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.     

High natural fusion rates in a botryllid ascidian

Many benthic colonial invertebrates have the ability to fuse and form chimeras with compatible colonies. Botryllid ascidians are model organisms for the study of the evolution of and molecular basis for allorecognition, and fusion rates have been determined for different populations and species by random sampling and fusion testing between individuals. However, natural fusion rates over time have not been documented. Nine settlement panels were deployed in Salem Harbor, Massachusetts, USA and Botrylloides violaceus settlement, growth, and fusion monitored from July to mid-August 2007. Seventy-three percent of the recruits observed fused with at least one other colony, while 4% neither fused nor were overgrown. Multifused colonies were not observed to grow faster than single colonies when growth was calculated as increase in size beyond the summation of fused entities; however, they were significantly larger. These results suggest that larvae settle in clumps of compatible individuals, and that large subtidal colonies may be the result of high numbers of fusions between compatible colonies.     

An agent-based model for simulating trading of multi-species fisheries quota

Individual transferable quotas (ITQs) are increasingly seen as a way to make fisheries more profitable and halt over-capitalisation. ITQs allocate to users of a resource a share of a total allowable catch (TAC) which they are free to use, lease, or sell. We outline an approach to modelling the effect of an ITQ system in a multi-species, multi-sector fishery and apply it to the Coral Reef Fin Fish Fishery (CRFFF) in Queensland, Australia. An ITQ model, based on the assumption that operators seek to maximize profits, simulates the use of tradeable quota units by operators in the fishery, taking account of the initial quota allocation to operators, seasonal fish prices and individual operator variable costs, their fishing efficiency and experience, and constraints on vessel movements. Rationalization of the fishery is predicted to occur under an ITQ system for the CRFFF, which will lead to reductions in effort, increases in profits, and changes over time in quota prices. The ecological consequences of transferable quota in the multi-species fishery are seen in the catch and discard levels of the less profitable species, even though a TAC was set. This had flow-on effects on biomass. For example, simulations showed that the TAC for the primary target species, coral trout, was used more fully than that for a less valuable target species, red throat emperor, and that this was achieved through increased discarding of red throat emperor. Catches of both coral trout and red throat emperor that were derived from the model were higher than those recently observed in the fishery. The effort predicted by the model, however, closely approximated the actual effort observed in the fishery following implementation of ITQ management.     

VALIDATION OF THE SWAT MODEL ON A LARGE RWER BASIN WITH POINT AND NONPOINT SOURCES1

ABSTRACT: The State of Texas has initiated the development of a Total Maximum Daily Load program in the Bosque River Watershed, where point and nonpoint sources of pollution are a concern. Soil Water Assessment Tool (SWAT) was validated for flow, sediment, and nutrients in the watershed to evaluate alternative management scenarios and estimate their effects in controlling pollution. This paper discusses the calibration and validation at two locations, Hico and Valley Mills, along the North Bosque River. Calibration for flow was performed from 1960 through 1998. Sediment and nutrient calibration was done from 1993 through 1997 at Hico and from 1996 through 1997 at Valley Mills. Model validation was performed for 1998. Time series plots and statistical measures were used to verify model predictions. Predicted values generally matched well with the observed values during calibration and validation (R²≥ 0.6 and Nash‐Suttcliffe Efficiency ≥ 0.5, in most instances) except for some underprediction of nitrogen during calibration at both locations and sediment and organic nutrients during validation at Valley Mills. This study showed that SWAT was able to predict flow, sediment, and nutrients successfully and can be used to study the effects of alternative management scenarios.     

SIMULATED ANNEALING WITH MEMORY AND DIRECTIONAL SEARCH FOR GROUND WATER REMEDIATION DESIGN1

ABSTRACT: Review of recent literature indicates an emergence in the use of combinatorial methods such as simulated annealing in ground water management during the past nine to ten years. While previous studies demonstrated the feasibility of using these methods, a general finding was that computational processing requirements were inordinately high relative to gradient‐based methods. An enhanced annealing algorithm was developed and used to demonstrate the potential for greatly improving the computational efficiency of simulated annealing as an optimization method for ground water management applications. The algorithm incorporates “directional search” and “memory” capabilities. Selecting search directions based on better understanding of the current neighborhood of the configuration space was shown to improve algorithm performance. Also, “memory” concepts derived from the Tabu Search Method show particular promise for improving the rate and quality of convergence. Performance of the enhanced annealing method was evaluated and the resultant management method was demonstrated using an example from the literature.     

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.     

El Niño periods increase growth of juvenile white seabass (<Emphasis Type="Italic">Atractoscion nobilis</Emphasis>) in the Southern California Bight

Studies of the impact of El Niño periods on marine species have usually focused on negative, highly visible effects, e.g., decreasing growth rates or increasing mortality due to a decline in primary productivity in typically nutrient rich upwelling zones; but positive effects related to elevated water temperature are also known. This study examined how the growth rate of juvenile white seabass, Atractoscion nobilis, responded to changes in ocean temperature in an El Niño period (1997–1998) in the northern portion of the Southern California Bight, USA. Growth rates of juvenile white seabass during their first 4 years of life were estimated as the slopes of linear relationships between body mass and age (from otoliths) of 800 fish collected at 11 stations throughout the bight. Growth rates differed significantly among cohorts hatched in 1996–2001. Specifically, white seabass that hatched in 1996 and 1997 grew significantly faster than those that hatched in 1998, 1999, and 2001. These differences in growth rates of cohorts appeared to be driven by variation in sea-surface temperature (SST). Growth rates averaged over the first three or 4 years of life were significantly positively correlated to average daily SST during the first 1–4 years of life. Increased growth of juvenile white seabass during the warm El Niño period likely provided a number of benefits to this warm-temperate species. This study demonstrated that some species will benefit from these warm-water periods despite reduced system-wide primary production.     

Exploratory Analysis of the Winter Chemistry of Five Lakes on the North Slope of Alaska1

Abstract: Lakes are important water resources on the North Slope of Alaska. Freshwater is required for oilfield production as well as exploration, which occurs largely on ice roads and pads. Since most North Slope lakes are shallow, the quantity and quality of the water under ice at the end of winter are important environmental management issues. Currently, water‐use permits are a function of the presence of overwintering fish populations, and their sensitivity to low oxygen concentrations. Sampling of five North Slope lakes during the winter of 2004‐2005 shed some light on the winter chemistry of four lakes that were used as water supplies and one undisturbed lake. Field analysis was conducted for oxygen, conductivity, pH, and temperature throughout the lake depth, as well as ice thickness and water depth. Water samples were retrieved from the lakes and analyzed for Na, Ca, K, Mg, Fe, dissolved‐organic carbon, and alkalinity in the laboratory. Lake properties, rather than pumping, were the best predictors of oxygen depletion, with the highest dissolved‐oxygen levels maintained in the lake with the lowest concentration of constituents. Volume weighted mean dissolved‐oxygen concentrations ranged from 4 to 94% of saturation in March. Dissolved oxygen and specific conductance data suggested that the lakes began to refresh in May.     

Characterizing ammonia emissions from swine farms in eastern North Carolina: part 1--conventional lagoon and spray technology for waste treatment

Ammonia (NH3) fluxes from waste treatment lagoons and barns at two conventional swine farms in eastern North Carolina were measured. The waste treatment lagoon data were analyzed to elucidate the temporal (seasonal and diurnal) variability and to derive regression relationships between NH3 flux and lagoon temperature, pH and ammonium content of the lagoon, and the most relevant meteorological parameters. NH3 fluxes were measured at various sampling locations on the lagoons by a flowthrough dynamic chamber system interfaced to an environmentally controlled mobile laboratory. Two sets of open-path Fourier transform infrared (FTIR) spectrometers were also used to measure NH3 concentrations for estimating NH3 emissions from the animal housing units (barns) at the lagoon and spray technology (LST) sites. Two different types of ventilation systems were used at the two farms. Moore farm used fan ventilation, and Stokes farm used natural ventilation. The early fall and winter season intensive measurement campaigns were conducted during September 9 to October 11, 2002 (lagoon temperature ranged from 21.2 to 33.6 degrees C) and January 6 to February 2, 2003 (lagoon temperature ranged from 1.7 to 12 degrees C), respectively. Significant differences in seasonal NH3 fluxes from the waste treatment lagoons were found at both farms. Typical diurnal variation of NH3 flux with its maximum value in the afternoon was observed during both experimental periods. Exponentially increasing flux with increasing surface lagoon temperature was observed, and a linear regression relationship between logarithm of NH3 flux and lagoon surface temperature (T1) was obtained. Correlations between lagoon NH3 flux and chemical parameters, such as pH, total Kjeldahl nitrogen (TKN), and total ammoniacal nitrogen (TAN) were found to be statistically insignificant or weak. In addition to lagoon surface temperature, the difference (D) between air temperature and the lagoon surface temperature was also found to influence the NH3 flux, especially when D > 0 (i.e., air hotter than lagoon). This hot-air effect is included in the statistical-observational model obtained in this study, which was used further in the companion study (Part II), to compare the emissions from potential environmental superior technologies to evaluate the effectiveness of each technology.