The probabilistic niche model reveals substantial variation in the niche structure of empirical food webs

The structure of food webs, complex networks of interspecies feeding interactions, plays a crucial role in ecosystem resilience and function, and understanding food web structure remains a central problem in ecology. Previous studies have shown that key features of empirical food webs can be reproduced by low-dimensional "niche" models. Here we examine the form and variability of food web niche structure by fitting a probabilistic niche model to 37 empirical food webs, a much larger number of food webs than used in previous studies. The model relaxes previous assumptions about parameter distributions and hierarchy and returns parameter estimates for each species in each web. The model significantly outperforms previous niche model variants and also performs well for several webs where a body-size-based niche model performs poorly, implying that traits other than body size are important in structuring these webs' niche space. Parameter estimates frequently violate previous models' assumptions: in 19 of 37 webs, parameter values are not significantly hierarchical, 32 of 37 webs have nonuniform niche value distributions, and 15 of 37 webs lack a correlation between niche width and niche position. Extending the model to a two-dimensional niche space yields networks with a mixture of one- and two-dimensional niches and provides a significantly better fit for webs with a large number of species and links. These results confirm that food webs are strongly niche-structured but reveal substantial variation in the form of the niche structuring, a result with fundamental implications for ecosystem resilience and function.     

Chemical defense in pelagic octopus paralarvae: Tetrodotoxin alone does not protect individual paralarvae of the greater blue-ringed octopus (Hapalochlaena lunulata) from common reef predators

Some pelagic marine larvae possess anti-predator chemical defenses. Occasionally, toxic adults imbue their young with their own defensive cocktails. We examined paralarvae of the greater blue-ringed octopus (Hapalochlaena lunulata) for the deadly neurotoxin tetrodotoxin (TTX), and if present, whether TTX conferred protection to individual paralarvae. Paralarvae of H. lunulata possessed 150 ± 17 ng TTX each. These paralarvae appeared distasteful to a variety of fish and stomatopod predators, yet food items spiked with 200 ng TTX were readily consumed by predators. We conclude that TTX alone does not confer individual protection to paralarvae of H. lunulata, and that they possess an alternative defense. In larger doses, tetrodotoxin is a deterrent to the predatory stomatopod Haptosquilla trispinosa (mean dose = 3.97 μg/g). This corresponds to 12–13 paralarvae per predator based on the TTX levels of the clutch we examined. Thus, the basic assumption that individual paralarvae of H. lunulata are defended by TTX alone was disproved. Instead, functionality of TTX levels in paralarvae may arise through alternative selective pathways, such as deterrence to parasites, through kin selection, or against predator species not tested here.     

Commentary: graduated licensing--moving forward or standing still?

The widespread application of graduated driver licensing (GDL), starting in the mid-1990s, has greatly reduced young driver crashes. Substantial further reductions are possible by raising the licensing age to 17. This can be done indirectly, through extension of GDL policies (minimum learner age of 16, one-year holding period), or by legislation directly establishing 17 as the licensing age. Other approaches are likely to have limited impact.     

The contribution of roadside soil to phosphorus loading in the eutrophic Lagos Lagoon, Nigeria

Roadside soils were sampled from the Lagos Lagoon catchment during the wet and dry seasons over the period 2005-2009. Lagoon sediment samples were also collected within the same period. All samples were digested with aqua regia to determine total phosphorus and extracted with 0.5 M sodium bicarbonate to determine the bioavailable fraction (Olsen-P). A segmented flow analyser method was used for analysis and good accuracy was demonstrated for two reference soils (SO-2 from CCMET and SRM 2711 from NIST). The Lagos Lagoon is a hypereutrophic water body (1270 ± 1170 μg P L(-1)), with significant areas of anoxia and water hyacinth growth. The total phosphorus concentrations in roadside soils (16 sites; mean ± 2 S.D.) were 285 ± 279 mg kg(-1) in the wet season and 424 ± 629 mg kg(-1) in the dry season, indicating that rainwater leaching is a major source of phosphorus in the lagoon. The bioavailable fractions were 5.17 ± 3.47 mg kg(-1) (2.1 ± 1.5% of the total) in the wet season and 13.0 ± 8.7 mg kg(-1) (4.3 ± 4.5% of the total) in the dry season.     

Potential world garbage and waste carbon sequestration

To offset the carbon dioxide released by fossil fuels, a proposed sequestration strategy relies on burying garbage and waste in landfills. This paper roughly estimates the current annual world supply of carbonaceous waste to be 35.5 billion metric tons and to contain about 18 billion metric tons of carbon. If landfills received all of this waste, sequestration of more than 5.6 billion metric tons of carbon seems theoretically possible—an amount well in excess of the 3.3 billion metric tons which the atmosphere is currently gaining.     

A field experiment characterizing variable detection rates during plant surveys

Surveys aimed at finding threatened and invasive species can be challenging due to individual rarity and low and variable individual detection rates. Detection rate in plant surveys typically varies due to differences among observers, among the individual plants being surveyed (targets), and across background environments. Interactions among these 3 components may occur but are rarely estimated due to limited replication and control during data collection. We conducted an experiment to investigate sources of variation in detection of 2 Pilosella species that are invasive and sparsely distributed in the Alpine National Park, Australia. These species are superficially similar in appearance to other yellow-flowered plants occurring in this landscape. We controlled the presence and color of flowers on target Pilosella plants and controlled their placement in plots, which were selected for their variation in cover of non-target yellow flowers and dominant vegetation type. Observers mimicked Pilosella surveys in the plots and reported 1 categorical and 4 quantitative indicators of their survey experience level. We applied survival analysis to detection data to model the influence of both controlled and uncontrolled variables on detection rate. Orange- and yellow-flowering Pilosella in grass- and heath-dominated vegetation were detected at a higher rate than nonflowering Pilosella. However, this detection gain diminished as the cover of other co-occurring yellow-flowering species increased. Recent experience with Pilosella surveys improved detection rate. Detection experiments are a direct and accessible means of understanding detection processes and interpreting survey data for threatened and invasive species. Our detection findings have been used for survey planning and can inform progress toward eradication. Interaction of target and background characteristics determined detection rate, which enhanced predictions in the Pilosella eradication program and demonstrated the difficulty of transferring detection findings into untested environments.     

Phylogenetic diversity of NO reductases,new tools for nor monitoring,and insights into N2O production in natural and engineered environments

● 548 representative nor genes were collected to create complete phylogenetic trees. ● The distribution of nor and nod genes were detected in 18 different phyla. ● The most conserved amino acids in NOR were located adjacent to the active site. ● nor-universal and Clade-specific primers were designed, suggested, and tested. Nitric oxide reductases (NORs) have a central role in denitrification, detoxification of nitric oxide (NO) in host-pathogen interactions, and NO-mediated cell-cell signaling. In this study, we focus on the phylogeny and detection of qNOR and cNOR genes because of their nucleotide sequence similarity and evolutionary relatedness to cytochrome oxidases, their key role in denitrification, and their abundance in natural, agricultural, and wastewater ecosystems. We also include nitric oxide dismutase (NOD) due to its similarity to qNOR. Using 548 nor sequences from publicly accessible databases and sequenced isolates from N₂O-producing bioreactors, we constructed phylogenetic trees for 289 qnor/nod genes and 259 cnorB genes. These trees contain evidence of horizontal gene transfer and gene duplication, with 13.4% of the sequenced strains containing two or more nor genes. By aligning amino acid sequences for qnor + cnor, qnor, and cnor, we identified four highly conserved regions for NOR and NOD, including two highly conserved histidine residues at the active site for qNOR and cNOR. Extending this approach, we identified conserved sequences for: 1) all nor (nor-universal); 2) all qnor (qnor-universal) and all cnor (cnor-universal); 3) qnor of Comamonadaceae; 4) Clade-specific sequences; and 5) nod of Candidatus Methylomirabilis oxyfera. Examples of primer performance were confirmed experimentally.     

Animals on marine flowers: does the presence of flowering shoots affect mobile epifaunal assemblage in an eelgrass meadow?

Eelgrass, Zostera marina, produces two types of shoots: morphologically simple vegetative shoots and highly branched flowering (reproductive) shoots, the latter found only in summer months. We examined whether the abundance and diversity of mobile epifaunal assemblage are affected by the presence of flowering shoots in an eelgrass meadow of Otsuchi Bay, northeastern Japan. Comparisons of epifauna in natural vegetation revealed that density and species richness did not differ significantly between sites consisting of both flowering and vegetative shoots, and those only of vegetative shoots. A transplant experiment, conducted to examine the colonization rates of epifauna to defaunated eelgrass planted with different combination of vegetative and flowering shoots, showed no obvious variation in abundance and species richness. At species level, the density of some species such as a tanaid Zeuxo sp. and a polychaete Platynereis sp. was higher at sites and/or treatments with flowering shoots, whereas that of some gastropods, such as Lirularia iridescens and Siphonacmea oblongata was higher at sites without flowering shoots. The species-specific response led to dissimilarity of epifaunal assemblage between sites and among treatments with different densities of vegetative and flowering shoots. Similar patterns observed for natural vegetation and the transplant experiment suggest that the variation in assemblage structure is caused by habitat selection of each species, for example, the utilization of flowering shoots as feeding ground and nursery by Zeuxo sp.     

A method for assigning species into groups based on generalized Mahalanobis distance between habitat model coefficients

Habitat association models are commonly developed for individual animal species using generalized linear modeling methods such as logistic regression. We considered the issue of grouping species based on their habitat use so that management decisions can be based on sets of species rather than individual species. This research was motivated by a study of western landbirds in northern Idaho forests. The method we examined was to separately fit models to each species and to use a generalized Mahalanobis distance between coefficient vectors to create a distance matrix among species. Clustering methods were used to group species from the distance matrix, and multidimensional scaling methods were used to visualize the relations among species groups. Methods were also discussed for evaluating the sensitivity of the conclusions because of outliers or influential data points. We illustrate these methods with data from the landbird study conducted in northern Idaho. Simulation results are presented to compare the success of this method to alternative methods using Euclidean distance between coefficient vectors and to methods that do not use habitat association models. These simulations demonstrate that our Mahalanobis-distance-based method was nearly always better than Euclidean-distance-based methods or methods not based on habitat association models. The methods used to develop candidate species groups are easily explained to other scientists and resource managers since they mainly rely on classical multivariate statistical methods.