Data-Mining Discovery of Pattern and Process in Ecological Systems

ABSTRACT Most ecologists use statistical methods as their main analytical tools when analyzing data to identify relationships between a response and a set of predictors; thus, they treat all analyses as hypothesis tests or exercises in parameter estimation. However, little or no prior knowledge about a system can lead to creation of a statistical model or models that do not accurately describe major sources of variation in the response variable. We suggest that under such circumstances data mining is more appropriate for analysis. In this paper we 1) present the distinctions between data-mining (usually exploratory) analyses and parametric statistical (confirmatory) analyses, 2) illustrate 3 strengths of data-mining tools for generating hypotheses from data, and 3) suggest useful ways in which data mining and statistical analyses can be integrated into a thorough analysis of data to facilitate rapid creation of accurate models and to guide further research.     

Geographical and seasonal gradients in hatching failure in Eastern Bluebirds Sialia sialis reinforce clutch size trends

Eggs untended during the laying phase can lose viability if exposed to high temperatures, such as those common at lower latitudes and late in the nesting season. The egg‐viability hypothesis states that constraints on viability during the laying phase could account for latitudinal and seasonal gradients in clutch size. We used 7 years’ worth of data collected by volunteers (The Birdhouse Network, co‐ordinated by the Cornell Laboratory of Ornithology) to look simultaneously at populations across the temperate breeding range of Eastern Bluebirds Sialia sialis in order to test three predictions of the egg‐viability hypothesis: the probability of hatching failure decreases at higher latitude and increases later in the season, and that these trends are strongest among large clutches. The overall average number of unhatched eggs relative to the total number of eggs laid was similar to that found by other studies (7.8%; range 6.8–8.9% annually; n = 32 567 eggs from 7231 nests from 530 study sites). Using generalized linear mixed models that controlled for the non‐independence of eggs within a clutch, we found that the ‘per‐egg’ probability of hatching failure was highest late in the season, highest at lower latitudes, and highest for both small (three‐egg) and large (six‐egg) clutches. The seasonal and geographical gradients in egg hatching failure reinforce documented seasonal and geographical trends in clutch size. Loss of egg viability prior to incubation currently provides the most parsimonious and consistent explanation of the observed patterns of hatching failure. However, alternative explanations for large‐scale patterns, particularly those not consistent with the egg‐viability hypothesis, warrant further research into other causes of hatching failure, such as microbes and infertility (related to extra‐pair mating). Our results demonstrate that investigating causes of variation in demography among local populations across a geographical gradient provides a potential means of identifying selection pressures on life‐history traits.     

Oxygen--A Key Regulatory Metabolite in Metabolic Defense Against Hypoxia

Two main defense strategies against hypoxia tolerant animalshave been identified in earlier studies: (i) reduction in energyturnover and (ii) improved energetic efficiency of those metabolicprocesses that remain. Two model systems were developed fromthe highly anoxia tolerant aquatic turtle—(i) tissue slicesof brain cortex (to probe cell level electrophysiological responsesto oxygen limitation) and (ii) isolated liver hepatocytes (toprobe signalling and defense). In the latter, a series of mechanismsunderpinning hypoxia defense is initiated with an oxygen sensor(probably a heme protein) and a message transduction pathwayleading to the specific activation of some genes (increasedexpression of several proteins) and to specific down regulationof other genes (decreased expression of several other proteins).The pathway seems similar to oxygen regulated schemes in othercells. The main roles for the oxygen sensing and signal transductionsystem appear to include coordinate down regulation of energydemand and energy supply pathways in metabolism. By this means,hypoxia tolerant cells stay in energy balance as they down regulateto extremely low levels of ATP turnover. The main ATP demandpathways in normoxia (protein synthesis, protein degradation,glucose synthesis, urea synthesis, and maintenance of electrochemicalgradients) are all depressed to variable degree during anoxiaor extreme hypoxia. However, Na⁺ K⁺ ATPase is the main energysink in anoxia—despite significant reductions in cellmembrane permeability ("channel arrest"). Turtle brain corticalcells also show lower permeability than do homologous hypoxiasensitive cells, but in this case under acute anoxia, thereis no further change in cell membrane conductivity. These twomodels may supply guidelines for further studies of estuarineanimals on how normoxic maintenance ATP turnover rates can bedown regulated by an order of magnitude or more—to newhypometabolic steady states prerequisite for surviving prolongedhypoxia or anoxia     

The Adaptation of Enzymes to Pressure II. A Comparison of Muscle Pyruvate Kinases from Surface and Midwater Fishes with the Homologous Enzyme from an Off-Shore Benthic Species

SYNOPSIS. Pyruvate kinase (PK) maximum catalytic rate is dramaticallydecelerated by increasing hydrostatic pressure. In four differentspecies inhabiting different portions of the water column, musclepyruvate kinase displays (1) a reduction in the volume changeof activation, V*. a t higher temperatures, (2) a pH independenceof V*, and (3) a general increase in the activation energy atincreased pressures. Although shared by the four different pyruvatekinases examined, none of these characteristics is criticallyinvolved in the regulation of PK catalysis. In contrast, pressureeffects on another set of characteristics, all vitally importantto control of PK catalytic function, depend upon the speciesorigin of the enzyme. In the case of the rainbow trout, Salmogairdneri, high pressure dramatically reduces pyruvate kinaseaffinities for the two substrates (PEP and ADP), the cationiccofactor (Mg²⁺), and the negative modulator (ATP). The homologousmuscle enzyme from Oligoplites mundus, another surface dwellingspecies, displays similar responses to pressure. On the otherhand, muscle PK affinities for the same key regulatory ligandsare much less pressure sensitive in the abyssal rattail fishes(Coryphaenoides sp.) and are essentially pressure independentin a vertically migrating midwater sea bass, Ectreposebastesimus. In these latter two species, PK catalytic rates underprobable physiological conditions are determined largely bythese kinetic properties rather than by energy-volume parameters.     

The Adaptation of Enzymes to Pressure I. A Comparison of Trout Liver Fructose Diphosphatase with the Homologous Enzyme from an Off-Shore Benthic Fish

SYNOPSIS. At low temperature (3°C), in the absence of substrateand cofactor, trout liver fructose diphosphatase (FDPase) isinactivated by exposures to relatively low pressures. FDP andMg²⁺ protect against this inactivation; hence, maximum catalysisat pH 7.5 is pressure insensitive, while at more alkaline pH,it is markedly accelerated by pressure. The volume change ofactivation, V*, at saturating FDP and Mg²⁺ concentrations isabout –40 cm₃/mole. The apparent Km for FDP and the Kafor Mg²⁺ are markedly increased by pressure. At low FDP or Mg²⁺levels these kinetic properties outweigh V* in determining thereaction rate; hence, under these conditions, piessure retardscatalysis. Similarly, the K₄ for AMP is notably pressure sensitive.Comparable effects of pressure on the kinetic constants forliver FDPase from benthic Corypliaenoides are much less pronounced,suggesting that in these off-shore species enzyme-substrate,enzyme-cofactor, and enzyme-modulator interactions have beentailored through evolution for pressure independent catalyticfunction.     

Effects of Hydrostatic Pressure on Catalysis by Different Lactate Dehydrogenase Isozymes from Tissues of an Abyssal Fish

SYNOPSIS. The predominant lactate dehydrogenases (LDH's) occurringin liver, heart, and muscle of a benthic Coryphaenoides speciesare electrophoretically distinguishable from each other. Maximumrates of pyruvate reduction catalyzed by heart and muscle LDH'sshow an optimum pH near neutrality, while liver LDH activitydisplays an unusual alkaline pH optimum. Pyruvate saturationcurves are Michaelis-Menten in form for all three preparations.Maximum catalytic rates and the apparent K_m (pyruvate) are pressureindependent for liver and heart LDH's. In the case of muscleLDH's, the maximum catalytic rate is also pressure insensitive,but the K_m is dramatically increased by pressure. These experimentsdearly indicate that, at low substrate concentrations, the preciseeffects of pressure on enzyme-catalyzed reactions depend uponthe nature and origin of the catalyst.     

Effects of Pressure and Temperature on the Catalytic and Regulatory Properties of Muscle Pyruvate Kinase from an Off-Shore Benthic Fish

SYNOPSIS. Muscle pyruvate kinase from an abyssal Coryphaenoidesspecies occurs as a single electrophoretic form with an isoelectricpoint of about pH 6.0. Maximum catalytic rates are dramaticallyreduced by pressure. For catalysis at 3°C, the volume changeof activation, V*, is about 44 cm³/mole (calculated between14.7 and 8000 psi). The value ot V* decreases at higher temperaturesbut is pH independent. The activation energy for rattail musclepyruvate kinase at 14.7 psi is about 13 Kcal/mole and doublesat 12,000 psi. Mg²⁺ saturation kinetics involve positive site-siteinteractions. Hill plots yield n values of about 2.4 and K_avalues of about 2 mM (at 3°C), and these constants are pressureindependent. The K_m values for ADP increase slightly with pressure.PEP saturation curves are complex: at high PEP concentrations,the n values are about 2–2.5, while at low PEP levels,values for the Hill constant are about 1.0. The Hill constantlor PEP is not affected by pressure, but the apparent K_m increasessomewhat with pressure. FDP dramatically activates rattail musclepyruvate kinase (500% activation with 0.1 mM FDP) by (1) reducingthe K_mPEP, (2) increasing the maximum velocity, and (3) overridingnegative ATP modulation of the enzyme. The latter control featureis strictly dependent upon pressure and is not observed at lowpressure. In the presence of FDP, the K_m for PEP decreases athigh pressures, in this way counteracting the inhibitory effectsof pressure. Under low concentrations of substrates, pyruvatekinase activity is probably determined by its kinetic propertiesand not by energy-volume relationships.     

Animal Life Without Oxygen: Basic Biochemical Mechanisms

A variety of animals are now known to be facultative anaerobes,capable of utilizing molecular oxygen when it is present andcapable of sustained anaerobiosis when it is absent. Duringanoxia these organisms rely upon the simultaneous catabolismof carbohydrate and amino acids. In probing the mechanisms utilized,this essay accounts for (1) the maintenance of redox balanceduring anoxia, (2) the sources of energy in the form of ATP,and (3) the formation of a multiplicity of anaerobic end products.     

Effects of Hydrostatic Pressure on Catalysis by Epaxial Muscle Phosphofructokinase from an Abyssal Fish

SYNOPSIS: Phosphofructokinase (PFK) extracted from muscle ofabyssal Coryphaenoides fishes common in the deep waters aroundthe Galápagos Archipelago is extremely unstable upondecompression and extraction and can be recovered only in lowactivities. Preliminary studies indicate that the pressure responsesof the enzyme are complex: At low pressures, the enzyme is activated;at moderate pressures, activity passes through a pressure optimum;at high pressures, maximum catalytic activity is decelerated.At low pressures, the volume change of activation is about –11cm³/mole at 3°C and increases to about –46 cm³/moleat 28°C. The homologous enzyme from a surface species (Oligoplitesmundus) appears to be more pressure sensitive at low temperatures.     

Biochemical Adaptation to the Environment

SYNOPSIS. Biochemical adaptation to environmental parameterssuch as temperature appears to involve two distinct types ofchanges in the organism's chemistry. On the one hand, the quantitiesof certain molecular species present in the cells may change.Alternatively, the actual types of molecules present may vary.Rainbow trout (Salmo gairdneri) acclimated to warm and coldtemperatures exhibit a striking example of this latter typeof adaptation. For all enzymes we have examined in this species,distinct "warm" and "cold" isozymes are present. The isozymesfound in warmacclimated (18°C) trout function well onlyat temperatures above 10–12°C. The isozymes presentin cold-acclimated (4°C) trout function optimally at 2-5°C,temperatures this species normally encounters in winter. Thesedata, plus information on comparable changes in membrane lipids,lead us to propose that adult poikilotherms may undergo a considerabledegree of "biochemical restructuring" on a seasonal basis. Thefactors which control this "restructuring," and the rates atwhich the process occurs at high and low temperatures, are topicsfor future investigation.