bluuebunny/crossref_metadata_2025 huggingface dataset:
BIOMASS DYNAMICS IN AMAZONIAN FOREST FRAGMENTS
Authors: Nascimento Henrique E. M. , Laurance William F.
Published: June 2007

Habitat fragmentation affects aboveground biomass in Amazonian forests, with potentially important implications for carbon storage and greenhouse gas emissions. We assessed the dynamics of aboveground‐biomass stocks by combining long‐term (10– 19 yr) data on mortality, damage, growth, and recruitment of large (≥10 cm diameter at breast height [dbh]) trees with measurements of nearly all other live and dead plant material (seedlings, saplings, small trees, palms, lianas, downed wood debris, snags, litter) in 50 1‐ha plots in fragmented and continuous Amazonian forests.

The key process altering biomass dynamics in fragmented forests is the chronically elevated mortality of large trees, which apparently results from microclimatic changes and increased wind turbulence near forest edges. This, in turn, accelerates the production of necromass and leads to significantly increased wood debris and litter on the forest floor. Near forest edges, frequent canopy disturbance increases the amount of light in the understory, resulting in accelerated tree recruitment, significantly higher biomass of small (5– 10 cm dbh) trees, and higher liana densities. Surprisingly, the estimated annual turnover of wood debris increases significantly near forest edges, suggesting that decomposition is occurring more rapidly in fragmented than continuous forests.

These results reveal that habitat fragmentation fundamentally alters the distribution and dynamics of aboveground biomass in Amazonian forests. The rate of carbon cycling probably increases sharply, both because long‐lived canopy and emergent trees decline in favor of shorter‐lived successional trees and lianas, and because necromass production and turnover both appear to increase. Carbon storage in live vegetation also declines because small successional trees and lianas (which typically have low wood density) store substantially less carbon than do large, old‐growth trees. Finally, the decline and rapid decay of live biomass in forest fragments may produce substantial atmospheric carbon emissions, above and beyond that resulting from deforestation per se.
NITROGEN AND PHOSPHORUS LIMITATION OF BIOMASS GROWTH IN A TROPICAL SECONDARY FOREST
Authors: Davidson Eric A. , Reis de Carvalho Cláudio J. , Vieira Ima C. G. , Figueiredo Ricardo de O. , Moutinho Paulo , Yoko Ishida Françoise , Primo dos Santos Maria Tereza , Benito Guerrero José , Kalif Kemel , Tuma Sabá Renata
Published: June 2007

Understanding secondary successional processes in Amazonian terrestrial ecosystems is becoming increasingly important as continued deforestation expands the area that has become secondary forest, or at least has been through a recent phase of secondary forest growth. Most Amazonian soils are highly weathered and relatively nutrient poor, but the role of nutrients as a factor determining successional processes is unclear. Soils testing and chronosequence studies have yielded equivocal results regarding the possible role of nutrient limitation. The objective of this paper is to report the first two years' results of a nitrogen (N) and phosphorus (P) fertilization experiment in a 6‐yr‐old secondary forest growing on an abandoned cattle pasture on a clayey Oxisol. Growth of remnant grasses responded significantly to the N + P treatment, whereas tree biomass increased significantly following N‐only and N + P treatments. The plants took up about 10% of the 50 kg P/ha of the first year's application, and recovery in soil fractions could account for the rest. The trees took up about 20% of the 100 kg N/ha of the first year's application. No changes in soil inorganic N, soil microbial biomass N, or litter decomposition rates have been observed so far, but soil faunal abundances increased in fertilized plots relative to the control in the second year of the study. A pulse of nitric oxide and nitrous oxide emissions was measured in the N‐treated plots only shortly after the second year's application. Net N mineralization and net nitrification assays demonstrated strong immobilization potential, indicating that much of the N was probably retained in the large soil organic‐N pool. Although P availability is low in these soils and may partially limit biomass growth, the most striking result of this study so far is the significant response of tree growth to N fertilization. Repeated fire and other losses of N from degraded pastures may render tree growth N limited in some young Amazonian forests. Changes in species composition and monitoring of long‐term effects on biomass accumulation will be addressed as this experiment is continued.
RESPIRATION FROM A TROPICAL FOREST ECOSYSTEM: PARTITIONING OF SOURCES AND LOW CARBON USE EFFICIENCY
Authors: Chambers Jeffrey Q. , Tribuzy Edgard S. , Toledo Ligia C. , Crispim Bianca F. , Higuchi Niro , Santos Joaquim dos , Araújo Alessandro C. , Kruijt Bart , Nobre Antonio D. , Trumbore Susan E.
Published: June 2007

Understanding how tropical forest carbon balance will respond to global change requires knowledge of individual heterotrophic and autotrophic respiratory sources, together with factors that control respiratory variability. We measured leaf, live wood, and soil respiration, along with additional environmental factors over a 1‐yr period in a Central Amazon terra firme forest. Scaling these fluxes to the ecosystem, and combining our data with results from other studies, we estimated an average total ecosystem respiration (Reco) of 7.8 μmol·m−2·s−1. Average estimates (per unit ground area) for leaf, wood, soil, total heterotrophic, and total autotrophic respiration were 2.6, 1.1, 3.2, 5.6, and 2.2 μmol·m−2·s−1, respectively. Comparing autotrophic respiration with net primary production (NPP) estimates indicated that only ∼30% of carbon assimilated in photosynthesis was used to construct new tissues, with the remaining 70% being respired back to the atmosphere as autotrophic respiration. This low ecosystem carbon use efficiency (CUE) differs considerably from the relatively constant CUE of ∼0.5 found for temperate forests. Our Reco estimate was comparable to the above‐canopy flux (Fac) from eddy covariance during defined sustained high turbulence conditions (when presumably Fac = Reco) of 8.4 (95% ci = 7.5– 9.4). Multiple regression analysis demonstrated that ∼50% of the nighttime variability in Fac was accounted for by friction velocity (u*, a measure of turbulence) variables. After accounting for u* variability, mean Fac varied significantly with seasonal and daily changes in precipitation. A seasonal increase in precipitation resulted in a decrease in Fac, similar to our soil respiration response to moisture. The effect of daily changes in precipitation was complex: precipitation after a dry period resulted in a large increase in Fac, whereas additional precipitation after a rainy period had little effect. This response was similar to that of surface litter (coarse and fine), where respiration is greatly reduced when moisture is limiting, but increases markedly and quickly saturates with an increase in moisture.
15N NATURAL ABUNDANCE IN WOODY PLANTS AND SOILS OF CENTRAL BRAZILIAN SAVANNAS (CERRADO)
Authors: Bustamante M. M. C. , Martinelli L. A. , Silva D. A. , Camargo P. B. , Klink C. A. , Domingues T. F. , Santos R. V.
Published: June 2007

We measured the 15N natural abundance values of 320 individuals belonging to 45 different plant species of the Brazilian cerrado. We also determined δ15N of soil nitrogen as a function of soil depth. Our purpose was to test the hypothesis that N‐limited cerrado would have a large range of plant δ15N values, similar to patterns seen in northern high‐latitude ecosystems. Foliar δ15N values did demonstrate the large range found in some other N‐limited ecosystems, varying from −5‰ to +7.9‰. Significant variability within individual species was also seen across cerrado community types. Several factors contributed to this variability, including the presence of N‐fixing legumes, associations with mycorrhizal fungi, δ15N variability of soil organic matter with depth, fire events, and the seasonality of N‐immobilization and mineralization processes in cerrado soils.
SOIL FLUXES OF CO2, CO, NO, AND N2O FROM AN OLD PASTURE AND FROM NATIVE SAVANNA IN BRAZIL
Authors: Varella R. F. , Bustamante M. M. C. , Pinto A. S. , Kisselle K. W. , Santos R. V. , Burke R. A. , Zepp R. G. , Viana L. T.
Published: June 2007

We compared fluxes of CO2, CO, NO, and N2O, soil microbial biomass, and N availability in a 20‐yr‐old Brachiaria pasture and a native cerrado area (savanna in central Brazil). Availability of N and NO fluxes were lower in the pasture than in the cerrado. N2O fluxes were below detection limit at both sites. The CO fluxes showed weak seasonal variation with slightly higher positive fluxes in the dry season and lower fluxes, including net consumption, during the wet season. The cerrado CO fluxes were higher and more variable than the fluxes in the pasture. Both sites showed a seasonal pattern in CO2 emissions with lower fluxes (∼2 μmol CO2·m−2·s−1) during the dry season. There were no significant differences in annual CO2 soil emissions between the cerrado and the pasture, but the temporal trends differed, with higher fluxes in the pasture during the transition from the wet to the dry season. Artificial water addition in the pasture during the dry season resulted in short‐lived pulses of NO and CO2.
CARBON AND NUTRIENT ACCUMULATION IN SECONDARY FORESTS REGENERATING ON PASTURES IN CENTRAL AMAZONIA
Authors: Feldpausch Ted R. , Rondon Marco A. , Fernandes Erick C. M. , Riha Susan J. , Wandelli Elisa
Published: June 2007

Over the past three decades, large expanses of forest in the Amazon Basin were converted to pasture, many of which later degraded to woody fallows and were abandoned. While the majority of tropical secondary forest (SF) studies have examined post‐deforestation or post‐agricultural succession, we examined post‐pasture forest recovery in 10 forests ranging in age from 0 to 14 years since abandonment. We measured aboveground biomass and soil nutrients to 45 cm depth and computed total site carbon (C) and nutrient stocks to gain an understanding of the dynamics of nutrient and C buildup in regenerating SF in central Amazonia.

Aboveground biomass accrual was rapid, 11.0 Mg·ha−1·yr−1, in the young SFs. Within 12–14 yr, they accumulated up to 128.1 Mg/ha of dry aboveground biomass, equivalent to 25–50% of primary forest biomass in the region. Wood nitrogen (N) and phosphorus (P) concentrations decreased with forest age. Aboveground P and calcium (Ca) stocks accumulated at a rate of 1.2 and 29.4 kg·ha−1·yr−1; extractable soil P stocks declined as forest age increased. Although soil stocks of exchangeable Ca (207.0 ± 23.7 kg/ha) and extractable P (8.3 ± 1.5 kg/ha) were low in the first 45 cm, both were rapidly translocated from soil to plant pools. Soil N stocks increased with forest age, probably due to N fixation, atmospheric deposition, and/or subsoil mining.

Total soil C storage to 45 cm depth ranged between 42 and 84 Mg/ha, with the first 15 cm storing 40–45% of the total. Total C accrual (7.04 Mg C·ha−1·yr−1) in both aboveground and soil pools was similar or higher than values reported in other studies. Tropical SFs regrowing on lightly to moderately used pasture rapidly sequester C and rebuild total nutrient capital following pasture abandonment. Translocation of some nutrients from deep soil (>45 cm depth) may be important to sustaining productivity and continuing biomass accumulation in these forests. The soil pool represents the greatest potential for long‐term C gains; however, soil nutrient deficits may limit future productivity.
APPLICATION OF IMPROVED ECOSYSTEM AERODYNAMICS IN REGIONAL WEATHER FORECASTS
Authors: Gustavo Goncalves de Goncalves L. , Burke Eleanor J. , Shuttleworth W. James , Chan Chou Sin , Marengo Jose A.
Published: June 2007

This paper reports the impact of applying improved representation of the area‐average aerodynamic properties of South American ecosystems on 7‐d weather forecasts made with the Brazilian regional forecast model (Eta‐SSiB). Two pairs of 7‐d forecasts were made, each pair starting from the same initial conditions on 1 January 1999 and on 24 June 1999, respectively. In one run, the aerodynamic properties of the ecosystem used for each modeled grid square were those of the most common vegetation present. In the second, the grid‐average aerodynamic properties of the vegetation were calculated using aggregation rules in combination with a high‐resolution land‐cover data set. There are marked differences in the aerodynamic properties of the underlying ecosystems in these two runs in some regions, notably around the Amazon River basin, in regions where there has been land‐cover change, and in portions of southern Brazil. The 7‐d average, predicted ecosystem–surface exchanges, near‐surface temperature, and precipitation for the two pairs of runs were compared. There were differences between the forecasts that were most noticeable in regions where the ecosystem's aerodynamic properties were most dissimilar, but also elsewhere. Given the limited nature of the experiments reported, these preliminary results should be treated with care. Nonetheless, they suggest the need for more systematic study of the significance of ecosystems on regional weather forecasts in South America.
EMISSIONS OF N2O AND CO2 FROM TERRA FIRME FORESTS IN RONDÔNIA, BRAZIL
Authors: Garcia-Montiel Diana C. , Melillo Jerry M. , Steudler Paul A. , Tian Hanqin , Neill Christopher , Kicklighter David W. , Feigl Brigette , Piccolo Marisa , Cerri Carlos C.
Published: June 2007

Nitrous oxide (N2O) functions as a greenhouse gas in the lower atmosphere and as a destroyer of the ozone layer in the upper atmosphere. Tropical forest soils are considered the largest natural N2O source, but the spatial pattern of the emissions is poorly understood because of the relatively small number of ground measurements and the lack of a good way to scale them. In this paper, we present a new approach for estimating the magnitude and spatial pattern of N2O emissions from tropical forest soils of the Amazon Basin. First, we develop an empirical relationship between N2O and CO2 emissions from tropical soils based on seven years of field measurements made in forests of Rondônia, Brazil. Second, we combine this empirical relationship with monthly estimates of forest soil respiration across the basin from a process‐based biogeochemistry model, the terrestrial ecosystem model, to estimate annual N2O fluxes and the spatial pattern of these fluxes from the region's undisturbed forests for the period 1980–1995. For this time interval, we estimate the average flux from the forest soils of the Amazon Basin was 7.9 × 1011 g N2O‐N/yr, with the highest subregional fluxes coming from the most productive forests in the northwestern part of the basin.
LANDSCAPE AND REGIONAL IMPACTS OF HURRICANES IN PUERTO RICO
Authors: Boose Emery R. , Serrano Mayra I. , Foster David R.
Published: June 2007

Puerto Rico is subject to frequent and severe impacts from hurricanes, whose long‐term ecological role must be assessed on a scale of centuries. In this study we applied a method for reconstructing hurricane disturbance regimes developed in an earlier study of hurricanes in New England. Patterns of actual wind damage from historical records were analyzed for 85 hurricanes since European settlement in 1508. A simple meteorological model (HURRECON) was used to reconstruct the impacts of 43 hurricanes since 1851. Long‐term effects of topography on a landscape scale in the Luquillo Experimental Forest (LEF) were simulated with a simple topographic exposure model (EXPOS).

Average return intervals across Puerto Rico for F0 damage (loss of leaves and branches) and F1 damage (scattered blowdowns, small gaps) on the Fujita scale were 4 and 6 years, respectively. At higher damage levels, a gradient was created by the direction of the storm tracks and the weakening of hurricanes over the interior mountains. Average return intervals for F2 damage (extensive blowdowns) and F3 damage (forests leveled) ranged from 15 to 33 years and 50 to 150 years, respectively, from east to west. In the LEF, the combination of steep topography and constrained peak wind directions created a complex mosaic of topographic exposure and protection, with average return intervals for F3 damage ranging from 50 years to >150 years. Actual forest damage was strongly dependent on land‐use history and the effects of recent hurricanes. Annual and decadal timing of hurricanes varied widely. There was no clear centennial‐scale trend in the number of major hurricanes over the historical period.
QUANTITATIVE FATTY ACID SIGNATURE ANALYSIS: A NEW METHOD OF ESTIMATING PREDATOR DIETS
Authors: Iverson Sara J. , Field Chris , Don Bowen W. , Blanchard Wade
Published: June 2007

Accurate estimates of the diets of predators are required in many areas of ecology, but for many species current methods are imprecise, limited to the last meal, and often biased. The diversity of fatty acids and their patterns in organisms, coupled with the narrow limitations on their biosynthesis, properties of digestion in monogastric animals, and the prevalence of large storage reservoirs of lipid in many predators, led us to propose the use of quantitative fatty acid signature analysis (QFASA) to study predator diets. We present a statistical model that provides quantitative estimates of the proportions of prey species in the diets of individual predators using fatty acid signatures. We conducted simulation studies using a database of 28 prey species (n= 954 individuals) from the Scotian Shelf off eastern Canada to investigate properties of the model and to evaluate the reliability with which prey could be distinguished in the model. We then conducted experiments on grey seals (Halichoerus grypus,n= 25) and harp seals (Phoca groenlandica,n= 5) to assess quantitative characteristics of fatty acid deposition and to develop calibration coefficients for individual fatty acids to account for predator lipid metabolism. We then tested the model and calibration coefficients by estimating the diets of experimentally fed captive grey seals (n= 6, switched from herring to a mackerel/capelin diet) and mink kits (Mustela vison,n= 46, switched from milk to one of three oil‐supplemented diets). The diets of all experimentally fed animals were generally well estimated using QFASA and were consistent with qualitative and quantitative expectations, provided that appropriate calibration coefficients were used. In a final case, we compared video data of foraging by individual free‐ ranging harbor seals (Phoca vitulina,n= 23) fitted with Crittercams and QFASA estimates of the diet of those same seals using a complex ecosystem‐wide prey database. Among the 28 prey species in the database, QFASA estimated sandlance to be the dominant prey species in the diet of all seals (averaging 62% of diet), followed primarily by flounders, but also capelin and minor amounts of other species, although there was also considerable individual variability among seals. These estimates were consistent with video data showing sandlance to be the predominant prey, followed by flatfish. We conclude that QFASA provides estimates of diets for individuals at time scales that are relevant to the ecological processes affecting survival, and can be used to study diet variability within individuals over time, which will provide important opportunities rarely possible with other indirect methods. We propose that the QFASA model we have set forth will be applicable to a wide range of predators and ecosystems.
IMPLICATIONS OF RIPARIAN MANAGEMENT STRATEGIES ON WOOD IN STREAMS OF THE PACIFIC NORTHWEST
Authors: Meleason Mark A. , Gregory Stanley V. , Bolte John P.
Published: June 2007

Riparian forest management plans for numerous regions throughout the world must consider long‐term supply of wood to streams. The simulation model OSU STREAMWOOD was used to evaluate the potential effects of riparian management scenarios on the standing stock of wood in a hypothetical stream in the Pacific Northwest, USA. OSU STREAMWOOD simulates riparian forest growth, tree entry (including breakage), and in‐channel processes (log breakage, movement, and decomposition). Results of three simulation scenarios are reported. The first scenario assessed total wood volume in the channel from Douglas‐fir plantations clearcut to the stream bank using three rotation periods (60, 90, and 120 yr). Without a forested riparian management zone, accumulation of wood in the channel was minimal and did not increase through time. In the second scenario, response of total wood volume to forested riparian management zones of widths between 6 m and 75 m was evaluated. Total wood volume associated with the 6 m wide nonharvested forest for forest ages ≥240 yr was 32% of the standing stock associated with a nonharvested forest buffer one potential tree height in width. Maximum standing stock associated with the channel for nonharvested riparian forests ≥30 m required 500‐yr‐old forests. In the third scenario, contribution of wood from forest plantations beyond nonharvested forests of various widths was explored. Forest plantations associated with nonharvested riparian buffers with widths >10 m contributed minimal amounts of wood volume to the stream. These results suggest that forest age and width of the nonharvested buffers are more important than the rotation age of plantation forests in providing long‐term supplies of wood to streams.
PROJECTING THE BIOLOGICAL CONDITION OF STREAMS UNDER ALTERNATIVE SCENARIOS OF HUMAN LAND USE
Authors: Van Sickle John , Baker Joan , Herlihy Alan , Bayley Peter , Gregory Stanley , Haggerty Patti , Ashkenas Linda , Li Judith
Published: June 2007

We present regression models for estimating the status of fish and aquatic invertebrate communities in all second to fourth–order streams (1:100 000 scale; total stream length = 6476 km) throughout the Willamette River Basin, Oregon (USA). The models project fish and invertebrate status as a function of physiographic, land‐use/land‐cover, and stream flow variables, with the latter two sets of variables subject to change under historical and alternative future scenarios of human development. Models are developed using sample data collected between 1993 and 1997 from 149 wadeable streams in the basin. Model uncertainties are propagated through model projections and into aggregated estimates of regional status. The projections show no significant change in basin‐wide status in year 2050, relative to Circa 1990, for scenarios either of increased human development or continuation of current development trends, because landscape change under these scenarios is dominated by conversion of agricultural land to rural residential and urban uses, and because these changes affect only a small percentage of the basin. However, under a scenario of increased conservation, regional medians of biotic status indicators are projected to improve by 9–24% by year 2050. None of the changes projected between Circa 1990 and year 2050 is as large in magnitude as the decline in status projected to have occurred between the time of pre‐European settlement and Circa 1990.
PROJECTING WILDLIFE RESPONSES TO ALTERNATIVE FUTURE LANDSCAPES IN OREGON'S WILLAMETTE BASIN
Authors: Schumaker Nathan H. , Ernst Ted , White Denis , Baker Joan , Haggerty Patti
Published: June 2007

Increasingly, environmental quality is becoming recognized as a critical factor that should constrain land use planning. One important measure of a landscape's quality is its capacity to support viable populations of wildlife species. But the ability of land managers to balance conservation with other competing objectives is limited by a shortage of methodologies for assessing landscape quality. In response to this shortage, the research community has begun developing a variety of multispecies, landscape‐level, assessment models. Useful models must strike a balance between parsimony and biological realism and must be designed to make the most of limited life history data. This paper applies two such assessments to an examination of wildlife responses to scenarios of landscape change within Oregon's Willamette River Basin. The study uses GIS maps of pre‐European settlement and circa 1990 habitat conditions, and three possible realizations of how the Basin might appear in the year 2050. Our simpler assessment generated statistics of landscape change from the GIS imagery and species–habitat relationships for all 279 amphibian, reptile, bird, and mammal species in the basin. Our more complex assessment used an individual‐based life history simulator to estimate population sizes for a small subset of this fauna. These two assessments offer complementary kinds of information about wildlife responses to landscape change: estimates of habitat changes for a large number of species representing a region's biodiversity, and estimates of changes in the persistence of populations of key species. We found both good and poor correlations between our two assessments, depending upon the species and landscape. Both assessments agreed in their overall ranking of the landscapes' quality for wildlife. In most cases, the percentage change in habitat quality underestimated the percentage change in population size. In a few cases, small gains in habitat quality were accompanied by very large increases in wildlife populations. We attribute discrepancies in our two assessments to the influence habitat fragmentation had on our individual‐based model. As such, our study provides a methodology for separating the influences of habitat quality and quantity from those of habitat pattern.
ALTERNATIVE FUTURES FOR THE WILLAMETTE RIVER BASIN, OREGON
Authors: Baker Joan P. , Hulse David W. , Gregory Stanley V. , White Denis , Van Sickle John , Berger Patricia A. , Dole David , Schumaker Nathan H.
Published: June 2007

Alternative futures analysis can inform community decisions regarding land and water use. We conducted an alternative futures analysis in the Willamette River Basin in western Oregon. Based on detailed input from local stakeholders, three alternative future landscapes for the year 2050 were created and compared to present‐day (circa 1990) and historical (pre‐EuroAmerican settlement) landscapes. We evaluated the likely effects of these landscape changes on four endpoints: water availability, Willamette River, stream condition, and terrestrial wildlife. All three futures assume a doubling of the 1990 human population by 2050. The Plan Trend 2050 scenario assumes current policies and trends continue. Because Oregon has several conservation‐oriented policies in place, landscape changes and projected environmental effects associated with this scenario were surprisingly small (most ≤10% change relative to 1990). The scenario did, however, engender a debate among stakeholders about the reasonableness of assuming that existing policies would be implemented exactly as written if no further policy actions were taken. The Development 2050 scenario reflects a loosening of current policies, more market‐oriented approach, as proposed by some stakeholders. Estimated effects of this scenario include loss of 24% of prime farmland; 39% more wildlife species would lose habitat than gain habitat relative to the 1990 landscape. Projected effects on aquatic biota were less severe, primarily because many of the land use changes involved conversion of agricultural lands into urban or rural development, both of which adversely impact streams. Finally, Conservation 2050 assumes that ecosystem protection and restoration are given higher priority, although still within the bounds of what stakeholders considered plausible. In response, most ecological indicators (both terrestrial and aquatic) recovered 20–70% of the losses sustained since EuroAmerican settlement. The one exception is water availability. Water consumed for out‐of‐stream uses increased under all three future scenarios (by 40–60%), with accompanying decreases in stream flow. Although the conservation measures incorporated into Conservation 2050 moderated the increase in consumption, they were not sufficient to reverse the trend. Results from these analyses have been actively discussed by stakeholder groups charged with developing a vision for the basin's future and a basin‐wide restoration strategy.
RESPONSE OF BIRDS TO THINNING YOUNG DOUGLAS‐FIR FORESTS
Authors: Hayes John P. , Weikel Jennifer M. , Huso Manuela M. P.
Published: June 2007

Silvicultural practices, such as thinning, are increasingly performed both for commodity production and to help achieve biodiversity goals and promote ecological restoration. However, relatively little research has examined effects of thinning conifer forests on vertebrates. We experimentally manipulated stands using a randomized block design to evaluate influences of two thinning intensities on populations of diurnal breeding birds in western Oregon. We conducted point counts of birds seven times each year in 1994 (prior to treatment) and from 1995 through 2000 (subsequent to treatment). We analyzed data using multiple linear regression and information‐theoretic approaches to model selection. Of the 22 species for which we had sufficient data for analysis, detections of nine species decreased and eight species increased in thinned stands relative to controls, and there was no strong evidence that thinning influenced numbers of five species. Of the 17 species that responded to thinning, the magnitude of response of eight species varied with thinning intensity; for each of these species, response was greatest in the more heavily thinned stands. Although no species was extirpated from stands following thinning, detections of Hutton's Vireos (Vireo huttoni), Golden‐crowned Kinglets (Regulus satrapa), Brown Creepers (Certhia americana), Black‐throated Gray Warblers (Dendroica nigrescens), and Varied Thrushes (Ixoreus naevius) decreased to less than half of the detections in controls in one or more treatment types, suggesting thinning significantly reduces their numbers. In contrast, American Robins (Turdus migratorius), Townsend's Solitaires (Myadestes townsendi), and Hammond's Flycatchers (Empidonax hammondii) were rare or absent in controls but regularly present in thinned stands, and detections of Western Tanagers (Piranga ludoviciana), Evening Grosbeaks (Coccothraustes vespertinus), and Hairy Woodpeckers (Picoides villosus) increased by threefold or more in thinned stands relative to controls. Only Pacific‐slope Flycatchers (Empidonax difficilis), Warbling Vireos (Vireo gilvus), and Western Tanagers showed strong evidence of temporal trends in response. For these species, differences between numbers in controls and treated stands became more extreme through time. Our findings suggest that thinning densely stocked conifer stands in landscapes dominated by younger stands enhances habitat suitability for several species of birds, but that some unthinned patches and stands should be retained to provide refugia for species that are impacted by thinning.
IMPROVING PRECISION AND REDUCING BIAS IN BIOLOGICAL SURVEYS: ESTIMATING FALSE‐NEGATIVE ERROR RATES
Authors: Tyre Andrew J. , Tenhumberg Brigitte , Field Scott A. , Niejalke Darren , Parris Kirsten , Possingham Hugh P.
Published: June 2007

The use of presence/absence data in wildlife management and biological surveys is widespread. There is a growing interest in quantifying the sources of error associated with these data. We show that false‐negative errors (failure to record a species when in fact it is present) can have a significant impact on statistical estimation of habitat models using simulated data. Then we introduce an extension of logistic modeling, the zero‐inflated binomial (ZIB) model that permits the estimation of the rate of false‐negative errors and the correction of estimates of the probability of occurrence for false‐negative errors by using repeated visits to the same site. Our simulations show that even relatively low rates of false negatives bias statistical estimates of habitat effects. The method with three repeated visits eliminates the bias, but estimates are relatively imprecise. Six repeated visits improve precision of estimates to levels comparable to that achieved with conventional statistics in the absence of false‐negative errors. In general, when error rates are ≤50% greater efficiency is gained by adding more sites, whereas when error rates are >50% it is better to increase the number of repeated visits. We highlight the flexibility of the method with three case studies, clearly demonstrating the effect of false‐negative errors for a range of commonly used survey methods.
IDENTIFYING BREEDING HABITAT FOR THE IBERIAN LYNX: INFERENCES FROM A FINE‐SCALE SPATIAL ANALYSIS
Authors: Fernández Néstor , Delibes Miguel , Palomares Francisco , Mladenoff David J.
Published: June 2007

Empirical landscape habitat models are valuable tools for addressing species conservation issues in heterogeneous landscapes. These have been particularly useful for animal populations requiring extensive areas, like large mammalian carnivores. Although models are scale‐dependent, they are often based exclusively on coarse‐grained information on landscape structure and species distribution. However, accurate discrimination and quality assessment of breeding habitats may require more detailed information on both individuals' habitat use and landscape patterns.

Here, we modeled breeding habitat for the Iberian lynx (Lynx pardinus), an endangered specialist of Mediterranean native ecosystems, in a human‐dominated landscape. For this, we used radiotelemetry data on breeding individuals and fine‐grained landscape variables obtained over an areal extent encompassing an entire lynx metapopulation. In addition, we restricted the study domain to areas of potential presence within this extent based on previous habitat analyses. This fine‐scale landscape analysis and design aimed to test whether it was possible to obtain detailed inferences on breeding habitat distribution and quality within more coarsely defined habitats that only indicate where the species can be found. Landscape composition factors (i.e., fine‐grain variables of landscape pattern within territories) and context factors (variables on geographical location of territories) were combined in different candidate habitat models. These reflected various hypotheses involving territory presence and size, including vegetation structure characteristics, landscape heterogeneity and complexity, favorable prey habitat, and human disturbance. The best approximating model for territory presence included only one landscape composition variable, namely, density of ecotones between scrubland and pastureland, which favored presence. For this model, classification accuracy was >80% in 94% of cross‐validation tests performed. The best approximating model for territory size explained 65% of the variation in size and included also density of ecotones, plus mean coverage of tall shrubs within territories; both correlated negatively with size. We show how these predictors are also related to prey density and suggest that this low‐hierarchical‐level relationship between the prey and patterns of the landscape can be interpreted as a likely mechanism explaining breeding habitat distribution and quality at a higher level. Our approach shows the potential of fine‐scale landscape analysis to understand patterns of breeder abundance, and to better manage population viability of threatened species in human‐populated areas.
OF MICE AND MEN AND TRILLIUM: CASCADING EFFECTS OF FOREST FRAGMENTATION
Authors: Tallmon David A. , Jules Erik S. , Radke Nikki J. , Mills L. Scott
Published: June 2007

Cascading ecological effects of anthropogenic habitat fragmentation have been studied primarily in extreme cases (e.g., the isolation of habitat fragments in a novel habitat matrix such as suburban developments, reservoirs, or agricultural fields), with less attention to more subtle and widespread cases, such as habitat fragmentation due to timber harvest. Few studies have used rigorous demographic data to demonstrate the direct and indirect effects of habitat fragmentation. We trapped deer mice (Peromyscus maniculatus) at five sites over two years in southwest Oregon, USA, and used multi‐state capture–recapture models to estimate deer mouse survival and movement in clearcuts, forest‐fragment edges, forest‐fragment interiors, and contiguous forests. We also estimated deer mouse densities in fragmented and unfragmented forests and combined deer mouse demographic studies with trillium (Trillium ovatum) seed predation trials to link deer mouse changes to reduced trillium recruitment previously observed at the same study sites. Mouse survival was highest in clearcuts, intermediate in forest fragments, and lowest in unfragmented (control) forests. Mouse movement among clearcuts, forest edges, and forest interiors was common over short time intervals. Collectively, demographic rates led to mouse densities that were 3–4 times higher at forest‐fragment sites than at unfragmented sites. Trillium seeds were ∼3 times more likely to be depredated in areas of elevated relative mouse abundance than in areas of lower relative abundance. Forest fragmentation has favored mouse populations, resulting in increased seed predation that may decrease recruitment rates and increase local extinction risks for trillium.
COMPETITION AND PREDATION MEDIATE THE INDIRECT EFFECTS OF AN INSECTICIDE ON SOUTHERN LEOPARD FROGS
Authors: Mills Nathan E. , Semlitsch Raymond D.
Published: June 2007

Pesticides are widely used by humans to eliminate or reduce populations of unwanted species. These pesticides often cause collateral damage by killing nontarget species and altering biological communities. Our study examined the relative importance of direct and indirect effects of the insecticide carbaryl on southern leopard frog tadpoles, Rana sphenocephala, in a simple aquatic community. We did not detect any significant direct effects of carbaryl on the anuran life‐history traits examined in this study. Rather, environmentally relevant concentrations of carbaryl indirectly affected R. sphenocephala life‐history traits by causing changes in the intensity of competition and predation within the community. Carbaryl generally increased the survival of R. sphenocephala tadpoles. However, the increase in survival was greatest in mesocosms containing predators, largely due to pesticide‐induced mortality of the predators. Carbaryl also exacerbated the effects of competition by decreasing periphyton abundance, which resulted in smaller metamorphs. Thus, we conclude that investigations of the effects of pesticides on a species of interest should go beyond standard toxicological protocols and examine the effects of the pesticide within the context of the community, placing special emphasis on understanding how competition and predation mediate indirect effects.
DISTURBANCE‐MEDIATED COMPETITION AND THE SPREAD OF PHRAGMITES AUSTRALIS IN A COASTAL MARSH
Authors: Minchinton Todd E. , Bertness Mark D.
Published: June 2007

In recent decades the grass Phragmites australis has been aggressively invading coastal, tidal marshes of North America, and in many areas it is now considered a nuisance species. While P. australis has historically been restricted to the relatively benign upper border of brackish and salt marshes, it has been expanding seaward into more physiologically stressful regions. Here we test a leading hypothesis that the spread of P. australis is due to anthropogenic modification of coastal marshes. We did a field experiment along natural borders between stands of P. australis and the other dominant grasses and rushes (i.e., matrix vegetation) in a brackish marsh in Rhode Island, USA. We applied a pulse disturbance in one year by removing or not removing neighboring matrix vegetation and adding three levels of nutrients (specifically nitrogen) in a factorial design, and then we monitored the aboveground performance of P. australis and the matrix vegetation. Both disturbances increased the density, height, and biomass of shoots of P. australis, and the effects of fertilization were more pronounced where matrix vegetation was removed. Clearing competing matrix vegetation also increased the distance that shoots expanded and their reproductive output, both indicators of the potential for P. australis to spread within and among local marshes. In contrast, the biomass of the matrix vegetation decreased with increasing severity of disturbance. Disturbance increased the total aboveground production of plants in the marsh as matrix vegetation was displaced by P. australis. A greenhouse experiment showed that, with increasing nutrient levels, P. australis allocates proportionally more of its biomass to aboveground structures used for spread than to belowground structures used for nutrient acquisition. Therefore, disturbances that enrich nutrients or remove competitors promote the spread of P. australis by reducing belowground competition for nutrients between P. australis and the matrix vegetation, thus allowing P. australis, the largest plant in the marsh, to expand and displace the matrix vegetation. Reducing nutrient load and maintaining buffers of matrix vegetation along the terrestrial–marsh ecotone will, therefore, be important methods of control for this nuisance species.
REMOTE MEASUREMENT OF ENERGY AND CARBON FLUX FROM WILDFIRES IN BRAZIL
Authors: Riggan Philip J. , Tissell Robert G. , Lockwood Robert N. , Brass James A. , Pereira João Antônio Raposo , Miranda Heloisa S. , Miranda Antônio C. , Campos Teresa , Higgins Robert
Published: June 2007

Temperature, intensity, spread, and dimensions of fires burning in tropical savanna and slashed tropical forest in central Brazil were measured for the first time by remote sensing with an infrared imaging spectrometer that was designed to accommodate the high radiances of wildland fires. Furthermore, the first in situ airborne measurements of sensible heat and carbon fluxes in fire plumes were combined with remote measurements of flame properties to provide consistent remote‐sensing‐based estimators of these fluxes. These estimators provide a means to determine rates of fuel consumption and carbon emission to the atmosphere by wildland fires as required for assessments of fire impacts on regional air pollution or global emissions of greenhouse gases. Observed fires developed complex fire‐line geometry and thermal structure, even as average whole‐fire temperatures varied little. Flame temperatures sometimes exceeded 1600 K along the leading edge of actively spreading fire lines, yet >90% of the radiant energy from observed fires was associated with temperatures of 830–1440 K. Fire in a partially slashed forest encompassed a high‐intensity flaming front and a trailing reach of residual combustion extending 400 m. Fire fronts in tropical savanna typically formed with little depth and a high proportion of their radiant flux density associated with high temperatures due to low levels of residual combustion. Measured fires had such low and variable radiance compared with that of a blackbody of comparable temperature as to preclude the use of fire radiance at a single wavelength as a measure of fire intensity or temperature. One‐half of the radiant flux density from a measured savanna fire was associated with values of a combined emissivity–fractional‐area parameter <0.091 m2/m2; for a slash fire this fraction was associated with values <0.37 m2/m2. Observations reported here show wildland fires to be so complex and dynamic as to require frequent high‐resolution measurements over their course and duration in order to specify their effects in the environment; an understanding of global fire impacts may require such measurements over a large sample of individual fires.
PRECISION AND BIAS OF METHODS FOR ESTIMATING POINT SURVEY DETECTION PROBABILITIES
Authors: Wintle Brendan A. , McCarthy Michael A. , Parris Kirsten M. , Burgman Mark A.
Published: June 2007

Wildlife surveys often seek to determine the presence or absence of species at sites. Such data may be used in population monitoring, impact assessment, and species– habitat analyses. An implicit assumption of presence/absence surveys is that if a species is not detected in one or more visits to a site, it is absent from that site. However, it is rarely if ever possible to be completely sure that a species is absent, and false negative observation errors may arise when detection probabilities are less than 1. The detectability of species in wildlife surveys is one of the most important sources of uncertainty in determining the proportion of a landscape that is occupied by a species. Recent studies emphasize the need to acknowledge and incorporate false negative observation error rates in the analysis of site occupancy data, although a comparative study of the range of available methods for estimating detectability and occupancy is notably absent. The motivation for this study stems from the lack of guidance in the literature about the relative merits of alternative methods for estimating detection probabilities and site occupancy proportions from presence/absence survey data. Six approaches to estimating underlying detection probabilities and the proportion of sites occupied from binary observation data are reviewed. These include three parametric methods based on binomial mixtures, one nonparametric approach based on mark–recapture theory, and two approaches based on simplistic assumptions about occupancy rates. We compare the performance of each method using simulated data for which the “true” underlying detection rate is known. Simulated data were realized from a beta‐binomial distribution, incorporating a realistic level of variation in detection rates. Estimation methods varied in their precision and bias. The “binomial‐with‐added‐zeros” mixture model, estimated by maximum likelihood, was the least biased estimator of detection probability and, therefore, occupancy rate. We provide an Excel spreadsheet to execute all of the methods reviewed. Stand‐alone programs such as PRESENCE may be used to estimate all models including the “binomial with added zeros” model. Our findings lend support to the use of maximum likelihood methods in estimating site occupancy and detectability rates.