Trees - Science topic

Restoration ecology in rainforests is complex due to the intricate relationships between all species. There are a few studies that have approached the subject in these areas, see below and sources within:

Yes, Forest managers, scientists, and policy makers have long assumed that 50 percent of wood biomass in trees is carbon.

https://www.fs.usda.gov/research/nrs/news/highlights/how-much-carbon-tree-biomass#:~:text=Forest%20managers%2C%20scientists%2C%20and%20policy,carbon%20stocks%20and%20stock%20changes.

Your question is not well-clear but you can find more here www.Stats4Edu.com/services

Abdullah Salim Khan

This plant is Barringtonia acutangula (L.) Gaertn. of Lecythidaceae family.

Thanks!

Planting trees would affect the water cycle because it would increase transpiration. Transpiration is a process where plants lose water to the atmosphere due to evaporation through their leaves. Forests play important role in maintaining water cycle. Plants bind the soil and help in the percolation of water in the soil and thus add in water table. The water is absorbed back by roots and maximum portion of which is lost into the atmosphere in the form of vapours by transpiration. Transpiration is the process in which plant roots absorb water and then release the water in the form of vapour through the leaves. Transpiration is an important factor in the water cycle as it is one of the major sources of water into the atmosphere. It is easier for water to evaporate into dryer air than into more saturated air. Temperature: Transpiration rates go up as the temperature goes up, especially during the growing season, when the air is warmer due to stronger sunlight and warmer air masses. Most of the water a plant loses is lost due to a natural process called transpiration. Plants have little pores (holes or openings) on the underside of their leaves, called stomata. Plants will absorb water through their roots and release water as vapor into the air through these stomata. The role of trees in the water cycle is to add water to the atmosphere through the process of transpiration. During this process, the plants release water from their leaves. This moisture contributes to the formation of rain clouds, which release the water back onto the Earth's surface.

Have you seen these papers?

;

chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/http://jkv.50megs.com/R051_fem.pdf

I hope they could help you.

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.

Dr. Arvind identified the species.

You can use object detection and classification software to count plants

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.

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:

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.

Ricarda Koopmann thank you for your addition. I will clarify these points.

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

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.

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.

As you present your tree, there is 99% percent support. No question.

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.

Ok. maybe it is a pice po decorticated wood but the question is what is on the left sied of the photo?

Dr J C Tarafdar thank you for your contribution to the discussion

In principle, you could edit the text-base tree files to include both types of measures in the resulting tree and open it in something like FigTree. Easier, I think, is to simply open on of the trees in Figure or Mesquite without labels and export the tree as a jpg or PDF. then import the tree is Amandine or other image editors and add the labels to each branch with on measure above and the other below the branch line. As below:

I had the same problem with MegaX, try running it with lower threads. Was able to construct a ML tree using only 6 threads (My laptop has 12 threads).

The size of sliding window has a key influence on the statistical significance. If the window is too small, it is difficult to obtain reliable significance based on T-tests. However, you can try using the methods like Monte carlo or bootstrap that are persuasive even in small samples. Dplr uses the bootstrap method. So even using a small sliding window, even 10 years, it still can give a reliable statistical test and still be convincing.

From https://www.megasoftware.net/known_issues:

"...My Tree Explorer window has a floating blue box that I can't get rid of

In the above, the actual path to your Ini directory will depend on the version of MEGA you are using. The path will look something like %localappdata%\MEGA11\MEGA_11220624-x86_64\Private\Ini or ~/.config/MEGA11/MEGA11_11220624-x86_64/Private/IniSome users have experienced an issue where a blue rectangular box appears in the Tree Explorer window. To get rid of the box one can restore MEGA to its default settings by deleting MEGA's saved settings files:Close MEGA if it is open. In a file system explorer window navigate to the folder where MEGA keeps its settings files and delete the folder that contains the settings files: On Windows: open a File Explorer window and type %localappdata% in the address bar and press enter button on your keyboard. Navigate to your MEGA\MEGA_buildnumber\Private folder and delete the Ini folder that is there. On Linux: navigate to your ~/.config/MEGA/MEGA_buildnumber/Private directory and delete the Ini directory On macOS For MEGA12 and later, right-click MEGA in your Applications folder and select Show Package Contents. Navigate to Contents/Resources/Private and delete the Ini folder For MEGA11 and earlier, navigate to your ~/.config/MEGA/MEGA_buildnumber/Private folder and delete the Ini folder..."

Regards;

My observation from RG Question column is, Whenever, we put a practical (application of science) question, the response is poor but for theorical questions it is good.

This type of weathering is caused by plants and animals. The plants and animals have acids inside them and when they release their acid it converts into chemicals that further results in weathering and breaking down of rocks and minerals and other types of land forms. Biological weathering occurs when plants break up rocks with roots or root exudates. Chemical weathering describes the process of chemicals in rainwater making changes to the minerals in a rock. Carbon dioxide from the air is dissolved in rainwater, making it slightly acidic. A reaction can occur when the rainwater comes into contact with minerals in the rock, causing weathering. Plants grow around rocks where roots penetrate and crack the rocks. Plants grow around rocks and disintegrate the rock into soil. Mechanical weathering caused by ice wedging and plant roots cause rocks to 'break' from the inside out. Water seeping into rocks will freeze and expand, pushing the rock apart from the inside. Plant roots can slowly grow inside rocks through small holes or cracks. As plant roots take in nutrients, they remove elements from the minerals. This causes a chemical change in the rock that is as oxidation. Carbonic acid is a common, weak acid found in nature. This acid works to dissolve rock. Chemical Weathering Chemical weathering changes the molecular structure of rocks and soil. For instance, carbon dioxide from the air or soil sometimes combines with water in a process called carbonation. This produces a weak acid as carbonic acid that can dissolve rock. Acids are one substance that can cause chemical weathering. When rocks are exposed to acidic substances the acids react with minerals inside the rocks, weakening the structure of the rock and causing it to break down more quickly. Chemical weathering describes the process of chemicals in rainwater making changes to the minerals in a rock. Carbon dioxide from the air is dissolved in rainwater, making it slightly acidic. A reaction can occur when the rainwater comes into contact with minerals in the rock, causing weathering.

Pi is a mathematical constant that represents the ratio of the circumference of a circle to its diameter. It is approximately equal to 3.14159, but its decimal expansion goes on infinitely without repeating.

Fractal numbers, on the other hand, are numbers that exhibit self-similarity at different scales. This means that they can be broken down into smaller parts that look like a smaller version of the whole. Fractals are often used to describe natural phenomena such as coastlines, clouds, and snowflakes.

While pi and fractals may seem unrelated at first, there are actually some interesting connections between the two. For example, the formula for calculating the circumference of a circle involves pi, and circles are examples of geometric shapes that exhibit self-similarity. In fact, the Mandelbrot set, one of the most famous fractals, is closely related to the mathematical concept of complex numbers, which are used to calculate the circumference of circles.

Furthermore, pi also appears in some formulas used to describe fractal patterns. For example, the Hausdorff dimension, which is a way of measuring the "fractional dimension" of a fractal, involves pi in its calculation.

Overall, while pi and fractal numbers may seem like unrelated mathematical concepts, they are actually connected in some interesting and surprising ways

Mohammad Kheiri Harshita Negi Anjana Chauhan Anil Kumar Arbind K. Choudhary

I would like to share five of my research articles for read since I believe that they would provide insightful information in sustainable vegetation practices.

1.

2.

3.

4.

5.

Before we had Lintab, we scanned archaeological and subfossil sample. We didn't have to save the samples, so we split the sample along the radius and prepare the edge at a cross section with a razor blade at a slight angle. It turns out a fairly flat surface, which is more or less convenient to put on the scanner. The scanner resolution is usually enough to get a good image even if the surface is not always adjacent to the scanner glass.

Another option is to put a ruler near to the prepared surface and take a pictures series with a camera and use them. We did this for some of the structures in churches where it was not possible to take samples, but the camera resolution must be very good.

The best method for any phylogeny of any species collection is model-based Maximum Likelihood. NJ and especially UPGMA are prone to biased results. NJ better by far than UPGMA.

If you want to define a set of taxa as resulting in monophyletic you could use:

constraint NAME hard = taxon1 taxon2 ...;

prset topologypr = constraints (NAME);

As the command says it is a hard constraint, thus no other taxon can be placed within the monophyletic clade. If you would like to keep the possibility that yet non-included taxa could still be included, then replace the 'hard' by 'soft'.

Hope this helps,

Cheers, Patrick

Hi,

I don't know much about flatworms, but for a great many types of organisms, including invertebrates and vertebrates, the mitochondrial genomes and even more often mitochondrial genes such as nadh and cox-1 are studied for phylogenetic classification and taxonomy.nomenclature. I searched GenBank for Macrogyrodactylus and only found one mitochondrial genome. I then used BLAST with the cox-1 gene from that genome and again found only one Macrogyrodactylus plus a few related flatworms. I aligned the cox-1 genes and have attached the alignment and tree here.

As for outgroups, in general you should select the next closest relative of the group you are interested in, and not something very distant like mouse or insect, for many reasons. Even within the flatworms, the 0.5 scale bar in my attached tree indicates a huge distance between these organisms. You can see that within a species (G. lucii, G. botnicus) there are variable degrees of diversity which is probably more of a nomenclature issue than a biological issue.

Growing seaweed on a global scale also has ecological risks; too much seaweed could impact the amount of light that goes down to other species affecting photosynthesis processes and could have dangerous effects on ecosystems by removing too many nutrients from wild ecosystems. Seaweed farmers, many of whom are women, face a number of environmental, social and economic challenges. These include climate change, weak representation of women producers, difficulties in accessing international markets and insufficient protection of coastal ecosystems. However, inorganic arsenic is known to increase the risk of cancer, and some seaweed species can contain high levels. Eutrophication due to human sewage rich in phosphate and nitrate from major municipalities and small towns has negative impacts on seaweed growth. Run-off from land-based agriculture, thermal power plants and chemical factories inundates near-shore waters and contributes to commercial cultivation challenges. Seaweed is a crop that scientists believe can help to effectively reverse the climate crisis. A 2019 study found it 20 times more effective than plants at carbon sequestration: taking CO2 from the atmosphere and “locking” it up in solid or liquid form. Seaweed farming is a simple and eco-friendly approach for sustainable development. Because of relatively small expenditure required to set up seaweed farming, marine algae farming is a viable option for coastal developed countries to help mitigate climate change concerns. Based on the current selling price of $ 0.50 per kg of dried seaweed, if you are engaged in a 320 line farm, you can expect to earn about $ 60.00 per week. If you have a bigger farm, let's say 480 line farms, you can earn up to $ 90.00 per week. This means $ 15.00 to $ 22.50 per each of the four working days. Seaweed absorbs CO2 more effectively than trees and it's estimated that it stores around 175 million tonnes of carbon each year –that's equal to 10% of the world's car emissions. Seaweed could play a vital role in the sustainable future of our planet; it has a low carbon footprint, doesn't require fresh water, needs minimal land-based infrastructure, and can be used in a number of industries aside from food, including agriculture, cosmetics and pharmaceuticals, and as a biofuel.

Hi,

I have the same error as you when running the BayesTraits. Have you solved this problem?

Yours,

Just to add some detail to Andrew and Natalya’s answers:

Most night lighting affects the seasonal rhythms of plants such as growth and dormancy, as well as flowering, that are regulated by daylength. The growing season may be lengthened, and in Bristol UK it is said that some night-lighted London plane trees remain in leaf throughout the winter.

An urban area is warmer than the surrounding rural areas, and is called an ‘urban heat island’ (UHI), mainly because: (i) The buildings have a higher surface area than the ground, increasing heat absorption. (ii) The building materials and other urban fabric (including vehicles) store heat. (iii) Heat is emitted by vehicular traffic, space heating and cooling, people and animals. (iv) Heat tends to be trapped by air pollution. (v) There is less cooling from evapotranspiration. (vi) Air movement close to the ground may be reduced. Other effects of the UHI are that elevated CO2 may promote growth, hot sunshine can reduce air quality and excessive heat can give rise to physiological stress.

It depends what do you mean by long branches. You should attach an image and point them out. Sometimes Bayesian methods are known overestimate branch lengths.

Best,

Denis

Also, check the links below.

Contact the maintainer whose name and email is on the R pdf document describing the package. Best wishes David Booth.

Your could use the k-mer analysis (k={3,4} seems appropriate) to compute a similarity matrix. Would be the opposite of the distance matrix, which, as you say, is quite incomplete.

Hi Hannah,

allcompat = strict consensus tree.

Nikola Makedonski Sorry to say thanks for your comment. Later I found out that the Python DEAP framework does not support CGP, I wish it could. Although someone(very expert) can add this functionality into this.

See what Google says "randomly swap it, or compose it out of two parts of two parental (sub)trees", where it = tree/ subtree.

Perhaps ChatGPT would provide you with even smarter guesses.

Technically, Fig. 3 and 4, next, show crossover and mutation.

We haven't tried to cultivate it yet. But we have already selected young shoots and will do so.

Here, our analysis of IAS control methods with black plastic:

The major objectives of community based conservation in forestry are:

1. Engaging local stakeholders and empowering them to take part in the management of their forests;

2. Promoting local knowledge and traditional ecological practices to maintain sustainable forest resources;

3. Encouraging sustainable economic development through the use of forest products;

4. Restoring the genetic diversity of native tree species;

5. Protecting wildlife habitats and preserving biodiversity;

6. Establishing conservation areas and establishing buffer zones to protect sensitive ecosystems;

7. Promoting sustainable forestry practices that are ecologically sound and economically viable;

8. Developing educational and training programs to increase awareness and understanding of the importance of sustainable forestry.

Generally, Community based conservation can be done in any type of forest tree species, from coniferous to deciduous and from tropical to temperate.

Thank you very much

Please also go through the following RG links.

Unifrac distances are no the same thing as phylogenetic distances. So it does not matter.

Diagram illustrates evolutionary lineage of different species, organisms, or genes from a common ancestor. Root represents ancestral lineage; tips of the branches represent descendants of that ancestor. As you move from the root to the tips, you are moving forward.

Matthew Wheal Thanks for the help

Prisilla Jayanthi INRE: 'Extinction'. No, I mean the cognitive model of the dynamics of the relationships and interactions between tree limbs ( and their attributes) and long rope things (vines, ropes, cables) - like how and when they break goes way, way, way back in time since most likely we are descended from some sort of arboreal species back in the depths of time.

Overall, since you are interested in the relationships among the members of the ingroup (the outgroup is assumed to be outside), then you are better off with missing data there than you are if you have a lot of missing data among the ingroup taxa. The really tricky problem is when you have complementary patterns of missing data, such as

agctagct--------

--------agctagct

Many of the phylogenetic programs will view these two taxa as identical, because missing character states are treated as a wild card that is considered to be the same as the character state of a taxon it is compared to. This is definitely something to avoid. See Cladistics 34:467 (2018) for an example.

Yes, dust and pollution accumulated on the leaves of trees can be dangerous to health, as it can cause respiratory problems and other health issues. Pollutants such as lead, carbon dioxide, and nitrogen dioxide can be absorbed into the leaves, and when the leaves shed, these pollutants can become airborne and be inhaled by humans. Additionally, dust and particulate matter can accumulate on the leaves, which can be breathed in and cause a variety of health issues.

So you are short three trees. You must have another three ways to root the tree.

Hi,

I, Pedro P write to you all for I have been trying for quite some time to get my trees (originally derived from MrBayes 3.2.5) fixed in the xmls generated with Beauti in order to get the estimation of the evolutionary rates of the distinct clades and taxa, without the quite troublesome assumption of Molecular Clock for my analyses and without having to deal with the trees generated by Beast given the constitutive widespread failures generated within, including in branch lengths and obviously in the evolutionary rates (my endgame), using of course GTR and Random local clock or flexible log-normal clock. However, I'm still far from an expert in the xml editing procedure and not just one, but both current procedures for fixing the tree with xml editing described on Beast2

Hi Teresa. Did you check if the weird sequence is in the right orientation? i.e. maybe you need to reverse-complement it. Good luck!

This may involve, time or season in relationship to species number per time or season, with respect to suitability of the Environment, food, water, diseases etc.

This can be achieved by Simpson's Diversity Index is a measure of diversity which takes into account the number of species present per given period.

Plant authentication is very important for any research. in order to have findings that will help both the current and future crop of scientists, the plant in question, should be authenticated/validated. There are so many methods for plant authentication, though the most common and reliable method is DNA analysis. Especially if there are any doubts, DNA analysis is very handy in such cases.

I recommend using a different outgroup with a longer sequence.

This is a useful article that can answer your question.

I think you can, maybe if it's just for the thesis the research scope is about identification and distribution. Then for the dissertation, it's better to discuss the typical pests on the tree. Maybe anatomically or genetically

Against the background of the obviously critical population situation of the species and the fact that - as far as I understand it correctly - there has been no substantial improvement over the last decades, it seems to me that it is appropriate to suspend the trade. At the same time, those who are locally dependent on the wood product should be supported structurally and financially in order to rebuild tree populations of the species in the medium and long term that will later be suitable for economic exploitation again. This may be the case in 30, 60 or 120 years. The decisive factor for that point in time is that the conservation status of the tree species has significantly improved.

This is just an opinion, I am not personally involved with work on this tree species or similar cases.

I understand that the background and interrelationships are otherwise complex and should certainly be taken into account (see Lichtenberg et al 2022). However, this should not affect the basic decision to protect the species.

Lichtenberg, S., E. Huber-Sannwald, J. Reyes-Agüero, D. Anhuf, and U. Nehren. 2022. Pau-brasil and string instrument bows

telecouple nature, art, and heritage. Ecology and Society 27(1):32. https://doi.org/10.5751/ES-13047-270132

Research

Please check it.

Please learn from youtube. Follow the thats steps

Hi, our research group recently published these works on biomass estimation and allometric equations:

Hope they are useful,

Best regards

any answers here? to di with outer and inner wood of a tree?

Holger Steinmetz thank you for your response and I understand your requirements.

I think you can give feature selection techniques a run then, to see which features are more strongly related to the class determination. After seeing your requirements, I think it will be more appropriate to try them. I personally have experience of using selection technique and reduced the number of features by 50% and got better outcome from my models.