Computational visual ecology in the pelagic realm

Visual performance and visual interactions in pelagic animals are notoriously hard to investigate because of our restricted access to the habitat. The pelagic visual world is also dramatically different from benthic or terrestrial habitats, and our intuition is less helpful in understanding vision in unfamiliar environments. Here, we develop a computational approach to investigate visual ecology in the pelagic realm. Using information on eye size, key retinal properties, optical properties of the water and radiance, we develop expressions for calculating the visual range for detection of important types of pelagic targets. We also briefly apply the computations to a number of central questions in pelagic visual ecology, such as the relationship between eye size and visual performance, the maximum depth at which daylight is useful for vision, visual range relations between prey and predators, counter-illumination and the importance of various aspects of retinal physiology. We also argue that our present addition to computational visual ecology can be developed further, and that a computational approach offers plenty of unused potential for investigations of visual ecology in both aquatic and terrestrial habitats.     

The mycorrhizal colonization of six wetland plant species at sites differing in land use history

 Five wetland prairie sites and six native plant species in western Oregon were examined to determine patterns of vesicular-arbuscular mycorrhizal fungal (VAMF) colonization. The sites differed in type and intensity of past land use. VAMF colonization was tested in situ on seedlings from both field-sown seeds and from transplants. Colonization was measured as the percentage of root length with arbuscles or vesicles. All species (Deschampsia cespitosa, Downingia elegans, Eriophyllum lanatum, Hordeum brachyantherum, Microseris laciniata, and Plagiobothrys figuratus) became colonized by VAMF during the study. This is the first report of mycorrhizal colonization of these important native species. All sites supported mycorrhizal colonization of some of the experimental species. Average VAMF colonization ranged from 58% to 92% but was unrelated to subjective rankings of land use intensity. These results suggest that VAMF inoculum at all sites was sufficient to support revegetation by at least some species of native plants. Accepted: 16 September 1999     

Colonization of the pelagic realm by calanoid copepods

The evolution of calanoid copepods probably extends back into the mid-Paleozoic. Environmental change from the Paleozoic through to the Tertiary is reviewed. Turbidity, water clarity, oxygen, pelagic primary production, and tectonically induced changes in the morphology of the oceans are probably all important drivers of calanoid evolution and their invasion of the pelagic realm. Current views of the phylogeny of the Calanoida are presented as well as a review of some recent work on metabolic potential, female genital system, and nervous system. It is hypothesized that ancestors of the Arietelloidea and Diaptomoidea invaded the water column in the Devonian at a similar time to the Ostracoda and that the ancestors of the Calanoidea–Clausocalanoidea, with their myelinated axons, arose in the Permian during the major deep ventilation of the ocean. Present day distributions of some Diaptomidae, Centropagidae, and Calanidae suggest that these families successfully came through the Jurassic/Cretaceous expansion of the oxygen minimum zone and the K-T boundary event. Some Arietelloidea and Clausocalanoidea became secondarily benthic and may have survived the K-T boundary event in this environment. It is postulated that some Clausocalanoidea reinvaded the water column (e.g. Clausocalanidae, Aetideidae, Phaennidae, Scolecitrichidae) in the Tertiary after finding refuge in deep, low oxygen water away from the sea surface. It is possible that these hypotheses may be testable using genetic information in the near future.     

Early evolutionary origin of the planktic foraminifera inferred from small subunit rDNA sequence comparisons

Phylogenetic analysis of five partial planktic foraminiferal small subunit (SSU) ribosomal (r) DNA sequences with representatives of a diverse range of eukaryote, archaebacterial, and eubacterial taxa has revealed that the evolutionary origin of the foraminiferal lineage precedes the rapid eukaryote diversification represented by the crown of the eukaryotic tree and probably represents one of the earliest splits among extant free-living aerobic eukaryotes. The foraminiferal rDNA sequences could be clearly separated from known symbionts, commensals, and food organisms. All five species formed a single monophyletic group distinguished from the crown group by unique foraminiferal specific insertions as well as considerable nucleotide distance in aligned regions.     

Molecular adaptation and the origin of land plants

The origin and diversification of land plants was one of the most important biological radiations. Land plants are crucial components of all modern terrestrial ecosystems. The first land plants had to adapt to a wide array of new environmental challenges including desiccation, varying temperatures, and increased UV radiation. There have been numerous studies of the morphological adaptations to life on land. However the molecular adaptations to life on land have only recently gained attention. These studies have greatly benefited from the recent advances in our understanding of the phylogenetic relationships between and among the charophycean algae and the basal land plant groups. In this review I summarize the current knowledge of a variety of physiological and biochemical adaptations to land including plant growth hormones, isoprene, phenolics, and heat shock proteins.     

A comparison of visualization techniques for recording arbuscular mycorrhizal colonization

The extent of arbuscular mycorrhizal colonization was assessed in 10 field-collected plant species, representing three annual forbs, three perennial forbs, three perennial grasses and one annual grass. Each root system of each plant was split into four portions, and for each portion, mycorrhizal structures were revealed with epifluorescence microscopy (under which only arbuscules are generally visible) and three commonly used stains (Chlorazol Black E, Acid Fuchsin and Trypan Blue). The aim of the study was not to evaluate the efficacy of each method, but to compare results obtained by each under standard laboratory conditions. The recorded colonization levels of arbuscules, total arbuscular mycorrhizal fungal material and total fungal (arbuscular mycorrhizal+non-arbuscular mycorrhizal) material differed significantly between visualization methods in a number of species. However, there were also interactions between stain and plant species, indicating that the performance of a stain is dependent on the plant species being examined. In some cases (e.g. Plantago lanceolata ), each visualization method produced the same colonization level, while in others (e.g. Dactylis glomerata ), each method gave a different result. These data therefore suggest that the level of mycorrhizal colonization recorded in any particular plant species at a particular time is dependent on the technique employed.     

A comparison of vascular vegetation and protozoan communities in some freshwater wetlands of Northern Lower Michigan

Vascular vegetation and protozoan communities were sampled in seven wetland sites — two bogs, two fens, two marshes, and one swamp — in summer 1977. Two similarity indices were used to compare vascular vegetation and Protozoa from each site with all the other sites. Bog sites were the most distinct from other wetland types with respect to chemical and physical characteristics, dominant vascular vegetation, and protozoan species composition. The swamp site had the highest similarity to all other sites with respect to both dominant vascular vegetation and protozoan species. Protozoan communities from different wetland types were much more similar than dominant vascular species; however, the pattern of similarity between wetland sites was very similar for both groups (Pearson product-moment correlation coefficient = 0.76).Protozoan communities were also compared with those from several nearby lakes with respect to colonization rate onto polyurethane foam artificial substrates. The structure and dynamics of protozoan communities of wetlands were broadly different from those of other freshwaters, and somewhat unique to the other wetland types. Evidence for a high degree of eutrophy in certain bog lakes is presented.     

A review of Morphological and Behavioural Changes in the Cave Molly, Poecilia Mexicana, from Tabasco, Mexico

The poeciliid fish Poecilia mexicana successfully colonised a sulfur cave in Tabasco, Mexico. The eye size, melanin pigmentation and scale tuberances as well as aggressive and schooling behaviour are reduced in the cave fish. Besides these regressive characters some constructive ones have been found. The genital region of the female is enlarged to a genital pad and in both sexes the number of taste buds is considerably increased on the upper side of the head. The cephalic lateral line shows a hyperdevelopment with an incomplete covering of some channels. Nearly all of these characters studied form a genetically based gradient from the beginning to the end of the cave, which seems to be the result of gene flow from the outside to the inner part of the cave. A special behavioural adaptation was found among females which prefer bigger males during courtship. In darkness, only the cave females show this preference.     

A prolegomenon to nonlinear empiricism in the human behavioral sciences

We propose a general framework for integrating theory and empiricism in human evolutionary ecology. We specifically emphasize the joint use of stochastic nonlinear dynamics and information theory. To illustrate critical ideas associated with historical contingency and complex dynamics, we review recent research on social preferences and social learning from behavioral economics. We additionally examine recent work on ecological approaches in history, the modeling of chaotic populations, and statistical application of information theory.     

A comparison of autoclaved and gamma-irradiated soils as media for microbial colonization experiments

Summary The effects on various properties of Lincoln Clay of a sterilizing dose of gamma radiation (3.0 megarads) were compared to the effects resulting from autoclaving the soil (121°C) for 1 hour. Effects of both treatments were much more drastic when moist, rather than air-dry soil was treated but, in general, radiation had less effect on soluble organic matter and on total water-extractable electrolyte than did autoclaving. Radiation caused a greater release of NH₄-N from soil treated moist than did autoclaving but the reverse was true in dry soil. Alcohol-soluble ninhydrin-positive material was increased by both sterilization procedures with irradiation having the greater effect. The aggregate stability of Lincoln clay was decreased by irradiation and increased by autoclaving.Pure cultures of bothArthrobacter sp. andPseudomonas sp. grew better, on the basis of cell yields, in irradiated than in autoclaved soil. Respiration of mixed soil organisms in an artificial soil amended with an extract of irradiated soil was almost identical with that in an extract of air-dried soil but auto-claved soil extract was only metabolized after a prolonged lag period.This work was supported by grant # A 1702 from the National Research Council of Canada, Ottawa, Canada.     

A comparison of the efficiencies of the shotgun and the bow in neotropical forest hunting

Whenever introduced into Amazonia and its neighboring regions, the shotgun has quickly replaced the bow and arrow and other aboriginal weapons of the hunt. The quick and widespread adoption of the shotgun is plainly a matter of its superiority over most aboriginal weapons. This paper compares the hunting efficiencies of the shotgun and the bow by means of a controlled field experiment among the Ye'kwana and Yanomamö Indians of the Upper Orinoco River of southern Venezuela. It also examines the impact of the shotgun on local animal populations and the economic changes brought about by the need to cash-crop in order to purchase Western hunting technology.Funds for the research and writing of this paper were made possible by an NIMH predoctoral fellowship to Napoleon A. Chagnon, Grant No. NIMH 5 R01 MH 26008-SSR.     

A conspectus of the Cladocera of the subterranean waters of the world

A synthesis of current knowledge of the Cladocera living in non-surface waters is provided. For all 94 species and subspecies recorded (Dec. 1994) we give information on their ranges, ecological characteristics, and a review of literature data. We also give a historic survey of the development of concepts, identify categories among groundwater-dwelling species, and discuss their adaptations and the evolutionary lines present. Of the estimated total of c. 450 non-marine Cladocera of the world, c. 20% may occur in underground aquatic habitats, but true groundwater forms (stygobionts or stygobites) are relatively few, possibly not more than 10 species (c. 2.5% of the total). This number may increase, as attention is given to subterranean habitats outside Europe.     

A comparison of the electrosensory morphology of a euryhaline and a marine stingray

The electrosensory system is found in all chondrichthyan fishes and is used for several biological functions, most notably prey detection. Variation in the physical parameters of a habitat type, i.e. water conductivity, may influence the morphology of the electrosensory system. Thus, the electrosensory systems of freshwater rays are considerably different from those of fully marine species; however, little research has so far examined the morphology and distribution of these systems in euryhaline elasmobranchs. The present study investigates and compares the morphology and distribution of electrosensory organs in two sympatric stingray species: the (euryhaline) estuary stingray, Dasyatis fluviorum, and the (marine) blue-spotted maskray, Neotrygon kuhlii. Both species possess a significantly higher number of ventral electrosensory pores than previously assessed elasmobranchs. This correlates with a diet consisting of benthic infaunal and epifaunal prey, where the electrosensory pore distribution patterns are likely to be a function of both ecology and phylogeny. The gross morphology of the electrosensory system in D. fluviorum is more similar to that of other marine elasmobranch species, rather than that of freshwater species. Both D. fluviorum and N. kuhlii possess ‘macro-ampullae’ with branching canals leading to several alveoli. The size of the pores and the length of the canals in D. fluviorum are smaller than in N. kuhlii, which is likely to be an adaptation to habitats with lower conductivity. This study indicates that the morphology of the electrosensory system in a euryhaline elasmobranch species seems very similar to that of their fully marine counterparts. However, some morphological differences are present between these two sympatric species, which are thought to be linked to their habitat type.     

The quest for a unified view of bacterial land colonization

Exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. We hypothesize that bacterial land colonization is dominated by a single-gene sweep, that is, the emergence of dnaE2 derived from an early duplication event of the primordial dnaE, followed by a series of niche-specific genomic adaptations, including GC content increase, intensive horizontal gene transfer and constant genome expansion. In addition, early bacterial radiation may be stimulated by an explosion of land-borne hosts (for example, plants and animals) after initial land colonization events.     

M.M. Kamshilov and Plankton Investigations in the Murmansk Region

In this paper, the results of plankton investigations from 1952 to 2000 in the Barents and Kara seas by the Laboratory of Plankton of the Murmansk Marine Biological Institute (Kola Branch, Russian Academy of Sciences) are briefly outlined. The development of ideas on the seasonal and long-term succession of plankton communities in the Barents Sea, which were propounded by M.M. Kamshilov, the founder of the Plankton Laboratory, is shown.     

Evolution and stability of the G-matrix during the colonization of a novel environment

Populations that undergo a process of rapid evolution present excellent opportunities to investigate the mechanisms driving or restraining adaptive divergence. The genetic variance-covariance matrix (G) is often considered to constrain adaptation but little is known about its potential to evolve during phenotypic divergence. We compared the G-matrices of ancestral and recently established ecotype populations of an aquatic isopod (Asellus aquaticus) that have diverged in parallel in two south Swedish lakes. Phenotypic changes after colonization involved a reduction in overall size, lost pigmentation and changes in shape. Comparisons between G-matrices reveal close similarity within the same ecotype from different lakes but some degree of differentiation among ecotypes. Phenotypic divergence has apparently not been much influenced by the orientation of G. Additive genetic variation in the newly colonized habitats has also decreased substantially. This suggests that a process of adaptation from standing genetic variation has occurred and has probably facilitated phenotypic divergence.     

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis,phototrophy, and the colonization of land

Background  

The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method.