Published by Wiley

Online ISSN: 1939-9170


Print ISSN: 0012-9658


To P or not to P?
  • Article

March 2014


70 Reads

Jarrett J Barber


Kiona Ogle

TABLE 1 . Selected vegetation and soil characteristics along the Franz Josef soil chronosequence (South Westland, New Zealand) from Richardson et al. (2004).
FIG. 2. Acetylene reduction activity: (a) Coriaria arborea, (b) foliose lichen, (c) bryophyte, and (d) litter acetylene reduction data are shown as a function of site age. Summer data are red, and winter data are blue. Although each datum comes from one of nine sites of discrete age, we have added a small random jitter to the horizontal value of each data point to improve readability of overlapping data. Data below the minimum detection limit are displayed as half this limit, but our statistical analyses do not make this assumption. Maximum likelihood estimates are shown as solid lines (in red and blue if there is a seasonal effect, otherwise in black), along with the 68% confidence interval of the mean (evaluated for each site age) in dashed lines of the same color. Units in panel (a) are micromoles of ethylene produced per gram of dry sample per hour, whereas units for panels (b)–(d) are nanomoles of ethylene produced per square centimeter of fresh sample per hour. Both axes are displayed on a logarithmic scale.  
FIG. 5. Proportional biological nitrogen fixation (BNF) as a function of soil inorganic N. Nitrogen fixation trends reflect the product of acetylene reduction activity and density data sets using soil inorganic N (extractable NO 3 À þ NH 4 þ ) and season as the independent variables, rather than soil age. Trends are shown as proportions of the maximum for each type, and all four types are shown. Two points only are shown for Coriaria arborea, rather than a continuous line.  
Nitrogen fixation in different biogeochemical niches along a 120 000-year chronosequence in New Zealand
  • Article
  • Full-text available

September 2009


223 Reads

Biological nitrogen fixation (BNF) is the major nitrogen (N) input in many terrestrial ecosystems, yet we know little about the mechanisms and feedbacks that control this process in natural ecosystems. We here examine BNF in four taxonomically and ecologically different groups over the course of forest ecosystem development. At nine sites along the Franz Josef soil chronosequence (South Westland, New Zealand) that range in age from 7 to 120000 yr old, we quantified BNF from the symbiotic plant Coriaria arborea, cyanolichens (primarily Pseudocyphellaria spp.), bryophytes (many species), and heterotrophic bacteria in leaf litter. We specifically examined whether these groups could act as "nitrostats" at the ecosystem level, turning BNF on when N is scarce (early in primary succession) and off when N is plentiful (later in succession and retrogression). Coriaria was abundant and actively fixing (approximately 11 kg N x ha(-1) x yr(-1)) in the youngest and most N-poor site (7 yr old), consistent with nitrostat dynamics. Coriaria maintained high BNF rates independent of soil N availability, however, until it was excluded from the community after a single generation. We infer that Coriaria is an obligate N fixer and that the nitrostat feedback is mechanistically governed by species replacement at the community level, rather than down-regulation of BNF at the physiological scale. Biological nitrogen fixation inputs from lichens (means of 0-2 kg N x ha(-1) x yr(-1)), bryophytes (0.7-10 kg N x ha(-1) x yr(-1)), and litter (1-2 kg N x ha(-1) x yr(-1)) were driven primarily by changes in density, which peaked at intermediate-aged sites (and increased with soil N availability) for both lichens and bryophytes, and grew monotonically with soil age (but did not change with soil N) for litter. This non-nitrostatic link between soil N availability and lichen/bryophyte BNF likely stems from increased tree biomass in more fertile sites, which increases epiphytic moisture conditions and habitable surface area. This apparent positive feedback could produce N-rich conditions.

Figure 1: Tree species distribution map of Stillberg, Central Alps, Switzerland, in: (a) 1975 and (b) 2005.
Figure 2: Survival curves for three high-elevation conifers (Larix decidua, Pinus mugo ssp. uncinata, and Pinus cembra) for the period 1975–2005. For each species, survival is expressed as a percentage of the ∼30 000 trees per species planted as seedlings.
Figure 3: Decision tree for mortality of all trees in the period 1975–2005. The relative frequencies of both response classes are shown in the inner nodes of the classification tree (the proportion of dead trees is shown in dark gray, and the proportion alive is shown in light gray).
Figure 6: Estimated GAM functions for significant predictors of height growth during three 10-year periods: (a) elevation and (b) snowmelt date (day of year, where day 1 is 1 January). Each plot shows the relationship of the fitted function with the response, scaled to zero. Values on the y-axes are residuals, the smooth-term coefficients (s) fitted from a generalized additive model. The plots include approximate 95% pointwise CI bands (in light gray).
FIG. 6. Continued.
Factors driving mortality and growth at treeline: A 30-year experiment of 92 000 conifers

February 2012


609 Reads






Understanding the interplay between environmental factors contributing to treeline formation and how these factors influence different life stages remains a major research challenge. We used an afforestation experiment including 92 000 trees to investigate the spatial and temporal dynamics of tree mortality and growth at treeline in the Swiss Alps. Seedlings of three high-elevation conifer species (Larix decidua, Pinus mugo ssp. uncinata, and Pinus cembra) were systematically planted along an altitudinal gradient at and above the current treeline (2075 to 2230 m above sea level [a.s.l.]) in 1975 and closely monitored during the following 30 years. We used decision-tree models and generalized additive models to identify patterns in mortality and growth along gradients in elevation, snow duration, wind speed, and solar radiation, and to quantify interactions between the different variables. For all three species, snowmelt date was always the most important environmental factor influencing mortality, and elevation was always the most important factor for growth over the entire period studied. Individuals of all species survived at the highest point of the afforestation for more than 30 years, although mortality was greater above 2160 m a.s.l., 50-100 m above the current treeline. Optimal conditions for height growth differed from those for survival in all three species: early snowmelt (ca. day of year 125-140 [where day 1 is 1 January]) yielded lowest mortality rates, but relatively later snowmelt (ca. day 145-150) yielded highest growth rates. Although snowmelt and elevation were important throughout all life stages of the trees, the importance of radiation decreased over time and that of wind speed increased. Our findings provide experimental evidence that tree survival and height growth require different environmental conditions and that even small changes in the duration of snow cover, in addition to changes in temperature, can strongly impact tree survival and growth patterns at treeline. Further, our results show that the relative importance of different environmental variables for tree seedlings changes during the juvenile phase as they grow taller.

FIG. 4. Relationship between mean effect sizes and level of ectomycorrhizal fungal colonization of inoculated seedlings for (A) total biomass, (B) shoot height, and (C) shoot : root ratio. Outliers in (A) and (B) (those data points above the 97th percentile of the distribution) are indicated as triangles; these were retained in the analysis.
FIG. 5. Relationship between mean effect sizes and magnitude of contamination for (A) total biomass, (B) shoot height, and (C) shoot : root ratio. 
FIG. 7. Relationship between the magnitude of contamination and the duration of association of ectomycorrhizal fungus and host. 
Karst J, Marczak L, Jones MD, Turkington R.. The mutualism-parasitism continuum in ectomycorrhizas: a quantitative assessment using meta-analysis. Ecology 89: 1032-1042

May 2008


366 Reads

Context dependency is deemed to position the outcomes of species interactions along a continuum of mutualism to parasitism. Thus, it is imperative to understand which factors determine where a particular interspecific interaction falls along the continuum. Over the past 20 years research on the ectomycorrhizal symbiosis has resulted in sufficient independent studies to now generalize about the factors and mechanisms that affect host response to ectomycorrhizas. Using meta-analysis we quantitatively evaluated the role of biotic (partner identity and colonization levels of ectomycorrhizal fungi) and abiotic (phosphorus levels) factors in determining host biomass, height, and shoot:root responses to ectomycorrhizal associations. On average, seedlings across multiple host genera increased in total biomass when inoculated with ectomycorrhizal fungi regardless of the identity of the fungal associate; host genera differed in the magnitude of response for both total biomass and shoot:root ratio. Association with different fungal genera modified only host allocation of biomass to shoots and roots. Neither level of colonization on inoculated seedlings nor the level of contamination on control seedlings relative to colonization levels by target fungi on inoculated seedlings was important in explaining variation in effect sizes for any growth response. None of our proposed factors (identity of partners, colonization level, magnitude of contamination, or duration of association) explained variation in effect sizes for shoot height, although in general seedlings were taller when inoculated with ectomycorrhizal fungi. Phosphorus additions did not influence effect sizes. Although the general trend across studies was for a positive response of hosts to ectomycorrhizal inoculation, publication bias and methodological issues effectively reduce and distort the spectrum on which we evaluate host responses to ectomycorrhizal inoculation. Our results indicate that the variation in ectomycorrhizal fungi perceived by the host may be of a discrete (presence/absence of ectomycorrhizal fungi) rather than continuous nature (variation in identity or abundance of ectomycorrhizal fungi).

Seifert EK, Bever JD, Maron JL.. Evidence for the evolution of reduced mycorrhizal dependence during plant invasion. Ecology 90: 1055-1062

May 2009


89 Reads

Introduced species inevitably experience novel selection pressures in their new environments as a result of changes in mutualist and antagonist relationships. While most previous work has examined how escape from specialist enemies has influenced herbivore or pathogen resistance of exotic species, post-introduction shifts in exotic dependence on mutualists have not been considered. In a common environment, we compared dependence on AM fungi of North American and European populations of Hypericum perforatum (St. John's Wort), a forb native to Europe. Introduced North American populations responded less to inoculation with AM fungi than did European populations. Root architecture was strongly correlated with mycorrhizal response, and introduced populations had finer root architecture than native populations. Finally, introduced populations exhibited decreased root and increased reproductive allocation relative to European populations, consistent with a transition to a weedier life history; however, biomass allocation patterns were uncorrelated with mycorrhizal response. These findings are the first demonstration of a genetically based reduction of mycorrhizal dependence and shift in root architecture in an introduced species.

Strength of evidence for density dependence in abundance time series of 1198 species

July 2006


106 Reads

Population limitation is a fundamental tenet of ecology, but the relative roles of exogenous and endogenous mechanisms remain unquantified for most species. Here we used multi-model inference (MMI), a form of model averaging, based on information theory (Akaike's Information Criterion) to evaluate the relative strength of evidence for density-dependent and density-independent population dynamical models in long-term abundance time series of 1198 species. We also compared the MMI results to more classic methods for detecting density dependence: Neyman-Pearson hypothesis-testing and best-model selection using the Bayesian Information Criterion or cross-validation. Using MMI on our large database, we show that density dependence is a pervasive feature of population dynamics (median MMI support for density dependence = 74.7-92.2%), and that this holds across widely different taxa. The weight of evidence for density dependence varied among species but increased consistently, with the number of generations monitored. Best-model selection methods yielded similar results to MMI (a density-dependent model was favored in 66.2-93.9% of species time series), while the hypothesis-testing methods detected density dependence less frequently (32.6-49.8%). There were no obvious differences in the prevalence of density dependence across major taxonomic groups under any of the statistical methods used. These results underscore the value of using multiple modes of analysis to quantify the relative empirical support for a set of working hypotheses that encompass a range of realistic population dynamical behaviors.

Gamfeldt L, Hillebrand H, Jonsson PR.. Multiple functions increase the importance of biodiversity for overall ecosystem functioning. Ecology 89: 1223-1231

June 2008


725 Reads

Biodiversity is proposed to be important for the rate of ecosystem functions. Most biodiversity-ecosystem function studies, however, consider only one response variable at a time, and even when multiple variables are examined they are analyzed separately. This means that a very important aspect of biodiversity is overlooked: the possibility for different species to carry out different functions at any one time. We propose a conceptual model to explore the effects of species loss on overall ecosystem functioning, where overall functioning is defined as the joint effect of many ecosystem functions. We show that, due to multifunctional complementarity among species, overall functioning is more susceptible to species loss than are single functions. Modeled relationships between species richness and overall ecosystem functioning using five empirical data sets on monocultures reflected the range of effects of species loss on multiple functions predicted by the model. Furthermore, an exploration of the correlations across functions and the degree of redundancy within functions revealed that multifunctional redundancy was generally lower than single-function redundancy in these empirical data sets. We suggest that by shifting the focus to the variety of functions maintained by a diversity of species, the full importance of biodiversity for the functioning of ecosystems can be uncovered. Our results are thus important for conservation and management of biota and ecosystem services.

Reconstructing patterns of temperature, phenology, and frost damage over 124 years: Spring damage risk is increasing

April 2013


179 Reads

Climate change, with both warmer spring temperatures and greater temperature fluctuations, has altered phenologies, possibly leading to greater risk of spring frost damage to temperate deciduous woody plants. Phenological observations of 20 woody species from 1993 to 2012 in Trelease Woods, Champaign County, Illinois, USA, were used to identify years with frost damage to vegetative and reproductive phases. Local temperature records were used in combination with the phenological observations to determine what combinations of the two were associated with damage. Finally, a long‐term temperature record (1889–1992) was evaluated to determine if the frequency of frost damage has risen in recent decades. Frost ≤−1.7°C occurred after bud‐break in 14 of the 20 years of observation. Frost damage occurred in five years in the interior and in three additional years at only the forest edge. The degree of damage varied with species, life stage, tissue (vegetative or reproductive), and phenological phase. Common features associated with the occurrence of damage to interior plants were (1) a period of unusual warm temperatures in March, followed by (2) a frost event in April with a minimum temperature ≤−6.1°C with (3) a period of 16–33 days between the extremes. In the long‐term record, 10 of 124 years met these conditions, but the yearly probability of frost damage increased significantly, from 0.03 during 1889–1979 to 0.21 during 1980–2012. When the criteria were “softened” to ≤−1.7°C in April and an interval of 16–37 days, 31 of 124 years met the conditions, and the yearly damage probability increased significantly to 0.19 for 1889–1979 and 0.42 for 1980–2012. In this forest, the combination of warming trends and temperature variability (extremes) associated with climate change is having ecologically important effects, making previously rare frost damage events more common.

Woodland-to-forest transition during prolonged drought in Minnesota after ca. AD 1300

October 2009


163 Reads

Interactions among multiple causes of ecological perturbation, such as climate change and disturbance, can produce "ecological surprises." Here, we examine whether climate-fire-vegetation interactions can produce ecological changes that differ in direction from those expected from the effects of climate change alone. To do so, we focus on the "Big Woods" of central Minnesota, USA, which was shaped both by climate and fire. The deciduous Big Woods forest replaced regional woodlands and savannas after the severity of regional fire regimes declined at ca. AD 1300. A trend toward wet conditions has long been assumed to explain the forest expansion, but we show that water levels at two lakes within the region (Wolsfeld Lake and Bufflehead Pond) were low when open woodlands were transformed into the Big Woods. Water levels were high instead at ca. 2240-795 BC when regional fire regimes were most severe. Based on the correlation between water levels and fire-regime severity, we infer that prolonged or repeated droughts after ca. AD 1265 reduced the biomass and connectivity of fine fuels (grasses) within the woodlands. As a result, regional fire severity declined and allowed tree populations to expand. Tree-ring data from the region show a peak in the recruitment of key Big Woods tree species during the AD 1930s drought and suggest that low regional moisture balance need not have been a limiting factor for forest expansion. The regional history, thus, demonstrates the types of counterintuitive ecosystem changes that may arise as climate changes in the future.

Leibold MA, McPeek MA.. Coexistence of the niche and neutral perspectives in community ecology. Ecology 87: 1399-1410

July 2006


351 Reads

The neutral theory for community structure and biodiversity is dependent on the assumption that species are equivalent to each other in all important ecological respects. We explore what this concept of equivalence means in ecological communities, how such species may arise evolutionarily, and how the possibility of ecological equivalents relates to previous ideas about niche differentiation. We also show that the co-occurrence of ecologically similar or equivalent species is not incompatible with niche theory as has been supposed, because niche relations can sometimes favor coexistence of similar species. We argue that both evolutionary and ecological processes operate to promote the introduction and to sustain the persistence of ecologically similar and in many cases nearly equivalent species embedded in highly structured food webs. Future work should focus on synthesizing niche and neutral perspectives rather than dichotomously debating whether neutral or niche models provide better explanations for community structure and biodiversity.

FIG. 1. (A) Oxygen, (B) temperature, and the concentrations of (C) bacteriochlorophyll d (Bchl d ) and (D) chlorophyll a (Chl a) in Mekkoja¨rviMekkoja¨rvi, southern Finland, through the open-water season of 2005.
FIG. 3. (A) The measured d 13 C of dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), adult female Daphnia (Dph, ad), juvenile Daphnia (Dph, juv), and particulate organic carbon (POC). (B) The d 15 N of adult female Daphnia and of juveniles during spring, summer, and autumn of 2005 in Mekkoja¨rviMekkoja¨rvi.  
FIG. 5. Stable isotope diet polygons for adult Daphnia (open circles) in Mekkoja¨rviMekkoja¨rvi and the d 13 C and d 15 N of the putative food sources: phytoplankton (PP), methanotrophic bacteria (MOB), heterotrophic bacteria (HB), and the green sulfur bacterium Chlorobium sp. (GSB), with measured or estimated deviation, and IsoSource model estimates (minimum–maximum) of the proportions of these major groups in adult Daphnia diet in (A) spring, (B) summer, (C) autumn1, and (D) autumn2 periods. Autumn1 and autumn2 refer respectively to the periods 12–22 September (before water column mixing) and 26 September–18 October (after water column mixing) in 2005.  
FIG. 6. Estimated proportions of different food sources (phytoplankton [PP], methanotrophic bacteria [MOB], heterotrophic bacteria [HB], and the green sulfur bacterium Chlorobium sp. [GSB]; mean 6 99% CI) in adult Daphnia diet during the spring, summer, autumn1, and autumn2 periods in Mekkoja¨rviMekkoja¨rvi.
Whole-lake dissolved inorganic 13C additions reveal seasonal shifts in zooplankton diet

March 2008


246 Reads

Sustained whole-lake additions of 13C-enriched dissolved inorganic carbon (DIC), intended to increase experimentally the delta13C of DIC in the epilimnion of a small lake with high dissolved organic carbon (DOC), were made during three seasonal periods (spring, summer, and autumn). Coupled with carbon and nitrogen stable isotope analysis of zooplankton and several of their putative food sources, these additions were used to investigate seasonal changes in the relative contributions of different food sources to zooplankton diet in the lake. Four main potential food sources were considered: phytoplankton, heterotrophic bacteria (HB), methanotrophic bacteria (MOB), and green sulfur bacteria (GSB). Because the number of potential food sources exceeded the number of isotopes analyzed, a computer program (IsoSource) was used to estimate the range of possible contributions of the various food sources. During all three periods the added inorganic 13C quickly increased the epilimnetic DIC delta13C by between 18 per thousand and 21 per thousand above the initial value of approximately -21 per thousand. This 13C enrichment of DIC was rapidly transmitted to the particulate organic matter (POM), which included photosynthetic phytoplankton. In spring and summer, delta13C of both adult and juvenile Daphnia increased by approximately 10 per thousand, indicating that Daphnia utilized autochthonous carbon. However, this 13C labeling of Daphnia was not so obvious during the autumn period, when their delta13C generally decreased. According to the IsoSource model outputs based on both delta13C and delta15N values, Daphnia utilized all four potential food source types during spring, summer, and autumn, but in different proportions. The possible contribution of phytoplankton to Daphnia diet was substantial (25-71%) in all seasons. The possible contributions of the bacterial food sources were more variable. The possible contribution of GSB was minor (0-20%) at all times and negligible in autumn. The possible contribution of HB was higher but very variable. Methanotrophic bacteria always made a significant contribution to Daphnia diet and were likely the single most important food source in autumn. Since both HB and MOB in this high-DOC lake probably depend largely on allochthonous organic carbon, our results highlight the seasonal variability in the potential importance of ecosystem subsidies in lake food webs.

Increased plant size in exotic populations: A common-garden test with 14 invasive species

December 2007


100 Reads

The "evolution of increased competitive ability" (EICA) hypothesis predicts that exotic species will adapt to reduced herbivore pressure by losing costly defenses in favor of competitive ability. Previous studies often support the prediction that plants from exotic populations will be less well defended than plants from native populations. However, results are mixed with respect to the question of whether plants from exotic populations have become more competitive. In a common-garden experiment involving plants from two native and two exotic populations of 14 different invasive species, we tested whether exotic plants generally grow larger than conspecific native plants, and whether patterns of relative growth depend on the intensity of competition. We found a quite consistent pattern of larger exotic than native plants, but only in the absence of competition. These results suggest that invasive species may often evolve increased growth, and that increased growth may facilitate adaptation to noncompetitive environments.

FIG. 1. Frequency distributions of medians in probability distributions of species-specific parameters in relative growth rate (RGR) and mortality models for 145 co-occurring Malaysian rain forest tree species. Vertical black lines show the median values of the parameters at community level (all 145 species). Gray bars show species with significant parameters whose 95% credible interval differed from the median of the parameter at the community level. These frequency distributions nearly approximate the prior distribution of parameters. Intercept and slope parameter r 1 and r 2 in the RGR model (see Eq. 1) are shown in panels (a) and (b), respectively. The parameters m 1 , m 2 , and m 3 in the mortality model (See Eq. 2) are shown in panels (c), (d), and (e). See the effect of each parameter on the curve in Appendix B: Fig. B1.  
FIG. 2. Size-dependent changes in relative growth rate and mortality. Lines show changes in RGR (R) and mortality (M ) with increasing stem diameter (D) by applying medians of probability distributions of R and M for 145 species. Note log scales for D and M.  
FIG. 3. Size-dependent changes in correlation coefficients between demographic rates and (a, c) upper diameter and (b, d) wood density. Symbols show medians of distributions of Kendall's correlation coefficients (s) between probability distributions of RGR (R) and mortality (M ) vs. upper diameter (D*) and wood density (WD) at different reference stem diameters (D) from 1 to 47 cm. Solid symbols indicate significant correlations (95% interval of s does not include zero), and open symbols indicate nonsignificant correlations (95% interval of s includes zero). Solid gray lines show a decline in the number of species to compare with increasing D, from 145 species at the smallest reference D to 20 species at the largest reference D.  
FIG. 4. Size-dependent changes in partial rank correlation coefficients between demographic rates and tree architectural variables. The upper panels (a–c) show each partial rank correlation of RGR (R) without the effect of upper diameter (D*), and the lower panels (d–f ) show each partial correlation of mortality (M ) without the effect of D*. Symbols show medians of distributions of Kendall's correlation coefficients (s) between probability distributions of R, M, and architectural traits for trees of different reference stem diameters (D) from 1 to 47 cm. Solid symbols indicate significant correlations (95% interval of s does not include zero), and open symbols indicate nonsignificant correlations (95% interval of s includes zero). Solid gray lines show a decline in the number of species to compare with an increase in size. The results of partial rank correlation without the effect of wood density are shown in Appendix D: Fig. D1.  
FIG. 5. Size-dependent changes in correlation coefficients between RGR and mortality. Different species sets were applied for correlations between RGR (R) and mortality (M ) as (a) all 145 species, (b) 50 small-statured species, (c) 50 intermediate-statured species, and (d) 45 large-statured species. Symbols show medians of distributions of Kendall's correlation coefficients (s) between probability distributions of R and M for trees of different reference stem diameters (D) from 1 to 47 cm. Solid symbols indicate significant correlations (95% interval of s does not include zero), and open symbols indicate nonsignificant correlations (95% interval of s includes zero). Solid gray lines show a decline in the number of species to compare with increasing D.
Linking size-dependent growth and mortality with architectural traits across 145 co-occurring tropical tree species

February 2014


717 Reads

Tree architecture, growth, and mortality change with increasing tree size and associated light conditions. To date, few studies have quantified how size-dependent changes in growth and mortality rates co-vary with architectural traits, and how such size-dependent changes differ across species and possible light capture strategies. We applied a hierarchical Bayesian model to quantify size-dependent changes in demographic rates and correlated demographic rates and architectural traits for 145 co-occurring Malaysian rain-forest tree species covering a wide range of tree sizes. Demographic rates were estimated using relative growth rate in stem diameter (RGR) and mortality rate as a function of stem diameter. Architectural traits examined were adult stature measured as the 95-percentile of the maximum stem diameter (upper diameter), wood density, and three tree architectural variables: tree height, foliage height, and crown width. Correlations between demographic rates and architectural traits were examined for stem diameters ranging from 1 to 47 cm. As a result, RGR and mortality varied significantly with increasing stem diameter across species. At smaller stem diameters, RGR was higher for tall trees with wide crowns, large upper diameter, and low wood density. Increased mortality was associated with low wood density at small diameters, and associated with small upper diameter and wide crowns over a wide range of stem diameters. Positive correlations between RGR and mortality were found over the whole range of stem diameters, but they were significant only at small stem diameters. Associations between architectural traits and demographic rates were strongest at small stem diameters. In the dark understory of tropical rain forests, the limiting amount of light is likely to make the interspecific difference in the effects of functional traits on demography more clear. Demographic performance is therefore tightly linked with architectural traits such as adult stature, wood density, and capacity for horizontal crown expansion. The enhancement of a demographic trade-off due to interspecific variation in functional traits in the understory helps to explain species coexistence in diverse rain forests.

A new method to track seed dispersal and recruitment using 15N isotope enrichment

December 2009


247 Reads

Seed dispersal has a powerful influence on population dynamics, genetic structuring, evolutionary rates, and community ecology. Yet, patterns of seed dispersal are difficult to measure due to methodological shortcomings in tracking dispersed seeds from sources of interest. Here we introduce a new method to track seed dispersal: stable isotope enrichment. It consists of leaf-feeding plants with sprays of 15N-urea during the flowering stage such that seeds developed after applications are isotopically enriched. We conducted a greenhouse experiment with Solanum americanum and two field experiments with wild Capsicum annuum in southern Arizona, USA, to field-validate the method. First, we show that plants sprayed with 15N-urea reliably produce isotopically enriched progeny, and that delta 15N (i.e., the isotopic ratio) of seeds and seedlings is a linear function of the 15N-urea concentration sprayed on mothers. We demonstrate that three urea dosages can be used to distinctly enrich plants and unambiguously differentiate their offspring after seeds are dispersed by birds. We found that, with high urea dosages, the resulting delta 15N values in seedlings are 10(3) - 10(4) times higher than the delta 15N values of normal plants. This feature allows tracking not only where seeds arrive, but in locations where seeds germinate and recruit, because delta 15N enrichment is detectable in seedlings that have increased in mass by at least two orders of magnitude before fading to normal delta 15N values. Last, we tested a mixing model to analyze seed samples in bulk. We used the delta 15N values of batches (i.e., combined seedlings or seeds captured in seed traps) to estimate the number of enriched seeds coming from isotopically enriched plants in the field. We confirm that isotope enrichment, combined with batch-sampling, is a cheap, reliable, and user-friendly method for bulk-processing seeds and is thus excellent for the detection of rare dispersal events. This method could further the study of dispersal biology, including the elusive, but critically important, estimation of long-distance seed dispersal.

TABLE 1 . Nonparametric correlations for total ecosystem percentage 15 N tracer recovery.
Figure 3: Mean 15N tracer recovery among terrestrial ecosystem pools for short-term (<1 week) and long-term (3–18 months) time periods following 15N addition. Not all studies are represented among each ecosystem pool, which may result in recovery >100%. Not all ecosystem pools or ecosystem types are available for each sampling time.
Figure 5: Total ecosystem 15N tracer recovery (mean and 95% confidence intervals) among forms of 15N addition, method of 15N addition, experimental treatment, and form of N within fertilizer for the long-term time period. Nonoverlapping 95% confidence intervals and data points with different lowercase letters indicate significant differences at P = 0.05. Sample size (the number of studies within each category) is given just above the x-axis.
Figure 6: Relationship between the percentage change in total ecosystem 15N tracer recovery and the rate of N addition for all time periods. Positive values indicate greater total ecosystem 15N tracer recovery following higher level of N addition. The Spearman rank correlation coefficient and P value are shown.
Sinks for Nitrogen Inputs in Terrestrial Ecosystems: A Meta-Analysis of 15N Tracer Field Studies

August 2012


667 Reads

Effects of anthropogenic nitrogen (N) deposition and the ability of terrestrial ecosystems to store carbon (C) depend in part on the amount of N retained in the system and its partitioning among plant and soil pools. We conducted a meta-analysis of studies at 48 sites across four continents that used enriched 15N isotope tracers in order to synthesize information about total ecosystem N retention (i.e., total ecosystem 15N recovery in plant and soil pools) across natural systems and N partitioning among ecosystem pools. The greatest recoveries of ecosystem 15N tracer occurred in shrublands (mean, 89.5%) and wetlands (84.8%) followed by forests (74.9%) and grasslands (51.8%). In the short term (<1 week after 15N tracer application), total ecosystem 15N recovery was negatively correlated with fine-root and soil 15N natural abundance, and organic soil C and N concentration but was positively correlated with mean annual temperature and mineral soil C:N. In the longer term (3-18 months after 15N tracer application), total ecosystem 15N retention was negatively correlated with foliar natural-abundance 15N but was positively correlated with mineral soil C and N concentration and C: N, showing that plant and soil natural-abundance 15N and soil C:N are good indicators of total ecosystem N retention. Foliar N concentration was not significantly related to ecosystem 15N tracer recovery, suggesting that plant N status is not a good predictor of total ecosystem N retention. Because the largest ecosystem sinks for 15N tracer were below ground in forests, shrublands, and grasslands, we conclude that growth enhancement and potential for increased C storage in aboveground biomass from atmospheric N deposition is likely to be modest in these ecosystems. Total ecosystem 15N recovery decreased with N fertilization, with an apparent threshold fertilization rate of 46 kg N·ha-1·yr -1 above which most ecosystems showed net losses of applied 15N tracer in response to N fertilizer addition.

Benthic algae stimulate leaf litter decomposition in detritus-based headwater streams: a case of aquatic priming effect? Ecology 94: 1604-1613

July 2013


204 Reads

In detritus-based ecosystems, autochthonous primary production contributes very little to the detritus pool. Yet primary producers may still influence the functioning of these ecosystems through complex interactions with decomposers and detritivores. Recent studies have suggested that, in aquatic systems, small amounts of labile carbon (C) (e.g., producer exudates), could increase the mineralization of more recalcitrant organic-matter pools (e.g., leaf litter). This process, called priming effect, should be exacerbated under low-nutrient conditions and may alter the nature of interactions among microbial groups, from competition under low-nutrient conditions to indirect mutualism under high-nutrient conditions. Theoretical models further predict that primary producers may be competitively excluded when allochthonous C sources enter an ecosystem. In this study, the effects of a benthic diatom on aquatic hyphomycetes, bacteria, and leaf litter decomposition were investigated under two nutrient levels in a factorial microcosm experiment simulating detritus-based, headwater stream ecosystems. Contrary to theoretical expectations, diatoms and decomposers were able to coexist under both nutrient conditions. Under low-nutrient conditions, diatoms increased leaf litter decomposition rate by 20% compared to treatments where they were absent. No effect was observed under high-nutrient conditions. The increase in leaf litter mineralization rate induced a positive feedback on diatom densities. We attribute these results to the priming effect of labile C exudates from primary producers. The presence of diatoms in combination with fungal decomposers also promoted decomposer diversity and, under low-nutrient conditions, led to a significant decrease in leaf litter C:P ratio that could improve secondary production. Results from our microcosm experiment suggest new mechanisms by which primary producers may influence organic matter dynamics even in ecosystems where autochthonous primary production is low.

Multi-season climate synchronized historical fires in dry forests (1650–1900), Northern Rockies, USA

March 2008


54 Reads

Our objective was to infer the climate drivers of regionally synchronous fire years in dry forests of the U.S. northern Rockies in Idaho and western Montana. During our analysis period (1650-1900), we reconstructed fires from 9245 fire scars on 576 trees (mostly ponderosa pine, Pinus ponderosa P. & C. Lawson) at 21 sites and compared them to existing tree-ring reconstructions of climate (temperature and the Palmer Drought Severity Index [PDSI]) and large-scale climate patterns that affect modern spring climate in this region (El Niño Southern Oscillation [ENSO] and the Pacific Decadal Oscillation [PDO]). We identified 32 regional-fire years as those with five or more sites with fire. Fires were remarkably widespread during such years, including one year (1748) in which fires were recorded at 10 sites across what are today seven national forests plus one site on state land. During regional-fire years, spring-summers were significantly warm and summers were significantly warm-dry whereas the opposite conditions prevailed during the 99 years when no fires were recorded at any of our sites (no-fire years). Climate in prior years was not significantly associated with regional- or no-fire years. Years when fire was recorded at only a few of our sites occurred under a broad range of climate conditions, highlighting the fact that the regional climate drivers of fire are most evident when fires are synchronized across a large area. No-fire years tended to occur during La Niña years, which tend to have anomalously deep snowpacks in this region. However, ENSO was not a significant driver of regional-fire years, consistent with the greater influence of La Niña than El Niño conditions on the spring climate of this region. PDO was not a significant driver of past fire, despite being a strong driver of modern spring climate and modern regional-fire years in the northern Rockies.

Millar RB, Anderson MJ, Tolimieri N.. Much ado about nothings: using zero similarity points in distance-decay curves. Ecology 92: 1717-1722

September 2011


286 Reads

Distance decay is used to describe the (usually exponential) decay in ecological similarity of assemblages between two sites as a function of their distance apart along an environmental gradient. Exponential distance-decay curves are routinely fitted by calculating the ecological similarity between each pair of sites, and fitting a linear regression to the points on a scatter plot of log-similarity vs. distance (x-axis). However, pairs of sites where the assemblages have no species in common pose a problem, because the similarity is zero, and the log transformation cannot be applied. Common fixes to this problem (i.e., either removing or transforming the zero values) are shown to have undesirable consequences and to give widely disparate estimates. A new method is presented as a special case of a generalized dissimilarity model. It is fitted very quickly and easily using existing software, and it does not require removal or transformation of the zero similarity points. Its simplicity makes it convenient for use in conjunction with the resampling methods that are routinely employed to test hypotheses, to obtain standard errors of estimated parameters, or to compare distance-decay curves. A word of caution about standard application of the bootstrap is noted, and modified bootstrap and jackknife alternatives are demonstrated.

Ulrich W, Gotelli NJ.. Null model analysis of species nestedness patterns. Ecology 88: 1824-1831

August 2007


331 Reads

Nestedness is a common biogeographic pattern in which small communities form proper subsets of large communities. However, the detection of nestedness in binary presence-absence matrices will be affected by both the metric used to quantify nestedness and the reference null distribution. In this study, we assessed the statistical performance of eight nestedness metrics and six null model algorithms. The metrics and algorithms were tested against a benchmark set of 200 random matrices and 200 nested matrices that were created by passive sampling. Many algorithms that have been used in nestedness studies are vulnerable to type I errors (falsely rejecting a true null hypothesis). The best-performing algorithm maintains fixed row and fixed column totals, but it is conservative and may not always detect nestedness when it is present. Among the eight indices, the popular matrix temperature metric did not have good statistical properties. Instead, the Brualdi and Sanderson discrepancy index and Cutler's index of unexpected presences performed best. When used with the fixed-fixed algorithm, these indices provide a conservative test for nestedness. Although previous studies have revealed a high frequency of nestedness, a reanalysis of 288 empirical matrices suggests that the true frequency of nested matrices is between 10% and 40%.

Controls on vegetation structure in Southwestern ponderosa pine forests, 1941 and 2004

October 2007


80 Reads

Long-term studies can broaden our ecological understanding and are particularly important when examining contingent effects that involve changes to dominance by long-lived species. Such a change occurred during the last century in Southwestern (USA) ponderosa pine (Pinus ponderosa) forests. We used five livestock grazing exclosures established in 1912 to quantify vegetation structure in 1941 and 2004. Our objectives were to (1) assess the effects of historical livestock grazing on overstory structure and age distribution, (2) assess the effects of recent livestock grazing and overstory on understory vegetation, and (3) quantify and explain changes in understory vegetation between 1941 and 2004. In 1941, canopy cover of tree regeneration was significantly higher inside exclosures. In 2004, total tree canopy cover was twice as high, density was three times higher, trees were smaller, and total basal area was 40% higher inside exclosures. Understory species density, herbaceous plant density, and herbaceous cover were negatively correlated with overstory vegetation in both years. Most understory variables did not differ between grazing treatments in 1941 but were lower inside exclosures in 2004. Differences between grazing treatments disappeared once overstory effects were accounted for, indicating that they were due to the differential overstory response to historical livestock grazing practices. Between 1941 and 2004, species density declined by 34%, herbaceous plant density by 37%, shrub cover by 69%, total herbaceous cover by 59%, graminoid cover by 39%, and forb cover by 82%. However, these variables did not differ between grazing treatments or years once overstory effects were accounted for, indicating that the declines were driven by the increased dominance of the overstory during this period. Our results demonstrate that historical livestock grazing practices are an aspect of land-use history that can affect ecosystem development. Grazing history must be considered when extrapolating results from one site to another. In addition, the understory vegetation was more strongly controlled by the ponderosa pine overstory than by recent livestock grazing or by temporal dynamics, indicating that overstory effects must be accounted for when examining understory responses in this ecosystem.

Increased plant biomass in a High Arctic heath community from 1981 to 2008

October 2009


250 Reads

The Canadian High Arctic has been warming for several decades. Over this period, tundra plant communities have been influenced by regional climate change, as well as other disturbances. At a site on Ellesmere Island, Nunavut, Canada, we measured biomass and composition changes in a heath community over 13 years using a point-intercept method in permanent plots (1995-2007) and over 27 years using a biomass harvest comparison (1981-2008). Results from both methods indicate that the community became more productive over time, suggesting that this ecosystem is currently in transition. Bryophyte and evergreen shrub abundances increased, while deciduous shrub, forb, graminoid, and lichen cover did not change. Species diversity also remained unchanged. Because of the greater evergreen shrub cover, canopy height increased. From 1995 to 2007, mean annual temperature and growing season length increased at the site. Maximum thaw depth increased, while soil water content did not change. We attribute the increased productivity of this community to regional warming over the past 30-50 years. This study provides the first plot-based evidence for the recent pan-Arctic increase in tundra productivity detected by satellite-based remote-sensing and repeat-photography studies. These types of ground-level observations are critical tools for detecting and projecting long-term community-level responses to warming.

Erratum: Methods to quantify variable importance: implications for the analysis of noisy ecological data (Ecology (2009) 90 (348-355))

March 2009


96 Reads

Determining the importance of independent variables is of practical relevance to ecologists and managers concerned with allocating limited resources to the management of natural systems. Although techniques that identify explanatory variables having the largest influence on the response variable are needed to design management actions effectively, the use of various indices to evaluate variable importance is poorly understood. Using Monte Carlo simulations, we compared six different indices commonly used to evaluate variable importance; zero-order correlations, partial correlations, semipartial correlations, standardized regression coefficients, Akaike weights, and independent effects. We simulated four scenarios to evaluate the indices under progressively more complex circumstances that included correlation between explanatory variables, as well as a spurious variable that was correlated with other explanatory variables, but not with the dependent variable. No index performed perfectly under all circumstances, but partial correlations and Akaike weights performed poorly in all cases. Zero-order correlations was the only measure that detected the presence of a spurious variable, whereas only independent effects assigned overlap areas correctly once the spurious variable was removed. We therefore recommend using zero-order correlations to eliminate predictor variables with correlations near zero, followed by the use of independent effects to assign overlap areas and rank variable importance.

Multi-season climate synchronized forest fires throughout the 20th century, Northern Rockies, USA

March 2008


38 Reads

We inferred climate drivers of 20th-century years with regionally synchronous forest fires in the U.S. northern Rockies. We derived annual fire extent from an existing fire atlas that includes 5038 fire polygons recorded from 12,070,086 ha, or 71% of the forested land in Idaho and Montana west of the Continental Divide. The 11 regional-fire years, those exceeding the 90th percentile in annual fire extent from 1900 to 2003 (>102,314 ha or approximately 1% of the fire atlas recording area), were concentrated early and late in the century (six from 1900 to 1934 and five from 1988 to 2003). During both periods, regional-fire years were ones when warm springs were followed by warm, dry summers and also when the Pacific Decadal Oscillation (PDO) was positive. Spring snowpack was likely reduced during warm springs and when PDO was positive, resulting in longer fire seasons. Regional-fire years did not vary with El Niño-Southern Oscillation (ENSO) or with climate in antecedent years. The long mid-20th century period lacking regional-fire years (1935-1987) had generally cool springs, generally negative PDO, and a lack of extremely dry summers; also, this was a period of active fire suppression. The climate drivers of regionally synchronous fire that we inferred are congruent with those of previous centuries in this region, suggesting a strong influence of spring and summer climate on fire activity throughout the 20th century despite major land-use change and fire suppression efforts. The relatively cool, moist climate during the mid-century gap in regional-fire years likely contributed to the success of fire suppression during that period. In every regional-fire year, fires burned across a range of vegetation types. Given our results and the projections for warmer springs and continued warm, dry summers, forests of the U.S. northern Rockies are likely to experience synchronous, large fires in the future.

P values are only an index to evidence: 20th-vs. 21st-century statistical science

March 2014


154 Reads

Early statistical methods focused on pre-data probability statements (i.e., data as random variables) such as P values; these are not really inferences nor are P values evidential. Statistical science clung to these principles throughout much of the 20th century as a wide variety of methods were developed for special cases. Looking back, it is clear that the underlying paradigm (i.e., testing and P values) was weak. As Kuhn (1970) suggests, new paradigms have taken the place of earlier ones: this is a goal of good science. New methods have been developed and older methods extended and these allow proper measures of strength of evidence and multimodel inference. It is time to move forward with sound theory and practice for the difficult practical problems that lie ahead. Given data the useful foundation shifts to post-data probability statements such as model probabilities (Akaike weights) or related quantities such as odds ratios and likelihood intervals. These new methods allow formal inference from multiple models in the a prior set. These quantities are properly evidential. The past century was aimed at finding the "best" model and making inferences from it. The goal in the 21st century is to base inference on all the models weighted by their model probabilities (model averaging). Estimates of precision can include model selection uncertainty leading to variances conditional on the model set. The 21st century will be about the quantification of information, proper measures of evidence, and multi-model inference. Nelder (1999:261) concludes, "The most important task before us in developing statistical science is to demolish the P-value culture, which has taken root to a frightening extent in many areas of both pure and applied science and technology".

FIG. 1. Spatial location of study site, including (a) map of the state of Alabama, USA, with the Mobile Bay basin indicated, and with the Cahaba River highlighted by the rectangle, (b) the Cahaba River watershed, with sampling sites marked within each of the three physiographic provinces, and images to illustrate differences in geomorphic features between them. Photo credit for Fall Line picture: Timothy Wynn.
TABLE 1 . Extended.
TABLE 2 . Mixed-model ANOVA results.
FIG. 3. Principal components analysis demonstrating variation in sediment characteristics between physiographic provinces (indicated by symbol shade).
Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure. Ecology 94: 2249-2262

October 2013


302 Reads

Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes.

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