scholarly journals Sticking around: plant persistence strategies on edaphic islands

2021 ◽  
Author(s):  
Gianluigi Ottaviani ◽  
Francisco Emmanuel Mendez Castro ◽  
Luisa Conti ◽  
David Zeleny ◽  
Milan Chytry ◽  
...  
Keyword(s):  
Soil Properties ◽  
Environmental Conditions ◽  
Linear Models ◽  
Extinction Risk ◽  
Distinct Species ◽  
Clonal Plants ◽  
Ordinary Least Squares ◽  
Mixed Effect ◽  
Persistence Strategies ◽  
Clonal Species

1. Species extinction risk at local scales can be partially offset by strategies promoting in-situ persistence. We explored how persistence-related traits of clonal and non-clonal plants in temperate dry grasslands respond intra- and interspecifically to variation in environmental conditions (soil, climate) and insularity. 2. We focused on edaphic island specialist species, hypothesizing that plants experiencing harsh soil environments and strong insularity are distinguished by traits supporting enhanced persistence, such as small stature, long lifespan and resource-conservative strategies. We used linear mixed-effect models and bivariate ordinary least squares linear models to explore the response of species triats to environmental and biogeographic predictors. 3. We found general support for this hypothesis. Soil properties and insularity emerged as the most important drivers of trait patterns. However, clonal species showed more consistent responses to variation in environmental conditions and insularity than non-clonal plants, which were characterized by distinct species-specific responses. 4. Soil properties and insularity confirmed their major role in shaping the persistence strategies of edaphic island plant species. These drivers may exert their effect on specific functions (e.g. belowground resource conservation captured by BDMC). Additionally, we unambiguously identified that clonal species had different persistence strategies than non-clonal ones.

scholarly journals Linear models for diallel crosses: a review with R functions

2020 ◽  
Author(s):  
Andrea Onofri ◽  
Niccolò Terzaroli ◽  
Luigi Russi
Keyword(s):  
Linear Model ◽  
Combining Ability ◽  
Linear Models ◽  
General Linear Model ◽  
Ordinary Least Squares ◽  
General Purpose ◽  
General Linear ◽  
Mixed Effect ◽  
Typical Process ◽  
R Functions

Abstract Key message A new R-software procedure for fixed/random Diallel models was developed. We eased the diallel schemes approach by considering them as specific cases with different parameterisations of a general linear model. Abstract Diallel experiments are based on a set of possible crosses between some homozygous (inbred) lines. For these experiments, six main diallel models are available in literature, to quantify genetic effects, such as general combining ability (GCA), specific combining ability (SCA), reciprocal (maternal) effects and heterosis. Those models tend to be presented as separate entities, to be fitted by using specialised software. In this manuscript, we reinforce the idea that diallel models should be better regarded as specific cases (different parameterisations) of a general linear model and might be fitted with general purpose software facilities, as used for all other types of linear models. We start from the estimation of fixed genetical effects within the R environment and try to bridge the gap between diallel models, linear models and ordinary least squares estimation (OLS). First, we review the main diallel models in literature. Second, we build a set of tools to enable geneticists, plant/animal breeders and students to fit diallel models by using the most widely known R functions for OLS fitting, i.e. the ‘lm()’ function and related methods. Here, we give three examples to show how diallel models can be built by using the typical process of GLMs and fitted, inspected and processed as all other types of linear models in R. Finally, we give a fourth example to show how our tools can be also used to fit random/mixed effect diallel models in the Bayesian framework.

scholarly journals Direct and indirect effects of environmental limitations on white spruce xylem anatomy at treeline

2021 ◽  
Author(s):  
Timo Pampuch ◽  
Mario Trouillier ◽  
Alba Anadon-Rosell ◽  
Jelena Lange ◽  
Martin Wilmking
Keyword(s):  
Tree Growth ◽  
Environmental Conditions ◽  
Indirect Effects ◽  
Tree Height ◽  
White Spruce ◽  
Vegetation Period ◽  
Lumen Diameter ◽  
Xylem Anatomy ◽  
Direct And Indirect Effects ◽  
Mixed Effect

<p>Treeline ecosystems are of great scientific interest to study the direct and indirect influence of limiting environmental conditions on tree growth. However, tree growth is complex and multidimensional, and its responses to the environment depend on a large number of abiotic and biotic factors and their interactions.</p><p>In this study, we analyze the growth and xylem anatomy of white spruce trees (<em>Picea glauca</em> [Moench] Voss) from three treelines in Alaska (one warm and drought-limited, and two cold and temperature-limited treelines). We hypothesized (1) no difference between the treelines regarding the relationship between tree DBH and height, yet in general (2) faster growing trees at the warmer site. Additionally, we expected to find differences in xylem anatomical traits with trees from the drought-limited site having adapted to drought conditions by (3) forming smaller lumen diameter due to water deficit but (4) a higher xylem anatomical density due to higher temperatures and a longer vegetation period.</p><p>Regarding growth in height and diameter, trees at the drought-limited treeline grew relatively (1) taller and (2) faster compared to trees at the temperature-limited treelines. Raw xylem anatomical measurements showed (3) smaller lumen diameters and (4) higher density in trees at the drought-limited treeline. However, using linear mixed-effect models, we found that (i) traits related to water transport like lumen diameter were not significantly correlated with the actual amount of precipitation during the vegetation period but with tree height. We also found that (ii) traits related to mechanical support like density were mainly positively influenced by the mean temperature during the vegetation period.</p><p>The differences in lumen diameter found in the raw data can be explained by differences in the growth rates of the trees, since lumen diameter at the lower part of the tree stem needs to increase over time with increasing tree height. The greater wood density at the drought-limited treeline is probably caused by the higher temperature that leads to more biomass production, and potentially longer vegetation periods.</p><p>Our study shows that xylem anatomical traits in white spruce can be directly and indirectly controlled by environmental conditions. While lumen diameter is not directly influenced by environmental conditions but indirectly through tree height, other traits like anatomical density show a direct correlation with environmental conditions. Our results highlight the importance of approaching tree growth in a multidimensional way and considering direct and indirect effects of environmental forcing.</p>

scholarly journals Invasive alien palm Pinanga coronata threatens native tree ferns in an oceanic island rainforest

2018 ◽  
Vol 66 (8) ◽  
pp. 647 ◽  
Author(s):  
Michael J. B. Dyer ◽  
Gunnar Keppel ◽  
Marika Tuiwawa ◽  
Sainivalati Vido ◽  
Hans Juergen Boehmer
Keyword(s):  
Linear Models ◽  
Management Strategies ◽  
Ornamental Plants ◽  
Native Plant ◽  
Ecological Processes ◽  
Mixed Effect ◽  
Mixed Effect Models ◽  
Tree Ferns ◽  
Native Tree ◽  
Negative Impacts

Invasive ornamental plants are a global problem that can have severe impacts on native biodiversity, especially on islands. To determine whether the invasive, ornamental ivory-cane palm Pinanga coronata could be displacing native biodiversity, we investigated its co-distribution with native tree ferns in a Fijian rainforest. We recorded the abundances of P. coronata and tree ferns and related these to environmental variables using linear models and generalised linear mixed-effect models (GLMMs). Distance to an introduction site was the most significant factor predicting the palm’s distribution and abundance, suggesting that its current distribution is limited by insufficient time for wider dispersal. P. coronata cover was strongly and negatively related with the abundance of native tree ferns and the palm may therefore be displacing native tree ferns. This relationship was strongest with tree fern seedlings and weakest with mature tree ferns, implying that the palm is preventing the establishment of native tree ferns. This study thus provides strong circumstantial evidence that P. coronata is progressively displacing native tree ferns by preventing seedling establishment and poses a severe threat to Fiji’s native biodiversity and ecological processes. Therefore, urgent management is required to control and prevent the further spread of P. coronata and its negative impacts on native plant biodiversity. Management should involve an initial feasibility study to determine the effectiveness of various management strategies, followed by targeted control and/or eradication campaigns and long-term monitoring. Ultimately, well implemented legislation to prevent the spread and introduction of P. coronata and other ornamental plants will be crucial to protect native biodiversity in Fiji and elsewhere.

scholarly journals Efficient construction of linear models in materials modeling and applications to force constant expansions

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Erik Fransson ◽  
Fredrik Eriksson ◽  
Paul Erhart
Keyword(s):  
Feature Selection ◽  
Thermodynamic Properties ◽  
Force Constant ◽  
Linear Models ◽  
Materials Science ◽  
Computational Cost ◽  
Ordinary Least Squares ◽  
High Order ◽  
Unit Cells ◽  
Low Symmetry

Abstract Linear models, such as force constant (FC) and cluster expansions, play a key role in physics and materials science. While they can in principle be parametrized using regression and feature selection approaches, the convergence behavior of these techniques, in particular with respect to thermodynamic properties is not well understood. Here, we therefore analyze the efficacy and efficiency of several state-of-the-art regression and feature selection methods, in particular in the context of FC extraction and the prediction of different thermodynamic properties. Generic feature selection algorithms such as recursive feature elimination with ordinary least-squares (OLS), automatic relevance determination regression, and the adaptive least absolute shrinkage and selection operator can yield physically sound models for systems with a modest number of degrees of freedom. For large unit cells with low symmetry and/or high-order expansions they come, however, with a non-negligible computational cost that can be more than two orders of magnitude higher than that of OLS. In such cases, OLS with cutoff selection provides a viable route as demonstrated here for both second-order FCs in large low-symmetry unit cells and high-order FCs in low-symmetry systems. While regression techniques are thus very powerful, they require well-tuned protocols. Here, the present work establishes guidelines for the design of protocols that are readily usable, e.g., in high-throughput and materials discovery schemes. Since the underlying algorithms are not specific to FC construction, the general conclusions drawn here also have a bearing on the construction of other linear models in physics and materials science.

scholarly journals Mathematical absurdities in the California net energy system

2019 ◽  
Vol 3 (3) ◽  
pp. 1018-1028
Author(s):  
Carl A Old ◽  
Ian J Lean ◽  
Heidi A Rossow
Keyword(s):  
Linear Models ◽  
Energy System ◽  
High Energy ◽  
Ordinary Least Squares ◽  
Mitochondrial Metabolism ◽  
Energy Utilization ◽  
Parameter Estimates ◽  
Net Energy ◽  
High Energy Phosphate ◽  
Laws Of Thermodynamics

Abstract Net energy systems, such as the California Net Energy System (CNES), are useful for prediction of input:output relationships not because of fidelity to the laws of thermodynamics, but because they were designed to predict well. Unless model descriptions of input:output relationships are consistent with the laws of thermodynamics, conclusions regarding those relationships may be incorrect. Heat energy (HE) + recovered energy (RE) = ME intake (MEI) is basic to descriptions of energy utilization found in the CNES and is consistent with the laws of thermodynamics; it may be the only relationship described in the CNES consistent with the first law of thermodynamics. In the CNES, efficiencies of ME utilization for maintenance (km) and gain (kg) were estimated using ordinary least squares (OLS) equations. Efficiencies thus estimated using static linear models are often inconsistent with the biochemistry of processes underlying maintenance and gain. Reactions in support of oxidative mitochondrial metabolism are thermodynamically favorable and irreversible; these reactions yield ATP, or other high-energy phosphate bonds, used for what is generally termed maintenance. Synthesis of biomass (gain) is less thermodynamically favorable; reactions do not proceed unless coupled with hydrolysis of high-energy phosphate bonds and lie closer to equilibrium than those in support of oxidative mitochondrial metabolism. The opposite is described in the CNES (km > kg) due to failure of partitioning of HE; insufficient HE is accounted for in maintenance. Efficiencies of ME utilization (km and kg) as described in the CNES are variable. Further neither km nor kg are uniformly monotonic f (ME, Mcal/kg); for ME (Mcal/kg) <0.512 or >4.26, km are inconsistent with thermodynamically allowed values for efficiencies (>1.0); kg are a monotonically positive f (ME) concentration (Mcal/kg) for ME <3.27 Mcal/kg. For ME <1.42 Mcal/kg, kg are not in the range of thermodynamically allowed values for efficiencies (0 to 1.0). Variable efficiencies of ME utilization require that the first law may not be observed in all cases. The CNES is an excellent empirical tool for prediction of input:output relationship, but many CNES parameter estimates evaluated in this study lack consistency with biology and the laws of thermodynamics.

Phenotypic plasticity of yield and related traits in rainfed durum wheat

2013 ◽  
Vol 152 (6) ◽  
pp. 873-884 ◽  
Author(s):  
R. MOHAMMADI
Keyword(s):  
Phenotypic Plasticity ◽  
Durum Wheat ◽  
Environmental Conditions ◽  
Linear Models ◽  
Agronomic Traits ◽  
Grain Weight ◽  
High Yield ◽  
Yield Improvement ◽  
Modern Cultivar ◽  
Breeding Lines

SUMMARYRainfall and temperature are unpredictable in Mediterranean environments, which results in inconsistent environmental conditions for crop growth and a critical source of uncertainty for farmers and growers. The objectives of the present study were to: (i) quantify and compare the plasticity of durum breeding lines, a modern cultivar and landraces on the basis of yield and agronomic traits and (ii) study associations between plasticity of yield and plasticity of agronomic and phenological traits. Plasticity was quantified using linear models for 11 durum breeding lines, one modern cultivar and two landraces grown in 21 diversified environments. The results showed that the effects due to environment, genotype and genotype×environment (G×E) interaction were significant, which indicates the existence of differences among genotypes for plasticity. Yield ranged from 1939 to 2419 kg/ha across environments and the range of plasticity was 0·66–1·13. The breeding lines and the modern cultivar had higher grain yields compared with the landraces at the same level of plasticity. The landraces with below-average plasticity in yield were characterized as tall in stature and late in heading and maturity, whereas the breeding lines and modern cultivar with above-average plasticity in yield were early in heading and maturity, semi-dwarf and high-yielding, which indicates the success in breeding the materials for unpredictable environmental conditions. In conclusion, yield plasticity was associated with yield improvement and high yield plasticity tends to associate with earliness, shorter plants and low grain weight.

scholarly journals Effects of supplementary feed for game birds on activity of brown rats Rattus norvegicus on arable farms

2020 ◽  
Author(s):  
Siti Md Saad ◽  
Roy Sanderson ◽  
Peter Robertson ◽  
Mark Lambert
Keyword(s):  
Linear Models ◽  
Camera Traps ◽  
Monitoring Methods ◽  
Mixed Effect ◽  
Factors Affecting ◽  
Game Bird ◽  
Game Birds ◽  
Bird Feeders ◽  
Brown Rat ◽  
Supplementary Feed

Abstract Brown rats are widespread in agroecosystems, but our understanding of factors affecting their activity is incomplete due to cryptic, nocturnal behaviours. Indirect monitoring methods include tracking plates and camera traps. Supplementary feeding of game birds may provide resources for rats away from farm buildings, allowing them to persist in winter when there is little other food available. Developing reliable methods to monitor such populations will facilitate landscape-scale studies of rat populations in farm environments and aid ecologically based approaches for controlling rats on farms. We compared camera traps and tracking plates to monitor brown rat activity near game bird feeders at a mixed farm in Northumberland, UK. Generalized linear models (GLM) were used to compare rat incidence estimated from camera traps and tracking plates. A strong positive relationship was found between the two methods, although tracking plate estimates were less reliable when rat activity was very low. Factors that affected populations of brown rats near game bird feeders were assessed via linear mixed-effect models (LMM) of monthly tracking plate data (October 2017 to September 2018). Populations were highest at the feeders (0 m) compared with further away (10 m, 20 m) and were also higher in periods of cold, wet weather and when more food was available from the feeders. Rodenticide application near feeders did not significantly affect activity, nor did land cover 100 m around each feeder. A highly significant relationship was detected with food supply, suggesting that the use of game bird feeders could potentially have major impacts on rat population dynamics.

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