Questions related to Trees
This question is focused on creating a list of tree species from the Lacandona Rainforest that could be used for a government project that seeks the equilibrium between an ecological restoration project and market production
I want to convert biomass from herbaceous/grassland plants to carbon. Most of the formulas I have come across are formulas for trees/forests. I am looking for a formula for herbaceous plants.
How does predictor importance calculate in SPSS Modeler? ( It is mentioned with the help of SW that the predictor importance is relative, So, it is not based on OR?)
In different models of DT such as C5.0 the branches of a tree are not according to the results of predictor importance. I mean the root is not the most important predictor followed by the next tree layers! why?
Also, how does predictor importance work in boosting?
The pic of the tree branches is attached.
How would planting trees most affect the water cycle decrease in evaporation increase in transpiration movement of water to new locations accelerate water pollution?
I am conducting a research to see the relationship between soil properties and wild ungulate browsing intensity on the tree saplings in the natural forest. I have analyzed soil data for some chemical properties. Since, the relationship between ungulate browsing intensity index and soil property can not be directly established, I wanted to calculate the vitality index. I have the structural parameters of the tree saplings such as sapling height, basal diameter, shoot diameter at the herbivore damaged point, crown length, crown height, and crown width for 6 tree species. But, I faced a challenge how to calculate the vitality index based on these parameters. If any body knows this please share with me. Thank you.
What, in your opinion, are the methods, ways, legal solutions, new material and other technologies to reduce paper consumption, save wood and trees?
What, in your opinion, are the actions and projects that can contribute to forest conservation, to convert deforestation into afforestation, to protect the climate, biosphere and biodiversity of the planet's natural ecosystems, to reduce greenhouse gas emissions and counteract the ongoing process of global warming?
As we know, trees, forests, especially old, natural forests, primeval forests with old-growth forests without human interference, without the influence of civilization, are the refuge of the greatest resources of biodiversity of natural ecosystems. Besides, forests play a particularly important role in the issue of slowing down the human-induced global warming process, which is progressing faster and faster. Forests also play a very important role in mitigating weather and climate anomalies, maintaining a mild microclimate friendly to living organisms, keeping the soil and air moist, maintaining the high level of biodiversity and soil fertility created over thousands or millions of years, and so on.
Deforestation still dominates over afforestation in many regions of the world. Forests are still being cut down and burned to acquire new areas for agricultural development, the cultivation of crops, which is usually carried out in the form of unsustainable robbery. In addition, this practice is carried out mainly in the tropics and subtropics, where after logging, forests created new arable land is quickly subject to drought and the soil becomes barren. Restoring a forest that has functioned for thousands of years or more in a specific area on the depleted soil requires huge expenditures. In addition, vegetable crops are grown on these new agricultural areas, which are either transported thousands of kilometers to other countries, which generates high greenhouse gas emissions, or are not used for human food but for livestock feed, which also generates high emissions, as industrial livestock farming is a source of high emissions of the potent greenhouse gas methane. Therefore, with a view to protecting the climate, biosphere and biodiversity of the planet's natural ecosystems, to reduce greenhouse gas emissions and counteract the ongoing process of global warming.
Various examples of reducing paper consumption and saving forests are as follows:
In some countries, the scale of printing notebooks, notebooks, books, including school books, has been reduced and students as early as elementary school write at school on tablets or laptops rather than in paper notebooks. Green economic activities involving, for example, the production of furniture from recycled materials are also emerging.
Another example is the replacement of dirty energy based on burning firewood with renewable and emission-free sources of clean energy. Unfortunately, in some countries, in order to falsify statistics on the development of renewable energy at the behest of the government, central statistical institutions, ministries and government agencies dealing with climate and environmental issues also count firewood as a renewable energy source. Such absurdities unfortunately still exist in some countries.
Another example is the use of secondary raw materials of various origins in the construction industry instead of using wood, and especially instead of newly harvested wood from companies producing building materials based on fresh, new wood raw material from a sawmill.
As of 1.8.2023, paper receipts are not printed in France to save trees. You have to ask for a printed receipt if the customer needs one.
What other examples of reducing paper consumption and saving forests are as follows?
In view of the above, I address the following question to the esteemed community of scientists and researchers:
What, in your opinion, are the actions and undertakings that can contribute to forest conservation, to convert deforestation into afforestation, to protect the climate, biosphere and biodiversity of the planet's natural ecosystems, to reduce greenhouse gas emissions and counteract the ongoing process of global warming?
What do you think are the methods, ways, legal solutions, new material technologies and others to reduce paper consumption, save wood and trees?
How can we reduce paper consumption, save wood, trees and reduce forest deforestation, protect biodiversity and climate?
What do you think about this topic?
What is your opinion on this issue?
I invite everyone to join the discussion,
Thank you very much,
Counting on your opinions, on getting to know your personal opinion, on a fair approach to the discussion of scientific issues, I deliberately used the phrase "in your opinion" in the question.
The above text is entirely my own work written by me on the basis of my research.
In writing this text I did not use other sources or automatic text generation systems.
Copyright by Dariusz Prokopowicz
My project is to count the number of trees using an UAV, with the help of an NDVI camera. Recently, while I was reading a research paper, I came across a term Leaf Area Index(LAI). Maybe i can use that to count the number of trees, I have not done much research on LAI though. Is there any algorithm that can count the number of trees? Or is there a research paper or papers that can help me on this project?
Inquiry on Conditional Inference Tree to assess the knowledge and attitude in conservation science
I am new to Random Forest. I understand how it is trained with random selection of features in each split, and so on. In the end we have n_trees, each of which will give a different estimate.
All codes and tutorials and papers I read so far (were not many, I confess) get solely one output, the average in case of regression or the most frequent class in case of classification.
I am very much interested in the distribution of values that all the n_trees give. Is there a theoretical reason why one should NOT do this? Is it conceptually not meaningful somehow?
In any case, does someone know how to get those values, if I want? I didn't find how to do this with R party and I'm currently still migrating to Python SKLearn.
Thank you very much and best regards!
I am working on Melaleuca alternifolia plant in my current project, and searching for a place to get the plant. If anyone here used it in their research, please provide me with s place or person selling it.
In a study dealing with the conservation and tree-related biodiversity, we also became interested in the climate protection protential of overmature, large trees. We are about to obtain accurate tree volumes and wood mass data out of terrestrial laserscanning (TLS) for >50 tree individuals of numerous tree species:
Quercus petraea, Q. robur, Q. rubra
Tilia cordata, T. platyphyllos, T. x europaea
Ulmus glabra, U. laevis, U. minor
At a first look on the available literature, I only found data on the C-sequestration of a few forest tree species...
Good day, I need advice.
My nucleotide sequence dataset (n=163; invertebrate mitochondrial DNA; 658 bp) was aligned by Muscle, manually adjusted to remove any stop codons and translates into a protein. I have been able to successfully create Neighbour-Joining trees with the dataset to date.
Now, I am attempting to produce a ML tree with the same dataset, using the bootstrap test method (1000 replicates), with the Kimura 2-parameter substitution model and the Nearest-Neighbour-Interchange (NNI) as the ML heuristic method. On more than one attempt, I started the process and it became "stuck" on a bootstrap replicate number for several hours before I stopped the process and started again. Please advise on how to avoid this and successfully create an ML tree by bootstrapping. Thank you.
What is the bootstrap score for the P.marinus clade containing the 5 P.marinus strains in the ML phylogenetic tree (attached) with aligned DNA sequences? Tree was constructed using Maximum Likelihood (ML) analysis, bootstrap scores<75% were removed.
This was found in shallow water (deltaic) deposits of late Cretaceous age - middle Campanian (central Poland, Europe).
On the left there is an imprint of a tree, but the most interesting structures are encircled by red lines. Additionally there are some "double hollows" marked by blue.
Do you have any proposition what is this?
I used to work with MEGA 11 to build the phylogenetic trees etc. And to this end I got Huawei MateBook D 16 16" i7-12700H - 16GB RAM - 512GB with Win11. And I have a problems with runnig trees - e.g. 60-70 seq with 500 bootstrap - it mostly stops and MEGA collapses itself. I tried to increase the efficiency of CPU in system option and it helped a little with smaller trees - up to 30-40 seq.
Does Anybody know if I can do something more with this configuration or this will not work together?
Thank You a lot :)
I am currently analyzing tree ring width data with the dplR package. The problem is that my series are very short and I'm not sure how to choose the optimal window.length. My series range from 6 to 27 years. Is there a rule of thumb about how wide the window should be? Is that even possible with this age range?
Reports are coming up that Conocarpus tree is harmful. It has both beneficial as well as harmful effects. Plant it cautiously.
Please share your experiences and comments?
What is weathering of rocks caused by roots of trees and water and chemical composition of rocks change when acid is produced by roots of plants?
I am going to calculate the carbon sequestration potential of some trees in arid and semi-arid regions using trunk diameter and tree height. Is there a way to calculate carbon sequestration potential without destroying trees?
What is the most suited reliable method?
Selected trees include apple, walnut, elm and almond.
I am interested does anyone tried to measure tree rings from sub-fossil oak cross-sections using an image analysis technique? When working with tree-ring measuring table, I usually do the measurements when the wood is still wet. I prepare a band on surface with a razor blade and treat it with chalk. However, the taking scans is problematic because the samples usually are quite big/heavy and the preparation of entire smooth surface is too difficult. What are your thoughts or experience with such samples?
I am trying to use a partial (backbone) constraint in MrBayes, to force some relations that were postulated in another paper. As I understood from the command reference, I need to define a partial constrain with the monophyletic taxa in one side and the taxa I do not want to get in the middle of the other clade in the other:
constraint name partial = 41 42 48 : 14 15 16;
and them apply said constraint
prset topologypr=constraints(ingroup,name); [note I also have an ingroup constraint defined]
The analysis runs great, but in the end I got trees that do not fulfil the constraint at all.
Any ideas what is going wrong?
I am constructing the phylogenetic tree of a monogenean parasite called Macrogyrodactylus species (28 isolates)(MEGA original) but always I found the outgroup lies inside the ingroups.I used several parasites species which looks related but from diffferent genera and families of monogenea bu again the outgroup lies inside the ingroups (inside the tree). I would be most grateful if you could help me in getting the outgroup outside the tree?
Is seaweed farming profitable in India, risks of seaweed farming and good for the environment and seaweed better than trees?
I'm really struggling to get any tree file to work in BayesTraits. I was able to generate a tree successfully in Seaview of the phylogeny I need (attached). The coding that generates this tree is the exact same that I put into BayesTree (also attached). When uploading into BayesTree, it only generates the first 6 taxa in a tree. I was *hoping* that this was potentially a display error (as the tree generated fine in Seaview) but I have the same issues in BayesTraits (attached).
I have created a mega-phylogeny tree for angiosperms using Mr.Bayes software after concatenation of rbcl, matK, Trnh-psba and ITS genes. My final tree consist with several exceptionally long branches. What is the reason for such long branches ? is that incorrect to have such a long branched in a phylogenetic tree?. (I rechecked the possible alignments errors but for me there is nothing wrong with the alignments).
Thank you all.
Researches and scientists' data show us that an area of 18.1 million square kilometers have been modified for buildings and constructions, around the world.
This area is considered as the missing soil on the Earth's surface (like our skin) which has been left uncovered since the first house was built in Tanzania, since the first factory was built in the United States and since the first sales of land for commercial purposes.
Is it a responsibility to return the missing soil back to the roofs of buildings for "MORE OXYGEN"? (About 14.5 million square kilometers, 80% of 18.1 million square kilometers have been modified).
Because only trees can produce natural oxygen, right?
I'm trying to calculate the cophenetic distance by R function cophentic from a phylogenetic tree (with size 16.8MB, generated by package V.phylomaker2), and the RStudio raise the error: "Error in dist.nodes(x) : tree too big", as the picture shows. How can I solve it? Or is there any other method to calculate NRI when the tree is too big(I'm using the function "ses_mpd" from package "picante") ?
Thanks a lot!
Good day! I have a list (~10000) of unique DNA sequences about 10-20 bp.
I want to find out if they could evolve from one or several sequences, or emerged independently.
Some of the sequences have similar motifs and could be aligned, others haven't at all - so I can't just perform MSA and make a tree - the distance matrix contains many NAs.
I've tried using principal components analysis on k-mers (1-4) frequencies but it gives me nothing - the frequencies form one dense cloud of points with PC1 that have only ~4% explained variance.
And I found that universalmotif R package is capable of performing similar analysis using motif_comparison(), so I converted the sequences into sequence motif format (one for each), but when tried it on a short set of data - found that the algorithm works in a very strange way on list of motifs created each from only one sequence. Different methods gives the same result (added tree to the question) - the sequences that are different are placed near instead of sequences that are someway similar...
I am new to the world of Bayesian phylogenetics and I am trying to get my head around the two types of consensus tree MrBayes offers. I understand the Majority-Rule consensus but I am struggling to grasp the allcompat option. Is there another name for it which I may be more familiar with? Any help would be much appreciated!
I am starting to learn Evolutionary Algorithms. I have used Python DEAP framework to implement small projects/programs using Genetic Algorithm and Genetic Programming(Tree based). DEAP has builtin support for GA and GP.
Now I have come across another term called Cartesian Genetic Programming (CGP). There is nothing mentioned in the documentation of DEAP. I don't know the details of CGP as well.
My question : Can we use DEAP framework for CGP based solutions as well ? If not then which platforms are better ? Your answer will be really helpful.
In the city of Dnepr and Dnipropetrovsk region (Ukraine) many damaged trees Ulmus pumila are found in 2021 -2022. Other elm species are not damaged. These are mainly mature trees. Young trees are affected less frequently. Those trees that became diseased in 2021 are practically dead in 2022. As I understand it, the shoot growth point is damaged. Do you have any information on the possible cause of this elm disease? I would be very grateful for the information. I apologise immediately if I can't answer right away. I often don't have electricity or the internet.
I am looking for information about non-chemical control methods of invasive species in Europe. Thanks for your help.
Is there any simple method to calculate above ground biomass of a forest area without taking into consideration the height of trees?
If not then what is the best way to measure the tree height?
I have 16s sequences from the V3-V4 region. I was wondering if it is correct to use a neighbor joining tree to calculate unifrac distances, instead of a maximum likelihood tree.
Any help will be deeply appreciated,
I have constructed a phylogenetic tree by using the MEGA 11.0.3 package. However, I cannot write details for understanding the tree. My question is that how can we write descriptions or how can we discuss a phylogenetic tree?
I request you to post your opinion for the discussion-- "WHY ON HEAVILY RAINY DAY, ONE IS NOT SUPPOSE TO STAND OR SIT UNDER THE TREES"?. What does the scientists say about this? What is the scientific reason behind not standing under the trees while it is raining heavily??
IS IT ADVISABLE TO COOK UNDER THE TREE IN RAINY OR WINTER SEASON?
WHAT IS THE SCIENTIFIC REASON FOR THIS??
WHAT WILL HAPPEN IF TREES ARE PLACED VERY CLOSE TO HOUSES WHEN THE LIGHTING SPARK THE TREE?? WILL THE HOUSE BE SAFE ACCORDING TO SCIENTIFIC REASONS??
Hello, I am researching the phylogenetic tree of snakes. (bayesian Inference tree)
My sequences are 1300 bp, but sequences of outgroups are about 600 bp.
Can I change the difference of about 700bp to missing data and analyze it?
Since there is no appropriate length between related species,
I tried using outgroup with a long distance, but the resolution is poor.
Do I need to cut off the non-overlapping area before using it?
Dear Researcher on Air Pollution, Respiratory illness and Dust pollution.
Are the trees planted in front of the houses, building safe for inhaling clean and fresh air?
The dust accumulated on the leaves of the trees after rainy season carry many toxic particle, which are harmful to human respiratory system. The research proves the rainfall cleans the pollution and improves air quality in the atmosphere. With the increase ib heavy transportation, dust and pollution accumulates on the leaves of the big trees, these leaves are left unwashed for several months till next rainfall. The trees are watered in ground but are unaware of dust on the leaves, bringing lot of diseases like lung cancer, respiratory illness, asthma and many more infection to eyes too.
I REQUEST TO PLEASE SHARE YOUR VIEWS ON THIS DISCUSSION. ARE WE ATTAINING NET ZERO CARBON OR POLLUTING OUR LIVING AREA.
ALSO WHICH TREES ARE TO BE PLANTED INSIDE THE APARTMENT AND IN FRONT OF THE HOUSES, MOST OF PEOPLE ARE ILLITERATE TO UNDERSTAND THE SCIENTIFIC PLANTS WHICH ARE REALLY USEFUL TO HEALTH, NOT SHOW TO THE BUILDING. THESE SHOW TREES JUST ACCUMULATED DUST ON THE LEAVES. LEAST THE APARTMENT PEOPLE SENSE THE FACT OF IT.
ARE THE BANANA TREES GOOD FOR VASTU IN THE BUILDING, THE LEAVES JUST ARE FILLED WITH THE DUST. THE TEAR IN THE LEAVE GIVES DIRTY LOOK, THE DRIED LEAF ARE TANGLING TO ACCUMULATE FOR DUST.
I CALL THE DISCUSSION FOR AIR QUALITY AND DUST FREE LIVING WITH CLEAN AND FRESH AIR.
I have been given 4 organisms (insect) and need to manually construct the max possible trees and then choose the most parsimonious and back this up by research. they are arthropods.
first How can i verify what are the number of possible trees, I have already drawn 12, but got feedback that that is not enough. I am using 10 characters.
We think that the problem might be due to the number of sequences (200) or to fact that we only have a single calibration node, (11-22 m.y. at the base node of the phylogeny).
We have tried to use different formats for the starting tree, but none of the possible options has been useful!!!!!
When BEAST is not given any tree, it runs but we get something like this (negative branch lengths and incorrect taxonomic groups).
We just tried all in the online foros
Here is the message:
Error 110 parsing the xml input file validate and initialize error: Sample from prior flag is set, but distribution with id 'likelihood' is not an input to posterior.
Error detected about here:
<run id='mcmc' spec='MCMC'>
I created a phylogenetic tree of several closely related ASVs and included a few reference strains. I'm seeing a really odd, long branch length on one of the sequences. Most of the branches are 0.01-0.04, and this one branch is 0.6. It is not in a distinct node. Is this likely due to an error? I aligned the sequences with MUSCLE and created the ML tree in MEGA. All of these sequences (including references) are highly similar to each other; they should be >95% identity. Should I use a different alignment tool and/or tree builder?
I want to quantify the effect of biodiversity (and vegetation in general) on meteorological conditions in urban areas.
I'm currently thinking about biodiversity indices like Simpson or Shannon Index, which show the diversity on a numeric range between 0 and 1.
I want to formulate my question based on two examples:
1. One plot with two different individual trees (different tree species) would result in diversity index of 1 because both individuals are of different species.
2. One plot with 100 individual trees (2 trees of species A and 98 of species B) would result in an index of 0.96.
So the first scenario has higher biodiversity compared to scenario 2 but much less individuals.
Is it possible to calculate a mixed index of diversity and density of individuals?
At the same time I'm thinking about the "correct" reference area in order to calculate diversity but also density of individuals in urban areas.
Which reference area would you recommend in order to calculate diversity and density?
I did not want to authenticate my plant sample so Will this cause problems for me to publish papers in the future?
Manily, i have worked with one plant but now the problem is the tree is no longer available in the place where I collected it.I collected some scientific paper from internet and those paper said that my plant is present in my coutry.
Is it enough or plant authentication must be required?
Hello, I am researching the phylogenetic tree of snakes. (bayesian Inference tree and molecular clock..)
My sequences are 1300 bp, but sequences of outgroups are about 600 bp.
Can I change the difference of about 700bp to a missing data and analyze it?
especially phylogenetic tree(ML, BI tree) and Relaxed molecular clock(using BEAST2).
There is wide Research and Managment gap of serious insect pests on various indigenous and or invasive tree species including eucalyptus in the country
The wood of the endangered tree species Paubrasilia echinata (previously Caesalpinia echinata), has traditionally been used for making string instrument bows. Currently, there is a discussion about how best to conserve this species. In particular, there is an initiative to upgrade its international conservation status on CITES, which would lead restriction of Brazilwood trading . Bow makers and related industries are presently lobbying against the CITES upgrade. I find it difficult to obtain unbiased, objective information on how to best address this problem from a conservation perspective. Can anyone please comment? Many thanks,
What are the Methods available for non-destructive biomass estimation of young Miyawaki plantations (young mixed plantations of tree seedlings with DBH less than 5 cm) in tropical condition?
When you are opening a new file on Mega X and Mega 11, the software for some reason ignores the underscore. The actual problem happens when we build a tree in some other software after aligning it on MEGA. How can we avoid this? Any solution to this problem?
I am looking for publications with specific error metrics (BIAS, MAE, RMSE etc.) for allometric tree volume equations for European tree species. Preferably in comparison to destructive measurements. If anyone knows of such publications, please leave a link. Many thanks in advance.
Eleven months ago I girdled 17 trees and measured the moisture content, at the place where they had been girdled, with a wood moisture meter. Typically, the moisture meter showed a reading of about 30%. Now recently I have cut down the trees and cut them into pieces, and I have measured the moisture content at the same place as before, as well as at 5, 10, and 15 meters height, both externally (cutting of the bark with a machete) as well as internally (at the place where I have cut the trees in to short pieces with a chainsaw). The weird thing is that, in spite of that the trees now are dead and very light, the readings on the moisture meter indicate the opposite, they typically are around 40%, as if the moisture content would have _increased_, something which obviously is not the case.
All this happened in western Amazonia (Ecuador) where the climate is very humid, such that I think it sounds quite normal that wood has a moisture content of 40% even in trees that have been girdled 11 months ago. But what I do not understand is why the moisture meter showed just 30% when the trees were alive and the cells must have been basically full of water.
I am planning to run a decision tree model in order to identify profiles that are associated with the binary success variable in a hackathlon. Unfortunately, my colleagues who ran the hackathlon have collected up to 200 predictors--way too many to include them in a tree model (where I would guess only 4-5 are useful, correct?).
My hunch would be to first run a logistic LASSO to identify these highly important predictors that then go into the tree model.
I am aware that a variable may turn out as relevant in the tree model that have no main relationship that could become salient in the LASSO but as this is a exploratory study and I have to come up with a practical approach, I would neverthess assume that the LASSO can identify the relevant ones.
A more finegrained issue is whether there are problems to first run the LASSO on the training data (10fold CV) and then run the tree on the same training data. At the end, both have to face the test set, where the dues are paid :) I have only begun to run machine learning models for the case I don't see the obvious :)
I would appreciate any comments or alternative recommendations
All the best,