A review of fish swimming mechanics and behaviour in altered flows

Fishes suspended in water are subject to the complex nature of three-dimensional flows. Often, these flows are the result of abiotic and biotic sources that alter otherwise uniform flows, which then have the potential to perturb the swimming motions of fishes. The goal of this review is to highlight key studies that have contributed to a mechanistic and behavioural understanding of how perturbing flows affect fish. Most of our understanding of fish behaviour in turbulence comes from observations of natural conditions in the field and laboratory studies employing controlled perturbations, such as vortices generated in the wake behind simple geometric objects. Laboratory studies have employed motion analysis, flow visualization, electromyography, respirometry and sensory deprecation techniques to evaluate the mechanisms and physiological costs of swimming in altered flows. Studies show that flows which display chaotic and wide fluctuations in velocity can repel fishes, while flows that have a component of predictability can attract fishes. The ability to maintain stability in three-dimensional flows, either actively with powered movements or passively using the posture and intrinsic compliance of the body and fins, plays a large role in whether fish seek out or avoid turbulence. Fish in schools or current-swept habitats can benefit from altered flows using two distinct though not mutually exclusive mechanisms: flow refuging (exploiting regions of reduced flow relative to the earth frame of reference) and vortex capture (harnessing the energy of environmental vortices). Integrating how the physical environment affects organismal biomechanics with the more complex issue of behavioural choice requires consideration beyond simple body motions or metabolic costs. A fundamental link between these two ways of thinking about animal behaviour is how organisms sense and process information from the environment, which determines when locomotor behaviour is initiated and modulated. New data are presented here which show that behaviour changes in altered flows when either the lateral line or vision is blocked, showing that fish rely on multi-modal sensory inputs to negotiate complex flow environments. Integrating biomechanics and sensory biology to understand how fish swim in turbulent flow at the organismal level is necessary to better address population-level questions in the fields of fisheries management and ecology.     

Cranial morphological variation in Peromyscus maniculatus over nearly a century of environmental change in three areas of California

Determining how species respond to prolonged environmental change is critical to understanding both their evolutionary biology and their conservation needs. In general, organisms can respond to changing environmental conditions by moving, by adapting in situ, or by going locally or globally extinct. Morphological changes, whether plastic or adaptive, are one way that species may respond in situ to local environmental change. Because cranial morphology is influenced by selective pressures arising from an organism's abiotic and biotic environments, including aspects of thermal physiology, diet, and sensory ecology, studies of cranial morphology may generate important insights into how species are responding to environmental change. To assess potential response of deer mice (Peromyscus maniculatus) to changing conditions in the Sierra Nevada Mountains of California, we quantified cranial variation in museum specimens of this species collected approximately 100 years apart. Specifically, we examined how cranial morphology varies in three populations of this geographically widespread, ecological generalist over elevation and time. Our analyses indicate that cranial morphology does not differ with elevation within either modern or historical samples but does vary between time periods, suggesting that in situ responses to environmental change have occurred. Contrary to predictions based on Bergmann's rule, we found no consistent relationship between body size and either elevation or time, suggesting that morphological differences detected between historic and modern specimens are specific to factors influencing cranial structure. Collectively, these analyses demonstrate the potential importance of in situ changes in morphology as a response to changing environmental conditions. J. Morphol. 277:96–106, 2016. © 2016 Wiley Periodicals, Inc.     

The ecology of information: an overview on the ecological significance of making informed decisions

Information is characterized as the reduction of uncertainty and by a change in the state of a receiving organism. Thus, organisms can acquire information about their environment that reduces uncertainty and increases their likelihood of choosing a best‐matching strategy. We define the ecology of information as the study of how organisms acquire and use information in decision‐making and its significance for populations, communities, landscapes and ecosystems. As a whole, it encompasses the reception and processing of information, decision‐making, and the ecological consequences of making informed decisions. The first two stages constitute the domains of, e.g. sensory ecology and behavioral ecology. The exploration of the consequences of information use at larger spatial and temporal scales in ecology has lagged behind these other disciplines. In our overview we characterize information, discuss statistical decision theory as a quantitative framework to analyze information and decision‐making, and discuss potential ecological ramifications. Rather than attempt a cursory review of the enormity of the scope of information we highlight information use in development, breeding habitat selection, and interceptive eavesdropping on alarm calls. Through these topics we discuss specific examples of ecological information use and the emerging ecological consequences. We emphasize recurring themes: information is collected from multiple sources, over varying temporal and spatial scales, and in many cases links heterospecifics to one another. We conclude by breaking from specific ecological contexts to explore implications of information as a central organizing principle, including: information webs, information as a component of the niche concept, and information as an ecosystem process. With information having such an enormous reach in ecology we further cast a spotlight on the potential harmful effects of anthropogenic noise and info‐disruption.     

Don't put all your eggs in one basket: a cost‐effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

With the increasing democratization of high‐throughput sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer‐targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs in the sequenced organisms even when targeting the same community. This potential source of taxonomic bias in HTS makes it prudent to investigate how primer choice will affect the sequenced community prior to investing in a costly community‐wide sequencing effort. Here, we use Fluidigm's microfluidic Access Arrays (IFC) followed by Illumina^® MiSeq Nano sequencing on a culture‐derived local mock community to demonstrate how this approach allows for a low‐cost combinatorial investigation of primer pairs and experimental samples (up to 48 primer pairs and 48 samples) to determine the most effective primers that maximize obtained communities whilst minimizing taxonomic biases.     

Ecological annotation of genes and genomes through ecological genomics

Ecological genomics is a research field that aims to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. This matter was the central theme of the symposium on Ecological Genomics that took place at the First meeting of the Canadian Society for Ecology and Evolution, held at the University of Toronto in May 2007. Through their research on a diverse array of organisms, the various speakers illustrated how ecology and evolution benefit from genomics, and indirectly how genomics can benefit from evolutionary ecology.     

Sensory ecology and perceptual allocation: new prospects for neural networks

Sensory ecology provides a conceptual framework for considering how animals ought to design sensory systems to capture meaningful information from their environments. The framework has been particularly successful at describing how one should allocate sensory receptors to maximize performance on a given task. Neural networks, in contrast, have made unique contributions to understanding how 'hidden preferences' can emerge as a by-product of sensory design. The two frameworks comprise complementary techniques for understanding the design and the evolution of sensation. This article reviews empirical literature from multiple modalities and levels of sensory processing, considering vision, audition and touch from the viewpoints of sensory ecology and neuroethology. In the process, it presents modifications of extant neural network algorithms that would allow a more effective integration of these diverse approaches. Together, the reviewed literature suggests important advances that can be made by explicitly formulating neural network models in terms of sensory ecology, by incorporating neural costs into models of perceptual evolution and by exploring how such demands interact with historical forces.     

Conservation physiology for applied management of marine fish: an overview with perspectives on the role and value of telemetry

Physiological studies focus on the responses of cells, tissues and individuals to stressors, usually in laboratory situations. Conservation and management, on the other hand, focus on populations. The field of conservation physiology addresses the question of how abiotic drivers of physiological responses at the level of the individual alter requirements for successful conservation and management of populations. To achieve this, impacts of physiological effects at the individual level need to be scaled to impacts on population dynamics, which requires consideration of ecology. Successfully realizing the potential of conservation physiology requires interdisciplinary studies incorporating physiology and ecology, and requires that a constructive dialogue develops between these traditionally disparate fields. To encourage this dialogue, we consider the increasingly explicit incorporation of physiology into ecological models applied to marine fish conservation and management. Conservation physiology is further challenged as the physiology of an individual revealed under laboratory conditions is unlikely to reflect realized responses to the complex variable stressors to which it is exposed in the wild. Telemetry technology offers the capability to record an animal's behaviour while simultaneously recording environmental variables to which it is exposed. We consider how the emerging insights from telemetry can strengthen the incorporation of physiology into ecology.     

Facilitation in the conceptual melting pot

1. Here we present an introduction to this issue's Special Feature arising from the British Ecological Society Symposium: Facilitation in Plant Communities (20–22 April 2009).
2. Papers in the Special Feature demonstrate the benefits that arise from cross-system application of general concepts, for example, the well-known stress gradient hypothesis. Such comparisons challenge our definition of facilitation, as well as our pre-conceptions on the nature of intermediary organisms.
3. We suggest that under some circumstances a clear definition of the two-way nature of interactions is essential, e.g. when considering the evolutionary implications of facilitation. In other cases, however, we can perhaps be more relaxed, e.g. when facilitation is a component of conservation ecology.
4. Synthesis . Overall we believe that establishing facilitation as an independent concept has driven substantial progress towards a clearer understanding of how ecological systems work. Through the links established by work such as that presented in this Special Feature, we believe this field will continue to make rapid progress and aid ecological understanding in general.     

Recognition of flowers by pollinators

The flowers of angiosperm plants present us with a staggering diversity of signal designs, but how did this diversity evolve? Answering this question requires us to understand how pollinators analyze these signals with their visual and olfactory sense organs, and how the sensory systems work together with post-receptor neural wiring to produce a coherent percept of the world around them. Recent research on the dynamics with which bees store, manage and retrieve memories all have fundamental implications for how pollinators choose between flowers, and in turn for floral evolution. New findings regarding how attention, peak-shift phenomena, and speed-accuracy tradeoffs affect pollinator choice between flower species show that analyzing the evolutionary ecology of signal-receiver relationships can substantially benefit from knowledge about the neural mechanisms of visual and olfactory information processing.     

From low to high gear: there has been a paradigm shift in our understanding of evolution

Experimental studies of evolution performed in nature and the associated demonstration of rapid evolution, observable on a time scale of months to years, were an acclaimed novelty in the 1980–1990s. Contemporary evolution is now considered ordinary and is an integrated feature of many areas of research. This shift from extraordinary to ordinary reflects a change in the perception of evolution. It was formerly thought of as a historical process, perceived through the footprints left in the fossil record or living organisms. It is now seen as a contemporary process that acts in real time. Here we review how this shift occurred and its consequences for fields as diverse as wildlife management, conservation biology, and ecosystems ecology. Incorporating contemporary evolution in these fields has caused old questions to be recast, changed the answers, caused new and previously inconceivable questions to be addressed, and inspired the development of new subdisciplines. We argue further that the potential of contemporary evolution has yet to be fulfilled. Incorporating evolutionary dynamics in any research program can provide a better assessment of how and why organisms and communities came to be as they are than is attainable without an explicit treatment of these dynamics.     

Rapid assessment of invertebrate biodiversity on rocky shores: where there’s a whelk there’s a way

The lack of species inventory data for most marine habitats currently hampers the objective management of marine biodiversity. There is thus a clear need to find reliable indicator taxa that can be targeted in marine conservation studies, providing cost-effective data for planning and monitoring. Using the rocky shores of the Solitary Islands Marine Park, NSW, Australia, as a model, I evaluated macroinvertebrates and determined which taxa (i) best reflected ecological patterns of the broader intertidal community; and (ii) were able to accurately predict species richness of assemblages at the headland scale. Both molluscs and crustaceans showed high levels of correlation with overall species richness. However, molluscs, and in particular prosobranchs, most closely reflected patterns in the community data and provided the most accurate predictions of species richness at the scale of the headland. The potential time savings of using molluscs in rapid assessments are considerable and relate to reductions in field time (by up to 40%) as well as the reduced need to invest time developing extensive taxonomic knowledge of other invertebrate groups. Molluscs are widespread and easily sampled, with stable taxonomy and well-known ecology relative to other marine invertebrate taxa. Their use as surrogates of biodiversity shows great potential for future marine conservation studies.     

Colour spaces in ecology and evolutionary biology

The recognition that animals sense the world in a different way than we do has unlocked important lines of research in ecology and evolutionary biology. In practice, the subjective study of natural stimuli has been permitted by perceptual spaces, which are graphical models of how stimuli are perceived by a given animal. Because colour vision is arguably the best‐known sensory modality in most animals, a diversity of colour spaces are now available to visual ecologists, ranging from generalist and basic models allowing rough but robust predictions on colour perception, to species‐specific, more complex models giving accurate but context‐dependent predictions. Selecting among these models is most often influenced by historical contingencies that have associated models to specific questions and organisms; however, these associations are not always optimal. The aim of this review is to provide visual ecologists with a critical perspective on how models of colour space are built, how well they perform and where their main limitations are with regard to their most frequent uses in ecology and evolutionary biology. We propose a classification of models based on their complexity, defined as whether and how they model the mechanisms of chromatic adaptation and receptor opponency, the nonlinear association between the stimulus and its perception, and whether or not models have been fitted to experimental data. Then, we review the effect of modelling these mechanisms on predictions of colour detection and discrimination, colour conspicuousness, colour diversity and diversification, and for comparing the perception of colour traits between distinct perceivers. While a few rules emerge (e.g. opponent log–linear models should be preferred when analysing very distinct colours), in general model parameters still have poorly known effects. Colour spaces have nonetheless permitted significant advances in ecology and evolutionary biology, and more progress is expected if ecologists compare results between models and perform behavioural experiments more routinely. Such an approach would further contribute to a better understanding of colour vision and its links to the behavioural ecology of animals. While visual ecology is essentially a transfer of knowledge from visual sciences to evolutionary ecology, we hope that the discipline will benefit both fields more evenly in the future.     

A tale of four stories: soil ecology, theory, evolution and the publication system

Background

Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals.

Findings

We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals.

Conclusion

This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate “particularity” (empirical observations) and “generality” (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary.     

State-Dependent Changes in Auditory Sensory Gating in Different Cortical Areas in Rats

Sensory gating is a process in which the brain’s response to a repetitive stimulus is attenuated; it is thought to contribute to information processing by enabling organisms to filter extraneous sensory inputs from the environment. To date, sensory gating has typically been used to determine whether brain function is impaired, such as in individuals with schizophrenia or addiction. In healthy subjects, sensory gating is sensitive to a subject’s behavioral state, such as acute stress and attention. The cortical response to sensory stimulation significantly decreases during sleep; however, information processing continues throughout sleep, and an auditory evoked potential (AEP) can be elicited by sound. It is not known whether sensory gating changes during sleep. Sleep is a non-uniform process in the whole brain with regional differences in neural activities. Thus, another question arises concerning whether sensory gating changes are uniform in different brain areas from waking to sleep. To address these questions, we used the sound stimuli of a Conditioning-testing paradigm to examine sensory gating during waking, rapid eye movement (REM) sleep and Non-REM (NREM) sleep in different cortical areas in rats. We demonstrated the following: 1. Auditory sensory gating was affected by vigilant states in the frontal and parietal areas but not in the occipital areas. 2. Auditory sensory gating decreased in NREM sleep but not REM sleep from waking in the frontal and parietal areas. 3. The decreased sensory gating in the frontal and parietal areas during NREM sleep was the result of a significant increase in the test sound amplitude.     

Chemical information transfer between plants:: back to the future

Chemical information conveyance between organisms has been well established for a wide range of organisms including protozoa, invertebrates, vertebrates and plant-parasitic plants. During the past 20 years, various studies have addressed whether chemical information conveyance also occurs between damaged and undamaged plants and many interesting pieces of evidence have been presented. To date, this research field has been restricted to the question whether and how plants (in general) are involved in plant-to-plant communication. However, apart from mechanistic questions, evolutionary questions should be addressed asking why plants do (or do not) exploit their neighbour's information and whether their strategy is affected by e.g. environmental conditions or previous experience. Recent progress in the field of chemical information conveyance between damaged and undamaged plants warrants an intensified study of this exciting topic in chemical ecology.     

A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel

The class Prasinophyceae (Chlorophyta) contains several photosynthetic picoeukaryotic species described from cultured isolates. The ecology of these organisms and their contributions to the picoeukaryotic community in aquatic ecosystems have received little consideration. We have designed and tested eight new 18S ribosomal DNA oligonucleotide probes specific for different Prasinophyceae clades, genera, and species. Using fluorescent in situ hybridization associated with tyramide signal amplification, these probes, along with more general probes, have been applied to samples from a marine coastal site off Roscoff (France) collected every 2 weeks between July 2000 and September 2001. The abundance of eukaryotic picoplankton remained high (>10(3) cells ml(-1)) during the sampling period, with maxima in summer (up to 2 x 10(4) cells ml(-1)), and a single green algal species, Micromonas pusilla (Prasinophyceae), dominated the community all year round. Members of the order Prasinococcales and the species Bathycoccus prasinos (Mamiellales) displayed sporadic occurrences, while the abundances of all other Prasinophyceae groups targeted remained negligible.     

Thermodynamic Costs of Information Processing in Sensory Adaptation

Biological sensory systems react to changes in their surroundings. They are characterized by fast response and slow adaptation to varying environmental cues. Insofar as sensory adaptive systems map environmental changes to changes of their internal degrees of freedom, they can be regarded as computational devices manipulating information. Landauer established that information is ultimately physical, and its manipulation subject to the entropic and energetic bounds of thermodynamics. Thus the fundamental costs of biological sensory adaptation can be elucidated by tracking how the information the system has about its environment is altered. These bounds are particularly relevant for small organisms, which unlike everyday computers, operate at very low energies. In this paper, we establish a general framework for the thermodynamics of information processing in sensing. With it, we quantify how during sensory adaptation information about the past is erased, while information about the present is gathered. This process produces entropy larger than the amount of old information erased and has an energetic cost bounded by the amount of new information written to memory. We apply these principles to the E. coli''s chemotaxis pathway during binary ligand concentration changes. In this regime, we quantify the amount of information stored by each methyl group and show that receptors consume energy in the range of the information-theoretic minimum. Our work provides a basis for further inquiries into more complex phenomena, such as gradient sensing and frequency response.     

Climate change-integrated conservation strategies

Aim Conservation strategies currently include little consideration of climate change. Insights about the biotic impacts of climate change from biogeography and palaeoecology, therefore, have the potential to provide significant improvements in the effectiveness of conservation planning. We suggest a collaboration involving biogeography, ecology and applied conservation. The resulting Climate Change‐integrated Conservation Strategies (CCS) apply available tools to respond to the conservation challenges posed by climate change. Location The focus of this analysis is global, with special reference to high biodiversity areas vulnerable to climate change, particularly tropical montane settings. Methods Current tools from climatology, biogeography and ecology applicable to conservation planning in response to climate change are reviewed. Conservation challenges posed by climate change are summarized. CCS elements are elaborated that use available tools to respond to these challenges. Results Five elements of CCS are described: regional modelling; expanding protected areas; management of the matrix; regional coordination; and transfer of resources. Regional modelling uses regional climate models, biotic response models and sensitivity analysis to identify climate change impacts on biodiversity at a regional scale appropriate for conservation planning. Expansion of protected areas management and systems within the planning region are based on modelling results. Management of the matrix between protected areas provides continuity for processes and species range shifts outside of parks. Regional coordination of park and off‐park efforts allows harmonization of conservation goals across provincial and national boundaries. Finally, implementation of these CCS elements in the most biodiverse regions of the world will require technical and financial transfer of resources on a global scale. Main conclusions Collaboration across disciplines is necessary to plan conservation responses to climate change adequately. Biogeography and ecology provide insights into the effects of climate change on biodiversity that have not yet been fully integrated into conservation biology and applied conservation management. CCS provide a framework in which biogeographers, ecologists and conservation managers can collaborate to address this need. These planning exercises take place on a regional level, driven by regional climate models as well as general circulation models (GCMs), to ensure that regional climate drivers such as land use change and mesoscale topography are adequately represented. Sensitivity analysis can help address the substantial uncertainty inherent in projecting future climates and biodiversity response.     

Application of proteomics to ecology and population biology

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.