitutions. We demonstrated that there are statistically significant properties in the differences of orthologous sequences. The differential patterns, in combination with sequence similarity analysis, may lead to the identification of genes that are very divergent from the mammalian orthologs.     

The factor structure of horse personality

Abstract

Two hundred and ten owners or carers completed a specially modified version of the NEO-Personality Inventory-Five Factor Inventory (NEO-PI-FFI, a well established personality questionnaire for humans) for their chosen horse. Three and five-factor Principal Components Analysis (PCA) solutions are reported and compared with published studies on the factor structure of human personality. Participants were asked how confident they were in using each of the different Big Five scales in describing their horse: neuroticism and extraversion were rated with most confidence and openness to experience with least confidence. Taking both our own factors above and the NEO scales, some comparisons between the working roles of the horse were significant; for example, horses used for teaching were less extraverted than show jumpers. Sophistication of working role also related to personality; for example, international horses were less extraverted than novices. We conclude that the study provides some evidence for cross-species similarity in the structure of personality.     

Convergence of fish communities from the littoral zone of reservoirs

1. Understanding factors that regulate the assembly of communities is a main focus of ecology. Human‐engineered habitats, such as reservoirs, may provide insight into these assembly processes because they represent novel habitats that are subjected to colonization by fishes from the surrounding river basin or transported by humans. By contrasting community similarity within and among reservoirs from different drainage basins to nearby stream communities, we can test the relative constraints of reservoir habitats and regional species pools in determining species composition of reservoirs. 2. We used a large spatial database that included intensive collections from 143 stream and 28 reservoir sites within three major river basins in the Great Plains, U.S.A., to compare patterns of species diversity and community structure between streams and reservoirs and to characterize variation in fish community structure within and among major drainage basins. We expected reservoir fish faunas to reflect the regional species pool, but would be more homogeneous that stream communities because similar species are stocked and thrive in reservoirs (e.g. planktivores and piscivores), and they lack obligate stream organisms that are not shared among regional species pools. 3. We found that fish communities from reservoirs were a subset of fishes collected from streams and dominant taxa had ecological traits that would be favoured in lentic environments. Although there were regional differences in reservoir fish communities, species richness, patterns of rank abundance and community structure in reservoir communities were more homogonous across three major drainage basins than for stream communities. 4. The general pattern of convergence of reservoir fish community structure suggests their assembly is constrained by local factors such as habitat and biotic interactions, and facilitated by the introduction of species among basins. Because there is a reciprocal transfer of biota between reservoirs and streams, understanding factors structuring both habitats is necessary to evaluate the long‐term dynamics of impounded river networks.     

Interactions between Nile tilapia (Oreochromis niloticus) and cladocerans in ponds (Khartoum,Sudan)

Juvenile Nile tilapia (Oreochromis niloticus) are omnivorous, and the question asked in this study is how they affect on their environment? Do they mainly act as predators on the cladoceran zooplankton or do they compete with the cladocerans for phytoplankton? This problem was studied in three ponds with and three ponds without small tilapia (3–5 cm). The fish growth rate, the succession of plankton species and the changes in abiotic conditions, were monitored over a period of 67 days. The fish biomass was kept low and the mean was approximately constant (12.6 g m^?2) during the experiment. Phosphate was added to avoid phytoplankton nutrient limitation. Although the diet of Nile tilapia contained both phytoplankton and zooplankton, the fish affected the ecosystem in a similar way as zooplanktivorous fish. The fish ponds got more phytoplankton due to increase of Chlorophyta. Effects on the other phytoplankton groups Euglenophyta, Bacillariophyta, Cryptophyta and Cyanophyta could not be registered. The ponds without fish had higher densities of Daphnia lumholtzi and D. barbata. The other Cladocerans seemed less influenced by fish presence. The relative fish growth rate was most positively correlated with the density of Daphnia lumholtzi, Diaphanosmoa excisum and Bosmina longirostris. Tilapia seemes to have two feeding modes: (1) preying on large zooplankton and (2) unselective filtration of small planktonic organisms such as phytoplankton. In our experiment the first feeding mode affected the ecosystem more than the second.     

Detecting deception in movement: the case of the side-step in rugby

Although coordinated patterns of body movement can be used to communicate action intention, they can also be used to deceive. Often known as deceptive movements, these unpredictable patterns of body movement can give a competitive advantage to an attacker when trying to outwit a defender. In this particular study, we immersed novice and expert rugby players in an interactive virtual rugby environment to understand how the dynamics of deceptive body movement influence a defending player's decisions about how and when to act. When asked to judge final running direction, expert players who were found to tune into prospective tau-based information specified in the dynamics of 'honest' movement signals (Centre of Mass), performed significantly better than novices who tuned into the dynamics of 'deceptive' movement signals (upper trunk yaw and out-foot placement) (p<.001). These findings were further corroborated in a second experiment where players were able to move as if to intercept or 'tackle' the virtual attacker. An analysis of action responses showed that experts waited significantly longer before initiating movement (p<.001). By waiting longer and picking up more information that would inform about future running direction these experts made significantly fewer errors (p<.05). In this paper we not only present a mathematical model that describes how deception in body-based movement is detected, but we also show how perceptual expertise is manifested in action expertise. We conclude that being able to tune into the 'honest' information specifying true running action intention gives a strong competitive advantage.     

Art Expertise Reduces Influence of Visual Salience on Fixation in Viewing Abstract-Paintings

When viewing a painting, artists perceive more information from the painting on the basis of their experience and knowledge than art novices do. This difference can be reflected in eye scan paths during viewing of paintings. Distributions of scan paths of artists are different from those of novices even when the paintings contain no figurative object (i.e. abstract paintings). There are two possible explanations for this difference of scan paths. One is that artists have high sensitivity to high-level features such as textures and composition of colors and therefore their fixations are more driven by such features compared with novices. The other is that fixations of artists are more attracted by salient features than those of novices and the fixations are driven by low-level features. To test these, we measured eye fixations of artists and novices during the free viewing of various abstract paintings and compared the distribution of their fixations for each painting with a topological attentional map that quantifies the conspicuity of low-level features in the painting (i.e. saliency map). We found that the fixation distribution of artists was more distinguishable from the saliency map than that of novices. This difference indicates that fixations of artists are less driven by low-level features than those of novices. Our result suggests that artists may extract visual information from paintings based on high-level features. This ability of artists may be associated with artists’ deep aesthetic appreciation of paintings.     

Species-specific probe,based on 18S rDNA sequence,could be used for identification of the mucilage producer microalga <Emphasis Type="Italic">Gonyaulax fragilis</Emphasis> (Dinophyta)

Brook trout (Salvelinus fontinalis) in Appalachia experience prolonged periods of poor feeding conditions, particularly during summer and fall. To determine which prey organisms are important in sustaining brook trout populations, we monitored the feeding patterns of a population of brook trout over the course of 2 years with an emphasis on seasonal change. We employed a bioenergetics model to estimate whether or not each fish had obtained enough energy to meet daily metabolic demand. As a result, qualitative comparisons between fish feeding above maintenance ration (successfully feeding fish) and fish feeding below maintenance ration (unsuccessfully feeding fish) were possible. With the exception of winter, brook trout derived significantly more energy from terrestrial organisms than aquatic organisms. During each season, successfully feeding brook trout fed on greater proportions of specific prey types. Terrestrial Coleoptera and Lepidoptera consistently proved to be important prey during warmer seasons, while large organisms such as vertebrates and crayfish appeared to be important during winter. Our findings suggest that terrestrial organisms are more important than aquatic organisms in sustaining brook trout populations. Further, certain large and abundant terrestrial taxa are critical in providing energy to brook trout.     

A wide window of migration phenology captures inter‐annual variability of favourable conditions: Results of a whole‐lake experiment with juvenile Pacific salmon

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Experience Does Not Equal Expertise in Recognizing Infrequent Incoming Gunfire: Neural Markers for Experience and Task Expertise at Peak Behavioral Performance

For a soldier, decisions to use force can happen rapidly and sometimes lead to undesired consequences. In many of these situations, there is a rapid assessment by the shooter that recognizes a threat and responds to it with return fire. But the neural processes underlying these rapid decisions are largely unknown, especially amongst those with extensive weapons experience and expertise. In this paper, we investigate differences in weapons experts and non-experts during an incoming gunfire detection task. Specifically, we analyzed the electroencephalography (EEG) of eleven expert marksmen/soldiers and eleven non-experts while they listened to an audio scene consisting of a sequence of incoming and non-incoming gunfire events. Subjects were tasked with identifying each event as quickly as possible and committing their choice via a motor response. Contrary to our hypothesis, experts did not have significantly better behavioral performance or faster response time than novices. Rather, novices indicated trends of better behavioral performance than experts. These group differences were more dramatic in the EEG correlates of incoming gunfire detection. Using machine learning, we found condition-discriminating EEG activity among novices showing greater magnitude and covering longer periods than those found in experts. We also compared group-level source reconstruction on the maximum discriminating neural correlates and found that each group uses different neural structures to perform the task. From condition-discriminating EEG and source localization, we found that experts perceive more categorical overlap between incoming and non-incoming gunfire. Consequently, the experts did not perform as well behaviorally as the novices. We explain these unexpected group differences as a consequence of experience with gunfire not being equivalent to expertise in recognizing incoming gunfire.     

Cleaner fish use tactile dancing behavior as a preconflict management strategy

The most commonly asked question about cooperative interactions is how they are maintained when cheating is theoretically more profitable. In cleaning interactions, where cleaners remove parasites from apparently cooperating clients, the classical question asked is why cleaner fish can clean piscivorous client fish without being eaten, a problem Trivers used to explain reciprocal altruism. Trivers suggested that predators refrain from eating cleaners only when the repeated removal of parasites by a particular cleaner results in a greater benefit than eating the cleaner. Although several theoretical models have examined cheating behavior in clients, no empirical tests have been done (but see Darcy ). It has been observed that cleaners are susceptible to predation. Thus, cleaners should have evolved strategies to avoid conflict or being eaten. In primates, conflicts are often resolved with conflict or preconflict management behavior. Here, I show that cleaner fish tactically stimulate clients while swimming in an oscillating "dancing" manner (tactile dancing) more when exposed to hungry piscivorous clients than satiated ones, regardless of the client's parasite load. Tactile dancing thus may function as a preconflict management strategy that enables cleaner fish to avoid conflict with potentially "dangerous" clients.     

Piscivorous behavior of a temperate cone snail, Conus californicus

Most of the more than 500 species of predatory marine snails in the genus Conus are tropical or semitropical, and nearly all are thought to be highly selective regarding type of prey. Conus californicus Hinds, 1844, is unusual in that it is endemic to the North American Pacific coast and preys on a large variety of benthic organisms, primarily worms and other molluscs, and also scavenges. We studied the feeding behavior of C. californicus in captivity and found that it regularly killed and consumed live prickleback fishes (Cebidichthys violaceus and Xiphister spp.). Predation involved two behavioral methods similar to those employed by strictly piscivorous relatives. One method utilized stings delivered by radular teeth; the other involved engulfing the prey without stinging. Both methods were commonly used in combination, and individual snails sometimes employed multiple stings to subdue a fish. During the course of the study, snails became aroused by the presence of live fish more quickly, as evidenced by more rapid initiation of hunting behavior. Despite this apparent adaptation, details of prey-capture techniques and effectiveness of stings remained similar over the same period.     

A comparative evaluation of pairwise nestedness measures

This paper deals with nestedness measures that are based on pairwise comparisons of sites, evaluates their performance and suggests improvements and generalizations. There are several conceptual and technical criteria to judge their ecological applicability. It is of primary concern whether the measures 1) have a clear mathematical definition, 2) are influenced by the ordering of the data matrix, 3) incorporate similarity alone or similarity together with a dissimilarity component, 4) consider site pairs with identical species number negatively or positively, 5) show sensitivity to small changes in the data, and 6) are not vulnerable to type I and type II error rates. We performed a detailed comparison of the nestedness metric based on overlap and decreasing fill (NODF), the percentage relativized nestedness and the percentage relativized strict nestedness functions (PRN and PRSN, respectively), based on analytical results as well as on artificial and actual examples. We show that NODF is in fact the average Simpson similarity of sites with different species totals, and that its value depends on how the matrix is actually ordered. NODF is modified to always produce the maximum possible result (NODF_max), independently of the order of columns and rows. Being based on similarities, NODF and NODF_max overemphasize the overlap component of nestedness and underrate richness difference which is also an important constituent of nested pattern in meta‐community data. This latter feature is reflected adequately by PRN and PRSN. However, PRSN is similar to NODF and NODF_max in sharing the disadvantages that 1) complete agreement and segregation in species composition are not distinguished, 2) a random matrix can have a higher value than truly nested patterns, and 3) they are ill‐conditioned statistically. These problems are rooted mostly in that site pairs with tied totals affect the result negatively. We emphasize that PRN is free from these difficulties. PRN, PRSN, and NODF_max, together with mean Simpson similarity exhibit highly similar statistical performance: they are resistant to type I and type II errors for the less constrained null models, although there are subtle differences depending on matrix fill and algorithm of randomization. The most constrained null model, with all marginal totals fixed, makes all statistics more sensitive to type I errors, although vulnerability depends greatly on matrix fill.     

Update of microbial genome programs for bacteria and archaea

Since the Haemophilus influenzae genome sequence was completed in 1995, 172 other prokaryotic genomes have been completely sequenced, while 508 projects are underway. Besides pathogens, organisms important in several other fields, such as biotechnology and bioremediation, have also been sequenced. Institutions choose the organisms they wish to sequence according to the importance that these species represent to them, the availability of the microbes, and based on the similarity of a species of interest with others that have been sequenced previously. Improvements in sequencing techniques and in associated methodologies have been achieved; however, scientists need to continue working on the development of this field. In Brazil, a multicentered, centrally coordinated and research-focused network was adopted and successfully used for the sequencing of several important organisms. We analyzed the current status of microbial genomes, the trends for criteria used to choose new sequencing projects, the future of microbial sequencing, and the Brazilian genome network.     

River of the dammed: longitudinal changes in fish assemblages in response to dams

Although dams are a common feature on rivers throughout the world, their effects on diversity, composition, and structure of fish assemblages are often unclear. We used electrified benthic trawls and stable isotope analysis of δ¹³C and δ¹⁵N to determine the complex relationships between taxonomic diversity and food web structure of fish assemblages among sites in the free-flowing and impounded reaches of the Allegheny River, Pennsylvania, USA. We found higher gamma and beta fish diversity in the free-flowing section, where Brillouin diversity increased in a downstream direction; however, in the impounded section, we found decreasing diversity downstream. Analysis of similarity and non-metric multi-dimensional scaling revealed longitudinal differences in Bray–Curtis similarity between assemblages from impounded and those from free-flowing sites. Finally, using stable isotope analysis, we showed that fishes in the free-flowing section derived nutrients primarily from benthic sources while fishes in the impounded section had a stronger reliance on pelagic nutrients. Our findings reveal that dams can reduce fish taxonomic diversity, driven primarily by decreases in lotic taxa, while shifting resource use from benthic toward pelagic nutrients. A multi-faceted approach to assess the cumulative effects of dams on aquatic communities is, therefore, recommended.     

Detecting network communities: an application to phylogenetic analysis

This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis.     

More genes in fish?

Certain species of fish have recently become important model systems in comparative genomics and in developmental biology, in certain instances because of their small genome sizes (e.g., in the pufferfish) and, in other cases, because of the opportunity they provide to combine an easily accessible and experimentally manipulable embryology with the power of genetic approaches (e.g., in the zebrafish). The resulting accumulation of genomic information indicates that, surprisingly, many gene families of fish consist of more members than in mammals. Most modern fish, including the zebrafish and medakka, are diploid organisms; however, the greater number of genes in fish was possibly caused by additional ancient genome duplications which happened in the lineage leading to modern ray-finned fishes but not along the lineage leading to tetrapods. Since these two lineages shared their last common ancestor (in the Devonian about 360 million years ago) individual duplicated members of gene families were later lost in fish. Interestingly, comparative data indicate that, in some cases, genes in mammals even serve somewhat different functions than their homologues in fish, highlighting that the degree of evolutionary relatedness of genes is not always a reliable predictor of their evolutionary conservation and their similarity of function. Since fish are phenotypically probably not more complex than mammals, it is possible that evolution took alternative paths to the “economics of genomics” through alternative solutions to gene regulation. It is suggested that the more complex genomic architecture of fish permitted them to adapt and speciate quickly in response to changing selective regimes. BioEssays 20 :511–515, 1998. © 1998 John Wiley & Sons, Inc.     

Separating natural responses from experimental artefacts: habitat selection by a diadromous fish species using odours from conspecifics and natural stream water

Animals use sensory stimuli to assess and select habitats, mates and food as well as to communicate with other individuals. One way they do this is to use olfaction, whereby they identify and respond to chemical cues. All organisms release odours, which mix with other chemical substances and ambient environmental conditions. The result is that animals are frequently immersed in a complex, highly dynamic sensory environment where they must identify and respond to only some of the potential stimuli they encounter in the face of significant levels of background noise. Understanding how organisms respond to different chemical cues is therefore dependent on knowing how these responses might be influenced by potential interactions with other stimuli. To test this, we examined whether the diadromous fish Galaxias maculatus was attracted to conspecific odours and whether this response differed when cues were offered in an artificial environment lacking other potential chemical stimuli (tap water) or a more natural background environment (stream water). We found that (1) fish responded to both natural stream water odours and those from conspecifics but the response to the latter was stronger; (2) the attraction to conspecific odours was stronger in tap water than in stream water, which indicates the importance of these odours may be overestimated when they are offered in artificial media. We also conducted a brief literature review, which confirmed that artificial media are commonly used in experiments and that the background environment is often not considered. Our results show that future research testing the responses of organisms to auditory, olfactory and visual cues should carefully consider the context in which cues are presented. Without doing so, such studies may inaccurately assess the importance of sensory cues in natural situations in the wild. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Relationship of fish and macroinvertebrate assemblages to environmental factors: implications for community concordance

Community concordance describes similarity in distributions and abundances of organisms from different taxonomic groups across a region of interest, with highly concordant communities assumed to respond similarly to major environmental gradients, including anthropogenic stressors. While few studies have explicitly tested for concordance among stream-dwelling organisms, it frequently is assumed that both macroinvertebrates and fish respond in concert to environmental factors, an assumption that has implications for their management. We investigated concordance among fish and macroinvertebrates from tributaries of two catchments in southeastern Michigan having varied landscape characteristics. Classifications of fish and macroinvertebrate assemblages resulted in groups distinguished by differences in taxonomic characteristics, functional traits, and stressor tolerance of their respective dominant taxa. Biological groups were associated with principal landscape gradients of the study region, which ranged from forests and wetlands on coarse surficial geology to agricultural lands on finer, more impervious surficial geology. Measures of stream habitat indicated more stable stream flows and greater heterogeneity of conditions at site groups with catchments comprising forests and wetlands on the coarsest geology, but did not distinguish well among remaining site groups, suggesting that habitat degradation may not be the driving mechanism leading to differences in groups. Despite broadly similar interpretations of relationships of site groups with landscape characteristics for both fish and macroinvertebrates, examination of site representation within groups indicated weak community concordance. Our results suggest that explicit responses of fish and macroinvertebrates to landscape factors vary, due to potential differences in their susceptibility to controls or to differences in the scale at which landscape factors influence these organisms. Handling editor: Robert Bailey