Studying crop sequences with CarrotAge,a HMM-based data mining software

We have developed a knowledge discovery system based on high-order hidden Markov models for analyzing spatio-temporal data bases. This system, named CarrotAge , takes as input an array of discrete data – the rows represent the spatial sites and the columns the time slots – and builds a partition together with its a posteriori probability. CarrotAge has been developed for studying the cropping patterns of a territory. It uses therefore an agricultural drench database, named Ter-Uti , which records every year the land-use category of a set of sites regularly spaced. The results of CarrotAge are interpreted by agronomists and used in research works linking agricultural land use and water management. Moreover, CarrotAge can be used to find out and study crop sequences in large territories, that is a main question for agricultural and environmental research, as discussed in this paper.     

A test of reproductive skew models in a field population of a multiple-queen ant

Determining the evolutionary basis of variation in reproductive skew (degree of sharing of reproduction among coexisting individuals) is an important task both because skew varies widely across social taxa and because testing models of skew evolution permits tests of kin selection theory. Using parentage analyses based on microsatellite markers, we measured skew among female eggs (n=32.3 eggs per colony, range=20–68) in 17 polygynous colonies from a UK field population of the ant Leptothorax acervorum. We used skew among eggs as our principal measure of skew because of the high degree of queen turnover in the study population. Queens within colonies did not make significantly unequal contributions to queen and worker adult or pupal offspring, indicating that skew among female eggs reflected skew among daughter queens. On average, both skew among female eggs (measured by the B index) and queen–queen relatedness proved to be low (means±SE=0.06±0.02 and 0.28±0.08, respectively). However, contrary to current skew models, there was no significant association of skew with either relatedness or worker number (used as a measure of productivity). In L. acervorum, predictions of the concession model of skew may hold between but not within populations because queens are unable to assess their relatedness to other queens within colonies. Additional phenomena that may help maintain low skew in the study population include indiscriminate infanticide in the form of egg cannibalism and split sex ratios that penalize reproductive monopoly by single queens within polygynous colonies.     

Prediction of near-field shear dispersion in an emergent canopy with heterogeneous morphology

The evaluation of longitudinal dispersion in aquatic canopies is necessary to predict the behavior of dissolved species and suspended particles in marsh and wetland systems. Here we consider the influence of canopy morphology on longitudinal dispersion, focusing on transport before constituents have mixed over depth. Velocity and longitudinal dispersion were measured in a model canopy with vertically varying canopy density. The vertical variation in canopy morphology generates vertical variation in the mean velocity profile, which in turn creates mean-shear dispersion. We develop and verify a model that predicts the mean-shear dispersion in the near field from morphological characteristics of the canopy, such as stem diameter and frontal area. Close to the source, longitudinal dispersion is dominated by velocity heterogeneity at the scale of individual stems. However, within a distance of approximately 1 m, the shear dispersion associated with velocity heterogeneity over depth increases and eclipses this smaller-scale process.     

Extrinsic and intrinsic determinants of winter foraging and breeding phenology in a temperate seabird

In temperate regions, winter presents animals with a number of challenges including depressed food abundance, increased daily energy requirements, higher frequency of extreme weather events and shortened day length. Overcoming these constraints is critical for overwintering survival and scheduling of future breeding of long-lived species and is likely to be state dependent, associated with intrinsic abilities such as food acquisition rates. We examined the relationship between environmental and intrinsic factors on overwintering foraging and subsequent breeding phenology of the European shag Phalacrocorax aristotelis, a diurnal marine predator. We tested a range of hypotheses relating to overwintering foraging time and location. We found that individuals greatly increased their foraging time in winter to a peak of more than 90% of available daylight at the winter solstice. The seasonal patterns of foraging time appear to be driven by a combination of light levels and weather conditions and may be linked to the availability of the shag's principal prey, the lesser sandeel Ammodytes marinus. There was no evidence that shags dispersed south in winter to increase potential foraging time. Foraging time decreased after the winter solstice and, crucially, was correlated with subsequent breeding phenology, such that individuals that spent less time foraging in February bred earlier. The relationship was much stronger in females than males, in line with their more direct control of timing of breeding. Our results demonstrate that pre-breeding intrinsic foraging ability is critical in determining breeding phenology.     

Hypoxia increases the behavioural activity of schooling herring: a response to physiological stress or respiratory distress?

Atlantic herring, Clupea harengus, increase their swimming speed during low O₂ (hypoxia) and it has been hypothesised that the behavioural response is modulated by the degree of “respiratory distress” (i.e. a rise in anaerobic metabolism and severe physiological stress). To test directly whether a deviation in physiological homeostasis is associated with any change in behavioural activity, we exposed C. harengus in a school to a progressive stepwise decline in water oxygen pressure and measured fish swimming speed and valid indicators of primary and secondary stress (i.e. blood cortisol, lactate, glucose and osmolality). Herring in hypoxia increased their swimming speed by 11–39% but only when was <8.5 kPa and in an unsteady (i.e. declining) state. In parallel with the shift in behaviour, plasma cortisol also exhibited an increase with plasma osmolality was subject to a transient rise at 8.5 kPa and plasma glucose was generally reduced at However, without any rise in anaerobically derived lactate levels, there was no evidence of respiratory distress at any set We show that a shift in physiological homeostasis is indeed linked with an increase in the swimming speed of herring but the physiological response reflects a hypoxia-induced shift in metabolic fuel-use rather than respiratory distress per se. The significance of this behavioural–physiological reaction is discussed in terms of behavioural-energetic trade-offs, schooling dynamics and the hypoxia tolerance of herring.     

Whole-system nutrient enrichment increases secondary production in a detritus-based ecosystem

Although the effects of nutrient enrichment on consumer-resource dynamics are relatively well studied in ecosystems based on living plants, little is known about the manner in which enrichment influences the dynamics and productivity of consumers and resources in detritus-based ecosystems. Because nutrients can stimulate loss of carbon at the base of detrital food webs, effects on higher consumers may be fundamentally different than what is expected for living-plant-based food webs in which nutrients typically increase basal carbon. We experimentally enriched a detritus-based headwater stream for two years to examine the effects of nutrient-induced changes at the base of the food web on higher metazoan (predominantly invertebrate) consumers. Our paired-catchment design was aimed at quantifying organic matter and invertebrate dynamics in the enriched stream and an adjacent reference stream for two years prior to enrichment and two years during enrichment. Enrichment had a strong negative effect on standing crop of leaf litter, but no apparent effect on that of fine benthic organic matter. Despite large nutrient-induced reductions in the quantity of leaf litter, invertebrate secondary production during the enrichment was the highest ever reported for headwater streams at this Long Term Ecological Research site and was 1.2-3.3 times higher than predicted based on 15 years of data from these streams. Abundance, biomass, and secondary production of invertebrate consumers increased significantly in response to enrichment, and the response was greater among taxa with larval life spans < or = 1 yr than among those with larval life spans >1 yr. Production of invertebrate predators closely tracked the increased production of their prey. The response of invertebrates was largely habitat-specific with little effect of enrichment on food webs inhabiting bedrock outcrops. Our results demonstrate that positive nutrient-induced changes to food quality likely override negative changes to food quantity for consumers during the initial years of enrichment of detritus-based stream ecosystems. Longer-term enrichment may impact consumers through eventual reductions in the quantity of detritus.     

Cicada emergence in Southwestern riparian forest: influences of wildfire and vegetation composition.

Annually emerging cicadas are a numerically and ecologically dominant species in Southwestern riparian forests. Humans have altered disturbance regimes that structure these forests such that floods are less common and wildfires occur more frequently than was historically the case. Impacts of these changes on primary consumers such as riparian cicadas are unknown. Because cicadas are consumed by a variety of animal species, disturbances that alter timing of their emergence or abundance could have consequences for species at higher trophic levels. We trapped emerging cicadas (Tibicen dealbatus) in burned and unburned riparian forest plots along the Middle Rio Grande in central New Mexico (USA) to determine effects of wildfire and vegetation structure on their density and phenology. We measured vegetation variables and soil temperature at cicada traps and related these variables to variation in emergence density and phenology. We also experimentally heated soil under emergence traps to examine the relationship between soil temperature and emergence phenology. Emergence density was similar in wildfire and unburned plots, though emergence date averaged earlier in wildfire plots and experimentally heated traps. We identified models containing cottonwood proximity (distance from the nearest cottonwood tree) and cottonwood canopy coverage as the most parsimonious explanations of emergence density at each trap. Model selection results were consistent with the literature and field observations that showed that cottonwood trees are an essential resource for T. dealbatus. Cottonwood canopy was also correlated with low soil temperatures, which are associated with later emergence dates. Failure of cottonwoods to reestablish following wildfire could result in cicadas emerging at lower densities and at earlier dates. For cicadas to emerge at densities and times that provide the greatest benefits to birds and other riparian-obligate secondary consumers, riparian forests should be protected from fire, and native vegetation in wildfire sites should be restored.     

Riparian shading and groundwater enhance growth potential for smallmouth bass in Ozark streams.

Moderation of stream temperatures by riparian shading and groundwater are known to promote growth and survival of salmonid fishes, but effects of riparian shade and groundwater on to be growth of warmwater stream fishes are poorly understood or assumed to be negligible. We used stream temperature models to relate shading from riparian vegetation and groundwater inflow to summer water temperatures in Missouri Ozark streams and evaluated effects of summer water temperatures on smallmouth bass, Micropterus dolomieu, growth using a bioenergetics model. Bioenergetics model simulations revealed that adult smallmouth bass in non-spring-fed streams have lower growth potential during summer than fish in spring-fed streams, are subject to mass loss when stream temperatures exceed 27 degrees C, and will likely exhibit greater interannual variation in growth during summer if all growth-influencing factors, other than temperature, are identical between the two stream types. Temperature models indicated that increased riparian shading will expand the longitudinal extent of thermal habitat capable of supporting adult smallmouth bass growth in spring-fed stream reaches when mean daily air temperatures exceed 27 degrees C. Optimum growth temperature (22 degrees C) will be present only in spring-fed streams under these conditions. Potential for increasing shade through riparian restoration is greatest for streams <5 m wide and along north-south reaches of larger streams. However, temperature models also indicated that restoring riparian shading to maximum levels throughout a watershed would increase the total stream mileage capable of supporting positive growth of adult smallmouth bass by only 1-6% when air temperatures are at or near average summer maxima; increases in suitable thermal habitat would be greatest in watersheds with higher spring densities. Riparian management for maintenance or restoration of the thermal habitat of adult smallmouth bass during summer should be focused in areas strongly influenced by groundwater. Restoring riparian shading along spring-fed warmwater streams will likely benefit adult smallmouth bass growth and may ultimately influence population sizes.