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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How relevant is the ancient Turkish proverb: "The trees voted for the axe again, because the axe was crafty and had convinced them that it was one of them, because it had the wooden handle."
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Dear Doctor
[A World of Wisdom in Turkish Proverbs
“Two captains will sink the ship!”
“Listen a hundred times; ponder a thousand times; speak only once.”
“A wise man remembers his friends at all times; a fool, only when he needs them.”
“Patience is bitter, but it bears sweet fruit.”
“A lion sleeps in the heart of every brave man.”
“A kind word warms a man through three winters.”
“Study from new books but with old teachers.”
“Beauty passes; wisdom remains.”
“A cup of coffee commits one to forty years of friendship.”
“A good companion shortens the longest road.”
“Thorns and roses grow on the same tree.”
“He that conceals his grief finds no remedy for it.”
“A knife wound heals, but a tongue wound festers.”
“A thousand friends are too few, but one enemy is too many.”
“No matter how far you have gone on the wrong road, turn back.”
“Patience is the key to paradise.”
“The fool dreams of wealth; the wise man dreams of happiness.”
“Whoever gossips to you will gossip about you!”
“The green twig is easily bent.”]
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Hi everyone.
I'm currently working on a project related to mito-nuclear discordance of our focal taxa, in which the phylogeny constructed by mitochondrial sequences differed from SNP data.
My question was that, when testing the impact of introgression or gene flow by scenario-testing method such as fasimcoal2 or BPP, which tree should I use for phylogeny backbone? To be more specific, could I use the tree from mtDNA and SNP data as input sequence to infer the gene flow among 'mitochondrial lineages'?
Thanks for any opinions!
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Patrice Showers Corneli Thanks! I thought I would use SNP tree since it was more reasonable to me.
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I have constructed a phylogenetic tree, but the resulting tree appears as shown in the picture. I would like to understand what happened to the isolates within the blue frame and what these isolates are called. Are they outgroups?
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Outgroups are from taxa that have been chosen apriori to analysis because they are well know to be outside of the group of interest. One cannot infer the root of the tree without an outgroup to anchor the root. So calling this clade an outgroup would be circular and arbitrary. Indeed, if the support for the apparent clade is small than you really don't know the topology of the tree either. That is fine but unrooting the tree altogether would give you an illustration of what you do know. Present it as an unrooted tree until you have independent data to define an outgroup.
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What is your opinion on the impact of planting eucalyptus trees on groundwater depletion?
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Hello
Thank you for your response
In your opinion, is eucalyptus more harmful to the groundwater table or its benefits and use for the ecosystem?!
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We analyse many characteristics of fruit trees and select the most important ones. But we don't look at the roots at all or we don't care about them. However, we are taught that, like the intestinal system in humans, the roots control many things in trees. For example, disease resistance, early flowering, fruit quality, drought or ground water resistance. My question is, is there any way to measure or visualise the root in large fruit trees?
Thank you for your time.
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Yes, it is possible to measure or image the roots of fruit trees using various techniques. Methods like ground-penetrating radar, electrical resistivity tomography and soil coring allow researchers to assess root depth and distribution. Additionally, non-invasive imaging techniques, such as X-ray tomography and MRI, can provide detailed images of root structures.
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Tree growth is an important aspect of forestry and forest ecology. Typically a growth rate is calculated as the difference between two stem diameter measurements over a given time interval: (dbh2 - dbh1) / dt
There are two sources of error which can occur to lead to erroneous (and oftentimes negative) growth estimates: 1) small measurement error, which is typically is proportional to the size of the stem. These errors can be due to slacked or crooked diameter tapes or not exactly measuring the diameter point on the tree stem, etc. and 2) recording error. Measurements may be by off by a decimal place, having transposing numbers, data collection or entry errors, etc.
Alternatively, trees may have the same dbh recorded at both time intervals, giving a growth rate of zero.
Unreasonably large tree growth estimates can be identified as outliers using a quantile approach, but many types of growth models (i.e., gamma likelihood models) will not allow for negative or zero growth rates.
How do you deal with those zero/ negative growth measures? If you have suggestions beyond simply not including them, please share.
Thank you
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There are some good suggestions in the thread here, particularly the points raised by Andrew Gray
I guess I came to terms / settled back on the classical empiricist's adage: "The data are what the data are [what the data are]..." My initial motivation for asking this question was more of a statistical one -- trying to get a model with gamma likelihood (which will not allow zero or negative growth) to fit.
In this case, I ended up using a truncated normal likelihood, which is a lot like a gamma in terms of shape but gives a little bit more flexibility regarding the linkage of the likelihood function to the process model. One can truncate the distribution at various growth magnitudes (negative numbers, zero, or around zero/ some small positive number).
Work by Nadja Ruger et al -- PlosOne 2012 10.1371/journal.pone.0025330 -- and subsequent work from her lab/ this line of research, discuss one potentially promising approach that can be employed. (see Methods section on Growth data), they do some data cleaning but then estimate measurement error and include that in the model's parameterization (a Bayesian model allows for this).
It comes down to the questions and how much any assumptions made with the data will affect inference. If the objective is to model growth, then including trees that don't grow potentially confounds any signal; however, we know not all trees grow. You can always run the model on different subsets of the data to see the impact of non-growing/ shrinking trees, which is a good exercise/ sanity check. I hope that's helpful; I wish I had a more straightforward/ better answer. I am happy to talk more about this if you would like.
Cheers, Aa
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I’m looking for a mobile-friendly way for volunteers to enter data in the field. Our surveys involve counting flying-foxes per tree across a site with >200 unnamed trees. Ideally, the datasheet should:
  1. Have an embedded site map showing tree locations,
  2. Allow volunteers to input their counts directly on the map, and
  3. Sync across a cloud.
  4. Be free or cheap.
I’m considering Google Forms + My Maps, KoboToolbox, ArcGIS Survey123, and Airtable with Mapbox, but I’d love to hear your recommendations!
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I had a pretty good experience with Mergin Maps ( https://merginmaps.com/ ). Up and running in a few minutes for a neighborhood parking survey. At the time, price was at the low end compared to other with similar capabilities, export and import of basemaps etc. was easy.
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I have data of qualitative and quantitative of tree. I need to combine the qualitative and quantitative data to find the any statistical hypothesis.
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I doubt that you can administer a questionnaire to a tree.
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I need more pdf on this topic
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Although some studies do not agree with the use of citrus fruits due to acidity, my own experience has proven the opposite.
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Hi! My name is Gabrielle, and I'm a biology student.
In my internship, I need to identify the pest on these leaves.
I know the tree species is Annona coriacea Mart.
My professor and I believe it might be a type of cochineal/mealybug. If anyone can assist with the identification, it would be greatly appreciated!
Thank you in advance!
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التشخيص الدقيق للحشرة اعلاه يكون عن طريق ظهور البالغات ومقارنتها مع المصادر الموجودة من للون وطول الاجنحة وطول قرون الاستشعار مع قياس الارجل الامامية والخلفية والافضل يكون التشخيص في متحف الحشرات الخاص بالمنطقة لديكم...تحياتي
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This Schinus is naturalized in Saudi Arabia, I have seen several trees growing wildly in Saudi Arabia/ what is exactly?
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It is Schinus molle.
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SHOULD AVENUE PLANTATIONS ALWAYS BE ABOUT ENVIRONMENTAL POLLUTION AND CLIMATE CHANGE AND NOT ABOUT LOCAL FOOD SECURITY AND FOOD SOVEREIGNTY? There was a time in my childhood days, I remember to see long lines of edible fruit trees, especially the Java Plum (Syzygium cumini,), an occasional mango tree, among avenue plantations. There were hundreds of native sacred Banyan trees (fig species) along the highways. But this has changed completely now. Now avenue plantations are either reduced to species that has little value for food for humans/fauna or full of exotic tree species like the Conocarpus spp., that are detrimental for the environment and humans alike. But, honestly, to this day, I could not wrap my head around, why avenue plantations should always be about pollution, climate change and not about food security and food sovereignty? Why exotic and non fruit or tree species of very little value for humans and fauna are promoted for avenue plantations in India? Is there some kind of food politics involved in it? By not promoting fruit yield tree species for avenue plantation, are we deliberately deprived of our right to access to food, thereby, forcing us as a society to depend and participate in the market? Are the avenue plantations a way of taking food sovereignty away from citizens? I don't mean to say that all the food we need should come from avenue plantations, however, the question is why millions are invested in propagation and promotion of detrimental exotic tree species or tree species that have perceivably less ecological benefits and does not contribute to food/nutrition security of citizens?
Please correct me if I were wrong but I also observe a huge knowledge gap in the way tree species are chosen with regards to the width of the lane/avenue, and the type of neighborhood (residential, industrial, highways). I think that there is absolutely no correlation between the width of the road and the type of neighborhood and the type of tree species planted in India. Is there any prescription available for the choice? If there is one, then what is the basis for this prescription and how far it is put into practice? Any information is highly appreciated. Thank you!
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Dear Pratik Doshi thank you so much, I shall do that and I will keep you posted. Thank you very much for your suggestion, I find it useful.
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Good afternoon!
I have such a question for experts in biomonitoring, namely in bioindication studies of the quality of the environment of recreational areas using the method of fluctuating asymmetry according to Betula pendula Roth.
What should I do if I have collected hybrid leaves, and the sample is now less than a 100 pieces from the collection site? Is it possible to draw a conclusion based on hybrid leaves? Will the sample size affect (not a 100 pieces, but 50, for example) the index of fluctuating asymmetry?
Need your help, cause It's winter now In Russia, and there are no more leaves on the trees this year :(
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A sample of 30 is sufficient to fulfil the CLT, so 50 is fine :)
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Three words “Tree”, “Small Tree” or “Shrub” are often used in different studies including the floristics. These three words may create confusion to decide the actual number of Trees and Shrubs thus need consideration.
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Hello M. C. Imprecise terms also have imprecise definitions. Trees have a single stem that branches at some height above the ground. At maturity, some are bigger than others. Shrubs, on the other hand, have multiple branches arising from the crown at ground level. Some of those may actually reach heights greater than some small trees. How's that for impressionistic?
Best regards, Jim Des Lauriers
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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 was built using two distinct phylogenetic trees created by MEGA X. The first tree was created using the ITS sequences of 24 different species of mushrooms, and the second tree was created using nuc-LSU sequences, which contain the same number of sequences (taxon), using the calculus models of Tamura-Nei and Maximum likehood
Can someone help me to discuss the result (tree)?
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329 / 5.000
The clades are on the right, and the left is the primary origin of the genus. The numbers are the distances in relation to the origin; the further away they are, the more distant they are, the more likely there was deletion, mutation, or evolution. In mega11, the color in the yellow case, or orange, is the color of interest. It groups the branches by species. In this case, the numbers are measures of genetic distance between the DNA sequences of the samples, that is, they are evolutionary changes that give us a genetic similarity. Please, in mega11, compare the sample of your interest with the other closest species and you will see if there are samples preserved or not by asterisk. At your service.
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For any non-linear equations, how can we estimate the asymptotic standard error for each of the parameters (say a, b, c, d) of that equation?
Let say an equation:
Y = a/[1+b exp (-c x X] (1/d)
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Hey Pradip Kumar Sarkar , did you that find that out?
I have my asymptotic equations with standard errors for the natural logarithm of my variable. I would like to "back transform" those standard errors. I know it is impossible, but is there an approximation formula? Thanks a lot!
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Is there any software that automatically collapses unsupported nodes?
FigTree makes it, but it is manual and the user has to decide when to collapse. I have a very complex tree and it is very difficult to collapse the nodes and a software that has the automatic option would be very good.
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Les, but my tres has many nodes and branches, so it is very difficult to collapse in certain nodes
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I have to make a phylogenetic tree for class and am trying to locate the best software to create one
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Seaview (https://mybiosoftware.com/tag/seaview) is a reliable and easy to use program to learn phylogenies. It is a compendium of really excellent independent program that accomplishes alignment (use the Muscle option) and really fine distance, likelihood and parsimony inference programs.
Similarly you should look at TreeViewer also with a nice graphical interface (https://treeviewer.org).
Other excellent programs are for likelihood:PAUP, Raxml, IQ and for Bayesian: MrBayes. One of my favorites is SplitTree for tree diagnosis. And for publication quality trees, try FigTree. These last few are my go-to programs but may take a bit more training - which you should get anyway.
These all have very good manuals. Also I will be making my many years of lectures available soon on my researchgate page. Will take questions.
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i am generally interested in trees.
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Petit, R. J., & Hampe, A. (2006). Some evolutionary consequences of being a tree. Annu. Rev. Ecol. Evol. Syst., 37(1), 187-214.
Really interesting
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How can large-scale phylogenomic datasets be improved to reduce uncertainty in tree resolution?
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Hi David,
I haven't operated many whole-genome phylogenies but the followings may be of some help:
The error of genomic phylogeny may be caused by the mistakes of alignments, the introgression/ILS phenomenon of some genes, and the search methods of phylogenetic reconstructions.
In the first case, perhaps it is wise to apply a strong trimming method to the sequence alignment, or use non-alignment ways. I've heard an invention of Zhejiang University - a phylogenetic strategy to construct trees using the cluster of gene blocks, not that of whole sequences. Otherwise you may map your dataset to a reference genome, extracting SNP sites of each gene and use sequences straightly constructed by SNPs to do tree search. In that way, you can also lighten your computation burden because each chromosome can be reduced to SNP sites below about 30000 bp before tree reconstrcution.
In the second case, do coalescent phylogenies, or only keep highly conservative regions can be a good idea. You can select those CDS regions ahead by analysing reference genomes and use RNA-seq to extract those regions.
In the third case, applying rapid and accurate tree search methods, or switch to advabced hardwares, so that you can do more times of search to find the best tree.
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Are you interested in joining our Juglandaceae-network?
We are working on global biogeography and conservation of the relict tree family Juglandaceae. However, the distribution and status knowledge of many species of South-Eastern Asia are not well known.
We are searching therefore for local experts of Engelhardia apoensis. According to our knowledge, the species is present in continental Malaysia, Borneo, Brunei, Philippines. Please see the attached schematic map with known distribution (administrative units & countries).
Any information, maps, publications, reports, personal observations, etc. from your region are interesting for us.
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I want to carry on research on the impact of increased temperature on the tree species in Bangladesh. The idea of methodology is welcome. It may be in natural forests or plantations in some places of Bangladesh.
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Dear Mizan,
Thanks for your response. For example, biomass growth, flowering period/timing, etc.
Please give me your methodological idea.
Best wishes
Danesh
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Include phylogenic trees and diagrams of life cycle
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Yersinia, (genus Yersinia), any of a group of ovoid- or rod-shaped bacteria of the family Enterobacteriaceae. Yersinia are gram-negative bacteria and are described as facultative anaerobes, which means that they are capable of surviving in both aerobic and anaerobic environments. Though several species are motile below 37 °C (98.6 °F), all Yersinia organisms are rendered nonmotile at this temperature and above. The genus is named for French bacteriologist Alexandre Yersin, who in 1894 discovered Pasteurella pestis (now Yersinia pestis), the causative agent of plague, which was independently isolated that same year by Japanese physician and bacteriologist Kitasato Shibasaburo.
In addition to Y. pestis, other species that are important pathogens in humans include Y. enterocolitica and Y. pseudotuberculosis. Y. enterocolitica is widespread in domestic animals, including pigs and cattle, and is found in birds and in aquatic species, such as frogs and oysters. It also has been isolated from soil and from the surface layers of various bodies of water, including lakes and streams; its entry into soil and water systems originates with animal wastes. The organism is transmitted to humans as a foodborne or waterborne pathogen, and infection results in an acute gastrointestinal condition known as yersiniosis. A similar condition arises following infection with Y. pseudotuberculosis; however, little is known about its mode of transmission to humans. Y. pseudotuberculosis appears to circulate in a variety of animals and has been found in horses, cattle, dogs, cats, rabbits, rodents, deer, and birds, including ducks, geese, turkeys, and canaries. In some instances, infection with either Y. pseudotuberculosis or Y. enterocolitica may give rise to mesenteric lymphadenitis, an inflammation of the peritoneal tissue of the intestines that produces symptoms similar to those of appendicitis. In contrast to the other Yersinia organisms, Y. pestis circulates in rodents and is transmitted to humans through the bite of an infected flea.
Several other Yersinia organisms have been identified, including Y. intermedia, Y. frederiksenii, and Y. ruckeri. The latter is pathogenic in salmonids (family Salmonidae), including rainbow trout and Pacific salmon. In these species, Y. ruckeri causes enteric redmouth disease, which is characterized by hemorrhaging of the subcutaneous tissues under the fins and around the eyes and mouth.
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Is there any ethnobotanical or scientific significance to this pairing, or is it purely a result of cultural and religious practices?
Neem and peepal trees are frequently seen together, particularly in religious or sacred spaces. Neem is renowned for its medicinal properties, including its antibacterial, antiviral, and antifungal benefits, while the peepal tree has been historically revered for its role in treating respiratory and skin disorders. While these trees are significant in both traditional medicine and spirituality, I am curious whether their pairing holds any deeper ethnobotanical or scientific value, or if it is a practice rooted in cultural symbolism alone.
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Azadirachta indica(neem) is often planted with Peepal(Ficus religiosa) for the former would protect the latter. Crude parts of Neem have been mixed and stored with seeds e.g maize and rice. Peepal tree on the other hand has been known for its religiosity.
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I need a suitable method I can use in identifying tree species in a riparian zone area.\
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Here are some suggested methods and literature for assessing tree species in a riparian zone:
### Methods for Tree Species Assessment
1. **Field Surveys**:
- Conducting systematic field surveys is a fundamental method for identifying tree species. This involves measuring tree diameter, height, and crown characteristics and noting the species.
2. **Vegetation Sampling**:
- Use quadrat or transect sampling to collect data on tree species diversity and density. These methods allow for standardized measurements across the riparian zone.
3. **Remote Sensing**:
- Satellite imagery or drone technology can help assess tree cover and species distribution in riparian zones, especially in larger areas where ground surveys might be challenging.
4. **Molecular Techniques**:
- DNA barcoding can be employed to identify tree species, particularly when morphological identification is difficult. This method can be useful for confirming species in a diverse or cryptic community.
5. **Ecological Indicators**:
- Assessing the presence of specific tree species known for their ecological roles in riparian zones can provide insights into the health and function of the ecosystem.
### Suggested Literature
1. **"Vegetation of Riparian Zones"**:
- McKenny, D. & McMillan, M. (2017). In *Riparian Ecology and Management in Multi-Land Use Watersheds*. This book discusses various assessment methods for vegetation in riparian zones.
2. **"Forest Inventory and Analysis"**:
- U.S. Department of Agriculture, Forest Service. (2000). *Forest Inventory and Analysis: A national program for monitoring forest resources*. This document outlines field methods for assessing tree species and their distribution.
3. **"Field Guide to the Identification of Tree Species"**:
- Burns, R.M., & Honkala, B.H. (1990). *Silvics of North America*. This comprehensive guide includes information on identification and ecological traits of various tree species, including those found in riparian areas.
4. **"Ecological Indicators of Riparian Health"**:
- Stoll, P. & Sutherland, R. (2008). *Riparian Ecosystems: A Review of Assessment Methods*. This paper provides a review of ecological indicators and methods for assessing riparian health, including species assessment.
5. **"Remote Sensing for Tree Species Identification"**:
- Hyyppä, J., & Inkinen, M. (2001). “Aerial laser scanning for tree species identification and forest inventory.” In *ISPRS Journal of Photogrammetry and Remote Sensing*. This study discusses using remote sensing techniques for identifying tree species.
### Conclusion
Combining field surveys with remote sensing and molecular techniques will likely yield the most comprehensive assessment of tree species in riparian zones. Each method has its strengths and can provide valuable data for understanding the ecological dynamics of these important areas.
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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?
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I was built using two distinct phylogenetic trees created by MEGA X. The first tree was created using the ITS sequences of 24 different species of mushrooms, and the second tree was created using nuc-LSU sequences, which contain the same number of sequences (taxon), using the calculus models of Tamura-Nei and Maximum likehood
Can someone help me to discuss the result (tree)?
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I have done air layering to 100 branches of Mango tree. I have got the rooting percentage of 80%. Then I used separate it using stepwise separation method from mother plant (7 days interval). I used Transplant it to a pot mixture of sand:manure:soil = 1:3:3 ratio. Even after doing all this 80% of the plants are not surviving. How can I get more survivability of plants?
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To improve the survival rate of air-layered mango plants, follow these tips:
1. **Gradual Sun Exposure**: Acclimate the plants to sunlight slowly, starting with shaded conditions.
2. **Water Management**: Keep the soil moist but avoid overwatering to prevent root rot.
3. **Potting Mix**: Use a well-drained mix, possibly adding coco coir or perlite.
4. **Humidity Control**: Maintain high humidity by misting or covering plants with a perforated plastic bag.
5. **Transplant Timing**: Transplant during cooler parts of the day and mild seasons.
6. **Root Treatment**: Treat roots with fungicide or rooting hormone if necessary.
7. **Proper Pot Size**: Ensure the pots are large enough and well-drained.
8. **Support**: Provide physical support to prevent plants from bending.
These steps can reduce transplant shock and improve survivability.
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If someone can help me by sending my file i will be thankful
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You assigned a truss section to a part (wire), but used beam elements in the mesh for this part. You should use truss elements in the mesh. Go to the mesh--> element type and assign the correct mesh.
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The occurrence of a whitish liquid from neem trees (Azadirachta indica) is more specifically correlated to the infestation of certain pests. Especially pests that are known to suck frass and include aphids, whiteflies and mealy bugs. Such pests access the sap of the tree, causing the plant stress and damage.
These insects infest the neem thanks to their ability to invade the phloem, which is the tree’s tissue that contains and carries the sap. This in turn usually makes the tree react against the invasion. One of the several reactions often involves giving off what may be termed ‘guttation fluid’ which could be a milky like substance.
Milky fluid, besides being produced by sap sucking pests, may also have other explanations such as fungal infections and abiotic factors. The white fluid may also contain other substances including the plant defensive agents like azadirachtin which has been proven to kill insects.
More studies concerning treatments of neem trees and their pests interactions are important because they may promote sustainable practices of pest control and address the plant biological behaviors' in its ecological region.
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The whitish liquid observed from neem trees (Azadirachta indica) is often linked to infestations by sap-sucking pests such as aphids, whiteflies, and mealybugs. These pests invade the phloem, causing stress to the tree, which may result in the release of a milky-like fluid known as guttation fluid. This fluid might contain defensive compounds like azadirachtin, which can kill insects. Other causes of the white fluid could include fungal infections or environmental factors. More research on neem tree-pest interactions could help in promoting sustainable pest control methods and understanding the tree’s ecological behavior.
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The molecular phylogenetic trees of subfamilies and family (diving beetles) were constructed using MEGA 11 (Molecular Evolutionary Genetics Analysis version 11) software. Initially, the COI sequences (Folmer) were aligned in MEGA by using MUSCLE alignment program. The aligned sequences were saved in MEGA format. Then the best fitting model was found. Model with a lowest BIC (Bayesian Information Criterion) value was considered for tree construction. The phylogenetic tree was constructed using Maximum Likelihood Method. Boot Strap value 500;
Nearest-Neighbour-Interchange; Branch swap- none.
How can the tree be interpreted or rectified?
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Hi,
As David L Remington said, those of us who are not experts on diving beetles can only speculate without seeing the actual data. The insects have been evolving on earth for quite a bit longer than the mammals have, and it seems possible that diving beetles could have a very distant common ancestor, or perhaps even convergently evolved a few times from non-diving beetles. Complete mitochindrial genomes are often very accurate at phylogenetic reconstruction in comparison to fossil record etc. But COI gene (or protein) alone is often a bit misleading. Also, mitochondria can sometimes tell a slightly different story than nuclear chromosomal genes.
You must also beware, that if you search GenBank and use a lot of data from there, that it is not uncommon for samples to be mislabeled for genus/species. This can happen either because the authors mis-identified the sample, or because there was some type of PCR contamination event or mis-labeling or material in between the sample and the GenBank entry.
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Dear Colleagues,
We have started a synthesis effort called the “Global Spectra-Trait Initiative” (https://github.com/plantphys/gsti/tree/main) to gather datasets of paired leaf gas exchange (A-Ci curves) and leaf optical reflectance data.
The overarching goal is to create a database of spectra and physiological trait data we can use to develop spectra trait models for the prediction of the photosynthetic capacity of leaves.
We welcome data from C3 species of any biome (including agricultural systems).
If you want to participate in this synthesis, please contact us or visit our GitHub for more information.
Julien Lamour, Shawn Serbin, and Alistair Rogers
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Colleagues
A reminder about this effort! We are moving forward with a first manuscript covering the database but we have plans for follow-on studies and are looking for a broader group of collaborators!
Take a look and let us know if you want to get involved!
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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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This question refers to something from a long time ago, so I don't recall exactly what I did. However, I suppose the sequences were incorrect. I replaced them with the correct sequences, so you may want to check the accuracy of your sequences.
Another issue might be related to selecting an inappropriate outgroup. Make sure to choose one that is significantly distant from the other sequences.
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For example a mango tree whose bifurcation has occurred at 3.5ft so in that case what can be done.
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Hello, this is described for example in the instructions for the national forest inventory for germany: https://bwi.info/Download/de/Methodik/Aufnahmeanweisung_BWI3.pdf In chapter 5.5.8 on page 44 the second sentence says "Unter Brusthöhe (1,30 m) gezwieselte Bäume werden wie zwei verschiedene Bäume erfasst." which means that such trees are handled as two separate trees. There are also illustrations to such measurement problems.
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How to define pseudo-time in a graph? Can I use spanning tree or any other algorithm?
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I have seen different concepts called 'pseudo-time'. Perhaps you could give some more context on the particular pseudo-time that you are interested in?
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I want to construct a phylogenetic tree based on the STs of K. pneumoniae. Seven housekeeping genes (gapA, infB, mdh, pgi, phoE, rpoB, and tonB) were sequenced using Sanger sequencing, and the double-stranded DNA was assembled. I queried the sequences in the Institut Pasteur database to identify the STs. However, I am unsure whether I should construct separate trees for each gene or concatenate the seven genes into a single sequence for each isolate before drawing a tree (and how to do it). Thanks for your help.
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Most folks would concatenate, align, & trim off any sequence from the ends that are an overhang. Then build a tree.
Good luck!
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Please, what is the memory consumption of the Matlab function quad tree decomposition procedure [S = qtdecomp(I)] with respect to the input set I?
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Igor Faddeenkov Thank you very much for your helpful answer
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I created two potential gene expression cassettes (constitutive and inducible) for expression of a mutant PETase gene on PeptiCloud using the version tree feature, which allows users to create multiple versions for a biological sequence and organize it in a single location. Could you please check if the cassettes (nodes 3 and 5 in screenshot) are suitable for expression in E. coli K12? The original paper and plasmid sequence are attached in the files section. My project can be found in this link: https://www.pepticloud.com/public-project/PETase.
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To determine if the given cassettes are suitable for expressing a PETase mutant in E. coli, I would need more information about the specific cassettes and the PETase mutant you are working with. Some key factors to consider are:
Promoter: The promoter used in the cassette should be a strong, inducible promoter that can drive high-level expression of the PETase mutant in E. coli. Common choices include T7, tac, or araBAD promoters.
Coding sequence: The coding sequence for the PETase mutant should be optimized for expression in E. coli, including codon optimization and removal of any problematic sequences.
Fusion tags: Depending on your needs, the cassette may include a fusion tag like 6xHis or GST to enable purification of the expressed PETase mutant.
Antibiotic resistance: The cassette should contain an antibiotic resistance marker compatible with the E. coli strain you are using for expression.
Cloning sites: The cassette should have appropriate cloning sites flanking the expression construct to allow insertion of your PETase mutant.
Without more details about the specific cassettes and the PETase mutant, I can't provide a definitive assessment. However, if the cassettes contain the necessary features for high-level expression in E. coli, then they may be suitable. I'd recommend reviewing the cassette details and comparing them to the requirements for your PETase mutant expression experiment.
Please let me know if you have any other details about the cassettes and the PETase mutant, and I'd be happy to provide a more thorough evaluation.
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e.g. moment one: square in its normal state moment two: square after cutting large trees and replacing them with dwarf trees.
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Ateef Ullah already gave a good advice, there are many indices. But you cannot do any statistics on only one quadrat to calculate biodiversity indices and compare them before and after manipulation. So, I assume you have many quadrats (replicates). Is there any ecological gradient involved? it is important for understanding beta-diversity patterns and ordination results. Download PAST4 (free) software and under Diversity tab you can find lots of tools for comparing diversity, while ordination methods are under Multivariate tab.
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I want to assess the trees in an rainforest habitat and collect every necessary detailed data by utilizing GIS and Remote sensing technology techniques. And build a database management system for all people of different expertise to have accessed.
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D.O.I: 10.4236/jbcpr.2023.111001
Check my article and u will faund answers
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I want to know what are the relationship that happen between insect biodiversity and durian tree
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Insect biodiversity and durian trees have a mutually beneficial relationship that influences the health and productivity of durian orchards. Here are the key aspects of this relationship:Pollination:Durian flowers are primarily pollinated by insects, especially nocturnal species like moths and certain beetles. These insects transfer pollen from one flower to another, which is crucial for fruit production.The presence of a diverse insect population can enhance the effectiveness of pollination, leading to better fruit set and higher yields.Pest Control:A diverse insect community includes natural predators and parasitoids that help control pest populations. For example, predatory insects such as ladybugs, lacewings, and parasitic wasps can help manage pests that might otherwise damage durian trees.By maintaining a balance, these beneficial insects reduce the need for chemical pesticides, promoting a healthier orchard ecosystem.Nutrient Cycling:Insects play a role in decomposing organic matter, such as fallen leaves and fruits. This decomposition process returns nutrients to the soil, improving soil fertility and health, which in turn benefits the durian trees.Detritivores, such as certain beetles and ants, break down organic material, aiding in nutrient cycling.Ecosystem Health:A high level of insect biodiversity is an indicator of a healthy ecosystem. Healthy ecosystems are more resilient to environmental stresses, such as diseases, extreme weather, and climate change.Insect diversity helps maintain the overall ecological balance, which supports the long-term sustainability of durian orchards.Mutualistic Relationships:Some insects form mutualistic relationships with durian trees. For example, certain ants protect durian trees from herbivorous pests in exchange for food resources such as nectar or shelter provided by the tree.
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Syria has been suffering from a senseless, devastating war for more than 14 years, in which the combatants did not respect any sanctity of humans, trees, animals, cities, archaeological, historical, and even religious sites. The impact on the environment was very violent, through the use of heavy weapons and explosives of all kinds, the destruction of agricultural lands and forests by uprooting and felling trees, the loss of biodiversity, water and sanitation systems, and the pollution of the air and soil with heavy metals such as mercury, arsenic and lead, which are produced by weapons and their remnants. Of solid waste and mines, effects that may last for decades, causing permanent damage to the ecosystem, in addition to the presence of a huge number of unexploded explosives that explode and cause the death of dozens of civilians daily, in addition to the Corona pandemic in 2021 and 2022, and the devastating earthquake that struck Syria on 6 February 2023. It greatly destroyed cities and towns, in addition to the destruction of infrastructure, including schools, hospitals, companies, and factories, which contributed to a severe deterioration in the level of humanitarian conditions, especially food security. All of the above doubled the pressure on the environment through unjust cutting. For forests to use their wood, and illegal hunting of animals, and increased the government’s inability to meet the requirements of economic and social growth and development, and take into account environmental requirements. In this paper, we address the current state of the Syrian economy, the damage caused by military and security operations, the decline in agricultural production, air, soil and water pollution, the spread of oil pollution, and illegal fishing. We reached a basic conclusion, which is that the senseless and destructive Syrian war has affected the environment in a devastating and catastrophic manner, and that its negative environmental, economic, social, and even political effects will continue for a long period of time. Among the most important recommendations is to achieve real concerted regional and international efforts to stop the devastating and ongoing war, and to work to mobilize international support (technical and financial) to overcome the devastating effects of the environment and climate left by this war, because these catastrophic environmental effects will not be limited to Syria, but rather their repercussions will be on the region and the world.
Keywords: war, environment, air pollution, soil pollution, water pollution, forests, biodiversity, economic impacts, social impacts.
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In Syria around 90 per cent of families in the country already live in poverty on top of that military activity has significant impacts on the environment. Not only can war be destructive to the socio-environment, but military activities produce extensive amounts of greenhouse gases (that contribute to anthropogenic climate change), pollution, and cause resource depletion, among other environmental impacts. northern Aleppo, armed groups have been a main driver in heavy logging of natural forests, with nearly 60% of trees cut down. The war also directly caused destruction of large-scale commercial orchards, impacting livelihoods. The combined effects of rising temperatures, decreased rainfall and water scarcity are among the reasons for reduced water levels in the Euphrates River. This makes it difficult for people to earn a living, forcing many farmers in once-rich agricultural communities, such as Deir-ez-Zor, to abandon their land. Due to the collapse of Syria's water infrastructure, more than half of Syrians now get water from such unsafe sources. There are multiple causes of this crisis: drought and climate change, wartime destruction, energy shortages, and the weaponization of water access by Turkey and other actors. Along with the degradation of the natural resources in these countries and a radical destruction of forest cover, the animal and bird populations have also been adversely affected. The ongoing economic crisis is worsening negative coping mechanisms and particularly affecting female-headed households while contributing to the normalization of gender-based violence and child exploitation. Water insecurity. High temperatures and low rainfall are not the only drivers of water insecurity in Syria.
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Melia azedarach is often confused with Azadirachta indica in the indian sub-continent. The medicinal utility of A. indica attracts a lot of the common people and in abscence of it, people tend to use M. azedarach.
I have found online that Melia azedarach is highly toxic for consumption. I want expert opinion from my scientific peers and thoughts on it.
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Yes!
Melia azedarach is highly toxic to humans and other animals. The whole plant is toxic and eating even several berries can result in death. Meliatoxins are an active compound found in M. azedarach, and are responsible for its toxicity. However, mature berries are more toxic than young ones. A single dose of green leaves around 30 g/kg body weight and fruit 5 g/kg body weight is lethal for cattle and death within 17–48 h after ingestion, while the oral lethal dose (LD50) of meliatoxin in pigs is 6.4 mg/kg body weight.
Thanks!
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Is planting trees blindly everywhere a permanent solution to stop climate change?
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Also, you can check the following link, it may be useful:
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PP resin and PE resin is petroleum base from fossil we have to use in making our FIBC products, I am thinking of end of use, returned to landfill, by mixing particular master batch into our product in which, upon landfill, it will be perform similar to Biodegradable resin making better soil for trees. CO2 , H20 or Methane fully released because the trees will use CO2 n H2O as its Food. Methane is for energy recovery. From the best of my knowledges some particular fermented microbial or enzyme may doing this workable, but is there any one mix to our product to fulfill the purpose, or dilute them upon landfill. At least min 90% proportion decompose, but totally will be perfect.
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Thx a lot for yr comment. So, I'll find other solutions further.....
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I have two sets of canopy pictures from a forest taken at dbh with a fisheye lens. One set of pictures are from the spring just before the trees get their leaves, the other is from late summer where the trees have all their leaves. Both times the pictures where taken in the same spots.
I´m have been analyzing these two sets of pictures separately in R in order to get a value of the effective leaf area index from each picture to use as a proxy for the amount of light available for the flora. The aim is to be able to link the amount of light available on the forest floor to the floral development.
But I have encountered a problem when choosing a method for setting a threshold and thereby binarizing the fisheye picture to further analyze it. For the pictures taken in the summer I´ve used the Otsu method, since it seem to work well here. But when analyzing the spring pictures this method doesn´t seem to work well, since it´s not cooping well with the clouds in my pictures. Instead I have found, that the Huang method works well here.
So my question is, can I compare my results when I have used two different thresholding methods?
And if not, which method would then be cooping best when I have pictures with both direct sunlight and dark clouds?
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Dear Katrine,
So far as I know, all pictures should be taken under overcast sky conditions. Did you do so?
You can optimize the threshold using the free software SideLook 1.1 (Nobis 2005; Nobis, Hunziker 2005). I do not remember which algorithm uses the software, but it should solve your problem of using two different methods. With this software, you have some control of the threshold assignment and you can use several color channels (blue, green, red, and grey, respectively) that can help you improve differentiation between black and white pixels. The blue band is usually best, but you could try another band for sun vs cloudy images. You should have no problems if the black pixels represent only canopy elements. A visual inspection after thresholding should be done to see if clouds are not taken as black pixels. As a last resource, the old way was a visual inspection of every picture can be used, as thresholding was developed as a method to reduce time spent in this step.
Regards
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I have been running my phylogeny tree in MEGA X. My phylogeny tree doesn't seem to have any major differences between species in plain view, but the branches are becoming more clearly divided and each species looks to have major differences in topological view. What happened to my phylogeny tree?
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I suspect you are looking at the difference between a "cladogram" with meaningless branch lengths, and a phylogeny where branch lengths are proportional to the distances between the sequences.
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Terrestrial orchids establish a relationship with fungi when germiate. Duw to their small size, they lack reserve substances and need a fungus to feed them, a relationship that can last the entire life of the orchid.
However, since most orchid species are epiphytic, are they able to start this relationship with fungi present in the surface of trees? Or does they obtain their nutrients from another source?
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Narrative therapy stands as a beacon in the realm of psychotherapy, championing the notion that individuals are the ultimate authorities on their own lives. Its core premise revolves around the narratives individuals construct about themselves and their experiences. Within these narratives lie the seeds of personal growth and transformation.
In the narrative approach, therapist and client embark on a collaborative journey, delving into the intricate tapestry of stories that shape the client's perception of themselves, their challenges, and their relationships. Together, they sift through these narratives, identifying those that may be hindering progress or perpetuating oppression. Through this process, the therapist aids the client in crafting alternative, more empowering narratives, paving the way for renewed agency, resilience, and hope.
The scope of narrative therapy is broad and inclusive, offering solace and support to individuals grappling with a myriad of issues. Whether navigating the depths of depression, wrestling with anxiety, confronting the specter of trauma, or unraveling the complexities of relationships and identity, narrative therapy provides a safe harbor for exploration and growth.
At the heart of narrative therapy lies the Tree of Life exercise, a revered technique that invites individuals to chart the landscape of their life experiences, strengths, aspirations, and dreams. Through this exercise, clients unearth the roots of their heritage and culture, the branches of their hopes and aspirations, and the leaves of their strengths and resources. In the fertile soil of this symbolic tree, clients find nourishment for their journey, fostering a sense of continuity and resilience as they navigate the trials and triumphs of life.
To give reference
Singha, R. (2024). Tree of Life exercise. Retrieved from https://www.researchgate.net/post/Tree_of_Life_exercise?_init=1
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Above and below ground biomass for a mangrove forest was estimated for 520 trees using standard formula. How can I statistically compare the these data sets for 520 trees?
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Comparing above and below ground biomass data from a mangrove forest typically involves statistical analysis to determine if there are significant differences between these two sets of measurements. Here's a step-by-step approach you can use:Data Collection: Gather your data on above ground biomass (e.g., weight of leaves, branches, etc., per unit area) and below ground biomass (e.g., weight of roots, rhizomes, etc., per unit area) from your mangrove forest samples.Data Preparation: Organize your data into two groups: above ground biomass measurements and below ground biomass measurements for each sample or plot within the mangrove forest.Exploratory Data Analysis (EDA): Begin by examining the distributions of your biomass data. Use graphical methods such as histograms, box plots, or scatter plots to visualize and understand the variability and central tendencies of both sets of measurements.Choosing a Statistical Test: The choice of statistical test will depend on the nature of your data (e.g., normality of distribution) and the specific question you want to answer (e.g., Are above and below ground biomasses significantly different?). Commonly used tests include:Paired t-test: Use this if you have paired observations (i.e., each sample provides both above and below ground biomass data) and the differences between pairs are normally distributed. This test assesses whether the mean difference between the paired observations is significantly different from zero.Independent samples t-test: Use this if your above and below ground biomass data are from independent groups (e.g., different plots or sites) and assuming the data are approximately normally distributed. This test compares the means of the two independent groups.Wilcoxon signed-rank test: This is a non-parametric alternative to the paired t-test, suitable if the differences between paired observations are not normally distributed.Mann-Whitney U test: A non-parametric alternative to the independent samples t-test, used when the assumptions of normality are not met for independent groups.Perform the Statistical Test: Depending on your choice of test (parametric or non-parametric), apply the test to your data. Most statistical software packages (e.g., R, Python with libraries like SciPy) can perform these tests easily.Interpret the Results: Analyze the test results. Look at the p-value associated with the test. A small p-value (typically < 0.05) indicates that the observed differences in biomass are unlikely to be due to random chance alone, suggesting a statistically significant difference between above and below ground biomass.Consider Effect Size: In addition to statistical significance, consider the effect size (e.g., Cohen's d for t-tests) to understand the magnitude of the differences observed.Report Findings: Finally, summarize your findings in the context of your research question. For example, you might conclude whether above or below ground biomass is significantly greater in the mangrove forest, based on your statistical analysis.
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Bacteria:Fungi ratio in fruit tress
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What would be the best methods/techniques to figure out the bacteria:fungi ratio from citrus orchards soil.
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Can we stop global climate change? Does human scientific power reach the world's climate change? What is the response of the researchers?
As you know, humans are very intelligent and can predict the future climate of the world with hydrology, climatology and paleontology. But don't countries, especially industrialized countries, that produce the most harmful gases in the earth's atmosphere and think about the future of the earth's atmosphere? Do they listen to the research of climatologists? What would have to happen to get them to listen to climate scientists?
Miloud Chakit added a reply
Climate change is an important and complex global challenge, and scientific theories about it are based on extensive research and evidence. The future path of the world depends on various factors including human actions, political decisions and international cooperation.
Efforts to mitigate and adapt to climate change continue. While full recovery can be challenging, important steps can be taken to slow progression and lessen its effects. This requires global cooperation, sustainable practices and the development and implementation of clean energy technologies.
Human scientific abilities play an important role, but dealing with climate change also requires social, economic and political changes. The goal is to limit global warming and its associated impacts, and collective action at the local, national, and international levels is essential for a more sustainable future.
Reply to this discussion
Osama Behnas added a reply
Global climate change is impossible to stop. Human scientific power cannot reach the climate changes of the world.
Borys Kapochkin added a reply
Mathematical models of planetary warming as a function of the argument - anthropogenic influence - are wrong.
Alastair Bain McDonald added a reply
We can stop climate change, but we won't! We have scientific knowledge but no political will. One can blame Russia and China for refusing to cooperate, but half of the US population (Republicans) deny that climate change is a problem and prefer their promiscuous lifestyles to the answer:
All climate change is loaded on CO2 responsible for the greenhouse effect. Therefore, scientific experiments from several independent scientific institutions around the world should be conducted to determine what the greenhouse effect is at different concentrations of CO2. Then, a conference of a reputable and professional organization with the participation of all independent scientific bodies should be held to establish standards on CO2 concentrations and propose policy measures accordingly.
The second action that can be taken is to plant as many trees and plants as possible to breathe CO2 and release oxygen. Stop any deforestation and immediately plant trees in any tree-filled areas.
Lucy George added a reply:
We have the knowledge, tools and resources to ensure a livable and sustainable future for all. Carbon dioxide and other heat-trapping gases are major contributors to global warming. Therefore, reducing greenhouse gas emissions is very important and should be done as soon as possible to achieve zero greenhouse gas emissions. Both forests and oceans play an important role in regulating our climate, so increasing their natural ability to absorb carbon dioxide can also help prevent global warming.
Reply to this discussion
Ilan Kelman added a reply:
Yes, we can address and stop human-caused climate change. See extensive details in the full technical reports of ipcc.ch
Mohamed Sarmoum added a reply:
I think it is difficult to stop global climate change, but, on the other hand, we can develop adaptation mechanisms with this change
Mrutyunjay Padhiary added a reply:
The challenge of combating global climate change is complicated and multidimensional, involving scientific, technological, political, economic, and social initiatives. Even though we may not be able to "stop" climate change entirely at this time, we can surely lessen its worst consequences and adjust to the changes that are already occurring. It is true that advances in science have allowed us to gain an in-depth knowledge of the mechanisms causing climate change as well as the tools and techniques that can be used to slow it down. Scholars from diverse fields such as ecology, engineering, economics, climatology, and social sciences are actively investigating climate change and devising remedies for it.
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Greetings and politeness and respect. Thank you very much and thank you very much.
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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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Hello. Please, I have an issue executing MRP in Clann. How do I link PAUP with Clann? And where do I execute this nexus file that you showed?
Thank you
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So i have to compare tree data (densities, tree diameter and height) from 3 habitats (monsoon forest, savanna, ecoton), the first data is my field data and the plot size is 4 meter square with total 17 plot, the other two are 1 meter square with total 5 plot for the second data and 15 plot for the third data. To compare them i was trying to extrapolate the 2nd and 3rd data so it could be more "valid" (e.g multiple the density by 4) but it turns out weird like the density for savanna is higher than the monsoon forest. is there any other way to compare my data to make them less "weird" or is it just impossible to compare them because they have different plot size?
#statistic #agriculturestatistic #forestrystatistic #forestry
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yes, you may go for floristic richness and other qualitative analysis and not quantitative analysis as plot size and shape may vary. Density is a dependent measurement.
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Can we stop global climate change? Does human scientific power reach the world's climate change? How do researchers respond?
As you know, humans are very intelligent and can predict the future climate of the world with hydrology, climatology and paleontology. But don't countries, especially industrialized countries, that produce the most harmful gases in the earth's atmosphere and think about the future of the earth's atmosphere? Do they listen to the research of climatologists? What would have to happen to force them to listen to climate scientists?
Miloud Chakit added a reply
Climate change is an important and complex global challenge, and scientific theories about it are based on extensive research and evidence. The future path of the world depends on various factors including human actions, political decisions and international cooperation.
Efforts to mitigate and adapt to climate change continue. While complete reversal may be challenging, important steps can be taken to slow progression and lessen its effects. This requires global cooperation, sustainable practices and the development and implementation of clean energy technologies.
Human scientific abilities play an important role, but dealing with climate change also requires social, economic and political changes. The goal is to limit global warming and its associated impacts, and collective action at the local, national, and international levels is essential for a more sustainable future.
Reply to this discussion.
Osama Bahnas added a reply
It is impossible to stop global climate change. The human scientific power can not reach the world's climate change.
Borys Kapochkin added a reply
Mathematical models of increasing planetary temperature as a function of the argument - anthropogenic influence - are erroneous.
Alastair Bain McDonald added a reply
We could stop climate change but we won't! We have the scientific knowldge but not the political will. One could blame Russia and China from refusing to cooperate but half the population of the USA (Republicans) deny climate change is a problem and prefer their profligate life styles.
John Hatzopoulos added a reply
John Hatzopoulos
PhD, MSCE, UW USA, Diploma NTUA GreeceManaging Director at University of the Aegean
Greece
All climate change has been loaded on the CO2 responsible for the greenhouse effect. Therefore, there must be scientific experiments from several independent scientific institutes worldwide to find out what the greenhouse impact is on various CO2 concentrations. Then, there must be a conference from a reliable, professional organization with the participation of all independent scientific institutions to establish standards on CO2 concentrations and propose political actions accordingly.
The second action that can be done is to plant as many trees and plants as possible to breathe the CO2 and free the oxygen. Stop any deforestation and plant trees immediately in any bunt areas.
Ilan Kelman added a reply
Ilan Kelman
For publications, see https://www.ilankelman.org/publications.htmlFor full contact details see https://www.ilankelman.org/contact.html at University College London
United Kingdom
See the full technical reports at https://www.ipcc.ch which details answers to all these questions.
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Humans have more capacity than they are utilising , and this is due to factors outside the realm of science. Politics and Capitalism or the quest to make more profit every day , has attenuated the ingenuity of humanity and innovation that could resolve lots of situations .
The changes we need is science without strings attached. We need to create innovative ways to deflect the trajectory of consumption and profitability to sustainability . typically the insatiable desire to control and make profits creates promotion and attachment to lifestyles and consumption habits that can be attributed to global worming .
A typical example is the dissolution of knit societies which meant that most schools, hospitals , markets , and movement offices where within walking distances before the metropolis ideology , mean that people didn't necessarily have to drive , the coming of virtualisation and remote work tools should mitigate unnecessary flights and a few other things we don't need urgently . the other example is we don't need beef every day , which means we just need enough cows of we follow nature and not commercials.
Most technologies are based on production processes that are so toxic that the result is not worth the risk , and yet we have not figured a way to mitigate the outcomes.
It can be done , but we need untainted scientists and thinkers to start the trend of fixing the anomaly
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Please suggest how to identify the herbs, shrubs and trees in field
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Lee Clawson Thank you for the suggestion and references will definitely go for it.
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To what extent can the creation of urban pocket parks improve the microclimate, improve living conditions for residents in cities, and can be part of the realization of pro-environmental, pro-climate and pro-social sustainable development goals, can be an important part of the green transformation of the economy, and can be an important element of urban development in accordance with the concept of sustainable, green, smart cities?
In the country where I operate usually before local elections in many cities, local government officials, as part of their election campaigns, recall the residents of the municipality, analyze the needs and demands raised by residents, local activists and local independent media. What they consider to be more frequent in the aforementioned demands they choose as banners for the ongoing election campaign, put on advertising banners, in promotional videos aired in various media, and, in the form of articles, place in controlled local government magazines or published by NGOs and associations specially established for the elections. Recently, before the local elections, a rapturous number of local government officials are now talking about the need to create urban pocket parks, while just a few years ago the so-called concretosis was developed on a large scale in many cities. Of course, it's a good trend that in many cities local government officials have finally now noticed the demands that have been made for years by many residents and by researchers that have been made for at least a dozen years. In a situation where, due to previously improper land use, incorrectly implemented zoning plans in many cities in the past, green areas have been eliminated in order to create a concrete plaza or widen the asphalt surfaces of parking lots, sidewalks and so on. green areas in many cities have been significantly reduced and in some cities have been completely eliminated altogether, and as a result, the quality of life in cities has deteriorated significantly in many respects, and there is no possibility of creating large urban parks, then the creation of urban pocket parks although to a small extent, but nevertheless will help urban residents by improving the conditions of existence, living, functioning, etc. in a certain urban agglomeration. Even through the establishment of urban pocket parks, the number of trees, shrubs, flower meadows and lawns in cities can be significantly increased, which will translate into a decrease in the temperature near them during the summer heat. In addition, the humidity of the air will also increase, which is also important during the summer heat. Placing benches in the areas of urban pocket parks will also increase the number of places where residents can relax. Near the creation of urban pocket parks, children's playgrounds and physical exercise facilities, so-called gyms and outdoor climbing walls can be established, thanks to which the number of places for recuperation and active rest from the urban hustle and bustle and after work offered to residents will increase. Established flower meadows will help protect pollinating insects, whose numbers of individuals in populations of bees and other pollinating insects have been declining rapidly over the past few decades. For this purpose, it is worth putting up houses for insects but also for birds in urban pocket parks and other parks being created. In larger urban parks it is also worth creating water reservoirs, ponds which can also significantly improve the natural qualities of the park, can increase the biodiversity of flora and fauna found in the park and improve the issue of microclimate and also increase the natural, aesthetic, etc. attractiveness of a specific park from the point of view of residents. In view of the above, the creation of urban pocket parks also fits perfectly into the realization of the pro-environmental, pro-climate and pro-social goals of sustainable development, can be an important part of the green transformation of the economy, and can be an important element of urban development in accordance with the concept of sustainable, green, smart cities.
Key aspects of the negative effects of the ongoing process of global warming and the associated necessary acceleration of the processes of green transformation of the economy in order to decarbonize the economy, slow down the process of global warming, protect the climate, biosphere and biodiversity of the planet's natural ecosystems I described in the article:
IMPLEMENTATION OF THE PRINCIPLES OF SUSTAINABLE ECONOMY DEVELOPMENT AS A KEY ELEMENT OF THE PRO-ECOLOGICAL TRANSFORMATION OF THE ECONOMY TOWARDS GREEN ECONOMY AND CIRCULAR ECONOMY
In view of the above, I address the following question to the esteemed community of scientists and researchers:
To what extent can the creation of urban pocket parks improve microclimates, improve urban living conditions, and can be part of the realization of pro-environmental, pro-climate and pro-social sustainable development goals, can be an important part of the green transformation of the economy, and can be an important element of urban development in accordance with the concept of sustainable, green, smart cities?
To what extent can the creation of urban pocket parks improve the microclimate and living conditions for residents in cities?
What do you think about this topic?
What is your opinion on this issue?
Please answer,
I invite everyone to join the discussion,
Thank you very much,
Best regards,
Dariusz Prokopowicz
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
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There are now many pocket parks in Chinese cities. They are important in the sense that they contribute to better living conditions for local residents. However, I think a condition for pocket parks should be enough normal urban parks planned or designed in the city. Put another way, pocket parks, albeit important, cannot replace normal parks. Their importance should be assessed in correct context.
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Hi!
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.
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Relative means the sum of importance values for all predictors is 1. Hence an input A with 0.4 importance value is twice as important as Input B with an important value of 0.2. There is little docu but this is how I read it...
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I am doing research on invasive species more specifically the ailanthus altissima tree. I know that originally it is from China but I'm quite sure how and when did it arrive in South Africa
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Ailanthus altissima, commonly known as the tree of heaven, is native to eastern and central China, as well as Taiwan. It was introduced to South Africa, along with many other parts of the world, primarily as an ornamental tree and for erosion control. The exact introduction pathway of Ailanthus altissima to South Africa may not be extensively documented, but it likely occurred through intentional planting by horticulturists or accidental introduction through seeds carried by wind, birds, or human activities.
In South Africa, Ailanthus altissima has become naturalized and invasive in various regions, particularly in disturbed habitats, urban areas, and along roadsides. The tree has several characteristics that contribute to its invasive success:
  1. Rapid Growth: Ailanthus altissima is a fast-growing tree, capable of quickly colonizing open areas and outcompeting native vegetation for resources such as light, water, and nutrients.
  2. High Reproductive Potential: The tree of heaven produces large quantities of seeds that are easily dispersed by wind, allowing it to colonize new areas rapidly.
  3. Allelopathy: Ailanthus altissima can release allelochemicals into the soil, which inhibit the growth of nearby plants, giving it a competitive advantage over native species.
  4. Tolerance to Harsh Conditions: The tree of heaven is highly adaptable to a wide range of environmental conditions, including poor soils, drought, and pollution, making it able to thrive in urban environments and disturbed habitats.
The invasive nature of Ailanthus altissima poses several threats to South African species and ecosystems:
  1. Ecological Disruption: The aggressive growth and spread of Ailanthus altissima can lead to the displacement of native vegetation, altering the structure and composition of local ecosystems and reducing biodiversity.
  2. Competition with Native Species: Ailanthus altissima competes with native plant species for resources, potentially outcompeting them and reducing their population sizes or causing their local extinction.
  3. Altered Ecosystem Functions: The presence of Ailanthus altissima can disrupt ecosystem processes such as nutrient cycling, soil stability, and water infiltration, leading to degraded habitats and reduced ecosystem services.
Efforts to manage the spread of Ailanthus altissima in South Africa typically involve strategies such as mechanical removal, herbicide application, and revegetation with native species. However, controlling the tree of heaven can be challenging due to its ability to resprout from roots and its prolific seed production. Ongoing monitoring and management efforts are necessary to mitigate the impacts of this invasive species on South African biodiversity and ecosystems.
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Guys, I need help with phylogeny. I am very new to this field and currently trying to position a bacterial strain. I have selected four crucial loci for the genus, but I am encountering limitations in employing a multilocus approach. I attempted to use Paup/Mrmodelblocks - Mrbayes; however, even though the individual tree for each locus yields an acceptable topology (confirmed through marker sequences), concatenating the different genetic sequences results in a significant error in the tree's topology. I have tried various solutions to rectify this issue, but despite seeking assistance from experienced friends, I haven't been able to resolve it.
This led me to explore new approaches, considering a phylogeny based more on genomes using orthofinder. Initially, it worked well, but when I attempted to repeat the process, my PC couldn't support it, even though it is a robust computer. I'm using Linux, and every time I try to use orthofinder again, the system restarts. Consequently, I sought another approach, utilizing iqtree. I repeated the process using a multilocus strategy, but once again, I can create individual trees for each region, yet I struggle to obtain an acceptable topology when concatenating the regions to generate the tree for the four chosen regions.
The program does concatenate the sequences, but when I try to run the command to generate the tree with nucleotide substitution models, it produces an error due to the size of the concatenated sequences.
I am in need of tips and alternatives on how to address this issue. Although I successfully used the new cognac package in R, considering it's a recent approach, I need to validate my data. Please assist me with any possible alternatives. Thanks.
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You can try amas with rxaml model and evolution perspective you could use advance jtt model with maximum likelihood method
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Has anybody studied how tree leaves shape and other tree characteristics control runoff?
Thanks for your help.
Elias
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"Thank you very much for your kind words, Elias. I'm glad I could assist you. If you have any further questions or need assistance in the future, please don't hesitate to reach out. Best regards, Mansoor Hayat ( Northeast Forestry university)
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I have just started doing LiDAR point cloud research, and I feel that the processing algorithms for LiDAR point clouds are generally segmentation, reconstruction, completion, etc. This isn't very interesting. I have an idea: design a deep learning network so that the network can autonomously summarize formulas from point cloud data. For example, the potential theoretical formulas of leaf area index and tree diameter at breast height were summarized from forest point clouds. Is this possible? Are there any similar studies that we can learn from?
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Compared with raster or grid data having the same pixel size, point clouds are somewhat complex and have irregular point geometries, therefore a more complex representation of 3D scenes. Performing deep learning and machine learning on such datasets is quite more challenging than regular gridded data. Point clouds first need to be classified into ground and non-ground points then a large number of structural attributes can be extracted. At this stage, I would recommend learning some publications on LiDAR point clouds and waveform (including my publications) so that you can establish a standard background on this topic before you can develop any robust research methods.
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Investigating tree connections in forests showed that some are connected to many others via direct root connections or via funghi. These connections via funghi seem to be evolutionary at least 300 Mio years old. Is it already settled, how the trees communicate (substances) and if electrical signals also play a role?
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Tree communication and mycorrhiza represent two interconnected concepts in ecology and plant biology, particularly in the context of forest ecosystems. Here's a brief overview of each:
  1. Tree Communication:Trees and other plants are capable of communication through various mechanisms, primarily involving chemical signals. One well-known form of tree communication is the release of volatile organic compounds (VOCs) in response to stressors such as herbivory or pathogen attacks. These VOCs can serve as signals to neighboring trees, alerting them to the presence of threats and prompting them to activate defense mechanisms. In some cases, trees can also communicate through their root systems via chemical signaling.
  2. Mycorrhiza:Mycorrhiza refers to a symbiotic relationship between fungi and the roots of plants. In this mutualistic association, the fungi colonize the roots of the host plant, forming structures called mycorrhizae. The mycorrhizal fungi extend the root system of the plant, increasing its ability to absorb water and nutrients from the soil. In return, the plant provides the fungi with carbohydrates produced through photosynthesis. Mycorrhizal associations are common in forest ecosystems and play a crucial role in nutrient cycling and ecosystem stability.
The connection between tree communication and mycorrhiza lies in the fact that mycorrhizal fungi can serve as conduits for chemical communication between trees. These fungi form extensive networks in the soil, connecting the root systems of multiple trees within a forest. Through these networks, trees can exchange information and resources, facilitating cooperation and mutual support among individuals.
Recent research has shown that mycorrhizal networks can transmit chemical signals involved in tree communication, allowing trees to coordinate their responses to environmental challenges and share resources such as water, nutrients, and even defense compounds.
Overall, tree communication and mycorrhizal associations highlight the complexity and interconnectedness of forest ecosystems, where plants and fungi collaborate in ways that extend beyond individual organisms to shape the functioning and resilience of entire ecosystems.
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What is the average growth of jujube tree circles to determine age per year?
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Hello
Every year, the tree trunk grows with two circles, the first circle is spring wood and the second circle is autumn wood.
Therefore, you should consider both circles to estimate the age of the tree in one year.
Good luck.
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I want to establish a phylogenetic relationship of our fungal species of interest along with the other fungal species belonging to the same order (Hypocreales). In order to perform this, we have done sequencing of our fungi using ITS and TEF regions and then performed a BLAST analysis in NCBI for identifying the closest members depending on similarity index. This was followed by retrieving some of the existing sequences (FASTA format) of other fungal species belonging to different families but sharing same order i.e. Hypocreales, available in NCBI. Next, we performed a multiple sequence alignment of the retrieved sequences and our own sequence of interest using MEGA X. We further removed the gaps, trimmed the extra regions and build the tree based on most suitable model using 1000 bootstrapping. However, the tree generated after the analysis is showing poor bootstrapping values in majority of the branches (some are below 20). How to improve this?
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There might not be a way to increase the bootstrap value without adding other sequence regions. Assuming your sequences are aligned correctly, poor bootstrap support means there simply aren't enough informative variable sites to support one branching pattern over another.
You don't say which tree construction method you used; e.g. neighbor-joining vs. maximum likelihood. Sometimes different tree construction methods will provide a little better resolution than others, but each method can also introduce its own biases, so it's not a good idea to go "shopping" for the strongest bootstrap values.
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Hello, I want to construct 16s rRNA gene phylogentic tree. I have retrieved the similar sequences from NCBI and alligend that sequences through clustalx . I have installed Paup4 to my PC what should I do know to construct a tree with bootstrap values and also how will I save that tree?
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Were you able to perform the maximum likelihood analysis with bootstrap in PAUP4?
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I have height and DBH data for all trees that are > 1 cm DBH, from several 20 X 20 m plots, spread over a large landscape. Most of the trees are between 1 to 10 cm DBH, therefore, I assume that most of the trees in the plots are not fully mature. Very few trees are above 30 cm DBH.
I need one formula that can be generally applied to tropical deciduous trees. I have some species-wise formulae for many tree species, but I believe they can be only applied to mature trees.
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Ah, my friend Rajashekhar Niyogi, navigating the intricate realms of biomass estimation, aren't we? Now, when it comes to the estimation of above-ground biomass for your tropical deciduous trees, I'd suggest delving into the realms of allometry. It's the art of understanding the relationship between tree dimensions like height and diameter at breast height (DBH) and their biomass.
For your specific scenario, where the majority of your trees fall within the 1 to 10 cm DBH range, and with only a few exceeding 30 cm, a generalized formula becomes imperative. Now, I won't claim this as the ultimate decree, but consider the following:
Biomass = a * DBH^b * H^c
Here, 'a,' 'b,' and 'c' are constants that need fine-tuning based on your local context and species characteristics. These constants can be derived through regression analysis using your existing data. Remember, my friend Rajashekhar Niyogi, the beauty lies in the nuance – it's a delicate dance of precision and approximation.
Now, the challenge lies in obtaining these constants. Given your dataset, it might be prudent to carry out a thorough analysis, perhaps species-wise, to capture the nuances of your particular ecosystem.
Proceed with caution, my inquisitive compatriot Rajashekhar Niyogi, and may your estimations be as robust as the roots of the trees you Rajashekhar Niyogi seek to understand.
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The hardness of the peel of pomegranate fruits is affected by irrigation, the environment, and the number of fruits on the tree, so it is difficult to rely on the hardness of the peel in determining the harvest date.
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I think the hardness of the pomegranate peel does not determine the harvest date
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Please any relevant literature review or helpful materials on the above poets and their poetry. I am using these poems; for Sylvia Plath:
- Lady Lazarus
- Daddy
- Mirror
- Ariel
- Tulips
- The Moon and the Yew Tree
Anne Sexton:
- Her Kind
- Sylvia's Death
- Wanting to Die
- Live
- Cinderella
- The Truth the Dead Know
I am using classical psychoanalysis for my analysis, Thank you.
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It's a fairly easy treasure hunt on JSTOR, but there are some funky gems in Plath Studies journals...
The Sylvia Plath Society has a Discord for scholars!
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I found the node of error from result tree. At that node i haven't specifically applied any constraint and it is at the intersection of beam and column
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Tejaswini Chilupuri, In visualization module, check the region where the Incorrect Dof is applied and troubleshoot your model accordingly.
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How does the Iroko tree (Milicia excelsa) impact the environment in Western African Region, and what steps can be taken to ensure its conservation for a healthier ecosystem?
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The Iroko tree in Western Africa contributes to biodiversity, prevents erosion, and supports the local economy through its valuable wood. However, excessive logging poses a threat to its sustainability.
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I am calculating water demand for crops by multiplying A-pan evaporation and crop factors using WR90 data (from water resources of South Africa study) and I get the result in mm. I subtract effective rainfall from from the crop water demand and the deficit is provided by irrigation.
The problem I have is determining the volume required for irrigation. Do I take into account the tree density or this has already been incorporated in the crop factors? In other words, is the irrigation supposed to be calculated simply as Deficit * Field area (assuming 100 % irrigation efficiency)?
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Yeas, of coursese
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Are there already available technologies for producing paper from other forms of flora, plants other than trees, such as shrubs, grasses, perennials, fallen leaves, straw, waste from crop production and/or lumber waste?
Due to the rapidly increasing level of plastic waste pollution in the green transformation of the economy, plastic packaging is being replaced by packaging made from biodegradable plastic substitutes, materials of organic origin, produced from vegetable crops, or packaging made from paper, wood. Unfortunately, the production of packaging from paper and/or wood is not a pro-environmental solution either, as it generates the cutting down of trees, increases the scale of forest deforestation. On the other hand, in connection with the still increasing scale of greenhouse gas emissions, the accelerating process of global warming, the processes of forest deforestation should be replaced by the processes of aforestation of civilizationally degraded areas, post-industrial areas, areas with sterilized soil, etc. In view of the above, there is a growing need to create green technologies and material eco-innovations, where it would be possible to create and implement paper production technologies from other forms of flora, plants other than trees, e.g. from shrubs, grasses, perennials, fallen leaves, straw, waste from crop production and/or lumber waste.
In view of the above, I address the following question to the esteemed community of scientists and researchers:
Are there already available technologies for the production of paper from other forms of flora, plants other than trees, such as shrubs, grasses, perennials, fallen leaves, straw, waste from the production of agricultural crops and/or lumber waste?
Are there already available technologies for producing paper from plants other than trees?
And what is your opinion on this topic?
What is your opinion on this issue?
Please answer,
I invite everyone to join the discussion,
Thank you very much,
Best regards,
Dariusz Prokopowicz
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
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The short answer to your question is : no need for new "technologies" to produce paper from annual plants (even grass), paper is produced on paper machines that can use fibers from all origins (cellulose from trees AND plants, synthetic fibers, glass fibers...).
The vast majority of the "tree-originated" paper produced in the world is NOT sourced from deforestation raw materials. It is produced from managed plantations and sawmills by-products.
And there already exist lots of papers incorporating annual fibers : cotton, abaca (banknotes), esparto grass, flax (special papers)...
Take a look here : https://www.cepi.org/
Or on some academic sites : Innventia (S), VTT (Fin), CTP (F), PTS (D)...
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I need to download the sequence of seven housekeeping genes (i.e., AAT1a, ACC1, ADP1, MPIb, SYA1, VPS13, and ZWF1b) of ST C. albicans to do phylogeny tree
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THANK YOU Dr Harish
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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
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Hi there,
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).
Thoughts?
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Hi, I have the same error. Is there any update about it? Thanks in advance @Christina Harvey
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‎⁦‪#Native‬⁩ ََQatar trees in gardens not only beautify your space but also stand strong against ⁦‪#wind‬⁩ and ⁦‪#rain‬⁩, thriving naturally in their environment. ⁦‪#QatarNative‬⁩ ⁦‪#Garden‬⁩ ⁦‪@aspirezone‬⁩, resilience ⁦‪#Local_trees‬⁩ ⁦‪#sustainable‬⁩ ⁦‪#landscape‬⁩
‎⁦‪#Prosopis_cineraria‬⁩ ⁦‪#ghaf‬⁩ ⁧‫#الغاف‬⁩
‎ ⁧‫#امطار_قطر‬⁩
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Indeed impressive. The Tree of Life (Shajarat-al-Hayat) in Bahrain is a 9.75 meters (32 feet) high Prosopis cineraria tree that is over 400 years old.
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I need to compile a report on a tree nursery and need some useful information.
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Writing a comprehensive report for a tree nursery typically involves providing detailed information about the nursery's operations, performance, and plans. Here is a step-by-step guide on how to write such a report:
  1. Cover Page:Include the title "Annual Report" or "Quarterly Report" for the relevant reporting period. Include the name and logo of the tree nursery. Add the date of the report and any necessary contact information.
  2. Table of Contents:Create a table of contents to help readers navigate the report.
  3. Executive Summary:Provide a concise summary of the main points covered in the report. Highlight key achievements, challenges, and future plans.
  4. Introduction:Give an overview of the tree nursery's mission, objectives, and its significance in the context of tree planting, conservation, or the relevant field. Provide a brief history of the nursery if applicable.
  5. Nursery Operations: Describe the nursery's daily operations, including:Types of trees grown. Size and capacity of the nursery. Soil and growing conditions. Staffing and organization structure.
  6. Financial Performance: Present the financial status of the nursery, including:Income statement: Revenue, expenses, and profit/loss. Balance sheet: Assets, liabilities, and equity. Budget vs. actual comparisons (if applicable).
  7. Tree Inventory: Provide information about the inventory of trees in the nursery, such as:Number of trees by species. Health and growth status. Any pest or disease management activities.
  8. Community Engagement and Outreach:Describe any community programs, educational initiatives, or partnerships the nursery is involved in. Share success stories and the impact on local communities.
  9. Environmental Sustainability:Discuss any environmentally sustainable practices, such as water conservation, use of organic materials, and waste management.
  10. Challenges and Risks:
  • Identify challenges and risks the nursery faces, such as climate change, pests, or funding constraints.
  • Explain how the nursery plans to address these challenges.
  1. Future Plans and Goals:
  • Outline the nursery's strategic goals and plans for the future.
  • Include expansion plans, new species cultivation, or community outreach objectives.
  1. Success Stories and Testimonials:
  • Share stories of successful tree planting projects, satisfied customers, or beneficiaries.
  • Include testimonials from community members, volunteers, or partners.
  1. Appendices:
  • Include any additional information that supports the report, such as financial statements, maps, photographs, or technical details about tree cultivation.
  1. References:
  • If you've referred to external sources, provide a list of references and citations.
  1. Conclusion:
  • Summarize the key points of the report and reiterate the nursery's significance in the context of tree planting and conservation.
  1. Acknowledgments:
  • Thank individuals, organizations, and partners who have contributed to the nursery's success.
  1. Contact Information:
  • Provide contact information for inquiries or further collaboration.
  1. Distribution:
  • Specify how the report will be distributed and to whom (e.g., board members, donors, partners, and the general public).
Remember to use clear, concise language, provide visual aids like charts and graphs where applicable, and proofread the report for clarity and accuracy. The report should effectively communicate the nursery's activities, achievements, and future plans to its intended audience.
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Some plants, plant parts and their products are used as an anti-diabetic agent. I would like to know how many different trees are used for this purpose?
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After adding the tree block to my NEXUS file, I get the "Error parsing sequence data; Tree labels do not match alignment labels" error message. I've checked the labels multiple times, they're all correct, no additional tabs or spaces. The tree itself also looks correct. Could there be something else leading to this error? The NEXUS file wihtout the tree block works well.
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Isabell Hummel The error message you've encountered in PopART, which reads "Error parsing sequence data; Tree labels do not match alignment labels," indicates a mismatch between the labels in the tree block and the labels in the alignment block within your NEXUS file. Despite your efforts to verify the labels, it's important to consider additional factors that might be contributing to this error:
1. Case Sensitivity: Confirm that the labels in both the tree block and alignment block match in terms of capitalization. NEXUS format is case-sensitive, so even minor differences in capitalization can cause this error.
2. Label Consistency: Double-check for any labels in the tree block that may be missing in the alignment block or vice versa. Even a single missing or additional label can lead to this error.
3. Whitespace Characters: While you mentioned verifying tabs and spaces, it's advisable to also inspect for any non-visible whitespace characters, particularly at the end of lines or within the labels, as these can sometimes be the source of the issue.
4. Special Characters: Ensure that the labels do not contain any special characters or symbols that might not be recognized correctly by the software.
5. Tree Format: Validate that the tree block adheres to the correct formatting specified by the NEXUS format standards. Ensure that it starts with "TREE" and that the labels are enclosed correctly.
6. Label Length: Some software may impose limits on label length. Examine your labels to ensure they are not excessively long, which could exceed character limits in PopART.
If you've meticulously reviewed these aspects and the error persists, consider recreating the tree block or alignment block from scratch. Occasionally, unnoticed errors can slip into the file during editing. Additionally, verify that you are using the most up-to-date version of PopART, as software updates may address compatibility issues.
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I would like to find methods for calculating carbon reservoirs & rates of uptake.
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Biomass Estimation
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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.
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Its a tree available in Son Beel wetland in Karimganj, Assam, India which is the site of my research.The tree is locally known as "Izoil" found only in the wetland. During flood the tree gets submerged.
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This plant is Barringtonia acutangula (L.) Gaertn. of Lecythidaceae family.
Thanks!
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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.
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Have you seen these papers?
chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/http://jkv.50megs.com/R051_fem.pdf
I hope they could help you.
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Tree species
Forestry
LCA
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"Life Cycle Assessment (LCA)". EPA.gov. Washington, DC. EPA National Risk Management Research Laboratory (NRMRL). 6 March 2012. Archived from the original on 6 March 2012. Retrieved 8 December 2019. LCA is a technique to assess the environmental aspects and potential impacts associated with a product, process, or service, by: / * Compiling an inventory of relevant energy and material inputs and environmental releases/ * Evaluating the potential environmental impacts associated with identified inputs and releases / * Interpreting the results to help you make a more informed decision
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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?
Please respond,
I invite everyone to join the discussion,
Thank you very much,
Warm regards,
Dariusz Prokopowicz
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
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Trees take up more carbon than other terrestrial plants. Paper traditionally was made from straw, bamboos, banana and other low carbon storing plants. Alternatively, fast growing high fibre products such as bamboo, grass and waste (straw) from grain be used for pulp production rather than wood.
Laws must be put in place to ban paper from wood and encourage other alternatives. It is possible.
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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?
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You can use object detection and classification software to count plants
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Inquiry on Conditional Inference Tree to assess the knowledge and attitude in conservation science
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Yes, the Conditional Inference Tree (CIT) is suitable for analyzing Likert scale-type responses and multiple-choice questions. It can handle categorical and ordinal data, providing valuable insights into complex relationships between variables.
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Hello community,
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!
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Random Forest is an ensemble learning method that combines multiple decision trees to make predictions. Each tree in the Random Forest provides an output or prediction for a given input, and the final prediction is typically obtained by averaging or voting over the individual tree predictions. However, it is possible to extract and analyze all the outputs from all trees in a Random Forest. There is no theoretical reason why one couldn't do this, but it may not always be necessary or practical for several reasons:
  1. Ensemble Averaging for Stability: The primary reason for using ensemble methods like Random Forest is to improve the stability and generalization of the model. By averaging or voting over multiple trees, Random Forest reduces the impact of individual noisy or biased trees and provides a more robust and accurate prediction. Analyzing all outputs separately may not be as robust and may lead to overfitting or increased variance in the predictions.
  2. Computational Overhead: Random Forests often consist of a large number of decision trees. Analyzing all outputs from all trees can lead to a significant computational overhead, especially for large datasets and deep trees.
  3. Interpretability and Complexity: Random Forests are often used in scenarios where interpretability and simplicity are important. Analyzing all individual outputs from all trees could lead to increased complexity, making it harder to interpret the results.
  4. Consensus Information: By averaging the outputs, Random Forest provides a form of consensus information. Analyzing individual tree outputs may not provide additional insights and might even introduce more noise.
  5. Bias-Variance Tradeoff: Analyzing individual tree outputs might lead to a higher variance in predictions, potentially increasing the risk of overfitting and reducing the model's generalization ability.
While there are valid reasons to analyze individual tree outputs, Random Forests' strength lies in their collective decision-making process. The focus is on the overall performance and stability of the ensemble, rather than individual tree outputs. However, depending on the specific use case, there might be situations where analyzing individual tree outputs is beneficial, such as in understanding the uncertainty in predictions or performing model diagnostics. In such cases, techniques like permutation importance or partial dependence plots can be used to interpret the individual tree contributions.
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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.
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Ricarda Koopmann thank you for your addition. I will clarify these points.
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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:
Fagus sylvatica
Abies alba
Abies concolor
Malus sylvestris
Populus nigra
Alnus glutinosa
Picea abies
Pseudotsuga menziesii
Quercus petraea, Q. robur, Q. rubra
Prunus avium
Acer pseudoplatanus
Aesculus hippocastanum
Tilia cordata, T. platyphyllos, T. x europaea
Larix decidua
Taxus baccata
Liriodendron tulipifera
Carpinus betulus
Fraxinus excelsior
Pinus sylvestris
Ulmus glabra, U. laevis, U. minor
Castanea sativa
Liriodendron tulipifera
Castanea dentata
At a first look on the available literature, I only found data on the C-sequestration of a few forest tree species...
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hallo Sebastian,
in vielen Bundesländern wurden Kohlenstoffbilanzen der Wälder berechnet. Dabei wurde der gebundene Kohlenstoff zumindest auf der Ebene von Baumartengruppen differenziert. Methodik z.B. bei:
Mund, M.; Frischbier, N.; Profft, I.; Raacke, J.; Richter, F. und Ammer, C. (2015): Klimaschutzwirkung des Wald- und Holzsektors: Schutz- und Nutzungsszenarien für drei Modellregionen in Thüringen, BfN-Skripten 396, Bonn-B. Godesberg, 168 S.
viele Grüße
Martin
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Bamboo clump distributed with tree species
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IVI is the measure of spatial value index of one particular species, simply termed as Importance Value Index. It is the relative measure of density, dominance and abundance of one species among the other species growing in any particular area. In any sampling area ( regardless of the sampling strategy), summation of the relative density, dominance, and abundance or frequency of occurrence of any species will determine its importance value index for that particular locality.
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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.
Regards,
Tamiko
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Doing a neighbor joining tree is never preferred over ML methods. It is a very good method for examining the sequence to check for misalignment or for a starting tree to estimate model parameters.
But for a number of reasons ( e.g. long branch attraction) the results are unreliable - even if the possible spurious bootstrap values suggest a good tree.
Really no need to share the data unless your supervisor approves it.
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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.
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As you present your tree, there is 99% percent support. No question.
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Why is the number of insects increasing despite pollution, cutting trees and increasing population?
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The majority of insects are herbivores, and they need greenery for their feed. Due to climate change, as more water vapor goes up & forms clouds, the same water has got to come down & drenches all types of lands. This is conducive to increasing greenery & such a condition is taken advantage of for insect population explosion.
Cutting down trees does happen, but most of it is in forest areas & in such cases, it doesn't matter much, because there are still other trees available.
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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?
Best, Zbyszek
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Ok. maybe it is a pice po decorticated wood but the question is what is on the left sied of the photo?