Taxonomy - Science topic

Hi Sean,

the orchid genus Ophrys also comprises between 9 and 354 species according to authors and criteria.

Cheers,

Joris

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

La comunicazione oggi è in acronimi ed espressa per grafici di algoritmi e....

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

A paper was published in Taxon sometimes back: Sleepless nights - please do not describe your species based on molecular differences.

I hope this helps.

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'

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."

Stefan Ziemendorff

I suspect that Utricularia caerulea is found in South America.

Thanks!

James Des Lauriers, Thank you!

Hello Juan; Here is a link with a little discussion and some citations. Maybe they will be useful. Best regards, Jim Des Lauriers

You can have any classification you like if it makes sense to you :)

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.

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.

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.

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.

on the internet there is this adress for Philippe Lebreton

ph.lebreton01@free.fr.

and yes it is the one you are looking for

he retired since a while

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

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.

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

you can do it by xlstst to make a hierarchical clustering

Dear Antipova, there is a drawing in the original description, see plate XXXIII

It's too late, but I will be interested

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."

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 , 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...?

It looks difficult to reach any conclusion from the above posted pictures.

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

Bahadorreza Ofoghi , thanks for sharing, it looks interesting.

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):

https://pt.wikipedia.org/wiki/Ci%C3%AAncia_social_computacional

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.

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.

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.

Abhijit, Marc, and Marion thanks for replying and sharing your answers.

Also check please the following useful link: https://www.royalsociety.org.nz/what-we-do/our-expert-advice/all-expert-advice-papers/national-taxonomic-collections-in-new-zealand/process-of-taxonomy/

I am not an expert in this field

You are most welcome dear Ali A Moursi . Wish you the best always

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.

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:

https://elifesciences.org/articles/50989#:~:text=Baboons%20allow%20us%20to%20study,systems%20(Jolly%2C%202019).

I would say soil profile. Bcz it gives a comprehensive idea regarding horizons, and various elements present only by visual effects.

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.

Also check please the following very good RG link:

Also see https://www.researchgate.net/project/Systematics-of-Tomoceridae-and-Oncopoduridae-Collembola-Tomoceroidea

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.

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

ok thank you!!!

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.

Arvind Kumar GOYAL

It looks Paphiopedilum spicerianum (Rchb.f.) Pfitzer

Thanks!

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

Statistical analysis according to the nature of the data

Thank You for all recommendation

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.

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.

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.

With your proposal you raise three issues:

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.

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

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

the European Journal of Taxonomy is a 'diamond' open access journal, meaning that you don't pay to publish and nobody pays for reading.

https://europeanjournaloftaxonomy.eu/index.php/ejt

It should be critical taxonomists maintain their independence from the conservation community including IUCN.

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

https://www.alchemer.com › Blog

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

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

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.

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

Yes. It is possible. All you need is the appropriate database and software for analysis depending on the type of 16S (Illumina or PacBio)

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

Dear Sreekumar

I suggest you Dr. Enrico de Lillo and Dr. Parisa Lotfollahi who are both on researchgate.

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.

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.

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.

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)

Interesting topic.