Estimates of animal methane emissions

The enteric methane emissions into the atmospheric annually from domestic animals total about 77 Tg. Another 10 to 14 Tg are likely released from animal manure disposal systems. About 95% of global animal enteric methane is from ruminants, a consequence of their large populations, body size and appetites combined with the extensive degree of anaerobic microbial fermentation occurring in their gut. Accurate methane estimates are particularly sensitive to cattle and buffalo census numbers and estimated diet consumption. Since consumption is largely unknown and must be predicted, accuracy is limited often by the information required, i.e., distribution of animals by class, weight and productivity. Fraction of the diet lost as enteric methane mostly falls into the range of 5.5–6.5% of gross energy intake for the world's cattle, sheep and goats. Manure methane emissions are heavily influenced by fraction of disposal by anaerobic lagoon. Non-ruminants, i.e., swine, become major contributors to these emissions.     

Use of cluster and principal component analyses to profile areas in California where ground water has been contaminated by pesticides

An empirical approach to profiling areas of ground water contamination by pesticides was devised that did not rely upon determining the level of vulnerability between land areas and that did not assume any particular pathway for ground water contamination. Climatic and soil data were obtained for 1-square mile sections of land in California where pesticide residues had been found in well water samples and the detection was attributed to legal agricultural applications. These sections were designated as known contaminated (KC) sections. Climate and soil data were also obtained for sections which lacked either well sampling data or a positive pesticide detection. These sections were designated as candidate sections. Statistical procedures were used to cluster groups of KC sections first with respect to climate characteristics and then with respect to soil characteristics. Principal components analysis (PCA) was used to construct a statistical profile of soil variables for each cluster of KC sections. A method based on the PCA was developed to compare the similarity of soil profiles derived for each KC section cluster to individual candidate sections. Since the profiling scheme was based only on data from KC sections, candidate sections that did not match any KC cluster profile could only be considered dissimilar to contaminated sections, receiving a status of not-classified. This profiling method is flexible and it can be revised to incorporate updated well sampling information.     

The efficacy of a limestone doser to mitigate stream acidification in a Maryland coastal plain stream: Implications for migratory fish species

The objective of this two-year study was to determine the efficacy of an automated limestone slurry doser to neutralize acidic pulses and improve water quality conditions for enhancing survival of early life stages of migratory fish species in a Maryland coastal plain stream. Implications for survival of early life stages of migratory fish species such as yellow perch (Perca flavescens), white perch (Morone americana), blueback herring (Alosa aestivalis) and alewife (Alosa pseudoharengus) are discussed based on the improved chemical conditions in the dosed area of the stream. Despite problems with overdosing in 1991 and failure of the stage transducer to work properly in 1992, the doser was generally effective in neutralizing acidic pulses (pH depressions) in the stream during three major rain events in both years. Chemical conditions (pH and inorganic monomeric aluminum) reported in the non-dosed area during major rainfall events were potentially stressful to both alewife and blueback herring although neither species was reported spawning in the stream during either year. Mitigating the potential impact of acidic conditions on early life stages of important migratory fish species was not sufficient to ensure spawning. It is therefore recommended that habitat improvement measures and well designed fish stocking programs be implemented concurrently with doser operations if the goal is to create optimum spawning conditions for migratory species.     

Bottom-up effects of plant genotype on aphids, ants, and predators

Theory predicts that bottom-up ecological forces can affect community dynamics, but whether this extends to the effects of heritable plant variation on tritrophic communities is poorly understood. In a field experiment, I contrasted the effects of plant genotype (28 genotypes; 1064 plants), aphid density, and the presence/absence of mutualistic ants in affecting the per capita population growth of a specialist aphid herbivore, as well as the effects of plant genotype on the third trophic level. Plant genotype strongly affected aphid population growth rate, explaining 29% of the total variation in growth rate, whereas aphid density and ant-aphid interactions explained substantially less variation (< 2%) in aphid population growth rate. Plant genotype also had direct and indirect effects on the third trophic level, affecting the abundance of aphid-tending ants and the richness of predators. Multiple regression identified several heritable plant traits that explained 49% of the variation in aphid growth rate and 30% of the variation in ant abundance among plant genotypes. These bottom-up effects of plant genotype on tritrophic interactions were independent of the effects of either initial aphid density or the presence/absence of mutualistic ants. This study shows that plant genotype can be one of the most important ecological factors shaping tritrophic communities.     

Efficacy of stable isotope ratios in assigning endangered migrants to breeding and wintering sites.

A primary constraint on effective conservation of migratory animals is our inability to track individuals through their annual cycle. One such animal is the endangered southwestern subspecies of the Willow Flycatcher, which is difficult to distinguish from conspecifics. Identifying wintering regions used by the endangered subspecies would be an important step in formulating an effective conservation strategy. Our objective was to use stable isotope ratios as a means of identifying wintering sites of Southwestern Willow Flycatchers. We analyzed stable isotope ratios of carbon, nitrogen, and hydrogen from feathers of breeding and wintering Willow Flycatchers. Based on winter samples, we document a positive trend in hydrogen isotope ratios across latitude. We also found that Willow Flycatchers use C4 food webs south of 8 degrees N latitude, but we found no evidence of use of C4 food webs farther north. Nitrogen stable isotope ratios of feathers showed no discernable geographic variation. Discriminant function analyses, based on stable isotope ratios of wintering Willow Flycatchers, were only useful (>50% accurate) for assigning individuals to winter regions if the regions were large and the threshold probability for assignment was relatively high. When using these discriminant functions, most breeding samples of Southwestern Willow Flycatchers were assigned to two wintering regions: central Mexico and Ecuador. We think that assignment of Southwestern Willow Flycatchers to Ecuador is unrealistic. Given the large percentages of samples that could not be classified with certainty, we are not confident that these two regions are truly more likely to harbor wintering Southwestern Willow Flycatchers than other winter regions. We think our inconclusive results are due primarily to weak and nonlinear gradients in isotope ratios across the winter range of Willow Flycatchers.     

Continuous-time correlated random walk model for animal telemetry data

We propose a continuous-time version of the correlated random walk model for animal telemetry data. The continuous-time formulation allows data that have been nonuniformly collected over time to be modeled without subsampling, interpolation, or aggregation to obtain a set of locations uniformly spaced in time. The model is derived from a continuous-time Ornstein-Uhlenbeck velocity process that is integrated to form a location process. The continuous-time model was placed into a state-space framework to allow parameter estimation and location predictions from observed animal locations. Two previously unpublished marine mammal telemetry data sets were analyzed to illustrate use of the model, by-products available from the analysis, and different modifications which are possible. A harbor seal data set was analyzed with a model that incorporates the proportion of each hour spent on land. Also, a northern fur seal pup data set was analyzed with a random drift component to account for directed travel and ocean currents.     

Optimizing dispersal corridors for the Cape Proteaceae using network flow

We introduce a new way of measuring and optimizing connectivity in conservation landscapes through time, accounting for both the biological needs of multiple species and the social and financial constraint of minimizing land area requiring additional protection. Our method is based on the concept of network flow; we demonstrate its use by optimizing protected areas in the Western Cape of South Africa to facilitate autogenic species shifts in geographic range under climate change for a family of endemic plants, the Cape Proteaceae. In 2005, P. Williams and colleagues introduced a novel framework for this protected area design task. To ensure population viability, they assumed each species should have a range size of at least 100 km2 of predicted suitable conditions contained in protected areas at all times between 2000 and 2050. The goal was to design multiple dispersal corridors for each species, connecting suitable conditions between time periods, subject to each species' limited dispersal ability, and minimizing the total area requiring additional protection. We show that both minimum range size and limited dispersal abilities can be naturally modeled using the concept of network flow. This allows us to apply well-established tools from operations research and computer science for solving network flow problems. Using the same data and this novel modeling approach, we reduce the area requiring additional protection by a third compared to previous methods, from 4593 km2 to 3062 km , while still achieving the same conservation planning goals. We prove that this is the best solution mathematically possible: the given planning goals cannot be achieved with a smaller area, given our modeling assumptions and data. Our method allows for flexibility and refinement of the underlying climate-change, species-habitat-suitability, and dispersal models. In particular, we propose an alternate formalization of a minimum range size moving through time and use network flow to achieve the revised goals, again with the smallest possible newly protected area (2850 km2). We show how to relate total dispersal distance to probability of successful dispersal, and compute a trade-off curve between this quantity and the total amount of extra land that must be protected.     

Fish distributions and nutrient cycling in streams: can fish create biogeochemical hotspots?

Rates of biogeochemical processes often vary widely in space and time, and characterizing this variation is critical for understanding ecosystem functioning. In streams, spatial hotspots of nutrient transformations are generally attributed to physical and microbial processes. Here we examine the potential for heterogeneous distributions of fish to generate hotspots of nutrient recycling. We measured nitrogen (N) and phosphorus (P) excretion rates of 47 species of fish in an N-limited Neotropical stream, and we combined these data with population densities in each of 49 stream channel units to estimate unit- and reach-scale nutrient recycling. Species varied widely in rates of N and P excretion as well as excreted N:P ratios (6-176 molar). At the reach scale, fish excretion could meet >75% of ecosystem demand for dissolved inorganic N and turn over the ambient NH4 pool in <0.3 km. Areal N excretion estimates varied 47-fold among channel units, suggesting that fish distributions could influence local N availability. P excretion rates varied 14-fold among units but were low relative to ambient concentrations. Spatial variation in aggregate nutrient excretion by fish reflected the effects of habitat characteristics (depth, water velocity) on community structure (body size, density, species composition), and the preference of large-bodied species for deep runs was particularly important. We conclude that the spatial distribution of fish could indeed create hotspots of nutrient recycling during the dry season in this species-rich tropical stream. The prevalence of patchy distributions of stream fish and invertebrates suggests that hotspots of consumer nutrient recycling may often occur in stream ecosystems.     

Fine-scale chemical fingerprinting of an open coast crustacean for the assessment of population connectivity

Chemical fingerprinting techniques recently have been used to track larval dispersal of estuarine species that bear calcified structures, but the applicability of this important approach may be limited on the open coast where chemical signatures may be less distinctive and for the many species that do not retain calcified structures throughout development. Externally brooded embryos of the porcelain crab, Petrolisthes cinctipes, and inductively coupled plasma mass spectrometry were used to determine whether fine-scale variation in trace-elemental composition occurred along an open coast. Embryos were collected from 16 sites from 37.8° to 39.5° north latitude along the Pacific Coast of California, USA during late January and early February 2003. Discriminant function analysis revealed that collection sites, many separated by only a few kilometers along an open coast, could be differentiated with an overall accuracy of 73%, and combining the sites into three regions increased the accuracy to 88%. Thus, distinctive elemental signatures can be detected in open coast species even at a fine scale raising the possibility that larval tags can be developed for many more species than previously thought possible.     

New evidence for habitat-specific selection in Wadden Sea Zostera marina populations revealed by genome scanning using SNP and microsatellite markers

Eelgrass Zostera marina is an ecosystem-engineering species of outstanding importance for coastal soft sediment habitats that lives in widely diverging habitats. Our first goal was to detect divergent selection and habitat adaptation at the molecular genetic level; hence, we compared three pairs of permanently submerged versus intertidal populations using genome scans, a genetic marker-based approach. Three different statistical approaches for outlier identification revealed divergent selection at 6 loci among 46 markers (6 SNPs, 29 EST microsatellites and 11 anonymous microsatellites). These outlier loci were repeatedly detected in parallel habitat comparisons, suggesting the influence of habitat-specific selection. A second goal was to test the consistency of the general genome scan approach by doubling the number of gene-linked microsatellites and adding single nucleotide polymorphism (SNP) loci, a novel marker type for seagrasses, compared to a previous study. Reassuringly, results with respect to selection were consistent among most marker loci. Functionally interesting marker loci were linked to genes involved in osmoregulation and water balance, suggesting different osmotic stress, and reproductive processes (seed maturation), pointing to different life history strategies. The identified outlier loci are valuable candidates for further investigation into the genetic basis of natural selection.