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Taxonomy - Science topic

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Questions related to Taxonomy
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Hi All! Im looking for examples of taxonomies for different groups that have changed over time. For example, in the Mimulus clade that used to study, the number of described species has fluctuated between 2 and 13 species, as different taxonomists revised the group. Ideally, I'd like to be able to show the timeline in number of species varying across multiple taxonomic revisions for the same group. I don't what the organism is.
For a clarification, I'm not just looking for groups where the taxonomy has changed (this is literally true for all groups), but temporal summaries (timelines) of how the number of species has changed across different revisions.
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Hi Sean,
the orchid genus Ophrys also comprises between 9 and 354 species according to authors and criteria.
Cheers,
Joris
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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
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Hi Alex, I wanted to inform you that I finally received a response from AlgeaBase regarding the API key. I will be trying it out in the next couple of weeks and will get back to you with the results.
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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?
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Hello Alexandra; Among the ants that I study the place of "subgenus" in the taxonomic heirarchy is often referred to as a "species group". Since both terms are not formal parts of the taxonomic nomenclature, which term is used is probably a matter of taste within the group of taxonomists that specialize in that group. Hmmm. Best regards, Jim Des Lauriers
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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.
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La comunicazione oggi è in acronimi ed espressa per grafici di algoritmi e....
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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!
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I believe that it would be inevitable, sooner or later, to use AI in scientific articles and other types of science production, such as text or script correction, etc. It would be like using R for statistics…nobody conducts statistics by hand anymore. Furthermore, there are some editorial companies, such as Elsevier, that have already incorporated the use of AI into their author policy. For instance, they ask authors to only use these technologies to improve readability and language, not to replace key researcher tasks, to apply the technology with human oversight and control, and to disclose in their manuscript the use of AI and AI-assisted technologies. Authors are ultimately responsible and accountable for the content of their work. However, up to now using AI seems to be relatively limited or inefficient for certain tasks, since at least according to my experience with the chat of Bing (Microsoft), it is a system relatively limited in finding the most relevant papers in an area, and or for filtering between information produced by a scientific paper (with data evidence) or that is just mentioned on a web page. I believe AI is important for science, as an aid, but that so far it will not replace any mindful researchers. After all, the invention of calculators and of systems such as R did not end mathematics or statistics, respectively. On the contrary, they have helped them
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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
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A paper was published in Taxon sometimes back: Sleepless nights - please do not describe your species based on molecular differences.
I hope this helps.
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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.
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The contagious accomplices in these symbioses are right now positioned in the Zygomycetes in the request Glomnles. Little is had some significant awareness of their variety, particularly at the particular and sub-explicit level. The investigation of variety among arbuscular mycorrhizal growths (AMF) is mostly hampered by the restricted scope of helpful morphological characters and their inconsistent or deficient use in species portrayals. In an endeavor to defeat this issue, sub-atomic methods have been applied. Even though isozymes and DNA arrangement information can recognize growths at any taxonomic level, the species and family idea in the Glomnles are stiH, not distinct, and further work is expected to lay out the degree of ID helpful in investigations of the science and biodiversity of these naturally critical parasites. History Thaxter (1922) gave the basis to the scientific categorization of these organisms, however, their trophic status was not known around then, and both mycorrhizal and non-mycorrhizal parasites were ordered together in one family, Endogone. In 1953, the primary connection was made between 'Endogone' (= Glomus mosseae) spores and the mycorrhizal propensity for growth (Mosse, 1953). This was trailed by the casual portrayal of a few 'spore types'
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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
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Not researched any papers but perhaps more importantly the Code states:
"nomenclature, n. A system of names, and provisions for their formation and use. binominal nomenclature The system of nomenclature in which a species, but no taxon of any other rank, is denoted by a combination of two names (a binomen, q.v.).zoological nomenclature The system of scientific names for animal taxa and the provisions for the formation, treatment, and use of those names."
"taxonomy, n. (taxonomic, a.)The theory and practice of classifying organisms. See taxonomic information, taxonomic taxon."
"taxonomic taxon A taxon (e.g. family, genus, species) including whatever nominal taxa and individuals a zoologist at any time considers it to contain in his or her endeavour to define the boundaries of a zoological taxon (q.v.). A taxonomic taxon is denoted by the valid name determined from the available names of its included nominal taxa."
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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 ?
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I suspect that Utricularia caerulea is found in South America.
Thanks!
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Why is chaetotaxy (of Head and Thorax) given so much importance in taxonomy of flies? Does it bear any evolutionary significance?
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James Des Lauriers, Thank you!
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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!
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Hello Juan; Here is a link with a little discussion and some citations. Maybe they will be useful. Best regards, Jim Des Lauriers
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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?
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You can have any classification you like if it makes sense to you :)
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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
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Hi Stefan. It is a very troglomorphic and posible troglobite opiliones (endemic from these cave). Including can be a new species. Did you sample?. Please write me (marconisilva@ufla.br) then we can talk a Little more about this amazing animal.
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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.
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Finally, after an extensive search, and as stated by Miralles et al., (2020), we have not found the aforementioned repository.
Our solution (specific to the study group, in this case, the kinorhynchs) has been to create the database ourselves. For all those interested, the Kinorhyncha Measurement Databse is available at this link: https://sites.google.com/a/meiobenthos.com/laboratory/database/kinorhyncha-measurement-database.
However, we are aware that this is only a specific (and partial) solution for a small group of animals, and the fact that we had to create the database ourselves highlights the need for a global, official and organised repository of taxonomic measurements.
REFERENCES:
Miralles, A., Bruy, T., Wolcott, K., Scherz, M. D., et al. 2020. Repositories for Taxonomic Data: Where We Are and What is Missing. Systematic Biology 69, 6: 1231-1253. https://doi.org/10.1093/sysbio/syaa026.
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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.
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I think it is important to consider the ongoing discussion regarding the taxonomy of the genus Penaeus. It is clear that there is a lot of debate surrounding the use of the sub-genus Litopenaeus as a genus, and that there is no consensus on the matter. However, the Yang et al. (2023) study found that the sub-genus Litopenaeus is distinct from Penaeus, and I think it is important to consider this when deciding which taxonomy to use. I also think that Tim Flegel's suggestion of using the sub-genera in parenthesis is reasonable and could help to clarify the taxonomy for people who are not taxonomists. Ultimately, I think it is best to use whichever taxonomy is most accepted and widely used in the scientific community.
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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!
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You can identify a fiddler crab species by examining its enlarged claw: the sand fiddler crab's claw is smooth on the underside. If the claw is not smooth on the underside and had red joints, it is a red-jointed fiddler crab. Otherwise, it is a marsh fiddler crab.
Besides mud fiddlers, two other species of fiddler crabs are common along the southeastern Atlantic coast: Uca pugilator, the sand fiddler; and Uca minax, the red-jointed fiddler
Male fiddler crabs are lopsided. Females have two claws of about the same size. Males have one regular size claw and one outsized claw, really outsized.
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Hello,
I am looking for these two references dealing with the taxonomy of Juniperus phoenicea published by professor Philippe Lebreton et al., but I could not find any electronic version of these papers.
Thank you very much
Cordially
Lebreton Ph. (1983). — Nouvelles données sur la distribution au Portugal et en Espagne des sous espèces du Genévrier de Phénicie (Juniperus phoenicea L.). Agronom. Lusit., 42 : 55-62.
Lebreton Ph. et Rivera D., 1988. — Analyse du taxon Juniperus phoenicea L. sur des bases biochimiques et biométriques. Natur. monspel., Série bot. Fasc. 53 : 17-41.
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on the internet there is this adress for Philippe Lebreton
and yes it is the one you are looking for
he retired since a while
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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...
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Good question. The answer have existing at least half of century already. For clear I strongly recommend the brilliant book of Willi Hennig "Phylogenetic Systematics". Please, check it here: http://aracnologia.macn.gov.ar/st/biblio/Hennig%201966%20Phylogenetic%20Systematics.pdf
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I have been searching for the internet page on Nomenclator Zoologicus online by uBio but it seems that the link is not working.
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Dear Alice, I was able to get the most recent on-line version (2019) from the Queensland Museum but am unsure if it is still available on-line.
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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.
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I would recommend to look at:
History of Acarology - Google Books
https://books.google.com › books › about › History_of_A...
Bibliographic information ; Title, History of Acarology ; Editor, Vikram Prasad ; Publisher, Indira Publishing House, 1982 ; Length, 472 pages.
and these websites :
DIRECTORY OF ACAROLOGISTS OF THE WORLD 2002
https://www.nhm.ac.uk › hosted_sites › acarology › ica
Specialization: Area of specialization: Ticks and tick-borne diseases. Abou-Awad, Badawi National Research Centre Plant Protection Laboratory, 12311 Dokki, ...
Online directory and list of Acarologists of the World: Join online directory · ICA Directory of Acarologists (2010).
Directory: Society
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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!!
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you can do it by xlstst to make a hierarchical clustering
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Does anyone have photos of Entomobrya elegans Stach, 1963 and Entomobrya albanica Stach, 1922?
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Dear Antipova, there is a drawing in the original description, see plate XXXIII
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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!
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It's too late, but I will be interested
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It is normal situation, especially in the taxonomy of the small groups of invertebrates. A low number of specialists around a World means that self-citations are inevitable. We know from the last year that it can be a problem for journals focused on taxonomy (the case of Zootaxa). What do you think, what we should to do with this? Any idea?
Another problem. As you know citations of the species descriptions (i.e. author of the species name) are often not included, similarly like authors of barcode sequences. Should we lobby for the citation of such works and sequences or not? And how to do it? When you are writing the papers do you cite such papers and sequences in the References? When you revise papers of other authors do you suggest to cite such papers and sequences in the References?
I'm very curious of your opinion.
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Self-citation may be necessary in many cases to complete the research study according to the world's progress. There may be a room for self-citation - but it is a good practice to limit the practice when possible. Therefore, self-citation is a sensitive issue.
On the other hand, "Citation Farms", also known as "Citation Cartels", consist of authors who routinely and enormously self-cite or cite each other for the purpose of raising their citation counters and, in turn, promoting the impact of their publications.
Let me show you this paragraph:
"Self citation. Researchers may need to cite their previously published works in order to communicate an idea effectively in their present manuscript. While IGI Global encourages the use of self citations in these cases, it is important that self-cited works do not account for, at most, 50% of the total references in the manuscript."
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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
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Hello Mehdi Hadi
I return to your original question/heading/topic of "What makes bad articles". I think that bad articles are ones that do not adequately address the topic/aim/title of their study. That happens in many fields, unfortunately, and it is often quite a good thing that letters and comments are sent in response. If people stay silent, that is because people are lazy but should make an effort to point out the problem(s) with the study/paper. I support this approach and definitely do it myself. To answer your original question - the author(s) should be held responsible for this situation.
That, though, might still mean that it is a good paper and may be thought-provoking and draws responses from readers who have different points of view so I totally support what some - such as Suman Sarkar - have said that comments might actually mean it is a thought-provoking article.
As for transparent reviews, as mentioned by Suman Sarkar ,
Mike Simmons
and Lorenzo Consorti most recently - I can only think that as a reviewer, I like to remain anonymous for most times. I wonder if that would make potential reviewers less likely to accept the task when invited...?
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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
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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.
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It looks difficult to reach any conclusion from the above posted pictures.
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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?
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Hello Ishtiaque,
I have found that Kaiju (taxonomy based on sequence homology) and Metagenomic Intra-species Diversity Analysis System (MIDAS; taxonomy based on curated phylogenetic trees) work terrifically for analyzing relative abundances of taxa with WGS data. These two tools complement each other as well.
Ryan
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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.
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Bahadorreza Ofoghi , thanks for sharing, it looks interesting.
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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)
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Hi Omnia,
I believe that is very important to know most specificly the motivation about your ask.
If the motivation is to know how to aplly the "computational methods", i recommend the lectures in articles that use the same methods.
For exemplo in the google schoolar are 85.000 articles with this subject. So, is necessary aplly most criterious to decrease and to define the article's area.
But, i saw that you are a researcher in the social area. In this case, i recommend you see the article in the public encyclopedia in the link below (use the translate):
I know that the wikipedia is not a good reference in the champ universitary, but, when do you want do a first reading i think that is a good option.
I hope hep you,
Caio Serpa.
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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?
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Oh now I see. Do you mean taxonomies of phenomena in psychology? Of course now I understand that my answer is for the philosophical part and not so much for categories that are used in research on general psychological processes.
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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.
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Everything that is not published, in terms of scientific information and more in terms of changes or taxonomic proposals, does not exist! You must either publish it yourself and propose it or find the author and publish it together.
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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
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Abhijit, Marc, and Marion thanks for replying and sharing your answers.
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I do not understand what do you mean by taxonomy in it? Is it related to 4IR or the roles of management ?
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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.
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I am not an expert in this field
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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.
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You are most welcome dear Ali A Moursi . Wish you the best always
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I'm asking this question to know if it is possible to rely on carapace shade/color in order to determine the animal's taxonomical group.
Thank you in advance for your answer.
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Not my subject, but I think the shadow can be a distinction between species in a population.
In other words, an aid to sorting the individuals in a population. Absolute identification may require other criteria. Unfortunately, keys are often difficult to use. Once the species is known, one can often recognize it on the habitus.
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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?
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A relevant and valuable open-access source (with a very deep list of references) is available on 'eLife': "Insights into the evolution of social systems and species from baboon studies" by Fischer et al. (2019) -- see:
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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.
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I would say soil profile. Bcz it gives a comprehensive idea regarding horizons, and various elements present only by visual effects.
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I am trying to identify the snail of the attached image. It was photographed in Cuatro Cienegas, Coahuila, Mexico by I. Domínguez.
Based on the shell sculpture, this snail resembles to the banded snail Mexithauma quadripaludium, but I have not found any information about if there is a white morphotype of this species, like the case of another endemic snail Mexipyrgus churinceanus.
I would like to identify this specimen, any help with this is welcome. Thanks for your help and comments.
A description of Mexithauma quadripaludium can be consulted on page 72 from the following document:
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Hi Eréndira,
Sé que han pasado muchos años de ésta pregunta y quizás ya tuvo una respuesta. Pero sí es una concha de Mexithauma quadripaludium, no es que sea un morfotipo distinto por ser la concha blanca, lo que pasa es que las bandas en color oscuro que tienen estas conchas es una capa epidérmica que se llama periostraco, el cual suele desprenderse. En el sedimento de las pozas de Cuatro ciénegas hay miles de conchas como las de la fotografía, y son conchas ya vacías. Por lo que podría decirse que al morir el animal el periostraco se va desprendiendo y queda la concha en color blanco.
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I wonder what are the best ways to make arthropod collections (Collembola, Euscorpius, Diplopoda, Insects....)? What are your experiences? Do you have your own collection? What are you collecting and why?
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Also check please the following very good RG link:
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Tomoceroidea is common but among the most problematic Collembola group. Its position within Collembola and the relationships within the family remain obscure. Traditional concepts of the phylogeny of Collembola have been challenged in recent years and the traditional position of Tomoceroidea within Entomobryomorpha was rarely doubted until the application of molecular approaches. There are several studies on the phylogeny of this group, but it seems that the position of Tomoceroidea within the four known orders has not been resolved.
Below I enclose the sources I found, and you can find more there.
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Taxonomy (a branch of biology), for example, is a basic science discipline that primarily deals with the identification, classification, and nomenclature of plants. It also contributes to biodiversity and conservation. However, it has been largely overlooked in recent times due to the fact that it has been unable to grow broader impacts or, maybe, due to other emerging applied fields. This question is being posed to discuss the broader impacts of basic sciences in general, and taxonomy in particular.
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Basic science are the backbone of all advance research and technology..it will give you a proper insight for the innovative technology.for example if take aquaculture unless and until you are not able to identify the species your future research will be vain.so all basic science should be studied and then future research and enterpinersh I can be developed.
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In the field of taxonomy, How much importance do you give to learning in scientific illustration?
I prefer to create myself illustrations and schemes of brachyuran crabs, and I like to support my investigacion with illustrations. But, other people prefer to look for a collaborator, pay someone or even, do no use illustraions. But it is true that it takes much more time.
What is your opinion?
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For public education, scientific illustration is extremely important. It provides a way to share ideas in an engaging and educational way. Artists have the skill necessary to translate scientific information into accessible and understandable artwork that bypasses difficult scientific terms and explanations Isabel Muñoz
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What modern taxonomies are currently used to systematize lichens? I use www.gbif.org and https://inpn.mnhn.fr.
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ok thank you!!!
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In the case of Phylogeny, we consider all the taxa as OTU. So, how can we interpret the various rank below species level? Or Just morphological data can provide distinction below species rank?
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Difficult question to answer. If the species concept is complex and there is no general agreement among taxonomists, the subspecies concept is even less so.
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Can anyone help me identify this Orchid?
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It looks Paphiopedilum spicerianum (Rchb.f.) Pfitzer
Thanks!
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Recently, there is a new trend in the scientific community is to publish on Preprint servers, but the International Code of Zoological Nomenclature does not seem to fit such a trend (or is not designed for such a trend). If anyone is familiar with this issue, could you please let me how taxonomists have to handle this trend?
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Hello Katsuyuki; I agree wholeheartedly with David. A species description in a preprint is not a valid species description. Citing such a preprint would only confuse an already cluttered literature. Get the paper properly published so that it can be cited by other workers who are interested in the systematics of your group. Best regards, Jim Des Lauriers
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I'm looking for an overview of statistical analysis and the key criteria that can help to choose the appropriate technique for the data analysis
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Statistical analysis according to the nature of the data
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May You recommend me any publications about family business typologies, taxonomies, classifications in countries from Central Eastern Europe?
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Thank You for all recommendation
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Some researchers reject the idea of using only high definition pictures for species description but, at least in my case, I find that high definition pictures provides more nformation than most of the drawings and, of course, do not depend on the researcher´s artistic talent.
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It depends very much on the new species you are about to describe, and whether you describe in the macroscopic or microscopic ranges, and whether you have to describe internal or external structures. For descriptions in the macroscopic range, stacking software is most convenient, because you may convey all the useful information in a single picture, whereas the user of a binocular has to turn around his specimen many times to verify its identity with the stacked one.
However, if you need to illustrate microscopic features, such as for example the setation on maxillae of Baetidae or Heptageniidae (Ephemeroptera), you are bound to bidimensional aspects (unless you use SEM), and here, drawings amount very much to the same as photographs (you may even change your colour photographs into black and white drawings by software).
Good drawings (there are unfortunately a lot of bad ones, as there are also bad photographs in the field) are not necessarily artistic, but rather informative: accurate drawings show precisely the distinguishing aspects, easily perceived by an expert human eye, but often much harder to convey by photographs, where they necessitate the use of arrows.
The important feature in describing new species is always this: is anyone else, observing the same new species as you yourself, able to identify it in a non ambiguous way on the basis of your illustrations and not necessarily with the same optical means you have used to produce them? If your illustrative apparatus is very sophisticated, and being the only one to allow the identification of your species and is not reproducible with a different equipment, you would have to validate this as a principle for the whole range of your family, order or genus, and argue why this is so.
As a principle, you should use, whenever possible, illustrations (whatever their source) that are verifiable by anyone else examining the same or similar material. Images produced by stacking software do not always comply with this principle, and should not be used in the magnification ranges of 50x to 100x, where they often produce artificial images not corresponding to what you can actually observe on physical specimens. The photographs you provide for a new species should, as a rule, reproduce exactly the features any other researcher might be able to observe under his own microscopic equipment.
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Hello!
I'm trying to know where the holotype of Psammotettix confinis (described by Dahlbom in 1850) is conserved.
I searched informations on GBIF, INPN, EOL and internet, unfortunately, I didn't find anything.
Can you help me to know how can I find where the holotype is conserved?
Thank you
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Hello everyone!
Thank you very much for all your answers!
I found an answer on EOL (Encyclopedia of Life) : Dahlbom didn't create a holotype when he described the species in 1850.
According to EOL, in 1937, Ossiannilsson decided to create the holotype for Psammotettix confinis (conserved at Carices I Rohne, in Sweden). The type is a male.
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According to the evaluations we have made among our colleagues on this subject and our own inquiries, another requirement has emerged. This means that there is a lack of standardization of the numbers used in the world's herbaria and given as the plant type codes. For example, for a plant samples of a species, collected from Turkey, stored in Geneva (G) herbarium, it has a different codes in other herbarium. For this reason, the species should be presented with the herbarium codes to be added to the country origin codes. Or some other digitising and coding systems. In this way, both the origin is indicated and even the collected plants can be classified. What do you guys think about it?
"TUR-G 125" instead "G 125"
Country codes are given below:
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The idea of standardising herbarium numbers is ill advised. Apart from the fact that it may create uncalled-for additional work if implemented retroactively, it may hamper the purpose of herbarium numbers which, usually, are accession numbers. There is some tradition, in smaller institutions in particular, for using herbarium numbers as a surrogate for collectors' numbers, which means that they are assigned to duplicate specimens as well, whether stored in the original place or distributed as gifts or on exchange. This leads to problems and errors; in particular, accession numbers are unique and can thus be cited in order to differentiate between duplicates, which is sometimes essential when it comes to type designation.
As an aside, there is already a system in place that is well known and widely used, which having been implemented in the JStor Global Plants images database (https://plants.jstor.org). It is not confusing and does not cause additional labour: it uses any existing herbarium numbers prefixed by the official "Index herbariorum" herbarium code (or "acronym"). The numbers are prefixed by the adequate number of zeros to match the longest extant (or foreseen) number used in that herbarium.
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Is it appropriate to name organisms after people? Names convey messages and reflect attitudes! Is it ethically appropriate to dedicate a plant or animal to a person for whatever reasons? Sandra Knapp, Maria S. Vorontsova, and Nicholas J. Turland refer to this as "symbolic ownership" in "A Comment on Gillman & Wright (2020)" in Taxon https://doi.org/10.1002/tax.12411
BIOPAT e.V., for example, offers to name new species at wish for a donation of at least 2600 Euros (who do these organisms 'belong to'?). One can dedicate a scholarly work, as a book or journal article, to a person – but a living organism? Wouldn't it be preferable to adhere to the common practice of allocating descriptive names and to ban anthropocentric patronymic names and 'graveyard taxonomy' from biological nomenclature via the 'Code'!
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With your proposal you raise three issues:
  1. Switching to “indigenous” names in scientific nomenclature (your reference to Knapp’s paper).
  2. Abandoning the habit of creating scientific names after people.
  3. Abandoning an alleged “antropocentrism” in naming species.
1) As regards the first issue, we should always bear in mind why the Linnean system gained its key role in science: avoiding the Babel of local (= indigenous) names and establishing an universal naming system to vehiculate names within the scientific community. What Linnaeus did in his system was abandoning a plethora of local (=indigenous) names. Linnaeus’ Systema Naturae was mostly dealing with European species and as such he wiped thousands of European “indigenous” names off. In Europe the same species has often a different name not only depending on the country but often depending on the town/village or the valley or the small island (and this is normally true also elsewhere in the world). Nobody in Europe complains that local (=indigenous) names have been “shadowed” by scientific names. People are free to use local/indigenous names in their daily life but when switching to science they know that there is another language to follow, ie., scientific nomenclature. I don’t see any reason why this should not work outside Europe. Are “indigenous” people of Africa, Oceania, etc. different from us?
2) as regards the second issue: I don’t see anything bad about naming species after people. It’s an habit as old as scientific nomenclature and I don’t see any valid reason to abandon it. We still have millions of species to be named and relying exclusively on morphology for chosing their names would greatly limit our imagination and envetually would make remembering names more difficult. I suppose that you are aware that in zoological and botanical literature there is a fluorishing publishing of books on the etymology of zoological and botanical names and having patronymic is often felt much more entertaining than having only boring morphological names. The claim that some recipients of names were bad guys (of course, based on your own values) and that therefore we must “punish” them by eliminating those names is nonsensical. The past is the past and we cannot change history. Furthermore it would be utterly presumptuous to think that our values are the truth and that therefore we are entitled to judge other people and their political, religious or cultural habits and beliefs.
3) As regards your claim that naming species based on our cultural view is “antropocentric”, this is another extremely questionable point. Honestly: do we have any other point of view which is not ours (and therefore antropocentric)? The answer is obviusly not. We are the only intelligent organisms on this planet and we are the only ones who have created a complex language, which requires to have names for every animal and plant. Are animals and plants intelligent enough to appreciate or dislike names? Obviously not.
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What is taxonomy? what is not? what does it do? what doesn't it do? What would happen to humanity without taxonomy? what changes? How can taxonomy, as a basic science, gain the importance it deserves, especially in scientific and daily media sources, and how can it be brought into the focus of attention again? Why are auxiliary sciences receiving more attention? etc...
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Taxonomic theory can be developed as a meaningfully interpreted quasi-axiomatics, where O-models act as axioms, E-models act as inference rules (principles); The C-model serves as a "constructor" for all quasi-axioms. The problem of correct definition of taxonomic reality, in which the object component is taxonomic diversity as a specific aspect of biological diversity in general. Currently, taxonomic diversity cannot be defined uniformly for
all biological taxonomy. Taxonomic theory is built as a "conceptual pyramid", to the top of which the general theory belongs, to the middle level - its particular interpretations (particular theories), to the bottom - specific classifications. General taxonomic theory is "aspect", since its subject area is one of the aspects of biological diversity. Private taxonomic theories can be “aspect” (cladistics, typology, etc.), “elemental” (they consider the concepts of a species, character, etc.), “relational” (they consider the concepts of similarity, kinship, etc.), “methodological” (numerical taxonomy), “level” (macro- and microsystematics), “fragmentary” (for different groups of organisms). The ontological substantiation of the unity of biological systematics is the most important fundamental problem in the development of its theory.
Regards, Sergey
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I am tempted to purchase a miniPCR® Lab Starter Pack and use it for nematode analysis and reverse taxonomy ( )
I am wondering if anyone has used these for PCR analysis and how did the miniPCR® fair in comparison to alternatives? I thinking it may be fun to explore the wonderful world of PCR analysis!
Below is a link to a miniPCR® Lab Starter Pack for further information about the lab kit:
Or can someone can recommend a basic PCR functional lab setup?
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Thanks Miguel for the linking message. Hi Lawrence, in my opinion, @miniPCR is a versatile, precise and low cost equipment, useful for any process related to PCR and thermo block functions.
We have used in remote field work and in lab. Highly recomendable for education and portable research.
We currently have the https://www.minipcr.com/product/minipcr-lab-in-a-box-2/ with a Gyro mini centrifuge
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I have worked on a phylogenetic analysis based on morphological and molecular characters and the review of a genus of Cicadas. As the research results, we will describe a new genus and 20 new species. I am facing trouble searching for a zoological journal that accepts papers with this amount of taxonomic information. The MS has around 80 pages.
Do you have suggestions of biological/zoological journals that commonly publish large papers that include taxonomy?
For now, I have in mind Zootaxa and Zoological Journal of Linnean Society.
I really appreciate any help you can provide.
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the European Journal of Taxonomy is a 'diamond' open access journal, meaning that you don't pay to publish and nobody pays for reading.
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After a new taxonomy revision or new classification has been peer-reviewed and published in a scientific journal, is it necessary for the taxonomic status of the species recognized in the article to be re-evaluated by the IUCN? Is the scope of the IUCN to review and assess taxonomy of species?
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It should be critical taxonomists maintain their independence from the conservation community including IUCN.
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There are several protocols available to perform sampling for metagenomics, such as Splash freezing, freezing, EDTA etc. Each method has its own pros and cons. Which sampling and sample preservation protocol is the best to reduce biasnesss as well as the taxonomy consistent?
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Use random sampling, correct sample size, proper controls, consistent methodology, and true replication to avoid post-sampling bias :)
How to Avoid Sampling Bias in Research | Alchemer
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Morphological looks like buff striped keelback back but as you can see, this one has single stripe that too on the dorsal side.
Photograph Attached.
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Hello Dr. Amit Manhas ,
The dead snake in the photo appears to be a buff striped keel-back at first but the features do not add up to it as you have already pointed out. I believe what you have here is a very rare snake species called Indian egg-eater (common in south Bengal) Elachistodon westermanni. It ranges in both freshwater and mangrove swamps as well.
Regards,
Dr. Abhishek Mukherjee
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I am a part of Skill India, working on advance training and skilling of fresh graduates t make them industry ready. eg Automotive Crash analysis, EV design, etc.
How can we use all the three domains of Blooms Taxonomy to give feedback to them on area that he/she should focus on?
Are you aware about some software that can do this?
Thanks.
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Dear Dr. Alajmi!
Please let me point out - I do not understand you critique toward my input. I am not a county specialist of India, so I simply searched for case-studies that Mr. Patil can use the way he thinks it fits his interest. The application of Bloom taxonomy is a case - and context dependent task. I am not a guru to say - this way you should go. I only wanted to contribute to the discussion.
Yours sincerely, Bulcsu Szekely
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I know it's an unpleasant topic to discuss mycorrhizal taxonomy, but I just can't wrap my head around this: I have analysed some root samples (wheat, UK) regarding their fungal endophytes with specific focus on Glomeromycota (arbuscular mycorrhizal fungi, AMF) and with both ITS1 and ITS2 I got Glomus invermaium as the most abundant phylotype. Now two points:
1. According to AMF taxonomy, this species (or whatever we talk about in AMF) was renamed Rhizophagus invermaius by Walker (2016), why was this not updated in the UNITE-database?
2. I hardly find Glomus invermaium/Rhizophagus invermaius in the literature, therefore I find it a bit suspicious that my samples are dominated by it. Is this an ITS-artefact? I should probably ignore the species assignment based on this marker anyway, but perhaps other people have encountered the same. Thanks!
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The fungus Glomus invermaium is one of the Arbuscular Mycorrhizal Fungi (AMF) which belongs to the phylum Glomeromycota which recently established by Hibbett et al.
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I had been updating the old collection list from our museum and I found that there is some clash between family taxon for those three genera, some sources put them under Family Lonchodidae while some under Family Diapheromeridae.
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Hello,
According to the current taxonomy, these 3 genera, Marmessoidea, Lopaphus (please check spelling), Carausius (please check spelling, too) belong to the family Lonchodidae. Necrosciinae and Lonchodinae, formerly subfamilies of Diapheromeridae, are now subfamilies of Lonchodidae (Robertson et al. 2018).
Regards
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Dear Colleagues,
Is it possible/feasible to assign Gram-positive and Gram-negative bacteria in a sample purely based on 16S or metagenomic sequences without gram staining?
Thank you very much.
Regards,
Nathanael
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Yes. It is possible. All you need is the appropriate database and software for analysis depending on the type of 16S (Illumina or PacBio)
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better if includes recent knowledge in physiology taxonomy and diversity .
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1. Taxonomy of vascular plants- George HM Lawrence
2. The genera of flowering plants - J Hutchinson
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Sometimes abbreviations are more common than we ever thought. We can at least say some abbreviations are more common than others, and they appear frequently on literature. However, sometimes, the names are abbreviated and is one of the most difficult to understand. Although, there some common rules to it.
Are there more common abbreviations other than these ones? Var, spp, sp. Are there similar abbreviations to these ones?
Are there more abbreviations?
Could you also provide information, like books, papers explaining the basics regarding taxonomy?
I would like to give examples on taxonomy, for an explanation to be given. If anyone would like to set there own questions for an explanation to be given on taxonomy of different species, please feel free to do so.
Any contribution is welcome
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Dear @Mª Angeles Zorrilla Lopez-Perea
I have attached one pdf which mentions several taxonomic abbreviations and their full form. Moreover, I fully agree with the answer given by @ Subir Bandyopadhyay.
Best wishes, AKC
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I have reported one eriophyid mite attacking amaranthus from Kerala, India. its taxonomy is not worked out till date. can any body help me in this venture?
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Dear Sreekumar
I suggest you Dr. Enrico de Lillo and Dr. Parisa Lotfollahi who are both on researchgate.
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My question is about the inconsistency between the species authorship date and the journal publication date that appeared since Zoobank came into use.
I would like to extend my question with the following example:
Szabo et al. published a paper entitled "Gastropods from the Jurassic neptunian sills of Rocca Busambra (north-western Sicily, Italy): Patellogastropoda, Pleurotomarioidea, Scissurelloidea, Fissurelloidea and Eucycloidea" in Papers in Palaeontology. They registered their species to Zoobank in 2019, when the online first view was published. So when I refer a species from their publication, I cite the species as following "Trapanimaria gattoi Szabo et al., 2019". Their paper is included in an issue and printed in 2021. So when I cite their paper, I add the citation in the reference section as following "Szabó, J., Conti, M. A., Monari, S., & Wendt, J. (2021). Gastropods from the Jurassic neptunian sills of Rocca Busambra (north‐western Sicily, Italy): Patellogastropoda, Pleurotomarioidea, Scissurelloidea, Fissurelloidea and Eucycloidea. Papers in Palaeontology, 7(1), 27-110". This creates an inconsistency between the date of species authorship (2019) and the date of end-text reference (2021).
I wonder how other researchers solve this date inconsistency in their manuscripts.
Thanks in advance.
The article can be reached here:
Zoobank link for the publication:
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I wonder if the early view from 2019 meets the requirements of the Code. The new taxa have ZooBank LSIDs and the paper is registrered in ZooBank, but the latter needs to be mentioned explicitly for an electronic publication to be valid in the sense of the Code.
If the electronic version from 2019 complies with the Code, the publication date of the new names is 2019. But how to cite this paper, if the issue number and final pagination wasn't available until 2021? We have the very same problem in our database.
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I have a big collection of ivy (Hedera) but fail to identify this specimen as species. It has matt leaves all of the similar shapes and with unusual stellate trichomes of 7-8 (10) rays - nearly scale-like but of fully fr
ee rays. The trichomes of this specimen do differ from those of other Hedera species. This specimen came from a Saint Petersburg's Botanical garden but of unknown origin. I took the photo of the specimen in my garden. The help will be acknowledged.
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Yes, I tried to use all key available incl. this one. To say precisely, I grow all Hedera spp. known in my co
llection and can compare all characters of them. I just hope anybody has met this strange ivy at least to know where it is from.
Anyway many thanks to you for your efforts to help me. All I can now is to count chromosome number.
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In a recent paper submitted for peer-review I made the statement that ... "Despite their ecological importance and their ubiquity they (the coralline algae) are still a comparatively poorly known group of marine organisms whose taxonomy has remained in flux".  A reviewer commented that this was not correct because “if you look at the number of papers on corallines covered in scientific abstracting databases, it is actually correct to say that in the last 10-15 years corallines have been one of the best-studied algal groups".  I am not disputing the increased number of papers or the numerous scientists that have extensively worked on this group in recent years, but what I am suggesting is that despite all our efforts, this group still remains a largely poorly understood group of algae. This is evidenced by the extensive work on this group in recent years in which much debate on their taxonomy and phylogeny still remains.  I do agree though that our understanding of their taxonomy is expected to improve as we better understand their molecular characterisations.  I would be happy for any comments on these statements.
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Looking at its wide global distribution in the marine systems, yes, the coralline algae are still poorly known and deserve lot more recognition. Complex taxonomy is an issue but I think its poor applicability in biostratigraphy (obvious due to their very long, persistent stratigraphic records) makes them less attractive to researchers in comparison to several other marine groups.
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For part of my research I am attempting to assess the abundance and diversity of crustaceans in an aquatic habitat. I intend to take picture of the specimens once collected before they are preserved and lose their colour. I mainly wanted to know if there were any specific guideline to taking taxonomic photographs of shrimp e.g. how it should positioned/oriented, should the appendages be positioned in a specific way as well?
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Hi Maizah, I concur with James: each species has a different set of characters, so you will have to study them in advance. I prefer to start taking photo's of living specimens, because they show some behaviour I want to register (see https://nieuwewendingproducties.blogspot.com/2018/03/in-vitro-in-natura.html - http://micksmarinebiology.blogspot.com/2017/10/spookkreeften-determinatietabel.html)
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Dear all,
I am currently developing a framework about learning with immersive Virtual Reality. So far, I have categorized "Number of mistakes" and "Time to completion" as performance /objective factors and satisfaction, self-efficacy and motivation as affective factors. However, I also want to include embodiment, usability and cognitive load. I currently cannot come up with a suitable summary keyword. They all refer to the experience while learning, but I would prefer a different category than "learning experience". Do you have any ideas how I could categorize the three concepts?
Thank you very much in advance for your help!
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Interesting topic.