Science topic

Trees - Science topic

Woody, usually tall, perennial higher plants (Angiosperms, Gymnosperms, and some Pterophyta) having usually a main stem and numerous branches.
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I am looking for literature about "Tugai". The Tugai type of vegetation is a plant complex of river valleys of all altitudinal and landscape zones, and mainly desert, in which communities of the tree, shrub and herbaceous vegetation are combined. Typical Tugais grow in a narrow band in valleys and river deltas - along the banks, islands, on low-lying terraces, interspersed with meadows and thickets of herbaceous vegetation. I have some literature. I am looking for more information to further improve our research. If anyone has literature on this, please share with me. Thank you very much in advance.
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Кузьмина Жанна Вадимовна Динамика растительности речных пойм сухих субтропиков Туркменистана и вопросы её охраны. Автореферат диссертации на соискание учёной степени кандидата биологических наук.
ECOLOGICAL RESEARCH AND MONITORING OF THE ARAL SEA DELTAS.
Main Tendencies in the Dynamics of Floodplain Ecosystems
and Landscapes of the Lower Reaches of the Syr Darya River
under Modern Changing Conditions. ISSN 2079-0961, Arid Ecosystems, 2019, Vol. 9, No. 4, pp. 226–236. © Pleiades Publishing, Ltd., 2019.
Russian Text © The Author(s), 2019, published in Aridnye Ekosistemy, 2019, Vol. 25, No. 4(81), pp. 16–29.
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Could You suggest datasets containing 2d and 3d images from different sensors of apple trees with fruits / other fruit trees for automated robotic harvesting?
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I'm preparing my first tree for publication with iTol and there are four ways to represent bootstrap there (Symbol, Text, Color, Width). My tree is quite big, I have something like 150 taxa and there's a lot of information I want to display on the image, such as Location, Clades, and Mutations. Anyway, did you work with iTol before? How do you think is appropriate to present the bootstrap values for publication?
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Well your publication is only so big so I recommend most of that in an additional table. Best wishes David Booth
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I am working on fungal diseases of Jackfruit (Artocarpus heterophyllus) tree and will focus on controlling the diseases in an eco-friendly way by using Bio/Plant extracts and observing the inhibition of disease spread.
Can anyone mention any work that has been done on this or related to this? I will be grateful.
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See this recent paper concerning your subject:
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I am looking for information on the pressure tree roots (by expansion) can exert on structures as retaining walls and quay walls. Failure of retaining walls by root pressure is very common. Is there any way/model to determine this load?
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There are some experimental papers on force measurement by plant tree roots:
You may use an inverted analysis of paper B with rod theory to derive root pressure.
Hope it helps
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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.
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So far, these equations are the best for this estimation, and scientifically speaking, when we set an equation it should be compared to the real result. Regards.
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I am referring specifically to the distance from the fruiting body.
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I quote from Dahlberg & Mueller (2011)... A large tree trunk may support more than one genet, sometimes numerous, of a particular species (e.g. Rayner & Boddy 1988; Kay 1992, Kauserud & Schumacher, 2002; Stenlid, 2008). However, except for species that form rhizomorphs, a fungal genet usually occurs only on a single trunk (e.g. Barett & Uscuplic 1971; Adams et al. 1981; Huss 1993; Holmer et al. 1994; Prospero et al. 2003; Stenlid 2008)...
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I tried to solve this on my own, however, this is way out of my area of expertise. Can the remains of a snake become fossilized within the interior of a tree? My husband is big into woodworking and around a week ago he brought back a piece of oak that was down. It has been through a fire. On the edge of the piece of wood, there is clearly a snake. I can see what appear to be vertebrae in a section or two in the areas where the spine would be. It is absolutely stunningly beautiful. Can this happen? Does this happen? Thanks.
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Anything is possible :)
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I like to know what your suggestion is to implement an intercropping system in a date palm orchard to avoid bare soil in the distances between trees.
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Crops such as cowpea, groundnut, beans, bambara groundnut and other leguminous crops have roots that are able to make soil nitrogen available to other plants.
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Dear all, I have to draw the complete pedigree of a high number (>40) of dogs in a study regarding genetic diseases, so I started drawing the pedigree using the R package kinship2.
The problem is there are many common ancestors between the tested animals, and as soon as I add the grand-parents of the subjects the tree gets all "scrambled up", with dashed lines connecting the same individual present more than once in the pedigree and drawn in different spots of the tree. I know that human genealogic trees are usually far more simple than this scenario and this package should work at best.
Manually adjusting the branches to avoid subjects duplication is quite hard to do, so I was wondering if there is an easier way using a different software (possibly free) or a different R package best suited for complex animal pedigrees.
Thank you,
Riccardo
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This is a good online tool. You have to register to use it.
Sometimes it will get scrambled up as you describe for kinship2 but that is solved by pushing the "RE-LAYOUT" button.
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Last year I found a text in German in which Salomon Müller describes how he climbs Mount Singgalang in Sumatra, sees a pygmy squirrel on a mossy tree, and shoots it. I shared the text with a friend, who, like me was very excited about the finding. Since then she has lost the email in which I sent her the text, as have I, and I have absolutely no idea where I found the German text. I have searched as much as I could but not a trace of this text. Plenty of Dutch writings by Müller but not the detailed description in German of his ascent of Mt Singgalang. Am I losing my marbles or does that text indeed exist?
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Slender squirrel is to be expected there. The interesting thing about Pygmy Squirrel (Excilisciurus) was that Mueller's accounts of seeing the species in Sumatra has been dismissed as erroneous by subsequent experts. That's why the hunting account is of interest (and also because we did find the species on Sumatra, so Mueller was right).
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Do both the methods predict a similar form of output for considered data or they can be used for different purposes?
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Christian Geiser well, I live and learn! Thank you for adding yet another batch of publications to my to-read list!!
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I need to know which tree species can be beneficial to be planted close to date palm trees for better yield and soil improvement (with references).
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Thank you @Shuraik Kader for sharing this useful paper.
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Hi there,
is any good research as of yet available regarding the assessment of the impact of afforestation?
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Dear Thomas,
Yes, there are different estimates on this subject. But according to many research centres, including the IPCC the deforestation process that is still taking place is responsible for min. 1/4 of the increase in CO2 emissions into the atmosphere. Consequently, one of the main factors in reducing greenhouse gas emissions, reducing the scale of the greenhouse effect and slowing the process of global warming includes the aforestation of civilisationally degraded areas, wastelands, post-industrial and mining heaps, etc. As part of aforestations, forests with a multi-species, biodiverse forest ecosystem structure reminiscent of natural forests should be restored and not in the formula of plantation monocultures of forest formations consisting only or mainly of 1-2 tree species. Monocultures are susceptible to various viral, bacterial, fungal diseases and pest attacks. On the other hand, biodiverse forests created in the formula of multi-species forest ecosystems are more resistant to various negative biotic and abiotic environmental factors and contribute more to the local microclimate stabilising the climate of the region, positively influence water transpiration, retain water in the soil, fertilise the soil, provide habitat for many animal species, etc.
Greetings,
Dariusz
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Hi
I am working with the UAV image data.
my study area is a dense forest.
How can I extract the dieback of the trees with deep learning techniques? do you know any package for this aim?
I want to extract the steps of the dieback trees.
thank you so much
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Hi dear Shafagat
Thank you for sharing the information and article.
I downloaded the article.
Good luck
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Hello,
I am supervising a PhD study on water and irrigation in Egypt. To submerge in the context I would like to read a good environmental history book about Egypt and the Nile covering the period 1800-2000s.
Some books I already found:
Jennifer Derr (2019) The Lived Nile: Environment, Disease, and Material Colonial Economy in Egypt
Alan Mikhail (2017) Under Osman's Tree: The Ottoman Empire, Egypt, and Environmental History
What is your recommendation, and why?
Thanks in advance for your time to read and answer this question!
Kind regards
Chris Seijger
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I don't think you will find all the information you are looking for in a single book. You have to look for the subjects one by one to get the old and the new.
The Delta. past and present. Archaeological remains?
The Nile since its birth with the problems of sharing, the health issue and its impact on agricultural life in the past and today.
The Aswan dam which solved the problem of floods but created problems on the environment.
The demographic question of Egypt. Egyptians live from the Nile, on the Nile without using the Mediterranean Sea sufficiently, etc…
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Greetings Professors, scientists and lecturers,
In phylogenetic tree analysis/evolutionary trees, most of them have only two branches. Why is that?
Though there are subdivision of small branches from the ancestors, everything divides into two but not three or four or five or six? Why?
Please clarify my query.
Thank you in advance
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Thank you all for your replies.
Good day
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Hi everyone,
I am working with 14074 PAVs (presence/absence variations) in a panel of 99 accessions.
I converted the PAVs table into a binary matrix to construct a PAV-based NJ. Now I would like to test its stability by bootstrapping the tree.
Someone can inform me about the R code to do that?
Attached is the CSV input file.
Here below the commands that I run in R:
Data <- read.csv("Table.csv", sep=";", row.name=1)
dist_mat <- dist(Data, method = 'binary')
tree <- nj(dist_mat)
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Hii Gaia, try aboot function in poppr package.
Best of luck
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Hi, I have the DBH data of each species, now I have to calculate the approximate tree age by using formula. please guide me how to calculate the growth factor value?
please look the image below.
thanks in advance
Regards,
YASEEN MUHAMMAD
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Don't you just look up the growth factor in the table given?
if your species is not there take the closest biologically
then age = DBH x growth factor.
I may be missing something
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There is a lot of demand for information about the potential of different tree species (and also other types of crops) to capture and store carbon.
Such information is critical to designing farms with a better climate footprint.
This is particularly true for agroforestry farming systems relying on one or more tree species!
However, information on this topic seems completely scattered and not synthesized.
Does such a database exist?
Best regards,
Thomas Fungenzi
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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.
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Hello Dears
My goal is to classify dense forest tree species using drone images. Is it possible to classify dense cloud points? If yes, in what way and in what software?
Thankful
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Hello plant-water relations experts!
I've been trying to estimate minimum xylem water potentials (Pmin) in deciduous trees in Indian Savannas using a Scholander pressure chamber. I understand Pmin to be the mid-day water potential in the driest season i.e. the lowest water potential that a plant experiences. The problem is that most deciduous trees are leafless during the driest season. In our field site in the eastern ghats in India, leaf flush happens after a few showers and mature only by monsoon. Do you have any suggestions on how I could go about estimating Pmin for these deciduous species?
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thanks for the document I.V.Srinivasa Reddy
Thanks David W. Lawlor , Unfortunately frequent measurement is very difficult+expensive as our field sites are far away from where we are based.
Siddarth Machado I am seriously considering a psychrometer, but am also vary about how comparable it would be. Just trying to see if there is a way to work with pressure chambers since we already have that equipment.
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I am looking for information about reliability of sonic tomography for the detection of internal defects in trees growing in urban areas. Has anyone ever examined whether the trees designated for felling based on sonic tomography were really so sick? In general, what is the error rate of this method?
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Sonic tomography, or the use of sound waves to detect decay in trees, is a technology available to arborists to create a two- or three-dimensional image of the internal structure of a tree. Knowledge of the internal structure can then be used by a qualified arborist as part of an advanced tree risk assessment.
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I want to set a trap in the plantation area to get butterflies with the bait trap method. However, I still have trouble whether to install it as high as the tree canopy or not far from the ground. Then, in choosing bait to attract carrion-feeding butterfly, is it better to use fish or shrimp or a mixture of both?
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Sociological,in setting a bait for this species one need to be careful and set appropriately because it's not a stable animal, carefully study the culprit which will serve as guide
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Among different tool of investigations such as Fish bone analysis, tree analysis, 5 why , brainstorming which one is more scientific and reliable for identifying root cause of different quality events occurred in pharmaceutical industry ?
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A full standard (IEC 62740) has been developed for root cause analysis. This document analyses many approaches for this purpose.
The Fault tree has been developed to identify, a priori, the causes leading to a potential top event. Then it is very effective for forecasting reliability analyses. However when the top event has actually occurred, this technique can be used, a posteriori, by retaining only the causes which have been actually observed (and discover the root causes of this ecent). This is the base of the "Cause tree Analysis" used in France to identify the root causes of accident/incidents. In collaboration with the actual observations it is based on a "deductive" (top-down) approach which is rather "scientific"
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Can anyone suggest an application of combinatorial optimization in real life? I am considering TSP(Travelling Salesman Problem), Minimum Spanning Tree, etc.
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There are indeed many. As far as (spatial) networks are concerned, you can find for example optimal hub location problems (see the papers by M O'Kelly), or also problems for optimal spatial networks such as subways (what is the optimal shape of a subway ?). I guess that new mobility services such as bikes, etc also display some combinatorial optimization problems...
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We have a problem of snake predation on B type nest boxes (entrance hole diameter: 32 mm). The culprit is the Aesclupian snake (Zamenis longissimus), and they eat eggs and nestlings alike. The nest boxes are hanged on trees at c. 3-4 m height at a periurban forest. We already tried to cover the tree trunks with plastic sheets (following Navalpotro et al. 2021, DOI: https://doi.org/10.32800/abc.2021.44.0103) and also relocated the nest boxes to more stand alone trees (the canopy of which does not (too much) overlap with neighboring trees; this is not always100% as it is not easy to do so in a forest. But all in vain. It seemingly worked for a week or two but then the predation continued and the situation is the same this year. I attached some pictures that can help evaluate the situation.
So the question is: do you have any good suggestion for this problem? Perhaps to treat the plastic sheets with some smelly material?
Thank you in advance!
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Thank you for the helpful comments, you gave me some good ideas that I can work with. Unfortunately, the nest boxes we use are a bit specific (se the 3rd pic), therefore I cannot install a Noel guard on them. However, now we designed a spec. and cheap snake guard on some of the trees and are waiting to see if they work.
@ Michela: this was the first thing we tried (see my original post above) but it did not work. The snakes are probably capable of wrapping themeselves around the treetrunk by sheer muscle power regardless of the smooth plastic foil into which the tree trunks were wrapped.
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Ganoderma spp. causes mortality in several perennial tree species. There is no technique or methodology available through that we can easily detect the actual cause before the death of host plant.
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Yes, Ganoderma causes mortality in perennial trees in arid and semi-arid regions. We have couple of research articles for your references Wim Peeters
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im looking for someone with some experience on multipurpose tree foliages as supplements for sheep.
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I served as a Fodder Dev. Officer in govt. of Odisha,India.I have experience of using leaves of Moringa,Subabul etc. as feed suplliment for cattle,goat and poultry
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Hi,
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.
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Nikola. I will locate some papers and study Cartesian Genetic Programming. It seems to be similar to "Genetic operators for sequencing problems" published in 1991 and available in my ResearchGate Profile. I use this method and its variations in all of my optimization algorithms where the solutions can be described as a sequences. You should also take time to look at my more recent post on benchmarking evolutionary algorithms.
Pls provide a short summary of what you are trying to optimize in your work so that I can consider if my work may assist your research.
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I am greeting you all. I wonder if anyone here faces the same problem with me that I often cannot access a TreeBASE website? Also, can anyone suggest an alternative database that I can use to deposit my phylogenic tree? Thank you very much for your time and your support.
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Hi!
I'm working on a phylogenetic inference (molecular) with 205 taxa and 5350 characters (7 different genes).
I've ever made a phylogeny thanks to a supermatrix. There were some polytomies. The problem is that some have lacks of sequences. Thus, I'd like to make a supertree to compare and see if there will be polytomies again or not.
This way, I inferred trees for each genes in ML with IQtree2. Then, I used Clann to make a matrix as a MRP (Matrix Representation with Parsimony) with 7 source trees. Next, I used PAUP to start a heuristic search (in parsimony) with these command lines in my nexus file (as Clann suggested) :
begin paup;
set increase=auto notifybeep=no errorbeep=no;
hs nreps=10 swap=tbr addseq=random;
showtrees;
savetrees FILE=MRP.tree Format=nexus treeWts=yes Append=no replace=yes;
quit;
end;
However, the search is working for hours (since 8:00 pm, yesterday) and it doesn't stop. More than 10 billion rearrangement were tried 1 721 900 trees are already saved, whereas it's only the first replicate. The analysis tells that the best tree is the tree n°3088, but the heuristic search continues.
Regarding the number of taxa and characters, is it normal that it take so much time?
Is there an error in my command lines?
It is the first time I try to build a supertree.
Can you help me?
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Hi all,
I am building a phylogenetic tree based on 18S rDNA data. The tree consists of 32 sequences and for correct representation I included 5 strains as outgroup. Now I want to collapse my outgroup when the tree is imported in FigTree, but in a weird way it not only collapses my outgroup, but my complete tree (basically get my ourgroup collapsed as well as the rest of my tree).
Does anybody perhaps know what is going on here and how I can prevent this from happening?
Thanks!
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Hello, @Sebastiaan Koppelle, I don't know if I am late to answer this but, the reason the entire tree collapses is because your entire tree is basically a clade that is rooted to the outgroup. So, by selecting your outgroup you are selecting the all the clades upward of your outgroup and therefore you collapse the ingroup instead of the outgroup.
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Dear all of you, especially the plant physiologists,
Can you an explanation why this tree is blooming like this (see the photos attached). I tried to look for all theories related to flowering but not found any fitted to explain in this case.
Please give me a hint. Thank you very much.
Tri
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It could be because of the light it receives… Have you keely observed which side of it receives the most light (photoperiod)? May be the other side of the tree qualitatively receives more or lesser photoperiod that accounts for qualitative variation in blooming.
You should also check for air pockets. This can also lead to uneven distribution of water and translocation of nutrients, resulting in such a discrepancy in blooming.
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How to reasonably measure the elastic modulus of trees with different trunk heights, especially when the trunk is short and the crown is large?
Note: The tree must be measured intactly, therefore, we cannot cut the crown, we need the elastic modulus of the whole tree.
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Filippo Piccini Wow. Good. Thank you very much.
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Hi, everyone! I developed a ML tree using IQtree, then I uploaded output file (.treefile) into itol and Figtree. I got different tree topologies using itol and Figtree. Any idea why? If someone could assist me, I would be grateful. Thanks :)
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Follow
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Dear all,
Is it just a matter of preference or is there a solid theoretical basis for using the DBH instead basal area as a proxy for the size of a tree?
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Hi Dr. Neptalí, the height-diameter relationship can be found in Poorter et al. 2006
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I need the correct formula for calculating FIV and IVI of tree species in a biological community. I have found different estimations online.
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Biomass: M = aDb, where M is the oven-dry weight of the biomass component of a tree (kg), D is diameter at breast height (DBH) (cm), and a and b are parameters. Not sure about IVI :)
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The idea is to have a list of different trees species from different biogeographical areas which have been tested as the best carbon sequestration species.
So if people are planning to make a plantation, they have a guide to using local species to create a mixed forest using the best species for co2 sequestration.
Similar soil, water requirements, seasons, etc will be considered
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Thank you for this data !! I will use it .
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A tunable clock source will consist of a PLL circuit like the Si5319, configured by a microcontroller. The input frequency is fixed, e.g. 100 MHz. The user selects an output frequency with a resolution of, say, 1 Hz. The output frequency will always be lower than the input frequency.
The problem: The two registers of the PLL circuit which determine the ratio "output frequency/input frequency" are only 23 bit wide, i.e. the upper limit of both numerator and denominator is 8,388,607. As a consequence, when the user sets the frequency to x, the rational number x/108 has to be reduced or approximated.
If the greatest common divider (GCD) of x and 108 >= 12 then the solution is obvious. If not, the task is to find the element in the Farey sequence F8388607 that is closest to x/108. This can be done by descending from the root along the left half of the Stern-Brocot tree. However, this tree, with all elements beyond F8388607 pruned away, is far from balanced, resulting in a maximum number of descending steps in excess of 4 million; no problem on a desktop computer but a bit slow on an ordinary microcontroller.
F8388607 has about 21*1012 elements, so a balanced binary tree with these elements as leaves would have a depth of about 45. But since such a tree cannot be stored in the memory of a microcontroller, numerator and denominator of the searched Farey element have to be calculated somehow during the descent. This task is basically simple in the Stern-Brocot tree but I don't know of any solution in any other tree.
Do you know of a fast algorithm for this problem, maybe working along entirely different lines?
Many thanks in advance for any suggestions!
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Now I tested the idea of jumping downwards in the Stern-Brocot tree. This idea is based on the observation that long paths from the root to a Farey element always seem to contain long sequences of steps directed exclusively to the left or exclusively to the right. As long as the direction is constant, the values of numerator and denominator which are added to the current node are also constant, obviously. Therefore, the products of numerator and a certain jump width resp. denominator and a this jump width can be added to the node.
In order to determine the largest possible jump width, bitwise successive approximation is used in this first approach. The result is quite satisfactory:
With an input frequency of 100 MHz, and the output frequency in the range 1 Hz to 100 MHz - 1 Hz (at the extrema, the approximation by Farey elements is poor, of course), the sum of the passes through the outer loop (movement through the tree) and through the inner loop (determining the maximum jump width) never exceeds 386. Attached is my C source. Compared to the maximum number of single steps, this is an improvement of 4 orders of magnitude.
While this approach solves my practical problem, I would still be interested in other solutions because sometimes it's amazing how a problem can be tackled in different ways.
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Trees are known for their carbon sequestration ability (see the VDO attached)
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12 percent In the United States, forest and croplands currently sequester the equivalent of 12 percent of U.S. carbon dioxide emissions from the energy, transportation and indus- trial sectors (EPA, 2008b).
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I have made a tree on the online version of RAXML with bootstrap but the values aren't added to the tree. I have downloaded the files but I don't understand how the numbers associated with the DNA sequences I have are 0.00001 because I only did 10 bootstrap trees. Can you help?
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I have soil moisture dataset of woodland from four different soil depths like 0-5 cm,5-20cm,20-40 cm and 40-70 cm. I also have rainfall, and other climate data for Hydrus 1d model but I don't have any data about root water uptake. please suggest me what should I can do in place of the trees roots parameters. My woodland have Cypress trees.
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A water stress index introduces compensation in root water uptake. See detailed discussion in "Šimůnek, J., and J. W. Hopmans, Modeling compensated root water and nutrient uptake, Ecological Modeling, doi:10.1016/j.ecolmodel.2008.11.004, 220(4), 505-521, 2009." When the index is equal to one, there is no compensation, when it is smaller than one, there is compensation. This option allows the model to consider the fact that at high potential transpiration rates (r2H = 5 mm/day in the model simulation) stomata start to close at lower pressure heads (h2H) (in absolute value) than at low potential transpiration rates (r2L = 1 mm/d) (h2L), and thus an optimal range of pressure heads for root water uptake may vary.
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I have created a molecular clock tree for my term project. However, after creating my tree, I'm not sure how can I display the node age and posterior probability simultaneously in my node.
Also, another question is how can I make my graph less crowded. Currently, it is really hard for me to see my node ages since many nodes are extremely close to each other.
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A node represents a branching point from the ancestral population. Terminals occur at the topmost part of each branch, and they are labeled by the taxa of the population represented by that branch.
First thing you can do is expand the tree which will move it expand it height ways and this allows me now to see the names of the sequences
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Hi everyone!
For a publication on biogeography of Ulmaceae (in a strict sense) I am looking for images from the tropical members of this familiy, especially of the genera Ampelocera, Hemiptelea, Holoptelea and Phyllostylon. Rather looking for live photos than herbarium specimens.
Thanks in advance!
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Please open your RG message box for images of Holoptelea integrifolia (Roxb.) Planch.
Thanks!
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I use MEGA for making phyllo tree. But for poster presentation reason the tree is too big. Can I use MEGA to make clustering of multiple species? Or do I need something like ARB?
Do you have any other suggestion
Thank you in advance.
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With this you can collapse nodes and also change the spaces between lines.
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I sequenced two isolates of a virus and constructed a phylogenetic tree base on their partial sequence. Although both sequences are 100% identical, they are separated from each other by another NCBI sequence that has 99% identity to my sequences.
However, the number of sequences submitted in GenBank is limited (about four sequences) and when I constructed the tree based on a shorter sequence (but more sequences), this problem will be solved.
Is it possible the low number of sequences cause this issue? and which tree is more reliable? a tree with more sequences but shorter length or a tree with low number of isolates but longer sequence?
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I found the problem in Alignment. Changed the alignment method and the issue were solved.
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Hi Everyone,
I have read many articles that say there are countless studies that prove hemp is better at absorbing CO2 than trees, but I can't find any of these studies. Does anyone know where I can find one?
Thank you
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The following link is also very useful: https://www.mdpi.com/2071-1050/14/7/4159/pdf
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I am searching for a model that predicts the volume of forest trees in the Mediterranean region (preferably pine trees), to simulate the volume of a stand as a function of age, I did not find anything like that for this region, any help is highly appreciated. thanks
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Farah, this is a long shot and I hesitate to introduce you to the company which has probably done more harm to Portugal's environment than any other. But Navigator (previously Portucel) makes its money from converting industrial eucalyptus plantations into pulp and pellets and they may well have the data you need for gums. They may be able to refer you also to pine producers.
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Could anyone provine hints on how to extract and quantify protein from shoot samples of chestnut tree (Castanea sativa)? We have been trying to extract proteins from frozen leaf samples (between 200 and 500 mg) using 100 mM PK buffer with 1 mM EDTA, 8% glycerol, 1 mM PMSF, 5 mM ascorbate and PVPP, but unfortunately no protein was detectable using Bradford's method, even without diluting the supernatant. We have tried the exact same procedure with tomato and barley samples and protein levels were detectable and in normal ranges.
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Thank you
Rani P Ramachandran
!
Although it is interesting to know that the authors had also had difficulty in extracting protein from chestnut tissues, I'm afraid the extraction methods tested in this paper are too strong and would affect the structure and function of proteins, disrupting enzyme activity, which we aim to evaluate..
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Does vegetation structure (e.g. tree raminification pattern) affect bird nesting activity and nest abundance? Could you please recommend studies related to this topic? Thanks
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Thank you very much for the recommendations. In Moudrý et al. it is interesting to note that vegetation heterogeneity was strongly related to bird species richness, also that dead trees also provided shelters for nesting birds. Those were however somehow limited to the ground nesting/foraging species as the authors mentioned. How about tree-nesting species?
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hi everybodyi model a courtyard. when i add tree to model this error found:Error: Turbulence Updating got unstable **Max Change of E :247.57847 @ 3,22,13 (incl. Nest-Grids)Max Change of eps :7319.07903 @ 3,35,15 (incl. Nest-Grids)** The relax factor is 0.1, no sense in going lower !!**** There is nothing I can do from here 😞(** You will nedd to increase the model domain or the grid spacing !!** It might help, to turn of the buoyancy term on the "Advanced Settings" -Tab !!** ENVI-met will continiue form here, but will probably fail soon !!** PANIC DUMP TURB was written for your information. Maybe you can fix the problem
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Hi, I got the same trouble too.. anybody knows how to fix it?
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Most of the working based on Random Forest is to achieve regression or classification tasks without clearifing the underlying structure of trees that make up the forest. However, is there a way to derive the summarized or balanced unique tree structure to represent the whole batch of decision trees without minimizing the effectiveness and generalizing ability?
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Random forest tree is a best algorithm. Random Forest is suitable for situations when we have a large dataset, and interpretability is not a major concern.
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New books. Maybe 2010 till today and only about all fruit trees! Reference and handbook books nutrition fruit trees.
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I will definitely check them out.
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To construct a phylogenetic tree using data from different regions of the 16S gene, is it necessary to insert the short sequences into the full-length sequences before constructing the tree? If so, what is the current method usually used? Looking forward to your kind responses! Thanks a lot!
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If you would construct a full-length 16S tree, you need to align the sequences and make the sequence length as same as possible to reduce the missing data and improve the support value. MJ, ML, and BI tree are common for 16S.
RAxML and IQtree are good for inferring ML tree, MrBayes for BI tree, and FigTree for visualization.
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My nuclear and cpDNA are incongruent, and We keep them separate. I would like to do biogeography analyses. Which kid of trees, nuclear or cpDNA, are prefered for this analysis and why?
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To know the exact decease, it is best to use both nuclear and plastid data. However, using chloroplasts can give good insight into past episodes of hybridization, e.g:
Tian, X., Shi, L., Guo, J., Fu, L., Du, P., Huang, B., ... & Wang, Z. (2021). Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts. Frontiers in plant science, 12, 804568-804568.
If we are interested in variability between species or isolated populations, the less variable chloroplast markers seem to be a better choice.
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Especially, For enumuration the permanent plot to know the vegetation patterns. We are trying to do long term monitoring research of Forest vegetation in term of pace of climate change in such circumstances the tagging of individual tree is essential to ascertain the phenological behavior, growth patterns of existing individual tree species in the permanent plot.In such mechanism the tagging of tree is essential part with unique number hence, we are tagging individual tree with iron nail using hammer on the centre DBH, point of tree. I would like to know, does this process is harming the natural phenomenon of tree life cycle?
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There is no such report. You can consult the attached manuscript
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I am not ruling out that answers are already in some published papers.
Could you please give more references?
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With the data of each variables, PCA can give good results
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For my master's thesis I am conducting research about the feasibility of establishing carbon forests in the middle east and generating revenue through the selling of carbon credits, therefore, I need formulas of forest trees volume as a function of age/time to insert in NPV calculations and the Faustmann model, however, I did not find anything, particularly for : Aleppo pine Pinus halepensis, phoenician juniper, and Valonia Oak Quercus Aegilops.
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How many times greater will the elastic modulus of the trunks of mature urban street trees be than that of their seedlings? For example, Acacia confusa. Thank you for your generous help and suggestions.
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Philip John Wilson Thank you very much for the suggestion.
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my object was to identify the unknown species through comparing its relationship with other type species on a phylogenetic tree, and i used IQ TREE to infer trees. As far as i am concerned, i was supposed to infer a rooted tree with an outgroup.
But i got comfused of creating an rooted/unrooted tree and the assignation of outgroup. While specify an outgroup, does that meant i inferring a rooted tree at the same time. on the contrary, while i inferring a root tree, does that meant i also specify a outgroup.
Here's what i check on the website of iqtree (http://www.iqtree.org/doc/Rootstrap)
 1. The default setting of program was creating an unrooted tree, then reroot the tree (with FigTree) would obtain an outgroup-rooted tree
 2. Use the best partition scheme written by iqtree then applied with Lie Markov models would inferring rooted trees without outgroup
Therefore, if my goal was to identify through phylogentic tree, should i assign an outgroup with command lined then use the best partition scheme with Lie Markov models.
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A ML tree is always calculated as unrooted. Any options to provide an outgroup will do the same as your point 1 (the program will just place reroot the tree after it's done). So it's more of a cosmetic thing than anything else. This also assumes that you have a suitable outgroup (not always it's the case).
Rootstrapping allows you to find the most likely place for rooting a tree by using non-reversible substitution models without having to pick an outgroup, and given that you have enough information, e.g. multiple genes.
IQ-TREE has a Google Group and Github repository so it might be a good idea to look in there if you have technical questions about the program.
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I'm interested in compiling information regarding ideas/mechanis/projects at national/regional/local level of different countries regarding the protection of ancient/veteran/habitat trees by paying/compensating for ecosystem services provision to land owners.
I'm interested in promoting this kind of conservation in Portugal but I'm lacking examples from other regions.
Thank you all in advance for the help.
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What is its unit of measure?
How can it be calculated?
How can it be used when shaking the tree stem?
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the rate at which the amplitude of a free damped vibration decreases
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I am currently conducting research on how the growth stage affects the antioxidant activity of mangrove leaves (Rhizophora mucronata). I categorize mangrove growth into 3 groups: seedlings, saplings, and trees. Extraction was carried out by the maceration method for 24 hours (methanol solvent). All extracts were filtered through a vacuum filter before the solvent was evaporated using a rotary evaporator. After rotavap, only the tree extract has small granules.
I wonder what is this thing that solidified and why is that?
ps. based on the phytochemical analysis, the tree extract has higher polyphenol concentrations among those extracts, with the strongest antioxidant activity.
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It should be used a suitable extraction method and it is also to consider a specific type of solvent according to the desired metabolite. Of course, the fractions process of the prepared extract is also recommended for achieving into the appropriate result in these cases. However, the existence of various impurities are also observed in some cases.
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I am looking for information about non-chemical control methods of invasive species in Europe. Thanks for your help.
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Thank you for your interesting suggestions.
There is not much published about the control of tree species sprouting whit this method, although some grey literature publications suggest these methods as available for species like Eucalyptus spp. DiTomaso et al. (2013) https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwjVxIzflfj1AhXoxoUKHRd7BFQQFnoECAgQAQ&url=https%3A%2F%2Fwric.ucdavis.edu%2Finformation%2Fnatural%2520areas%2Fwr_E%2FEucalyptus.pdf&usg=AOvVaw20Eb2foNQ0auen8j7syDb7
Black plastic was used for the control of some herbaceous species like Arundo donax, Tradescantia fluminensis etc. with very good results.
I'm looking for research papers or books that describe and analyse the effects of this method on tree species.
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I have a question on the relationship between maximum tree height and sampling/plot area.
It is like that I have various sampling/plot size in different forest type, and tree height, DBH are measured in the plot. While I'd like to summary the maximum tree height in each forest type. Since the plot size is varied. Should I use i fixed plot size or the various plot size is OK?
Thank you in advance for your time and comment.
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" Hello everyone, Im a student fron the Philippines currently taking up Bachelor of science in forestry. As part of our requirements as undergraduate students, we would to ask you a favor, if we may. We would like to form a survey questionnaire to our study. Our study is Tree Diversity Assessment and Population Assessment of Long-tailed Macaque. With this, we would to ask a sets of sample question from you. If there is any.
Thank you.
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It is our great pleasure to Cooperate with each other
Good luck
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Hello,
If you see the logo used by the very renowned publishers Elsevier, there is a tree, a man standing beneath the tree and two words Non Solus. Anybody, please let explain the logo in short.
Thanks
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dear Andrew
My regards to you
May be a relative of the Illuminati.
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I want to evaluation of phytochemical and morphological studies on Iranian willow (Salix.) species. But I need to be the same age as the trees. Is there a way to measure the age of willow trees without cutting down?
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Willow is a tree that you may not be able to hit the center all the time with an increment borer (as mentioned by Dr. Mohl). Since Salix if cut sprouts back from the roots (coppice), sometimes an increment bore may have two or more stem centers that grew together with time. As I remember, if especially worried about health of tree, return the increment core to the tree, or apply the spray that horticulturalist sand tree surgeons use on cut surfaces. The annual rings can be counted visually, or get a hand lens if the rings are close. Typically, increment cores should not damage or kill tree. If you don’t have any sealant, candle wax would probably due to cover hole, and discourage insects, excess moisture or disease entry.
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I wonder that if I would know the mathematical relationship to find the root propagation of a fibrous rooted coconut tree (Coccus nucifera) or a tap rooted mango tree (Mangifera indica) then I can excavate the entire plant safely and install it in a better place if I need to have a building construction where already a tree was planted. This would be the most sustainable approach considering the human requirements and ecosystem wellbeing.
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Usually , both compliment each other ina mutualistically beneficial manner...
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I have a little confussion about the major soil minerals of rhizosphere of a tree species. Please address me, what are the major minerals like, essential, micro and macro elements...
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Dear Bipul,
First of all you should mentioned about which part of India you are talking about! As different parts of India has different types of soils with various types of minerals. As you are studying in Tripura University so here I am assuming that you talking about Tripura soils. So in Tripura mostly it is red soils. So there you will get Kaolinite (1:1) minerals with abundant amount of hematite ( iron oxides) with sesquioxides (aluminium and Iron oxides). And you are asking for elements. So better mentioned essential nutrients (17) rather than elements. As red soils of Tripura are mostly acidic in nature so definitely Al and Fe will be there along with Mn. Lowland Rice soils will face Zn deficiency. Nitrogen along with phosphorus will be deficient. But still you should mentioned about type of tree.. whether coniferous or deciduous!
Best regards
Deb
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Dear all,
I am involved in tree planting initiatives (TPIs) research since some months. I want to get some studies comparing the income generation of crops (any kind of crops) and trees plantions worldwide or particularly in Africa if possible.
Best,
Legrand Cirimwami.
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Hi everyone. I'm trying to specify the fruit tree types via ortophoto imageries at 25 cm resolution. In normal supervised classificstion techinques, I can seperate bare lands and trees. However, I need to specify fruit trees as a parcel which have same pattern. I have added a sample imagery. Please if it is posssible, suggest me any analysis, method or calculation in any GIS or RS software. Thank you for your intereset.
Sincerely.
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Fruit trees may be identified with more higher resolution rather than at 25 cm. However, in your case, First you classify the trees and mask them out from remaining part of image using supervised image classification. afterwards, you may reclassify the image using programming language like R and Python. It should be noted that at 25 cm resolution should be classified. If you can elaborate your outputs here, will be good to understand problem.
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Hi! everyone. When we do calculate the net diversification rates (NDR) based on the TREE. We must need to have a time tree? Or is there a R-package or method can calculate NDR without a time tree?
Any help will be great appreciate.
Tao
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Lin Zhang Wow, it is great! Thanks a lot, Lin
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???
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No, you can't delete a question once posted on RG. However, you can edit it.
Thanks!
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