Papers by David Ratkowsky
Plants
Measuring the inequality of leaf area distribution per plant (ILAD) can provide a useful tool for... more Measuring the inequality of leaf area distribution per plant (ILAD) can provide a useful tool for quantifying the influences of intra- and interspecific competition, foraging behavior of herbivores, and environmental stress on plants’ above-ground architectural structures and survival strategies. Despite its importance, there has been limited research on this issue. This paper aims to fill this gap by comparing four inequality indices to measure ILAD, using indices for quantifying household income that are commonly used in economics, including the Gini index (which is based on the Lorenz curve), the coefficient of variation, the Theil index, and the mean log deviation index. We measured the area of all leaves for 240 individual plants of the species Shibataea chinensis Nakai, a drought-tolerant landscape plant found in southern China. A three-parameter performance equation was fitted to observations of the cumulative proportion of leaf area vs. the cumulative proportion of leaves pe...
Frontiers in Plant Science
Leaf shape is an important leaf trait, with ovate leaves common in many floras. Recently, a new l... more Leaf shape is an important leaf trait, with ovate leaves common in many floras. Recently, a new leaf shape model (referred to as the MLRF equation) derived from temperature-dependent bacterial growth was proposed and demonstrated to be valid in describing leaf boundaries of many species with ovate leaf shape. The MLRF model’s parameters can provide valuable information of leaf shape, including the ratio of lamina width to length and the lamina centroid location on the lamina length axis. However, the model wasn’t tested on a large sample of a single species, thereby limiting its overall evaluation for describing leaf boundaries, for evaluating lamina bilateral asymmetry and for calculating lamina centroid location. In this study, we further test the model using data from two Lauraceae species,Cinnamomum camphoraandMachilus leptophylla, with >290 leaves for each species. The equation was found to be credible for describing those shapes, with all adjusted root-mean-square errors (R...
European Journal of Plant Pathology, 2022
Ceratocystis wilt and canker disease has devastated Acacia mangium plantations in south-east Asia... more Ceratocystis wilt and canker disease has devastated Acacia mangium plantations in south-east Asia. Current screening methodologies to identify resistant or tolerant germplasm use potted plants in a greenhouse as a preliminary screening to select material for field trials, but these tests are time-consuming, motivating a search for rapid screening protocols. In this study, inoculation procedures were tested on three species of Acacia, viz. A. mangium, A. crassicarpa and a hybrid of A. auriculiformis and A. mangium, using three isolates of Ceratocystis manginecans. Mycelial plugs were compared with spore suspensions as inoculum to infect artificial wounds on the stems of A. mangium potted plants. The rapid screening protocols involved inoculation of stem segments with mycelial plugs and detached phyllodes with a spore suspension, with susceptibility measured by lesion length on the stems or necrosis length on the phyllodes. Both mycelial plugs and spore suspensions produced a similar ...
Wildfires in wet eucalypt forests, depending on their intensity and frequency, generate dead wood... more Wildfires in wet eucalypt forests, depending on their intensity and frequency, generate dead wood of varying sizes and in many different stages of decay. Windthrow events also contribute to large dead wood lying on the forest floor. In this study, CWD (coarse woody debris), defined as dead wood at least 10 cm diameter and 1 m long, and dead standing trees (stags) were measured and their attributes recorded in four 50 x 50 m plots within ca. 1 km of each other but with differing wildfire histories in a tall, wet, native Eucalyptus obliqua forest in southern Tasmania. Maps of the CWD and stags for each of the four plots were drawn and show substantial differences between the four plots. Information from four other surveys of CWD in the same forest type provided a degree of replication to this study. Comparisons among the studies showed that the CWD volumes in plots of similar age since wildfire were very variable and most likely reflect the chance location of large fallen eucalypts in...
Leho Tedersoo,*† Mohammad Bahram,† Sergei Põlme, Urmas Kõljalg, Nourou S. Yorou, Ravi Wijesundera... more Leho Tedersoo,*† Mohammad Bahram,† Sergei Põlme, Urmas Kõljalg, Nourou S. Yorou, Ravi Wijesundera, Luis Villarreal Ruiz, Aída M. Vasco-Palacios, Pham Quang Thu, Ave Suija, Matthew E. Smith, Cathy Sharp, Erki Saluveer, Alessandro Saitta, Miguel Rosas, Taavi Riit, David Ratkowsky, Karin Pritsch, Kadri Põldmaa, Meike Piepenbring, Cherdchai Phosri, Marko Peterson, Kaarin Parts, Kadri Pärtel, Eveli Otsing, Eduardo Nouhra, André L. Njouonkou, R. Henrik Nilsson, Luis N. Morgado, Jordan Mayor, Tom W. May, Luiza Majuakim, D. Jean Lodge, Su See Lee, Karl-Henrik Larsson, Petr Kohout, Kentaro Hosaka, Indrek Hiiesalu, Terry W. Henkel, Helery Harend, Liang-dong Guo, Alina Greslebin, Gwen Grelet, Jozsef Geml, Genevieve Gates, William Dunstan, Chris Dunk, Rein Drenkhan, John Dearnaley, André De Kesel, Tan Dang, Xin Chen, Franz Buegger, Francis Q. Brearley, Gregory Bonito, Sten Anslan, Sandra Abell, Kessy Abarenkov RESEARCH ARTICLE SUMMARY
The present study compares the macrofungi at three study sites in the lowland wet eucalypt forest... more The present study compares the macrofungi at three study sites in the lowland wet eucalypt forest of southern Tasmania, all in early stages of regeneration, two from silvicultural treatments and one from wildfire. Although not part of a designed experiment, the three areas provided an unbroken, partially overlapping time-line in which macrofungi were recorded during the first 38 months of their development after disturbance and/or fire. Two of the three regenerating units had adjacent mature forest, the macrofungi of which were markedly different from those in the regeneration, the latter being dominated by opportunistic, predominantly saprotrophic species and very low in the symbiotic basidiomycetous ectomycorrhizal species that are abundant in the soils of mature forests. Studies such as these assist in a growing understanding of the nature of the early successional mycota in the southern forests of Tasmania.
Symmetry, 2021
Many plant species produce ovate leaves, but there is no general parametric model for describing ... more Many plant species produce ovate leaves, but there is no general parametric model for describing this shape. Here, we used two empirical nonlinear equations, the beta and Lobry–Rosso–Flandrois (LRF) equations, and their modified forms (referred to as the Mbeta and MLRF equations for convenience), to generate bilaterally symmetrical curves along the x-axis to form ovate leaf shapes. In order to evaluate which of these four equations best describes the ovate leaf shape, we used 14 leaves from 7 Neocinnamomum species (Lauraceae) and 72 leaves from Chimonanthus praecox (Calycanthaceae). Using the AIC and adjusted root mean square error to compare the fitted results, the modified equations fitted the leaf shapes better than the unmodified equations. However, the MLRF equation provided the best overall fit. As the parameters of the MLRF equation represent leaf length, maximum leaf width, and the distance from leaf apex to the point associated with the maximum leaf width along the leaf len...
Symmetry, 2020
Many natural shapes exhibit surprising symmetry and can be described by the Gielis equation, whic... more Many natural shapes exhibit surprising symmetry and can be described by the Gielis equation, which has several classical geometric equations (for example, the circle, ellipse and superellipse) as special cases. However, the original Gielis equation cannot reflect some diverse shapes due to limitations of its power-law hypothesis. In the present study, we propose a generalized version by introducing a link function. Thus, the original Gielis equation can be deemed to be a special case of the generalized Gielis equation (GGE) with a power-law link function. The link function can be based on the morphological features of different objects so that the GGE is more flexible in fitting the data of the shape than its original version. The GGE is shown to be valid in depicting the shapes of some starfish and plant leaves.
Applied and Environmental Microbiology, 1997
The growth rate responses of Escherichia coli M23 (a nonpathogenic strain) to suboptimal pH and l... more The growth rate responses of Escherichia coli M23 (a nonpathogenic strain) to suboptimal pH and lactic acid concentration were determined. Growth rates were measured turbidimetrically at 20 degrees C in the range of pH 2.71 to 8.45. The total concentration of lactic acid was fixed at specific values, and the pH was varied by the addition of a strong acid (hydrochloric) or base (sodium hydroxide) to enable the determination of undissociated and dissociated lactic acid concentrations under each condition. In the absence of lactic acid, E. coli grew at pH 4.0 but not at pH 3.7 and was unable to grow in the presence of > or = 8.32 mM undissociated lactic acid. Growth rate was linearly related to hydrogen ion concentration in the absence of lactic acid. In the range 0 to 100 mM lactic acid, growth rate was also linearly related to undissociated lactic acid concentration. A mathematical model to describe these observations was developed based on a Bĕlehrádek-like model for the effects ...
Global Ecology and Conservation, 2019
There is convincing evidence for a scaling relationship between leaf dry weight (DW) and leaf sur... more There is convincing evidence for a scaling relationship between leaf dry weight (DW) and leaf surface area (A) for broad-leaved plants, and most estimates of the scaling exponent of DW vs. A are greater than unity. However, the scaling relationship of leaf fresh weight (FW) vs. A has been largely neglected. In the present study, we examined whether there is a statistically strong scaling relationship between FW and A and compared the goodness of fit to that of DW vs. A. Between 250 and 520 leaves from each of 12 bamboo species within 2 genera (Phyllostachys and Pleioblastus) were investigated. The reduced major axis regression protocols were used to determine scaling relationships. The fit for the linearized scaling relationship of FW vs. A was compared with that of DW vs. A using the coefficient of determination (i.e., r 2). A stronger scaling relationship between FW and A than that between DW and A was observed for each of the 12 bamboo species investigated. Among the 12 species examined, five had significantly smaller scaling exponents of FW vs. A compared to those of DW vs. A; only one species had a scaling exponent of FW vs. A greater than that of DW vs. A. No significant difference between the two scaling exponents was observed for the remaining 6 species. Researchers conducting future studies might be well advised to consider the influence of leaf fresh weight when exploring the scaling relationships of foliar biomass allocation patterns.
Global Ecology and Conservation, 2019
The mean and variance of ecological measures usually follow a power-law relationship, referred to... more The mean and variance of ecological measures usually follow a power-law relationship, referred to as Taylor's power law (TPL). Leaves are important organs for photosynthesis, and leaf size is closely related to photosynthetic potential. Leaf size has different physical measures, such as leaf length, area, and fresh or dry weight. However, it has not been reported whether these leaf size measures follow TPL and whether the estimates of the TPL exponent reflect basic topological constraints. Considering that the variation of leaf size can affect the photosynthetic capacity of leaves and plant competitive abilities in communities, we examined the effects of different physical dimensions of leaf size (including leaf length, area, and fresh and dry weight) on the estimate of the scaling exponent and the goodness of fit of TPL for 101 bamboo species, varieties, forms, and cultivars, using 90e100 leaves for each type of plant. All leaf size measures follow TPL. However, the goodness of fit increases with the physical dimension of the leaf size measure (e.g., from 1D leaf length to 3D leaf weight). Interestingly, no significant differences in the estimates of the TPL exponent were detected among any of the physical dimensions (1D to 3D) because the 95% confidence intervals of the differences between any two groups of bootstrap replicates of the exponents of TPL obtained from different leaf size measures did not include 0. In other words, the TPL exponents of leaf size measures from the different physical dimensions could be deemed identical. We found that leaf dry weight provides the best fit of TPL and the most reliable estimate of the exponent among the four leaf size measures used in this study, perhaps because it is the best representative of the energy allocated to individual leaves.
Trees, 2019
According to Thompson's principle of similarity, the area of an object should be proportional to ... more According to Thompson's principle of similarity, the area of an object should be proportional to its length squared. However, leaf area-length data of some plants have been demonstrated not to follow the principle of similarity. We explore the reasons why the leaf area-length allometry deviates from the principle of similarity and also examine whether there is a general model describing the relationship among leaf area, width and length. More than 11,800 leaves from the six classes of woody and herbaceous plants were sampled to check the leaf area-length allometry. Six mathematical models were compared based on root-mean-square error as the measure of goodness-of-fit. The best supported model described a proportional relationship between leaf area and the product of leaf width and length (i.e., the Montgomery model). We found that the extent to which the leaf area-length allometry deviates from the principle of similarity depends upon the variation of the ratio of leaf width to length. Estimates of the parameter of the Montgomery model ranged between 1/2 and π/4 for the six classes of plants. This is a narrower range than imposed by the limits 1/2 (for a triangular leaf with leaf length as its height and leaf width as its base) to π/4 (for an elliptical leaf with leaf length as its major axis and leaf width as its minor axis). The narrow range in practice implies an evolutionary stability for the leaf area of large-leaved plants despite the fact that leaf shapes of these plants are rather different.
Forests, 2018
Leaf shape and symmetry is of interest because of the importance of leaves in photosynthesis. Rec... more Leaf shape and symmetry is of interest because of the importance of leaves in photosynthesis. Recently, a novel method was proposed to measure the extent of bilateral symmetry in leaves in which a leaf was divided into left and right sides by a straight line through the leaf apex and base, and a number of equidistant strips were drawn perpendicular to the straight line to generate an equivalent number of differences in area between the left and right parts. These areal differences are the basis for a measure of leaf bilateral symmetry, which was then examined to see how well it follows Taylor’s power law (TPL) using three classes of plants, namely, 10 geographical populations of Parrotia subaequalis (H.T. Chang) R.M. Hao et H.T. Wei, 10 species of Bambusoideae, and 10 species of Rosaceae. The measure of bilateral symmetry followed TPL for a single species or for a class of closely related species. The estimate of the exponent of TPL for bamboo plants was significantly larger than fo...
Forest Pathology, 2017
In Vietnam, the productivity of Acacia hybrid (Acacia mangium x A. auriculiformis) 14 plantations... more In Vietnam, the productivity of Acacia hybrid (Acacia mangium x A. auriculiformis) 14 plantations is being threatened by an aggressive canker pathogen, Ceratocystis manginecans 15 and selection for tolerance is the main control strategy. A pot trial was established in Binh 16 Duong province to screen for the host response of nine Acacia genotypes (six Acacia hybrid 17 clones, two A. auriculiformis clones and mixed provenance seedlings of A. mangium) to 18 artificial inoculation with three isolates of C. manginecans. Lesion lengths as measured on 19 the inner bark suggested that the two A. auriculiformis clones were relatively more tolerant to 20 C. manginecans than the A. mangium genotype. In contrast, the lesion lengths of all six 21 Acacia hybrid clones fell between the A. auriculiformis and A. mangium genotypes. The 22 results of this study indicate that among the Acacia hybrid clones, BV10 showed the most 23 tolerance to C. manginecans. Chemical analysis of crude sapwood extracts sampled from the 24 lesion provided some evidence that induced phenolic compounds, particularly 25 Page 1 of 32 Forest Pathology Manuscript Proof tetrahydroxyflavanone and condensed tannins may have a defensive role in the Acacia-C. 26 manginecans pathosystem. However, results were not consistent across individual Acacia 27 hybrid clones and A. mangium genotypes.
Forests, 2019
The leaf area, as an important leaf functional trait, is thought to be related to leaf length and... more The leaf area, as an important leaf functional trait, is thought to be related to leaf length and width. Our recent study showed that the Montgomery equation, which assumes that leaf area is proportional to the product of leaf length and width, applied to different leaf shapes, and the coefficient of proportionality (namely the Montgomery parameter) range from 1/2 to π/4. However, no relevant geometrical evidence has previously been provided to support the above findings. Here, four types of representative leaf shapes (the elliptical, sectorial, linear, and triangular shapes) were studied. We derived the range of the estimate of the Montgomery parameter for every type. For the elliptical and triangular leaf shapes, the estimates are π/4 and 1/2, respectively; for the linear leaf shape, especially for the plants of Poaceae that can be described by the simplified Gielis equation, the estimate ranges from 0.6795 to π/4; for the sectorial leaf shape, the estimate ranges from 1/2 to π/4....
Forests, 2018
Plant leaves exhibit diverse shapes that enable them to utilize a light resource maximally. If th... more Plant leaves exhibit diverse shapes that enable them to utilize a light resource maximally. If there were a general parametric model that could be used to calculate leaf area for different leaf shapes, it would help to elucidate the adaptive evolutional link among plants with the same or similar leaf shapes. We propose a simplified version of the original Gielis equation (SGE), which was developed to describe a variety of object shapes ranging from a droplet to an arbitrary polygon. We used this equation to fit the leaf profiles of 53 species (among which, 48 bamboo plants, 5 woody plants, and 10 geographical populations of a woody plant), totaling 3310 leaves. A third parameter (namely, the floating ratio c in leaf length) was introduced to account for the case when the theoretical leaf length deviates from the observed leaf length. For most datasets, the estimates of c were greater than zero but less than 10%, indicating that the leaf length predicted by the SGE was usually smalle...
PloS one, 2016
We identify and describe the distribution of temperature-dependent specific growth rates for life... more We identify and describe the distribution of temperature-dependent specific growth rates for life on Earth, which we term the biokinetic spectrum for temperature. The spectrum has the potential to provide for more robust modeling in thermal ecology since any conclusions derived from it will be based on observed data rather than using theoretical assumptions. It may also provide constraints for systems biology model predictions and provide insights in physiology. The spectrum has a Δ-shape with a sharp peak at around 42°C. At higher temperatures up to 60°C there was a gap of attenuated growth rates. We found another peak at 67°C and a steady decline in maximum rates thereafter. By using Bayesian quantile regression to summarise and explore the data we were able to conclude that the gap represented an actual biological transition between mesophiles and thermophiles that we term the Mesophile-Thermophile Gap (MTG). We have not identified any organism that grows above the maximum rate o...
Tasforests
The macrofungi of an aggregated retention coupe harvested and burnt in April 2004 at the Warra lo... more The macrofungi of an aggregated retention coupe harvested and burnt in April 2004 at the Warra long-term ecological research (LTER) site were documented at approximately fortnightly intervals over a period of 16 months between February 2005 and June 2006. In transects of approximately 400 m total length, 167 macrofungal species were recorded in the unharvested aggregates compared to 125 species in the regenerating harvested area, with 63 species common to both. The regenerating area was a source of many saprotrophic fungi and also contained many species that are characteristically opportunistic, appearing after disturbance or fire but not generally seen in forests that have progressed beyond the earliest stage of regeneration. The regenerating area also contained a few species normally associated with mature forest, the presence of which may be attributed to the proximity of mature forest retained in the aggregates. Comparison of the aggregates with an unharvested control coupe sampled at the same intensity and over the same time period indicated lower species richness in the aggregates. This suggests that there are factors present, such as effects of the initial site preparation, opening up of the canopy, and proximity of the surrounding harvested areas, which tend to suppress the full development of the mycota in the aggregates. Nevertheless, the majority of ectomycorrhizal species in the aggregated retention coupe were found only in the unharvested aggregates, indicating that the latter are important reservoirs of ectomycorrhizal fungal diversity, and that they may be expected to show an increased species richness at a later stage of regeneration of the surrounding forest.
Canonical correlations analysis uses a secondary set of multivariate observations to correlate wi... more Canonical correlations analysis uses a secondary set of multivariate observations to correlate with, and thereby help to explain, differences among a primary set of multivariate observations. In ecology, the variables of the primary data set may be of the "presence/absence" type, or they may be the abundances of individual species in a species list, whereas the secondary set often involves environmental variables. The non-Gaussian distribution of the primary data set precludes the use of traditional multivariate statistical methods, but recent developments in the application of canonical analysis enable similarities between the primary variates to be calculated using measures of similarity in common use in ecology. In this paper, we illustrate how one of these generalisations, the canonical analysis of principal coordinates (CAP), may explain differences in species assemblages of macrofungal survey data obtained from experimental units of differing floristic composition, or how lists of species obtained during different seasons may reflect weather variables. The canonical correlation analyses incorporate non-parametric permutation tests that give exact probability values, as well as ordination diagrams that display the differences in the experimental units that mirror the differences in the mycota. D. A. Ratkowsky and G. M. Gates (2008). Generalised canonical correlations analysis for explaining macrofungal species assemblages.
Tetrahedron Letters, 2011
The yellow dihydroanthracenone dimer, austrocolorin B 1 and the unique violet-red 1,4anthraquinon... more The yellow dihydroanthracenone dimer, austrocolorin B 1 and the unique violet-red 1,4anthraquinone dimer, austrocolorone B, were isolated from the Tasmanian mushroom Cortinarius vinosipes and their structures and stereochemistry were determined from spectroscopic data. Austrocolorin B 1 and austrocolorone B were found to exhibit potent cytotoxic activity in vitro against the murine lymphoblast (P388D 1) cell line with IC 50 values in the range 10-31 µg/mL.
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Papers by David Ratkowsky