Towards the extremes: A critical analysis of pointer year detection methods

To study growth responses of trees to extreme events, analyses of so-called ‘pointer years’ are often performed. Thereby, the term pointer year refers to years in which a majority of trees shows extraordinary growth responses, like very narrow (or wide) ring widths. A wide variety of methods has been used to analyze pointer years, hampering comparisons between studies. The latter illustrates that there is a strong need to harmonize pointer year detection methods. This review contributes to that by describing and comparing the main methods (and variants thereof) found in the literature for the last two decades, both in a qualitative and quantitative way. We discuss methodological considerations and provide recommendations how to proceed with pointer year detection in future. Given that the individual methods for pointer year detection were found to highlight different aspects of extraordinary growth, the one method cannot completely substitute the other. Hence, we suggest to use multiple methods in a harmonized way to get the deepest insight into the nature of pointer years.     

Climate sensitivity is affected by growth differentiation along the length of Juniperus communis L. shrub stems in the Ural Mountains

Arctic and alpine shrubs are valuable for future dendro-ecological and dendro-climatological studies in regions where trees are sparse or absent. A commonly accepted procedure of sampling shrub stem disks is at the root collar. However many shrub studies report low inter-series correlations in radial measurements as compared to trees. Many studies also report cross-dating difficulties with radial measurements from shrubs within a stand and commonly attribute this to differential growth along the length of the stem. So does one stem disk entirely represent the environmental parameters the shrub might be reacting to? Does change in sampling location of the stem disk affect the subsequent ring-width chronologies and climate sensitivity? To tackle these questions, we investigated Juniperus communis L. – a species wide spread in the circumpolar arctic – across a latitudinal gradient in the Ural Mountains. Based on traditional radial ring-width measurements we assessed growth synchronicity along the length of shrub stems. We also compared ring width chronologies representing different stem heights with respect to their relationships with temperature and the standardized precipitation evapotranspiration index (SPEI). Growth patterns often varied significantly among stems disks of the same shrubs, resulting in dissimilar climate-growth relationships of stem disk chronologies. For correlations with temperature, stem disks at 20 cm distance from the root collar captured the best signal. For correlations with SPEI data we could not find any specific stem disk chronology with highest sensitivity. At least in our dataset, no “perfect sampling height” with high climate sensitivity exists and our results thus highlight that a single stem disk from a shrub may not completely represent the shrub’s growth response to climate parameters.     

Growth releases of three shade‐tolerant species following canopy gap formation in old‐growth forests

Questions: Do the number, duration and magnitude of growth releases following formation of natural, fine‐scale canopy gaps differ among shade‐tolerant Thuja plicata, Tsuga heterophylla and Abies amabilis? What is the relative importance of tree‐level and gap‐level variables in predicting the magnitude and duration of releases? What does this tell us about mechanisms of tree species coexistence in such old‐growth forests? Location: Coastal British Columbia, Canada. Methods: We estimated the timing of formation of 20 gaps using dendroecological techniques and extracted increment cores from all three species growing around or within gaps. Using a species‐ and ecosystem‐specific release‐detection method, we determined the number of trees experiencing a release following gap formation. We quantified the duration and magnitude of individual releases and estimated the influence of tree‐level and gap‐level variables on these release attributes. Results: Eighty‐seven per cent (304 of 348) of all trees experienced a release following gap formation. T. heterophylla and A. amabilis experienced higher magnitude and longer duration releases than T. plicata. The effect of diameter on the duration of releases varied among species, with T. heterophylla and A. amabilis experiencing decreasing, and T. plicata experiencing increasing, duration of releases with increasing diameter. The effect of growth rate prior to a release on the magnitude of releases varied among trees of different diameters, with the slowest growing and smallest individuals of all species experiencing the most intensive releases. Conclusions: Our results provide detailed information on the number, duration and magnitude of growth releases of the above three species following gap formation. Differences in response to canopy gaps suggest differences in how these species ascend to the canopy strata. T. plicata may be less dependent on gaps to reach the canopy. Differing strategies for ascending to the canopy strata may be important in facilitating coexistence of these three species in old‐growth forests of coastal British Columbia.     

Development and application of boundary-line release criteria

Identifying releases from suppression represents one of the most fundamental dendroecological procedures for quantifying forest disturbance histories. In this study we evaluate boundary-line release criteria, which incorporates the effects of growth history on release response. In eastern hemlock (Tsuga canadensis L.) the maximum possible value of a pulse in percent-growth change is dependent on growth decline immediately prior to the pulse. Maximum values of percent-growth-change decline exponentially as prior growth rate increases. This negative exponential rate is quantified as a boundary line, which is used to scale each percent-growth change pulse by the maximum possible value predicted by prior growth rate. The consistency of the relationship between radial growth prior to a release and the magnitude of the release is evaluated in multiple eastern hemlock data sets. Trees from diverse sites show large releases that approach the maximum value predicted by the prior-growth rates. These sites tend to have a history of disturbance, suggesting that disturbance is the most influential variable determining the magnitude of release response. Possible exceptions are sites on the northern and western borders of eastern hemlock's range, which consistently fall short of the boundary line and may be exhibiting unique relationships between prior growth and percent-growth change. Yet overall the relationship between prior growth and percent-growth change appears to be consistent across much of eastern hemlock's range. Furthermore, we demonstrate that similar boundary lines occur in Pinus ponderosa (Laws.), Pinus echinata (Mill.), Quercus alba (L.), and Quercus macrocarpa (Michx.). This suggests that prior growth could form the basis of a more unified set of release criteria better able to standardize release responses within and among species. Standardized release criteria would allow more accurate comparisons of disturbance histories among sites, species, and even across landscapes.     

Ecological and methodological drivers of species’ distribution and phenology responses to climate change

Climate change is shifting species’ distribution and phenology. Ecological traits, such as mobility or reproductive mode, explain variation in observed rates of shift for some taxa. However, estimates of relationships between traits and climate responses could be influenced by how responses are measured. We compiled a global data set of 651 published marine species’ responses to climate change, from 47 papers on distribution shifts and 32 papers on phenology change. We assessed the relative importance of two classes of predictors of the rate of change, ecological traits of the responding taxa and methodological approaches for quantifying biological responses. Methodological differences explained 22% of the variation in range shifts, more than the 7.8% of the variation explained by ecological traits. For phenology change, methodological approaches accounted for 4% of the variation in measurements, whereas 8% of the variation was explained by ecological traits. Our ability to predict responses from traits was hindered by poor representation of species from the tropics, where temperature isotherms are moving most rapidly. Thus, the mean rate of distribution change may be underestimated by this and other global syntheses. Our analyses indicate that methodological approaches should be explicitly considered when designing, analysing and comparing results among studies. To improve climate impact studies, we recommend that (1) reanalyses of existing time series state how the existing data sets may limit the inferences about possible climate responses; (2) qualitative comparisons of species’ responses across different studies be limited to studies with similar methodological approaches; (3) meta‐analyses of climate responses include methodological attributes as covariates; and (4) that new time series be designed to include the detection of early warnings of change or ecologically relevant change. Greater consideration of methodological attributes will improve the accuracy of analyses that seek to quantify the role of climate change in species’ distribution and phenology changes.     

MtreeRing: An R package with graphical user interface for automatic measurement of tree ring widths using image processing techniques

Accurate measurements of ring-width series are essential for dendrochronological analyses. We present an R package MtreeRing for ring-width measurements on scanned digital images. A morphological alternate sequential filter is used for noise reduction in the original image. Ring boundaries are determined by the steepest negative slopes in the light reflectance of latewood-earlywood transitions. To automatically identify tree rings, the package provides three alternative methods (watershed-based segmentation, Canny edge detector, and a linear detection algorithm), each with advantages and disadvantages and suited to different wood anatomical features. The user can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. Differences in ring-width measurements between MtreeRing and WinDENDRO in a given coniferous species (Larix gmelinii) were assessed, and no significant difference between programs was found. Furthermore, the package provides an R-based web application which was developed using the Shiny framework. This beginner-friendly application allows viewing and interacting with tree ring images. It requires no programming experience and can run on either a local computer or a remote server.     

Variation in radial growth responses to drought among species, site, and canopy strata

 Radial growth responses to drought were examined in the tree-ring records of six species growing within two locations of differing land-use history and soil moisture characteristics, and in overstory and understory canopy positions in northern Virginia. Tree species experienced differential ring-width reductions during or immediately following four severe drought periods occurring from 1930 to 1965 and were influenced by climatic variables including annual and summer temperatures, annual precipitation, and annual Palmer Drought Severity Index. Relative growth comparisons averaged across species before and after drought years indicated that understory trees on dry-mesic sites grew 11% faster after drought compared to pre-drought rates while mesic site trees in both canopy positions grew approximately 4% slower. Superposed epoch analysis indicated that Liriodendron tulipifera growing on mesic sites experienced greater ring-width reductions associated with drought than co-occurring, more drought-tolerant Quercus alba and Q. velutina. On dry-mesic sites, L. tulipifera also experienced greatly reduced growth as a result of drought but exhibited significant growth increases following individual drought events. Quercus alba was the only species that exhibited a consistent, significant ring-width decrease associated with all droughts on dry-mesic sites. In contrast, Pinus virginiana was least impacted by drought on dry-mesic sites but was much more impacted by drought on mesic sites, indicating a drought×site interaction for this species. Overstory Carya glabra and Q. alba experienced larger growth decreases during drought on dry-mesic versus mesic sites. Understory tree growth reductions did not differ between site types but were often significantly larger than overstory responses of the same species on mesic sites. Following drought, most trees exhibited growth reductions lasting 2–3 years, although several species experienced reductions lasting up to 6 years. The results of this study suggest that tree rings represent an important long-term proxy for leaf-level ecophysiological measurements of growth responses to drought periods. Received: 31 July 1996 / Accepted: 16 April 1997     

Protein Networks Reveal Detection Bias and Species Consistency When Analysed by Information-Theoretic Methods

We apply our recently developed information-theoretic measures for the characterisation and comparison of protein–protein interaction networks. These measures are used to quantify topological network features via macroscopic statistical properties. Network differences are assessed based on these macroscopic properties as opposed to microscopic overlap, homology information or motif occurrences. We present the results of a large–scale analysis of protein–protein interaction networks. Precise null models are used in our analyses, allowing for reliable interpretation of the results. By quantifying the methodological biases of the experimental data, we can define an information threshold above which networks may be deemed to comprise consistent macroscopic topological properties, despite their small microscopic overlaps. Based on this rationale, data from yeast–two–hybrid methods are sufficiently consistent to allow for intra–species comparisons (between different experiments) and inter–species comparisons, while data from affinity–purification mass–spectrometry methods show large differences even within intra–species comparisons.     

Statistical analysis of structural compensatory growth: how can we reduce the rate of false detection?

Compensatory growth (CG) is a key issue in work aiming at a full understanding of the adaptive significance of growth plasticity and its carryover effects on life-history. The number of studies addressing evolutionary explanations for CG has increased rapidly during the last few years, but there has not been a parallel gain in our understanding of the methodological difficulties associated with the analysis of CG. We point out two features of growth that can have serious consequences for detecting CG: (1) size dependence of growth rates, which causes nonlinearity of growth trajectories, and; (2) temporal overlapping of structural growth and replenishment of energy reserves after a period of famine. We show that the currently used methods can be prone to spurious detection of CG (Type I error) under conditions of nonlinear growth, and therefore lead to the accumulation of a significant amount of false “empirical support.” True and simulated growth data provided consistent results suggesting that a substantial fraction of the existing evidence for CG may be spurious. A small curvature in the growth trajectory can lead to spurious “detection” of CG when control and manipulated trajectories are compared over the same time interval (the “simultaneous” approach). We present a novel, robust method (the “asynchronous” approach) based on the accurate selection of control trajectories and comparison of control and treatment growth rates at different times. This method enables a reliable test to be performed for compensation under asymptotic growth. While the general results of our simulations do not support the application of conventional methods to the general case of nonlinear growth trajectories under the simultaneous approach, simple methods may prove valid if the experimental design allows for asynchronous comparisons. We advocate an alternative approach to deal with “safe” detection of CG that overcomes the problems associated with the occurrence of nonlinear and asymptotic growth, and provide recommendations for improving CG study designs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biomass size distributions as a tool for characterizing lake fish communities

Biomass size distributions (BSDs) can be useful tools to (1) summarize complex information about fish community structure in a condensed graphical form, facilitating the characterization of freshwater fish communities, (2) compare the position of fish communities along environmental gradients and (3) elucidate major trophic interactions in freshwater fish communities. Biomass size distributions are presented by taxonomic and trophic group, for a selection of fish communities from 35 Scandinavian and eight Dutch lakes. They were used for the analysis of taxonomic and trophic shifts in the fish communities along a large environmental gradient, with productivity (expressed as total phosphorus concentration, TP) as its most important component. Regression analysis of fish community variables (such as proportion of cyprinids, or biomass of benthivores) were consistent with the semi‐quantitative conclusions drawn from BSDs, regarding taxonomic and trophic shifts with changes in TP in both Scandinavian and Dutch lakes, especially an increase in the amount and size of benthivorous fishes with increasing TP‐levels. In addition, differences in mortality and growth rates were shown to partly explain differences in BSDs. Biomass size distributions thus provide an integrative tool for qualitative and quantitative comparisons among fish communities.     

Variation in the self-incompatibility response within and among populations of the tropical shrub Witheringia solanacea (Solanaceae)

Breakdown of genetically enforced self-incompatibility (SI), an extremely common and important evolutionary transition in plants, has conventionally been conceived as a qualitative rather than a quantitative change. We evaluated qualitative and quantitative variation in SI for four populations of Witheringia solanacea in Costa Rica, examining growth of self-pollen tubes in pollinations of buds and mature flowers. We also measured levels of RNase production in styles to determine whether enzyme production was correlated with differences in self-rejection. The two small populations contained both self-compatible (SC) individuals and obligate outcrossers (female or SI). Plants in the two large populations were uniformly SI as revealed by pollen tube growth, although several of these individuals sporadically set seed autogamously. Stylar RNase activity did not differ significantly between bud and mature flowers, but self-pollen tube growth did differ, suggesting that a gene product in addition to S-RNase is responsible for developmental onset of SI. Population-level differences in RNase activity were consistent with differences in the strength of the rejection response in bud pollinations, suggesting that a threshold level of S-RNase, in combination with other factors, is necessary for SI. Our results support a growing body of evidence that not only qualitative variation in SI, but also quantitative variation may be functionally significant.     

Methodologically induced differences in oak site classifications in a homogeneous tree-ring network

Spatiotemporal variations in tree growth are induced by varying environmental conditions. Different methods like variants of the principal component analysis and the hierarchical cluster analysis are commonly applied in dendroecology to separate subsets of growth patterns within large tree-ring datasets. To seek for methodological differences in classification techniques and their specific characteristics, we compared three standard methods using a homogeneous oak (Quercus spp.) network from temperate forests in Central-West Germany. Classifications of the original dataset consisting of 46 oak ring-width sites, carried out with the varimax rotated principle component analysis, Ward's method and the average linkage method, reveal differences in the classification of approximately 20% of the sites. Analyses with modified datasets are calculated to evaluate effects of dataset extension, different time periods and different tree-ring detrendings. The application of the principal component analysis generally leads to the most stable site classifications, whereas the most sensitive response to changes in the dataset is obtained by Ward's method. The average linkage method separates single sites in the classification and thus emphasises outliers within the tree-ring network.     

Growth rate and nutritional status of wild and released reared juvenile turbot in southern Kattegat, Denmark

More than 800 000 reared juvenile turbot Psetta maxima were released in Danish waters during the period 1990 to 2002, as part of a stock enhancement programme. Performance of the released fish has been investigated using a combination of surveys and experimental studies. A total of 1278 wild fish and 439 alizarine marked released fish were caught in 16 surveys from 1993 to 1997. Recaptures were made over a period of c . 2 years after release. Results of growth analysis and measurements of nutritional status (condition factor, liver index, liver dry matter and otolith residual mass) showed only minor differences between wild and released fish. Growth rates of wild and of released fish were comparable to fish kept in the laboratory at the same temperature (specific length growth rate c . 0·5% day⁻¹ at 75–185 mm total length and 12·5° C). The results indicated sufficient food in the release area, but significant differences in growth and in nutritional status, between  years, were also observed. Nutritional status of both wild and released fish was comparable to fed fish in the experiments and significantly higher than in fish starved for  > 1 week. The effects of the transport and release procedures used were examined by simulated releases in laboratory tanks. The fish were observed to be feeding and growing normally during the first week after simulated release, suggesting this species to be relatively robust and unaffected by the handling and release procedures.     

Estimation of Staphylococcus aureus Growth Parameters from Turbidity Data: Characterization of Strain Variation and Comparison of Methods

Turbidity methods offer possibilities for generating data required for addressing microorganism variability in risk modeling given that the results of these methods correspond to those of viable count methods. The objectives of this study were to identify the best approach for determining growth parameters based on turbidity data and use of a Bioscreen instrument and to characterize variability in growth parameters of 34 Staphylococcus aureus strains of different biotypes isolated from broiler carcasses. Growth parameters were estimated by fitting primary growth models to turbidity growth curves or to detection times of serially diluted cultures either directly or by using an analysis of variance (ANOVA) approach. The maximum specific growth rates in chicken broth at 17°C estimated by time to detection methods were in good agreement with viable count estimates, whereas growth models (exponential and Richards) underestimated growth rates. Time to detection methods were selected for strain characterization. The variation of growth parameters among strains was best described by either the logistic or lognormal distribution, but definitive conclusions require a larger data set. The distribution of the physiological state parameter ranged from 0.01 to 0.92 and was not significantly different from a normal distribution. Strain variability was important, and the coefficient of variation of growth parameters was up to six times larger among strains than within strains. It is suggested to apply a time to detection (ANOVA) approach using turbidity measurements for convenient and accurate estimation of growth parameters. The results emphasize the need to consider implications of strain variability for predictive modeling and risk assessment.     

Genetic variation in resistance, but not tolerance, to a protozoan parasite in the monarch butterfly

Natural selection should strongly favour hosts that can protect themselves against parasites. Most studies on animals so far have focused on resistance, a series of mechanisms through which hosts prevent infection, reduce parasite growth or clear infection. However, animals may instead evolve tolerance, a defence mechanism by which hosts do not reduce parasite infection or growth, but instead alleviate the negative fitness consequences of such infection and growth. Here, we studied genetic variation in resistance and tolerance in the monarch butterfly (Danaus plexippus) to its naturally occurring protozoan parasite, Ophryocystis elektroscirrha. We exposed 560 monarch larvae of 19 different family lines to one of five different parasite inoculation doses (0, 1, 5, 10 and 100 infective spores) to create a range of parasite loads in infected butterflies. We then used two proxies of host fitness (adult lifespan and body mass) to quantify: (i) qualitative resistance (the ability to prevent infection; also known as avoidance or anti-infection resistance); (ii) quantitative resistance (the ability to limit parasite growth upon infection; also known as control or anti-growth resistance); and (iii) tolerance (the ability to maintain fitness with increasing parasite infection intensity). We found significant differences among host families in qualitative and quantitative resistance, indicating genetic variation in resistance. However, we found no genetic variation in tolerance. This may indicate that all butterflies in our studied population have evolved maximum tolerance, as predicted by some theoretical models.     

Natural growth and diet of known‐age pallid sturgeon (Scaphirhynchus albus) early life stages in the upper Missouri River basin,Montana and North Dakota

Prior to anthropogenic modifications, the historic Missouri River provided ecological conditions suitable for reproduction, growth, and survival of pallid sturgeon Scaphirhynchus albus. However, little information is available to discern whether altered conditions in the contemporary Missouri River are suitable for feeding, growth and survival of endangered pallid sturgeon during the early life stages. In 2004 and 2007, nearly 600 000 pallid sturgeon free embryos and larvae were released in the upper Missouri River and survivors from these releases were collected during 2004–2010 to quantify natural growth rates and diet composition. Based on genetic analysis and known‐age at release (1–17 days post‐hatch, dph), age at capture (dph, years) could be determined for each survivor. Totals of 23 and 28 survivors from the 2004 and 2007 releases, respectively, were sampled. Growth of pallid sturgeon was rapid (1.91 mm day^?1) during the initial 13–48 dph, then slowed as fish approached maximum length (120–140 mm) towards the end of the first growing season. The diet of young‐of‐year pallid sturgeon was comprised of Diptera larvae, Diptera pupae, and Ephemeroptera nymphs. Growth of pallid sturgeon from ages 1–6 years was about 48.0 mm year^?1. This study provides the first assessment of natural growth and diet of young pallid sturgeon in the wild. Results depict pallid sturgeon growth trajectories that may be expected for naturally produced wild stocks under contemporary habitat conditions in the Missouri River and Yellowstone River.     

Growth pattern of Picea rubens prior to canopy recruitment

A majority (72%) of Picea rubens Sarg. (red spruce) trees in an old-growth spruce-fir forest in the Great Smoky Mountains underwent episodes of radial growth suppression and release before they reached the forest canopy. Prior to canopy recruitment, trees experienced an average of 1.43 and a maximum of 7 suppression periods with an average ring width of 0.257 mm. Duration of suppression periods ranged from 4 to 79 years with an average of 19.05 years, which was significantly shorter than the average duration of release periods (29.00 years). Mean ring width in a suppression period was negatively correlated with duration of the suppression period. The opposite was true for release periods. The severity of suppression had no significant effect on mean ring width in subsequent release periods. Greater suppression was observed in the recent growth pattern of current non-canopy trees than in the historical growth pattern reconstructed from current canopy trees. Growth releases prior to canopy recruitment, triggered by small gaps or neighboring gaps, displayed a continuous pattern over the last two centuries and had consistent frequency in recent decades. By contrast, canopy recruitment resulting from large-gap disturbances was discontinuous over the last two centuries, and less frequent after 1850.     

Traditional Water Resource Management and Water Quality in Rural Tanzania

Traditional resource management (TRM) is largely based on local ecological knowledge (LEK). In regions where formal institutional control of natural resources is limited due to a lack of coordination or stakeholder involvement, communities rely on TRM to manage common-pool resources. This paper examines TRM among the Sonjo in rural Northern Tanzania, with particular reference to catchment forest protection and water quality. We first document the ecological knowledge of traditional resource managers, and then describe the differences between traditionally managed water sources and formal, government managed resources. Using both qualitative and quantitative methods to examine water use, perceptions of water quality, and bacterial water quality, significant differences were detected among river basins within seasons and between seasons. Our findings indicate that the Sonjo, well known for their traditional forest conservation practices and irrigation management, may also benefit from TRM through improved water quality. The examination of traditional methods of water conservation provides insight into how communities in resource-stressed regions thrive despite seasonal droughts and flooding.     

The analysis of recessive lethal mutations in mice by using two-dimensional gel electrophoresis of liver proteins

We have used two-dimensional gel electrophoresis (2DE) coupled with computer-assisted data analysis to analyze liver-protein expression in mice known to be heterozygous carriers of recessive lethal mutations induced in In(1)1Rk or In(7)13Rk inversion stocks by exposure to either triethylene melamine or ionizing radiation. Carriers of 8 different mutations and corresponding littermate controls (average of 17 individuals in each group) were screened for liver-protein differences. Both qualitative and quantitative protein differences were detected that correlated with unique pedigrees among the mouse stocks analyzed. Such strain-specific differences demonstrated that quantitative differences (either increases or decreases) in protein abundance of greater than 25% can be readily detected by using this 2DE system. Thus the 50% reduction in expression of a protein expected in the event of a structural gene deletion is well within the level of detection. No significant quantitative decreases in protein expression that correlated with the recessive lethal mutations were detected, however.