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Taxonomy - Science topic
Explore the latest questions and answers in Taxonomy, and find Taxonomy experts.
Questions related to Taxonomy
I have FASTQ files for metagenomic analysis of the 18S rRNA gene, and I began to analyze them using DADA2 in R, following the tutorial at DADA2 Tutorial(https://benjjneb.github.io/dada2/tutorial.html). However, I stopped at the taxonomy assignment step due to my laptop overheating, which means the device's performance is insufficient to complete the analysis.
My question is: Is there any way to complete the analysis and obtain the taxonomy results while using my laptop? Or is there an alternative to DADA2 that can yield similar results? I would appreciate your expert opinion.
Normally, a plant species need to have a scientific name as a prerequisite to be able to publish its newly discovered medicinal properties. However, in my situation, this specific plant has a common name widely known by the locals and lacks a scientific name. I'm curious if the publication of findings on an unidentified plant's medicinal properties is acceptable and justifiable?
Dear ResearchGate Community,
As I delve deeper into marine biology, I am particularly interested in expanding my knowledge of the taxonomy, ecology, and physiology of algae, with a focus on macroalgae (seaweeds). Unfortunately, my university does not offer a dedicated course on these topics (Phycology). Therefore, I am seeking to educate myself independently.
Could you kindly recommend essential books, guides, scientific papers, or any other academic resources that would help me gain a thorough understanding of marine algae? Your suggestions would be greatly appreciated.
Thank you in advance for your assistance.
Hi mates, I'm doing systematic work required for obtaining DNA from species that belong to a chaotic genus. I wonder if it's acceptable to apply an non-destructive extraction on the paratype? (we have more than 6 specimen for each species)
I want field guide for collection of dragonflies and damselflies to study taxonomy of odonates
I need a camera lucida to draw polychaeta's chaetae and other details for taxonomical purposes, but I don't know were I can find one. On the internet I found only some museum piece. I know that I could take photos, but sometimes drawings are more suitable for taxonomic works, specially when details are not in the same focal plane. Is there a chance of getting one suitable with my microscope, that has 45° inclined eyepieces?
Hi, I'm in Asia and dealing with the local freshwater benthic macroinvertebrates. I want to ask for suggestions on the best taxonomy book for benthic macroinvertebrates (freshwater). Googling around some books include aquatic worms, snails, etc. Thank you.
Hi everyone,
I've been struggling to identify the family these guys belong to. Does anyone have any ideas?
Taken from NE Atlantic 2200m depth.
+3
books and scientific papers on the morphology, taxonomy and so on of ticks of the suborder Trombidiformes
Recently, people working in faunal research have practice to photomontage when identifying a species (in most cases they are not professional taxon experts), and they make a mirror image of one half and copy it to the first half. However they publish this in quality journals. How correct is that? I've been working in traditional taxonomy for more than 30 years, and often a morphological character can only be presented on one side, or there's an anomaly on the other side, that can lead you down the wrong path.
My question is how correct is this position for traditional taxonomy?
Hi, what way blooms taxonomy will support innovators idea?
Kindly reply to me.
I want to do microbiome analysis using R, for which I have three folders that contain ASV data, metadata i.e. sample data, and taxonomy data for 56 sample studies. I want to read the data in those folders and create a separate phyloseq object for each sample study, then I have to make a merged phyloseq object. The issue I am facing is that while creating a phyloseq object the ASV table is said to be non-numeric. What should I do in such a case?
Paleontology/mammalogy/taxonomy colleagues! Does anyone have a complete citation (or, in a perfect world, a PDF) for Nordmann, 1850, the paper in which the Tribe Camelini was named?
explain its morphology, taxonomy and habitat distributiion
I am currently studying Camellia sinensis and am at a loss in the taxonomy of this plant, if anyone knows a detailed taxonomy can help.
In reading classes work on book content using action verbs of six levels of Bloom s taxonomy and also the technique of Q and A in such classes? As Benjamin Bloom claims that it works well in comprehension and increases students critical thinking.
Last weekend I took a photo of this cave-dwelling snail in a northern peruvian cave (1200 metres above sea level). Could you please help me to identify the Genus and Family? Thank you very much.
I am looking for a paper (or several) in which the difference between nomenclature and taxonomy has been described in a clear wording.
To me the difference of these concepts is so obvious that I never cared about something written on this.
In my current case the above is connected to resolving a homonymy.
Can someone help me with that?
Thanks
Stefan
Dear scientific community, does anyone know of a #taxonomy course for #microalgae and #cyanobacteria? I'm eager to continue learning and delving deeper into this fascinating field. Any recommendations would be greatly appreciated. Thank you!
O meu parecer do CNPq produtividade veio assim:
"Vou restringir minha análise à questão "taxonômica" do projeto, já que não me considero apto a opinar na área de Ecologia Aplicada. O projeto sugere que pelo fato de diversas espécies terem sido descritas para as bacias dos rios Grande, Tietê e Paranapanema existe a tendência de que muitas outras possam ser descritas nos próximos anos. Não há no projeto no entanto nenhuma descrição acerca da metodologia empregada na "descoberta" de novas espécies ou sobre a metodologia de descrição das mesmas. Não me parece ser um ponto relevante no projeto proposto."
Se o anônimo não está "... apto a opinar [julgar o projeto] na área de Ecologia Aplicada", que não aceitasse ser o revisor do projeto.
Seria conflito de interesse do revisor com essa tamanha indisposição?
Qual caminho seria mais justo na sua opinião?
I have been searching for the internet page on Nomenclator Zoologicus online by uBio but it seems that the link is not working.
Submit your abstract for the Symposium organised by Ivana Rešetnik and me at the XX International Botanical Congress in Madrid (21-27 July 2024)!
The deadline for abstract submission is November, 30 for oral presentations and February 1, 2024, for posters.
Here you can find the submission guidelines: https://ibcmadrid2024.com/index.php?seccion=scientificArea&subSeccion=abstractGuidelines
Link for abstract submission: https://ibcmadrid2024.com/index.php?seccion=scientificArea&subSeccion=abstractSubmission1
The general link to the congress: https://ibcmadrid2024.com/
Our symposium is the n. 13
Dear All
Please help me to identify the plant/
Thanks in advance
Rishad
+2
According to Andersson (1990), "The only thing generally agreed upon is that variation in phenetic parameters is not continuous and that character states are not combined randomly". In the same work, he defines species as clusters of individuals in a multidimensional space, where each character marks an axis (and thus a dimension).
However, in practice, when conducting taxonomy at the species level, we frequently encounter intermediate states, hybridizations of characters, etc., which can cause us to question whether the compartmentalization of the total character hyperspace that defines a species is, at least in part, a construct of ours rather than of nature.
So the question I would like to ask is: If biological diversity could be expressed as an n-dimensional mathematical function, what type would it be? Clearly, there are not infinite intermediate states between each species (as a continuous function would seem to require) and there does appear to be empty interstices between the hypervolumes, as Andersson asserts, but do the intermediate characters we find in practice not prevent the function from being entirely discrete?
REFERENCE:
Andersson, L. 1990. The driving force: Species concepts and Ecology. Taxon 39(3): 375-382.
Hi,
Dear Acarologists and everyone else.
I hope this day will bring you joy, happiness, and success.
I want to get your opinion. Which Software do you use to Illustrate mites or other arthropods? By Illustrate, I mean the usual line drawings in the publication. I use Adobe Illustrator, but I would love to try different options.
So, let me know what you are using or send your recommendations.
Does anyone have experience with AI in this regard? It would be great if we could use it.
Thank you for reading, and I am patiently awaiting your experiences and suggestions.
Regards.
What would be the correct way of stating that the particular taxon belongs to a species complex, during identification? For example, a gecko that belongs to the Hemidactylus brookii complex. Thank you for the help.
In the modern era of technology, many microcontrollers are equipped with multicore processors.
Hello:
I have a question about the definition of adaptive control, since I´m researching about making a model-free adaptive control system. I will appreciate your help.
The definition I found says that an adaptive control modifies its parameters or structure in order to achieve a performance index. Reading about the subject in different sources I noticed that when they refer to an adaptive controller, it always has a model of the plant and implies an adaptation law which is usually obtained by taking the model and manipulating expressions.
My deduction is that when these sources refers to adaptive control, is about a kind of this instead. Am I right? I will really appreciate your support on this.
Thanks.
Pablo.
Dear colleagues, especially from India -
Could you please share PDF file of this article: KOMAREKJ,. (1972). Reproduction process and
taxonomy of unicellular endosporine blue-green
algae. In Proceedings of the Symposium on
Taxonomy and Biology of Blue-Green Algae,
pp. 41-47. Edited by T. V. Desikachary. Madras,
India: University of Madras.
I'll appreciate your help very much.
Sincerely, Igor Brown
flowers in April in Lachung,Sikkim, 2600 m alt.
I recently observed this strange worm in a Northeast Peruvian cave, which seems to catch its prey with hanging strings. Any idea what it is? Thank you very much in advance.
These ants are closely related to Apis cerana bees in South India.
I have tried to id it but became confused. The crab on the photo looks more like an immature Uca perplexa (as of unbarred leg and lemon yellow color, pattern of dorsal carapace) though having superficial resemblance with Uca triangularis (due to angular spines of carapace).
Dear ResearchGate community,
I'm currently working with a large dataset of phytoplankton species, and I'm looking for a way to routinely update the taxonomy of these species. Specifically, I'm interested in identifying changes to scientific names, accepted names, synonyms, and higher-level taxonomic classifications.
I've tried using various R packages such as worrms to retrieve taxonomic information from online databases, but I've encountered some challenges with data quality and consistency.
I would appreciate any suggestions or advice on how to efficiently and accurately update the taxonomy of my dataset on a regular basis. Are there any reliable databases or APIs that I should be using, like AlgaeBase? Are there any best practices for handling taxonomic data in R?
Thank you for your help!
Nicolas
And why for some groups of organisms (for example, for insects) the presence of subgenera in the taxonomy of the group is more typical than for others?
It uses acronym to compile the taxonomies of electronic dictionaries. Give me that computer scientist a correct definition and a motivation. As a linguist I can give this definition /synthesis for a keyword.
I fear that even in my discipline (botanical taxonomy) some people will come up with manuscripts completely written by algorithms in the near future, especially since the whole academic world seems to only revolve around papers and impact factors. There are already way too much papers being published and their metrics have become largely meaningless or at least questionable for a lot of reasons. With the new sophisticated KI-applications, it seems possible, if not likely, that many "scientists" in need of output (early career, temporary employed, people without original thoughts...) will be tempted to let their papers be written at least partially by software. Wouldn´t it be a good idea to force the authors of a scientific paper to clearly state the usage and its extent of such programs in a respective paragraph? There is (at least here in germany) the obligation to make an affidavit statement when submitting a thesis, assuring that it was made without the help of others etc. I have never seen this in the context of publishing a scientific manuscript. Isn´t it time to get something like this into practice? I will be more than happy to make clear that I have written all my papers using my own mind and those of my co-authors only!
I have two morphologically similar species that differs molecularly only by 4 bases. Can I synonymmized them? If not, how many base differences can lead to this taxonomic revision? How do I deal with such taxa?
I am looking forward to hear from all experts regarding this unclear situation.
Best Regards
I want to do the taxonomy and the phylogeny of the Mycorrhizas (Ectomycorrhizas and Endomycorrhizas). Can you please recommend some necessary publications? Also the effcitive method to obtain the isolates of Mycorrhizas.
This beautiful orchid was recently seen by a friend in the north peruvian Andes (Amazonas). Does anybody know to which family and genus it belongs ?
Why is chaetotaxy (of Head and Thorax) given so much importance in taxonomy of flies? Does it bear any evolutionary significance?
I do not find clear to which specie the aforementioned organism belongs. On some sites, I read that it references to a group of unclassified species instead ofjust one. I would appreciate if anyone may enlighten me with a taxonomy/phylogenetic approach.
Thanks in advance!
When rever what is waterbird the obvious answer always said that waterbird is a type of bird that lives and depend their live around body of water. But is it just that? Does waterbird itself has special taxonomy like subclass or other? or is it classify by only their morphology?
Recently I took a photo of this cave-dwelling harvestman some 300 meters from the entrance in a northern peruvian cave (1500 metres above sea level). Could you please help me to identify the Genus and Family? Thank you very much.
Greatings from Peru and a happy new year!
Stefan
Taxonomic measurements are critical for formal descriptions of metazoans. However, often these measurements are only provided in a table within the manuscript, losing data from individual specimens in the process, which could be used for morphometric, morphological or other studies.
My question is if anyone knows of an online repository where files (mainly with .xls extension) can be included.
Such a repository that works like ZooBank but with files instead of nomenclatural acts would be extremely useful. When you upload the file, the repository will give you a link to include in the manuscript. This link will be private until the manuscript is published, and then everyone can access the file via the link in the manuscript.
This would provide a very interesting database with individual morphometric data that does not exist for several animal groups.
If you know of such a repository, please let me know.
Thank you in advance.
Best wishes,
Alberto.
What is your opinion on the ongoing discussion regarding the taxonomy of the genus Penaeus?
As someone that is not a taxonomist, when I began working with shrimp I was not aware of it and simply used Litopenaeus because it was the name that I mostly read in recent publications. Today I came upon a recent article published in Aquaculture "Making sense of the taxonomy of the most commercially important shrimps Penaeus Fabricius, 1798 s. l. (Crustacea: Decapoda: Penaeidae), a way forward" that drew my attention to it. There is also an older article by Tim Flegel that deals with this (See below). I am considering using his recommendation of placing the sub-genus in parenthesis, e.g., Penaeus (Litopenaeus) vannamei, because I find his arguments reasonable and what the Yang et al. (2023) study found, but I am concerned because it seems that the use of the sub-genera as genera is very prevalent already.
Would you agree its Minuca zacae?
It is from the Eastern Pacific. Coloration is true to living color as the specimen is fresh. Collected on high mangrove area. If there are questions that might help the ID, please let me know.
Thanks in advance for the feedback
Cheers!
At the point we have reached in taxonomy and systematics today, it seems that we are in a situation where details and extremes (in the popular sense) ignore the basics (in the classical sense). Therefore, in a popular sense, we seem to be in a situation (especially by amateur researchers) in which many researchers publish articles without adequate knowledge of the scientific foundations, or even if they do, ignoring these foundations. From this point of view, I think that we should remember the scientific foundations again and know what and how the studies serve.
In this sense, what is taxonomy iessentially and clearly? From what need and how did it arise? What is its main subject and approach? And again, what is systematic essentially and clearly? From what need and how did it arise? What is its main subject and approach?
I think these questions should be answered clearly.
Can a systematic study be done without knowing the taxonomy and a taxonomic study without knowing the systematics? Concisely and clearly, what is a taxonomic study and what does it encompass? What and how does it serve? Also concisely and clearly, what is a systematic study and what does it encompass? What and how does it serve?
I would appreciate if you could share your valuable ideas...
Hi, I hope all who are reading, will be fine.
I would like to know more and extend my knowledge about the expert researchers, scientists, and professors, who spent their lives and are spending their precious time exploring mite fauna. Is there any website or internet resource where we can search for names of expert Acarologists? Like in the field of Taxonomy, systematics, genetics, behavior etc.?
I found it difficult to individually search for experts in each field/subject.
Thanking in anticipation.
Hi everyone, I was wondering about the possibilities of performing numerical taxonomy with SPSS software. I would be very thankful to recieve advice!! For now I have been reading about hierarchical clustering, principal component and discriminant function analysis... Help!!
Does anyone have photos of Entomobrya elegans Stach, 1963 and Entomobrya albanica Stach, 1922?
Hello! Between mid-April and throughout June2017 we carried out an extensive sampling to estimate sea urchin settlers through collectors placed on the bottom floor along the Sinis Peninsula (Westcoast of Sardinia , Italy).
We placed 100 collectors at five metres depth, on rocky bottom and Posidonia oceanica meadows, inside and outside the Marine Protected Area of Sinis (according to the method described by Tomas F, Romero J, Turon X, 2004) to evaluate settlement and recruitment of sea urchin Paracentrotus lividus in two contrasting habitats in the Mediterranean (Marine Ecology Progress Series 282: 173-184). Altogether we collected about 500 samples kept at -20 deg. in 70% alcohol. Moreover, we characterized sampling stations calculating habitat and landscape metrics.
However we found many other species of organisms, especially polychaetes, molluscs, crustaceans, other echinoderms, etc.
At the moment we lack resources to perform taxonomic work on these communities.
We are happy to send over the samples to anyone who could be interested. Considering we do have all the environmental data metrics, it would be great to identify biodiversity hot spots in the study area once we have the taxonomic data.
If interested, please contact me at: s.farina@fondazioneimc.it
Cheers!
Recently there were published many “comment papers” in valid journals such as Palaeoworld, Geological Journal, Carbonates and Evaporites and ... regarding the larger benthic foraminifera where accurate identifications require a high level of experience and knowledge of their taxonomy, this is the main question who are really the cause of these mistakes and problems?
1- Authors
2- Reviewers
3- Editors
1. I suggest to prepare the paper devoted the issues of non-financial reporting (institutional approach; non-financial reporting as a source for decision-making; Taxonomy for non-financial reporting, etc.).
2. If someone has an option to publish an article in such a journal, we can prepare an article together. We can also join forces and conduct joint research in this area.
Waiting for response
I have completed taxonomy assignment of the assembled contig from raw data but I cannot get the relative abundance of the species present. Is there any tool that can do that?
This species is encountered in Kokrajhar town of Assam, India. It is thin walled bamboo. As per my knowledge it seems to be Schizostachyum sp. I request the peers to kindly help me identify the same.
I have set of tags per document, and want to create a tree structure of the tags, for example:
Tags:
- Student,
- Instructor,
- Student_profile,
- The_C_Programming_Language_(2nd Edition),
- Head_First_Java
I need to generate a hierarchy as per the attached example image.
Are there Free taxonomy/ontologies which can give Parent words? like
get_parent_word( "Student", "Instructor") = 'People'
get_parent_word("The_C_Programming_Language_(2nd Edition)", "Head_First_Java") = "Book"
is_correct_parent(parent: "Student", child: "Student_profile") = True
I have a corpus of English as well as Technical documents and use Python as the main language. I am exploring WordNet and SUMO Ontology currently, if anyone has used them previously for a similar task or if you know something better I would really appreciate your guidance on this.
I can't find a rigid reference defining which is considered computational and which is not and saw some taxonomies including the regression ( isn't this just statistics?)
I am a bit confused and I feel like the term is loosely defined within the literature (at least what I have looked up)
What are the most influential ontologies or taxonomies in the behavioral/social sciences? How did they make a difference? What does it mean to be an influential ontology or taxonomy? Citations? Use? Saved lives?
While describing or analyzing species taxonomy, we find some taxonomic changes proposed within thesis that we considered appropriate but, since they have never been published in peer reviewed articles they are not officially accepted.
I need help identifying eukaryotic microorganisms found in aquatic samples from a fish farm. Could somebody recommend a source I can use for the taxonomy identification? Or want to take a look at the pictures of my little creatures?
I appreciate any kind of help.
Cheers
I do not understand what do you mean by taxonomy in it? Is it related to 4IR or the roles of management ?
We are trying to better understand the taxonomy of liberica and excelsea to find ways to help farmers taking decisions of how to replant different fields and plots of coffee.
I have asked a question, If baboons appear more like us than any other of our primate relatives, is it sane if I think in reconstructing biological taxonomy on a Cultural basis? Now, I want to ask about the meaning which Culture is supposed to be if this taxonomy wants to go further.
If Ardrey suggested that 'because of its terrestrial life the baboon, as I have suggested, pursues an existence more resembling the human than any other of our primate relatives.' is it sane if I think in reconstruct biological taxonomy on Cultural basis?
Soil profile presents a two-dimensional view of the soil body. According to Hartemink (2009), the first depictions of soil profiles were made in the late 1700 long before soil science was established. The soil profile may also be taken as one side of a pedon, the three-dimensional conceptual soil body used as the basic unit of classification in the Soil Taxonomy of USDA. Simonson and Gardner (1960) who proposed the pedon concept compared it to the cell in biological systems. This comparison, however, has been criticized since cells are functional units with real boundaries (cell walls) while pedons have no boundaries since the soil is a continuum. The French pedologist A. Ruellan, past president of the International Union of Soil Sciences, has summarized the criticisms against the pedon concept, as follows: it is not a natural unit of the soil cover but only an abstraction, its morphological lateral limits are artificial, and its genesis is interpreted vertically without looking at the lateral dynamics and relationships (Ruellan, 2002). What is your opinion on this? Which is a better unit or model to use in the study of soils?
References
Simonson, R.W. and D.R. Gardner. 1960. Concepts and function of the pedon. Trans. 7th Intern. Congr. Soil Sci., Vol. 4, Madison, pp: 127-131.
Hartemink, A.E. 2009. The depiction of soil profiles since the late 1700s. Catena 79: 113–127
Ruellan A. 2002. Classification of pedological systems: a challenge for the future of soil science. Trans. 17th World Congr. Soil Science, Bangkok.