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Hello colleagues,
I was wondering if any of you have recently (2021/2022) submitted a manuscript to Environmental Microbiology or Functional Ecology and what are your thoughts?
I recently submitted my manuscript to a journal that provided only one reviewer (unprofessional for such an established journal!), and I am considering withdrawing the manuscript and submitting to one of the Wiley journals.
Have you had any experience, what is the quality of peer review in these two journals and how long it took for the paper to be rejected or accepted? Thank you in advance!
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Yes, I would not accept just one reviewer. Some journals have up to four! But two is perfect :)
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Leaves are one of key components of a plant which play a remarkable role in food manufacturing, therefore it is called as photosynthetic machinery. Moreover, leaves are more sensitive than other components, they also act as receivers of external environment. Therefore, if any changes occur in the environment and if the changes persist and are prolonged, leaves can be affected by changes. Therefore, morphological traits like leaf area, thickness, surface, texture, leaf mass, tissue density etc, will exhibit some indication of receiving climate change. Thus, it could be an indicator of changing climate.
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Dear Researcher
leaves morphological features have demonstrated association with climate and varies within species along climate gradients. We predicted that given within species variation along a climate gradient, a morphological shift should have occurred over time due to climate change .
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what is the general trend in the R:S ratio of tree species at the seedling stage? early-successional vs. late-successional which ones have big R:S ratio? i see some contradicting results published. Plus, could these trend vary with tropical and temperate tree species?
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May be 3:1
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I'm studying functional trait variation within and between tree species growing in natural conditions. The trees have a considerable variation in size (height and DBH), and I want to know how size affects functional traits. I performed some linear models including size as a covariate like this:
trait~species+site+height
Do you recommend any other method/or any article to correct by size effects?
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They include: whole plant traits, such as plant height or life form; leaf traits, such as specific leaf area (SLA), leaf size or leaf phenology; stem and belowground traits, such as specific root length or bark thickness; and finally regenerative traits, such as dispersal mode, seed mass or resprouting capacity
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I have built a phylogenetic tree using categorical functional traits, such as pollination and dispersion syndromes, phenology, etc. Now, I can see the dicotomies and the points in which the plant species diverge, lineages, and so on. However, the interpretation itself seems to be a little tricky because I want to go with quantitative and qualitative discussion but don't know where to start from.
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@Rutger A. Vos
First of all, thank you very much for your help. This answer solved many of my conflicts. I'll try to make the analysis again, taking into account these suggestions. I was particularly intrigued by the non-evolutive meaning of the tree, but now you clarified it way better. I appreciate your attention and support. Have a great day!
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Dear Colleagues,
Is there any parameters related to the term "Invasive". I mean when we can say that a species (plant) is invasive? Especially for tree species...
Thank you
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Thank you all of you
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I am now compiling the bibliography for the paper on the importance of the biological age concept for system ecology and look for the references to the ecological models describing the effect of environmental conditions on the organism development.
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In the course of microscopic observations on the litter system of a Scots pine stand, I found that the dominant ectomycorrhizal fungus (a basidiomycete belonging to the genus Hyphodontia, identified through its typical cystidia found in the mycorrhizal mantle) was also a white-rot fungus (still identified by its numerous cystidia within root debris). The observation was reported in the following paper:
More details can be found in the following technical report:
This allowed me to build a work hypothesis about the role of (at least some) ectomycorrhizal fungi in the carbon economy of pine stands. If it could be possible to grow on or several pine seedlings in xenobiotic conditions with this fungus (or other paying a similar role) as a mycorrhizal partner, decaying wood could be added as a potential carbon source under reduced light conditions, as this occurs during winter or in suppressed conditions. Hence a balance between two physiological strategies involving a plant and a fungus, the balance between both strategies being regulated by light intensity. Unfortunately researches were discontinued because of my specialization in soil fauna studies and lack of financial support for the use of tracer isotopes. If my hypothesis is true, it can have some importance for understanding how the well of the community overcomes that of the individual (an essential issue in evolutionary science), as well as applications in sustainable forestry. Catch as catch can…
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Hello to all
The relationship between species diversity and ecosystem stability and its maintenance mechanism has been one of the main topic in ecology research.
In the past, diversity indices frequently used for assessing of community stability. in other words, each community that had more diversity, it was more stable. in the last decade, Functional diversity (FD) that defined as the value, range, distribution and relative abundance of the functional characteristics of organisms in a community, was the most popular methods for evaluation of community stability and functioning. While, in the recent years, Functional Redundancy (FR) that defined as some species perform similar roles in communities and ecosystems, and redundant species can therefore be lost with minimal impact on ecosystem processes. In other words, redundant species are considered necessary to ensure ecosystem resilience (resilience  and resistance are two concept of stability). The redundancy hypothesis predicts that the species redundancy in a plant community enhances community stability.
Now, my main question is that: Is there another index that measure plant community stability directly?
Best regards
Reza
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If you are looking at stability then this would imply that you take repeated measures. Assuming that you are working on plant communities I would raise a few questions:
  • What system are you considering? For instance - very arid areas are strongly affected by rainfall, and species become visible very quickly (and briefly) in response to only a few mm of rain.
  • What time interval would you consider? You might have some short term variation in plant composition around a certain "central" point.
  • What part of the plant community would you look at? In arid areas you can expect more variation in ephemeral plants, but perennial composition may remain consistent. So the perennial plants might be considered stable, while the ephemerals would indicate variation.
I agree that remote sensing might help, that you might look at variation around a "mean", but you would probably need more detailed advice from an RS person considering how responsive the various vegetation indexes are
You could use bi-plots based on (N)MDS to get a visual impact of how plant communities "behave".
As I write I am wondering if one number will actually be able to encompass everything that you are looking at. It might, but then again, the index would have to be sufficiently sensitive to pick up on variations, but not over-sensitive so as to make its interpretation impossible.
My idea is much in the line of ... we use a mean and variance to describe a sample / population, no single number can do both. ... we use species richness, a diversity index and an evenness index to describe different aspects of a plant community - the individual measures have little meaning.
Would you split the vegetation up into ephemerals and perennials and consider them separately?
When you find something, could you post it here as well? I'd really like to see what you come up with.
Regards,
Patrick
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When we analyze phylogenetic structure of a species community, we need a phylogenetic tree to generate phylogenetic indexes to analyze the phylogenetic patterns. How accurately the phylogenetic tree should be built ? A tree based on morphological traits (based from the morphological taxonomy) or a ML tree based from one gene or several gene? A bayesian tree based also from one or several gene?
Thanks you
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HI Gregiore, 
This is a topic that has taken my attention for sometime, morphological vs molecular. With many people holding polarized views. 
It also comes from what your view of a species is. There are cases of morphologically distinct but molecular identification and vice versa. 
Certain organisms are classified as different 'species' but have the same DNA barcode and also the converse. 
If one is to go down the molecular route than it is a basic requirement to use mitochondrial and nuclear genes but certain fungi do not contain mitochondria. 
If going down the morphological route it is suggested that habitat preference ought to be taken into account also. Then there is the possibility of subspecies, ecotypes etc but not everybody agrees with. I'm a little on the fence at the moment (after having been solidly in the molecular camp). 
Very interested to hear your views and those of others. Hopefully this will provide for a fruitful discussion. 
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I have studied an area of rain forest which presents a strong gradient of variation in soil moisture and nutrient, established in a short distance (150 - 200 meters). After the florestal inventory were detected three distinct plants communities, varying strongly across the environmental gradient - 1) A floodable plain forest in a organic soil; 2) Intermediary assembly located in a soil with a steep slope; and 3) a dry forest located in the highest place, with poor white sand soil.
For now, i intend to investigate anatomical and functional traits, searching for common patterns that could explain the establishment of these plant assemblies.
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If the gradient is strong enough in your system, you should be able to find a zonation of some plant functional and anatomical traits. In that case, I would look for different growth rates, contrasting production and/or presence of fleshy tissues and leaf-structures, contrasting production of below-ground structures, presence of water storage structures.. However, independently of whatever you may find, you will have to have in mind conducting experiments to determine whether the correlation between soil characteristics and plant traits have a cause-effect association. Correlation does not imply causation per se. So, the finding of a given pattern won´t "explain" the causes that regulate the establishment of the species you find; it only will give you a clue about it. It will help you to design a better experiment.
Good luck!
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I have measured several functional traits mainly leaf traits (SLA, LDMC, LT …), root length and weight above-ground standing biomass, Branching architecture. I know Paula et al(2009) review article which introduced possible traits related to fire considering resprouting and regeneration traits. Could leaf traits and allocations also be considered as representative traits for interpretation of fire effects?
It would be my pleasure to have your advice
Warm regards
veria
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I would measure the tissue flammability. See more at Cornelissen J, Lavorel, Garnier, Díaz, Buchmann, Gurvich, Reich, ter Steege, Morgan, van der Heijden M, et al. 2003. A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Australian Journal of Botany 51: 335.
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Which is more important? How to interpret? When should to use?
For example, following this pattern in Amazon rain forests: Hyperdominance in Amazonian forest carbon cycling (Fauset et al. 2014), 
The dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only 1% of Amazon tree species responsible for 50% of carbon storage and productivity.
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I'm looking for papers in which researchers accessed the role of floral parts as signal (or mechanical-fit) trait by removing (or modifying) them and then recorded flower visits and plant fitness. Could anyone help me?
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I thought I'd provided an answer to this question but it's not showing.  Odd.  Anyway, I wanted to say that the kind of manipulation of floral parts that you are talking about has been quite commonly done and can be an effective test of floral function, as the examples here show.  He's one from my group (there's a PDF on ResearchGate):
 Lamborn, E. & Ollerton, J. (2000) Experimental assessment of the functional morphology of inflorescences of Daucus carota (Apiaceae): testing the “fly catcher effect”. Functional Ecology 14: 445-454
Also look for work by Scott Armbruster on Dalechampia, and Paul Wilson on Impatiens.
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Pool et al (2014) quantify alpha functional diversity as the volume of the convex hull filled by the fish species of each community in two-dimensional functional space using the values from the first two functional axes.
But I wonder taxonomic alpha diversity is simply the species richness, so the alpha functional diversity can be functional richness...
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Yes, they are. Functional richness is generally measured as the convex hull volume. But when there is only one continuous trait it is measured as the range (or the range of the ranks for an ordinal trait (from dbFD function in FD R package). 
Consider reading the following papers:
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I want to know N-competing species.
and What kind of example of N-competing species?
Is cyanobacteria N-competing species?
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Based on the way your question is written, I think you might be a little confused as to the concept of 'N competing species'. It is a term used not to describe the behaviour of a species, but in reference to the number of species (N) competing for resources in a specific environment.
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Hello, we are working on biological traits analysis with fuzzy coding and would like to make the link with abiotic conditions.
How do you do it?
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Nathalie,
I have already performed this kind of factorial analysis on an invertebrate dataset (biological traits). As suggested by Alain, the RLQ analysis is a first option to investigate the link between biological and environmental tables. But if you wish to assess only the relationship between a fuzzy-coded biological table (typically species traits) and an environmental table, you can also perform either a CCA or a CAIV.
Using the ade4 package in R as advised above, the two following sequences gave the same result in my case:
1) first perform a FCA on the fuzzy-coded array (needs the ‘prep.fuzzy.var’ and ‘dudi.fca’ functions in ade4) and then a CAIV between the FCA result and the environmental table (‘pcaiv’ function)
2) perform directly a CCA between the fuzzy-coded array and the environmental table (‘prep.fuzzy.var’ and ‘cca’ functions)
Hope that helps.
Mathieu
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Functional Ecology/ Grime strategies
From S to R, for example.
Thanks.
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In the exploratory analysis of my data, I see a clear pattern of relationships between certain environmental variables and species traits. When I carry out a fourth corner analysis it points out to those relationships, but with the p adjustments the significance is lost. 
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Dray et al. (2014) have just published a paper <http://www.esajournals.org/doi/abs/10.1890/13-0196.1> combining fourth corner and RLQ methods. In the appendix <http://www.esapubs.org/archive/ecol/E095/002/suppl-1.pdf> they show how you can obtain adjuted p values in R. You may also read this one <http://www.esajournals.org/doi/abs/10.1890/08-0349.1>
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Hello,
I want an ecological explanation: H' and E are theoretically kept in stable assemblages, so stable ecosystems.
I worked in disturbed areas affected by desertification, but planted with different species like prickly pear, pine and olive trees.
In these plantations, H and E have automatically increased in spring (increase therophytes after rain).
My question is: can we speak of a balanced plant assemblage in a degraded environment, disturbed even if planted because  the H' and E are elevated?
Thank you.
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I agree with Nicolas and personally would not rely on H' and E alone as surrogates for biodiversity and stabilty (whatever you mean by these). As for the structural comparison of the community structure at the two points in time (seasons) you can compute a diversity profile using Hill's numbers. However, when it comes to more functional issues, I would suggest to resort to functional groups and functional diversity analysis.
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Ecologists use different terms to understand the function of ecological patterns and species response to environment. I am interested to know what are plant ecologists ideas about these terms.
In the text books of plant functional ecology (Pugnaire and Valladares, 2007) and plant physiological ecology (Lambers et al,2008; Larcher,1994), their border or definition is not very clear. I couldn't find in other references either.
Could we select any of these terms as main branches of ecology and others as sub branches? Are there any differences in the views of ecologists, biochemists and plant physiologists? Is functional ecology similar to only comparative functional ecology or does it also cover plant physiological ecology? It would be my pleasure to know researchers' ideas about these specialties.
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Dear Mehdi,
First of all, I am pleased to see your such specific question on technical terminology in Ecological Sciences. For this, I am glad to see your fine interest to find out clarity.
However, I would like to give you some points on about Prof. Hans Lambers, who is an experienced and excellent Eco-physiologist known figure at a global level. I stood up in the field of ecology to read his books and ideas from his peer reviewed research articles.
Now I come to your question, Eco-physiology, Plant Functional Ecology and Plant Physiological Ecology.
If you look meaning at grass root level or at definition level it may express the same meaning at different angle of understanding. If you are taking this at specific level it has different meaning.
It is well known that ecology word is a suffix you may put anywhere with any words e.g. plant ecology, animal ecology, root ecology, nematode ecology etc..... But the meaning of ecology is the study of interactions between biotic and abiotic component means interaction between organism and abiotic component to understand that how and what extent an organism is interacting with the surroundings for food, survival and reproduction etc.
If I am putting word only functional Ecology instead of Plant Functional Ecology the meaning would be study of functional parameters of any organism (might be plant or animal) if I am putting Plant Functional Ecology then the specific meaning would be study of all functional attributes of a plant related with biotic and abiotic components.
Similarly, the little and slight differences at finer scale in between Plant Functional Ecology and Plant Physiological Ecology. If study encompasses for all kind of functional aspects at quantitative, qualitative and semi quantitative level be taken will come under Plant Functional Ecology when study encompasses more dynamically and more mechanistically for important functional parameters like growth, transpiration, photosynthesis, carbohydrate partitioning (these are the most important functional attributes of a plant) of an individual plant or at community level, will come under Plant Physiological Ecology.
In other words, I can say that more dynamic study on functional attributes of an individual or at community level may come in Plant Physiological Ecology and all kind of functional attributes (classic, mechanistic, evolutionary etc,) may come in the Plant Functional Ecology.
While in case of Plant Eco-physiology, study of structural and functional parameters of a plant with respect to ecological angle may come. These are the my personal views and ideas to giving you here on my experiences.
Dear Mehdi, if you need further elaboration and explanation, feel free to contact me(dranand1212@gmail.com) or carry on with your debate on your question.
In last, I am very grateful to Prof. Lambers whose contributions are very significant indeed for Plant Eco-physiology and even to other branch of ecology.
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The cost-benefit model for the evolution of carnivory in plants, proposed by Thomas Givnish (1984), was experimentally tested only a few times and the results are quite contradictory. Certain studies show the results expected according the model (Farnsworth & Ellison, 2008; Pavlovic, 2009), while others show the contrary (Mendéz and Karlsson, 1999; Wakefield et al. 200; Adamec, 2008). In spite of this ambiguity, Givnish’s theory is still considered to be true, at least by most authors. Is this the result of some kind of inertia in the area or because of the lack of a better explanation?
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The cost/benefit model proposed by Thomas Givnish is, with slight modifications, probably true and as far as I know, nothing can better explain evolution of botanical carnivory. of course, each experiment you perform is dependent on dose of nutrients and time needed for growth of new leaves. For example, mendez and karlsson measured photosynthesis only 1 week after feeding. Wakefield did not measure photosynthesis on new leaves but only on them that were fed. It seems that for aquatic carnivorous plants, carnivory stimulate growth of shoot apex and Ellison and Adamec (2011) modified cost/benefit model for aquatic carnivorous plants. Or see also Lubomír Adamec, 2011. By which mechanism does prey capture enhance plant growth in aquatic carnivorous plants: Stimulation of shoot apex?, Fundam. Appl. Limnol. Vol. 178/2, 171–176. Also the respiratory cost must be taken into account at least in plant with active trapping mechanism (e.g. see my publication in Ann Bot., Pavlovič et al., 2010 or Laakkonen modification in Utricularia: A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power. Plant Biol (Stuttg). 2006 Nov;8(6):758-64.
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I am studying the functional significance of tree species diversity on soil C, N and pH in mature semi-natural forests. We have plots selected with a rigorous selection procedures based on basal area threshold, soil types, previous land-use history, management, aspect, climatic factors. We established a gradient of 1-5 tree species richness. Apart from basal area threshold,we have also evenness restriction to each species in the plot (how much percentage of the basal area per plot a particular species should account for).
I am here to learn from your experiences if any of the researchers in the field have addressed the issue before.
Since the study focuses on the effect(s) of diversity, the main goal is to demonstrate whether diversity is positively, negatively or none related to the soil properties in question.
Using diversity indices and calculating net diversity effects (relative yield) can be two of the options.
1. How to address the diversity effect ? Many measure Diversity (richness, evenness, or both) using different indices. Which one of the known indices is more appropriate in this situation?
2. If you were calculating net diversity effects (observed yield in mixtures minus the expected yield in the corresponding mono-cultures) how did you take into account the variation of individual trees and their influence? i.e did you apply some weighting? if yes, which parameters of the trees (basal area, biomass, volume, height etc) you had weighted and how?
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maybe this study can help you...
Grossiord, Charlotte, et al. "Does Drought Influence the Relationship Between Biodiversity and Ecosystem Functioning in Boreal Forests?." Ecosystems: 1-11.
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I need advice for which plants I should resemble.
Inspired by Sapir and Dudley (2013), I would like to make some artificial flowers to attract free-ranging hummingbirds to test how floral orientation effects flight (e.g. flowers oriented horizontally and tilted 45° downwards).
I would like to resemble plants that occur in the study area and that have different floral orientation. Further, they should not be too difficult to resemble in plastic.
I'm interested in three different areas:
1. Ontario in Canada
2. U.S. state of Washington
3. The southern pacific region of Costa Rica
Sapir, N. and R. Dudley. 2013. Implications of floral orientation for flight kinematics and metabolic expenditure of hover-feeding hummingbirds. Functional Ecology 27:227-235.
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I forgot. here are some of the most common species of the Costa Rican south Pacific region: Amazilia decora, Amazilia tzacatl, Threnetes ruckeri, Phaethornis longirostris y Heliothryx barroti. You may want to search articles related to pollination or feeding strategies or pollination syndromes. Best wishes, Melania
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I have repeated measurements on wingbeat frequencies (WBF) on many individuals belonging to different hummingbird species. I would like to relate WBF to body mass (regression, mixed effect model), controlling for repeated measurements by including "ID" as random effect. I would also include "species" as a random effect to control for repeated measurements and to control for variation associated with species. I'm a bit unsure whether to include both as separate random effects ("crossed design") or is it more proper to use "nested design" (i.e. "ID" nested in "species")?
I use R and my script is:
Crossed: lmerfit1<-lmer(WBF~BM+(1|Species) + (1|ID), data=Wingbeat)
OR
Nested: lmerfit2<-lmer(WBF~BM+(1|Species/ID), data=Wingbeat)
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Hi Ronny,
in my understanding every "ID" in your data belongs to only one "Species", thus "ID" is nested in "Species".
Still, I would prefer your first model (but wouldn't call it "Crossed").
Maybe Chapter 2 of Douglas Bates' book draft is helpful:
On page 40:
"Fitting a model with simple, scalar random effects for nested factors is done
in exactly the same way as fitting a model with random effects for crossed
grouping factors."
Maybe it could be interesting to extend your model and set BM random with respect to Species, this will give you the variation of the regression coefficient over Species
( lmerfit3<-lmer(WBF~(1+BM|Species) + (1|ID), data=Wingbeat) )
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Due to native biodiversity loss as a consequence of anthropogenic factors (e.g. land use changes, invasive species, contamination, overexploitation, emergent diseases, climate change, between others)?
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I did not mean to suggest conducting an academic study concerned with abstract ecological changes. On the contrary, just because it is impossible to get a detailed estimate of all ecosystem services at work and their trade-offs in a certain area, in order to address the estimate of changes in the provision of ecosystem services, it is increasingly recognized that remote sensing indices and, in particular, NDVI-related indices are the most appropriate and easy-to-use methods to get the overall picture. As I said, NDVI is broadly recognized as a spatially explicit robust indicator of vegetation photosynthesis (i.e. a fundamental supporting service) related to social–ecological processes such as habitat-land use conversion (e.g.,urban sprawling) or crop rotation (Guerschman et al.2003; Potter et al. 2003; Young and Harris 2005). It is used to identify and assess the impact of disturbances such as drought, fire, flood, frost (Potter et al. 2003; Mildrexler et al. 2007), or other human-driven disturbances (Guerschman et al. 2003; Zurlini et al. 2006; Wylie et al. 2008; Zaccarelli et al. 2008.). Of course, remotely sensed NDVI does not directly provide estimates of specific ecosystem services like pollination, or water regulation, but because of its strong relationship with land cover, and its synoptic feature it can provide an overall landscape perspective of the ecosystem service flow (Costanza et al. 2010). Once you get the overall picture along with robust high frequency time series at the pixel level, you can then address real-world decision-making issues at different scales and play different games like: where can I put an element (e.g. roads, settlements etc) without interfering with the ecosystem service flow, or can I clean this out (e.g. a part of a forest, a meadow) and what does that imply in term of ecosystem service flow? In those cases, NDVI-related indices can provide basic support for a reasonable answer. In other terms, what can I gain and what am I going to loose in terms of ecosystems services as a result of certain decisions in planning or management? See e.g. http://link.springer.com/article/10.1007/s10980-012-9794-4. In any case, in order to make any decision you need to have a landscape perspective if not larger. So, for example, you could decide to reduce a certain ecosystem service at a location in favour of other services or to foster it in other locations (even in other parts of the world) to counterbalance such reduction or loss. If you want to refine the strategy further you can then make use of economic values for ecosystem services or PES (Payments for Ecosystem Services) methods to make more sound and appropriate decisions through e.g. cost-benefit analyses.