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.     

Sand stress as a non-determinant of habitat segregation of indigenous (Perna perna) and invasive (Mytilus galloprovincialis) mussels in South Africa

Periodical sand inundation influences diversity and distribution of intertidal species throughout the world. This study investigates the effect of sand stress on survival and on habitat segregation of the two dominant mussel species living in South Africa, the invasive Mytilus galloprovincialis and the indigenous Perna perna. P. perna occupies a lower intertidal zone which, monthly surveys over 1.5 years showed, is covered by sand for longer periods than the higher M. galloprovincialis zone. Despite this, when buried under sand, P. perna mortality rates were significantly higher than those of M. galloprovincialis in both laboratory and in field experiments. Under anoxic condition, P. perna mortality rates were still significantly higher than those for M. galloprovincialis, but both species died later than when exposed to sand burial, underlining the importance of the physical action of sand on mussel internal organs. When buried, both species accumulate sediments within the shell valves while still alive, but the quantities are much greater for P. perna. This suggests that P. perna gills are more severely damaged by sand abrasion and could explain its higher mortality rates. M. galloprovincialis has longer labial palps than P. perna, indicating a higher particle sorting ability and consequently explaining its lower mortality rates when exposed to sand in suspension. Habitat segregation is often explained by physiological tolerances, but in this case, such explanations fail. Although sand stress strongly affects the survival of the two species, it does not explain their vertical zonation. Contrary to our expectations, the species that is less well adapted to cope with sand stress maintains dominance in a habitat where such stress is high. GI Zardi, KR Nicastro contributed equally to the work     

Integrating quality and quantity of mutualistic service to contrast ant species protecting Ferocactus wislizeni

Generalized, facultative mutualisms are often characterized by great variation in the benefits provided by different partner species. This variation may be due to differences among species in the quality and quantity of their interactions, as well as their phenology. Many plant species produce extrafloral nectar, a carbohydrate-rich resource, to attract ant species that can act as "bodyguards" against a plant's natural enemies. Here, we explore differences in the quality and quantity of protective service that ants can provide a plant by contrasting the four most common ant visitors to Ferocactus wislizeni, an extrafloral nectary-bearing cactus in southern Arizona. The four species differ in abundance when tending plants, and in the frequency at which they visit plants. By adding surrogate herbivores (Manduca sexta caterpillars) to plants, we demonstrate that all four species recruit to and attack potential herbivores. However, their per capita effectiveness in deterring herbivores (measured as the inverse of the number of workers needed to remove half of the experimentally added caterpillars) differs. Using these among-species differences in quality (per capita effectiveness) and quantity (number of workers that visit a plant and frequency of visitation), we accurately predicted the variation in fruit production among plants with different histories of ant tending. We found that plant benefits (herbivore removal and maturation of buds and fruits) typically saturated at high levels of ant protection, although plants could be "well defended" via different combinations of interaction frequency, numbers of ant workers per interaction, and per capita effects. Our study documents variation among prospective mutualists, distinguishes the components of this variation, and integrates these components into a predictive measure of protection benefit to the plant. The method we used to average saturating benefits over time could prove useful for quantifying overall service in other mutualisms.     

Demography of northern flying squirrels informs ecosystem management of western interior forests.

We studied northern flying squirrel (Glaucomys sabrinus) demography in the eastern Washington Cascade Range to test hypotheses about regional and local abundance patterns and to inform managers of the possible effects of fire and fuels management on flying squirrels. We quantified habitat characteristics and squirrel density, population trends, and demography in three typical forest cover types over a four-year period. We had 2034 captures of flying squirrels over 41 000 trap nights from 1997 through 2000 and marked 879 squirrels for mark-recapture population analysis. Ponderosa pine (Pinus ponderosa) forest appeared to be poorer habitat for flying squirrels than young or mature mixed-conifer forest. About 35% fewer individuals were captured in open pine forest than in dry mixed-conifer Douglas-fir (Pseudotsuga menziesii) and grand fir (Abies grandis) forests. Home ranges were 85% larger in pine forest (4.6 ha) than in mixed-conifer forests (2.5 ha). Similarly, population density (Huggins estimator) in ponderosa pine forest was half (1.1 squirrels/ha) that of mixed-conifer forest (2.2 squirrels/ha). Tree canopy cover was the single best correlate of squirrel density (r = 0.77), with an apparent threshold of 55% canopy cover separating stands with low- from high-density populations. Pradel estimates of annual recruitment were lower in open pine (0.28) than in young (0.35) and mature (0.37) forest. High recruitment was most strongly associated with high understory plant species richness and truffle biomass. Annual survival rates ranged from 45% to 59% and did not vary among cover types. Survival was most strongly associated with understory species richness and forage lichen biomass. Maximum snow depth had a strong negative effect on survival. Rate of per capita increase showed a density-dependent response. Thinning and prescribed burning in ponderosa pine and dry mixed conifer forests to restore stable fire regimes and forest structure might reduce flying squirrel densities at stand levels by reducing forest canopy, woody debris, and the diversity or biomass of understory plants, truffles, and lichens. Those impacts might be ameliorated by patchy harvesting and the retention of large trees, woody debris, and mistletoe brooms. Negative stand-level impacts would be traded for increased resistance and resilience of dry-forest landscapes to now-common, large-scale stand replacement fires.     

Nutrient subsidies to belowground microbes impact aboveground food web interactions

Historically, terrestrial food web theory has been compartmentalized into interactions among aboveground or belowground communities. In this study we took a more synthetic approach to understanding food web interactions by simultaneously examining four trophic levels and investigating how nutrient (nitrogen and carbon) and detrital subsidies impact the ability of the belowground microbial community to alter the abundance of aboveground arthropods (herbivores and predators) associated with the intertidal cord grass Spartina alterniflora. We manipulated carbon, nitrogen, and detrital resources in a field experiment and measured decomposition rate, soil nitrogen pools, plant biomass and quality, herbivore density, and arthropod predator abundance. Because carbon subsidies impact plant growth only indirectly (microbial pathways), whereas nitrogen additions both directly (plant uptake) and indirectly (microbial pathways) impact plant primary productivity, we were able to assess the effect of both belowground soil microbes and nutrient availability on aboveground herbivores and their predators. Herbivore density in the field was suppressed by carbon supplements. Carbon addition altered soil microbial dynamics (net potential ammonification, litter decomposition rate, DON [dissolved organic N] concentration), which limited inorganic soil nitrogen availability and reduced plant size as well as predator abundance. Nitrogen addition enhanced herbivore density by increasing plant size and quality directly by increasing inorganic soil nitrogen pools, and indirectly by enhancing microbial nitrification. Detritus adversely affected aboveground herbivores mainly by promoting predator aggregation. To date, the effects of carbon and nitrogen subsidies on salt marshes have been examined as isolated effects on either the aboveground or the belowground community. Our results emphasize the importance of directly addressing the soil microbial community as a factor that influences aboveground food web structure by affecting plant size and aboveground plant nitrogen.     

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.     

Soleidae macroparasites along the Portuguese coast: latitudinal variation and host–parasite associations

Parasite assemblages are increasingly being used as indicators of their hosts’ biology and ecology, especially for economically important marine species such as the Soleidae. In this study, seven species inhabiting Portuguese coastal waters were examined for external and internal macroparasite infections using standard procedures: Dicologlossa cuneata, Microchirus azevia, Microchirus variegatus, Solea lascaris, Solea senegalensis, Solea solea and Synaptura lusitanica. Despite being closely related, these species present different life history patterns and ecological preferences which were expected to be mirrored by their macroparasite assemblages. The aim of the study was, therefore, to study the variation of these assemblages, within and between host species, along the Portuguese coast in order to evaluate the importance of the hosts’ features and environmental factors in the assemblage compositions. Flatfish were obtained seasonally from commercial fishing vessels operating in three areas (northern, central and southern) along the Portuguese coast. Prevalence and mean abundance were calculated and tested for differences between host sex, areas and seasons. The host specificity index and the importance of the host–parasite relationship were computed based on mean abundance. The total number of parasite individuals, species richness, total prevalence, total mean abundance, diversity and evenness were also calculated. A canonical correspondence analysis (CCA) was performed using prevalence and mean abundance data. A total of 44 macroparasite species were found. No significant differences were observed in prevalence and mean abundance between sexes and sampling seasons but, for three of the parasite species, significant differences were found between areas. The highest values of the parasitological and ecological indices were generally registered in the hosts S. lascaris and S. senegalensis and in the southern area. The CCA using the prevalence data revealed the differentiation of S. lascaris samples, which was mainly related to the total prevalence and to the number of important species of macroparasites. When using mean abundance data, the CCA revealed the differentiation of D. cuneata from the south, S. lascaris from the three areas and S. senegalensis from the south, mainly related to total prevalence and richness. The differences found between infection levels and assemblages’ composition were mainly due to differences in hosts’ diet, namely prey type consumption, given that most macroparasites found were transmitted through the food web. However, environmental factors were also important given that they regulate the distribution of ectoparasites and the availability of prey, and therefore the infections’ pattern. These findings were in agreement with the ones from similar studies performed in other species, revealing the importance of parasites as indicators of their hosts’ ecology.