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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; The incentives imposed on employed academics are perverse! We all hope that what we read is accurate, contemporary and an addition to our collective knowledge. Employers (universities, corporations, start-ups, etc) insist that the new contributions come quickly and are widely read. So, how careful can you afford to be? ...tenure review or, the next grant application deadline is just around the corner. That's the problem! Personally, I enjoy the privilege of being a retired, avocational researcher who is under no pressure to submit a manuscript until it is ready. It is clear that changing the incentive system is imperative.
Best regards, Jim Des Lauriers
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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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Hello everyone,
I did the assembly of chloroplast genomes for some Boraginaceae species, in a few species, I got an orientation problem where the rbcl gene position is within the circular shape in a clockwise direction, and the atpB and atpE genes position is are outside the circular shape in the anti-clockwise direction (please see the picture), and this is a different result from most assemblies of chloroplast genomes that have been published !!!. (usually, the rbcl gene is outside the circular shape and in the anti-clockwise direction while the atpB and atpE genes are within the circular shape and in a clockwise direction)
I am using Chlorobox to draw the gene map after Novoplast finishes the assembly, this issue happened with only two of 7 samples, the two samples are from the same family !!!, I change the seed and reference many times and still got the same result.
Any idea what I need to fix this?
Thanks!
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I think that maybe you have used blunt end digestion endonucleases, this makes inserts to be ligable in both directions (as your experimental results suggest). If that's the case, maybe this information is useful:
Both the Costa and Weiner or Delphi genetics Staby methods could fix this orientation problem.
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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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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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Whatsoever the advances may be, the basic objective of taxonomy remains unchanged. It still deals with the naming, identification and classification of living organisms as per certain systems.
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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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Thank you dear @Nikola Z. Grujic for proposing such interesting questions and discussions in the case of Collembola researches. I hereby like to attach the link of one recently published paper, which is revealing the comprehensive phylogeny reconstruction of subfamily Tomocerinae for the first time. It has been shown in this paper that trait evolution in the subfamily Tomocerinae shows a multiple ecological divergence, which leads to this point that three dominated genus in this subfamily, Tomocerus, Tomocerina and Tritomurus have been evidenced not to be monophyletic. Thus besides this conflict inside the family Tomoceridae, in a larger view, we see how much superfamily Tomoceroidea would be controversial in its phylogenetic position. Here below you can find the link.
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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.
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We used a single locus analysis (ITS) for the provided set of FASTA sequences. We're hoping you could give us advice or tips to make a cohesive interpretation of the phylogenetic tree given the limited data that we have which are morphological characteristics and genetic sequences only.
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For phylogenetic analysis is better to generate the Bootstrap tree and PP tree. Fasta file can be changed to Nexus or Phylip files for MrBayes and IQTREE (e.g. in Mesquite, PAUP, etc)
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Is it possible that different species of particular plant encountered in a specific forest area is totally different from the previous report when surveyed after about a decade? If yes, what can be the tentative reason?
I feel that it is probably due to lack of proper identification and authentication.
Please help to find a reason.
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Which is why journals should demand that voucher specimens be deposited in a given herbarium before accepting a paper for publication, so that identifications can be verified. As it is, journals, even of supposedly high standing, pullulate with irreproducible results.
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Dear marine biologists,
Thank you in advance for helping me in identifying this Mediterranean limpet. These beautiful limpets were collected from Lebanese rocky shores, Eastern Mediterranean Sea.
I need to know which species is this? Patella caerulea, Patella vulgata, or Patella rustica / lusitanica?
Thanks :)
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Most probably Patella rustica.
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While working with taxonomy of Indian Orchids in past two decades, I have witnessed many merger and splitting of genera mostly as a result of phylogenetic analysis mostly based on molecular evidences. The circumscription of larger genera like Bulbophyllum, Dendrobium etc. with wider morphological variability have been expanded with merger of well established smaller genera; whereas, genera like Eria, Habenaria etc. are being splitted with many combinations. The examples are unlimited, but everywhere the logic is to make the genera monophyletic. The problem in Vandaceous genera are even more inconsistent. The question is on the perception of the authors. When we have taxonomic hierarchy like sub-genus, Section, Sub-section etc. to fit all the heterogeneity, why not use them instead of creating many small, narrower genera or merging smaller ones into bigger genera with wider circumscription.
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Roman Bohdan Hołyński gave the answer in a nutshell. The bad thing about the monophyly requirement is, that by and large it has become a dogma. Any dogmatic approach to a scientific question is in itself suspect.
Be aware of the logical conflict in the monophyly concept that has been pointed out by Roman Bohdan Hołyński (an by others before him). And then, ask yourself, non-dogmatically, what do you wish to achieve. The monophyly concept is relevant for classification, and it is valuable as a method to assess the "value" of any proposed classification. Nomenclature is an entirely different concept, and serves communication. We have grown to accept that the names of organisms must reflect their classification; but when accepting this becomes axiomatic, it reflects negatively on the usefulness of names as information vectors. When we wish to address a taxon that is worth while being recognized, because it is recognizable and we want to communicate about it, it is not primarily relevant that the taxon be monophyletic. Changing names each time a new classification hypothesis is proposed impairs the usefulness of names as information vectors and, in the long term, is contra-productive.
Even when one is reluctant to abandon full congruence between classification and nomenclature, one should bear in mind that translation of the first into the second is not a strait-jacket but leaves options; and it is the duty of responsible biologists to choose the option that is least disruptive with respect to familiar usage, and is most robust under the variation in classifications, or phylogenies, that are likely, if not certain, to occur in the future.
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Hello,
I am currently working on my MSc. thesis on video conferencing in (management) consulting oriented SMEs. The goal is to develop a tool/model/format to support managers in making responsible choices to implement video conferencing in their company.
The idea is to first map the consultancy process (already done), then link a number of meeting types per phase in this consultancy process, and finally link these types of meetings to characteristics of video conferencing.
For this I am now looking for an existing classification/taxonomy of business meetings.
As you may have noticed, I am still struggling with what the model should look like and what the appropriate descriptive words might be.
Well my question is: Does anyone have any tips and/or ideas of existing literature where business meetings is discussed in this context?
Thanks in advance for your time and effort!
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Refer link for types of business meetings :
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I am looking for recommendations of scales (in English or Spanish) to measure learning styles according to Bloom's taxonomy of learning.
Thank you in advance!
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I can also recommend the framework of Skills Assessment partly based on Blooms Taxonomy, but also on 6 other frameworks.
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Biological experiments are nowadays being added as preprint in different archives such as biorixv.. Can an author add taxonomic descriptions as well before published as a journal article?
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Publishing descriptions of new taxa as preprints is definitely a bad idea.
(i) the name would very probably not be made available through use in a preprint
(ii) others could start using the name before the description has been officially published, causing confusion with regard to priority and date of publication
(iii) as Thierry Bouyer pointed out, someone else could come in and quickly describe the same taxon using their own name. Taxonomic vandalism is a thing...
Under the rules of the Code, nothing could modify that (although herpetology has challenged those rules in recent years).
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This is a climbing shrub grown in houses for the fragrant flowers in Salem, South India. I request the expert members for the species id of this Jasminum.
Thank you.
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It looks close to Jasminum azoricum L. of family Oleaceae.
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Hi guys! I wonder how to find if some species/genera contain a specific gene. I have some human gut microbiome data derived from human faeces. The data includes gene abundance in each sample (each sample is faeces from each individual), taxonomy abundance in each sample (family, phylum, kingdom, genera, species). There is a gene that I am interested in, and I want to figure out what species/genera in our study contain this gene. There are hundreds of species detected, so I wonder if there is any program or any protocols that are routinely used for this purpose.
Thank you for your help in advance!
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Близость – родство генов можно установить
Этот результат получается на математическом расчете
Метод позволяет выявить близкие виды
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In case of cyanobacterial taxonomy, what is the final status of the organism which forms phylogenetically distinct clade but are not distinguishable by any of the morphological feature? Can we conclude it as a novel taxon? If no, then how can we report them in a publication?
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If it were a taxon of the animal or plant kingdom, the answer is that it is a new taxon. In Monera I don't know that. I attach an example of a work on a cryptic species in sea urchins just in case it is of interest to you:
Bronstein, O., Kroh, A., Tautscher, B., Liggins, L & Haring, E. 2017. Cryptic speciation in pan-tropical sea urchins: a case study of an edge-of-range population of Tripneustes from the Kermadec Islands. Scientific Reports, 7: 5948. DOI:10.1038/s41598-017-06183-2.
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I am facing difficulty to find the gynoecium properly of Mimosa pudia L. which has capitulum or head inflorescence. I have found the androecium after many try. But pistill was too hard, How to be efficient in classical taxonomy study (Morphology based)? How did they described it in literature? I wonder!!!!
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I like to use syringe needles you can purchase from a pharmacy as a very precise "knife" or "scalpel". I have dissected many flowers (about 1-5 mm in diameter) of Stelis (Orchidaceae) with this under a common binocular microscopes with magnifications ranging from 8x to 24x. However, sometimes it is hard to fix the flower so it can be cut. In these cases very fine forceps are helpful. Those can be purchased from goldsmiths or clockmakers. If this is still too large, the flower may be fixed on an adhesive tape or sometimes a wet paper is enough.
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If a taxon is described using three specimens, one with flowers, one with fruits, and one sterile, considering fruits and flowers are essential for unambiguous identification of that species, and all but the sterile specimen are lost, it clearly needs to designate the sterile material as lectotype.
That is the obvious, but then a problem comes up. As the species can only be identified using flowers and fruits, a single epitype will never be sufficient dealing as type.
Would it hence be possible to designate two specimen as equally serving epitypes?
In another case, if an epitype, lets say with flowers, was already designated, would it be allowed to designate another epitype (or "epiparatype") due to amguity of the first epitype?
Unfortunately, I found this not addressed anywhere. Or maybe I just have overseen it?
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Dear Sergei L. Mosyakin,
this is exactly the issue. In case of ambiguous original material (of which anything is the holotype or a lectotype can be selected), we still have the possibility of designation of ONE additional epitype, which is "conserved" if it is not in conflict with the type.
This is clearly not desirable as taxonomy evolves and "additional" characters using for differetiation of taxa may be discovered. If these characters can not be derived from an existing epitype and epitype further supporting the holo-, lecto-, or neotype AND the previous epitype would be necessary.
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I have been trying to learn how to dissect out the genital anatomy of snails for the purposes of taxonomy but I haven't been able to find any good advice or resources on this. I am identifying some succineids (and occasionally smaller things) and the morphology of the genital system seems to be very important. Can anyone provide guidance in this area for resources that are useful?
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David Bullis, In this diagram red coloured organs can be considered as the genital anatomy of the Achatina sp. (Land snail). They are hermaphroditic (bear both sex organs in an individual). When you are going to dissect them please be careful to separate them without damaging the overall genital connections - hermaphrodite duct and talon tend to be damaged easily.
Here is the dissecting procedure,
1. Preserve the collected sample in 70% Alcohol. (Wear gloves because they may be an intermediate host of platyhelminths parasites (Digenean).
2. Remove the shell using a bone cutter without damaging the animal.
3. Find the Pneumatophore (a small hole close to the head, see the photograph)
4.Cuts should be made as I mentioned in the diagram.
5.Open the body wall as shown in the diagram.
6. Identify the systems carefully.....
All the best!
Lahiru, UOR, Sri Lanka
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Dear all taxonomists
Do you think that the problem which we had with Zootaxa in this year is an accidental or we should expect similar problems in the future? Not only for Zootaxa but also with other taxonomic journals. Do you think that we can do something with it? Any strategy or ideas? Do we have this problem only in zoology or also in botany?
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I don't understand this and similar discussions. There are hundreds of quality journals that publish alpha taxonomy articles in many fields. Why all attention is focused on Zootaxa?
I never publush my research in paid journals because this is a cheating business. However, this does not apply to journals of scientific societies, where member contributions are required.
Here is just a brief list of free quality international peer-reviewed journals (referring in Scopus and Web of Science core collection) that publish articles on animal alpha taxonomy (many of them are with open access; also many journals publish alpha-taxonomy on fossil records):
Zoology/Entomology:
1. Zoosystema (Scopus, WoS core collection) - chargeless
2. Acta zoologica academiae scientiarum hungaricae (Scopus, WoS core collection) - chargeless, open access
3. European journal of taxonomy (Scopus, WoS core collection) - chargeless, open access
4. Zoosystematica Rossica (Scopus) - chargeless, open access
5. Zoologicheskii zhurnal (Scopus, WoS core collection) - chargeless, open access
6. Zoology in the Middle East (Scopus, WoS core collection) - chargeless
7. Invertebrate zoology (Scopus) - chargeless, open access
8. Acta Zoologica Bulgarica (Scopus, WoS core collection) - chargeless, open access
9. Ecologica Montenegrina (Scopus) - chargeless
10. Annales zoologici (Scopus, WoS core collection) - chargeless
11. Arthropod sytematics and phylogeny (Scopus, WoS core collection) chargeless, open access
12. Zoologischer anzeiger (Scopus, WoS core collection) - chargeless
13. Turkish Journal of Zoology (Scopus, WoS core collection) - chargeless, open access
14. Arthropoda selecta (Scopus) - chargeless, open access
Entomology:
15. Annales de la Société entomologique de France, N.S. (Scopus, WoS core collection) - chargeless
16. Insect systematic & evolution (Scopus, WoS core collection) - chargeless
17. Far Eastern Entomologist (Scopus) - chargless
18. Entomological Review (Scopus) - chargless
19. Fragmenta entomologica (Scopus) - chargless
20. Caucasian Entomological Bulletin (Scopus) - chargeless, open access
21. Russian Entomological Journal (Scopus) - chargeless, open access
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Hello Everyone,
The past few years have seen a lot of new cyanobacterial taxa being described using a polyphasic approach. It will be interesting to know that what are the various good things about using this approach and importantly, are there some particular taxonomic groups/clusters that are still unresolved where the polyphasic approach is still to give any proper answer?
What further developments do we anticipate in the coming years? What are the new techniques/methods that can be further incorporated for a better understanding of cyanobacterial taxonomy?
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Although it is not my specialty, I advise you to read the following paper:
A polyphasic approach for the taxonomy of cyanobacteria: principles and applications, by Jiří Komárek (2016).
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How would this appear on a tree if COI only resolved those closely related species and not more distantly related species? Thank you
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support values would be low for deep branches and/or they would be unresolved (as Artur already mentioned). And COI is NOT suited to resolve deep branches. For closely related species it is fine, but also for closely related species you always have the problem that if you analyze a single gene, you will only receive a gene tree. Not the underlying species tree and that might be quite different
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Hi,
I am trying to analyse sequences produced using SMRT link from PacBio. My goal would be to produce asvs table and taxonomy as for a normal DADA2 pipeline, but I am struggling finding information about how to use the output sequences from PacBio in any bioinformatics pipeline.
Any suggestions?
P.s. still a newbie! ;)
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I am searching for a well accepted taxonomy of resistance to change and in terms of its underlying causes/roots.
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If I get the question right, you are looking for an absolute method to use in taxonomy. There is no absolute method in taxonomy, but the most recently used projection in this field is Integrative Taxonomy: This uses tools from other fields, just like Ecology, Evolution, Ethology, Phylogenetic, Morphometrics, etc, together these allow a more exact approximation, to define a species and its systematic.
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Based on Suhling et. al., 2014 which I use for identifying Odonatan larvae, this specimen corresponds with the description of Lestinogomphus (based on the long hind legs which reaches abdominal segment 9, excluding the breathing tube). However, no image of the habitus of Lestinogomphus is attached, nor can be found online, hence my question.
I also have the larvae of Phyllogomphus which is totally different from this, based on general size and other dimensions.
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I can't help you indentifying this insecta, but see this website (allow you knowing faster your sp according to its database)
Good luck,
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Can you share any interesting photo concerning butterflies you'd met in nature in your country or during your voyages abroad?
Can you also comment it shortly with a place and date you'd spot it? Also its name. If you are not sure you may ask other participants about the specy name, instead.
E.g.: In May 2019 I'd spend my holidays in Greece, and met there the above Epicallia villica, the cream-spot tiger, a moth of the family Erebidae.
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صورة جميلة لإحدى الفراشات النادرة
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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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I fully agree that studies on the biodiversity are one of the most important, and must be treated as 'top of the tops' under current circumstances and biological loss. The small groups are as important as the large ones, or even more. We are now suffering from effects of decline and discourage of taxonomy and focus on modern molecular approach as replacement for 'traditional' taxonomy and biodiversity studies. So the problem is wide and not a simple solution can resolve it.
Second point is putting in one bag for assessment wide variety of biological research - biomedical (with journals IF over 20 easy accessible for researchers), molecular and genetic engineering science publications (with easy acievement of IF = 10) to taxonomy with most journals IF =1. The point is 'modern' papers are cited intensively for short time (3 years as median time) - which leads to the effect of high IF in a short time scale as requested by analytical companies. Taxonomic papers are cited for over 250 years now (Linnaeus papers as base of modern taxonomy) so their long term impact is much higher than estimated by 5yr IF (most common long term index of journal quality).
Third point is 'taxonomic ignorance' in molecular approach (See Lis JA et al. 2008), almost nothing changed since then.
Fourth question is how to tweak of the analytical companies algorithms to be more reliable. These must be more sensitive for taxonomic papers on one hand and be able to recognize and eliminate bulky self-citations not related to taxa and taxonomic names. And yes, lobbying is necessary in this case.
In many palaeontological journals it is obligatory to cite all authors of names with papers listed in references (it is even recommendation of ICZN), but it is often ignored or not allowed by the journals limits of cited papers, or push to obscure supplementary materials never cited.
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Today we can speak of the existence of a global crisis of specialists taxonomy. However, a little-addressed topic is undergraduate training in this important branch of the biological sciences. How is taxonomy research motivated in Biological Sciences majors? Is the teaching of taxonomy adequately and intentionally approached? Final Degree Projects are done today on topics related to taxonomy?
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Hello Abdiel;
1. Earning tenure requires publishing in high impact journals. Taxonomic papers aren't often published in those journals.
2. Requirements for undergraduate degrees no longer emphasize Organismic biology and so our students aren't often exposed to the subject.
3. Job opportunities in fields where taxonomy is essential aren't well publicized...at least not in the USA.
4. Natural history collections in colleges and universities are badly undervalued and so the raw material of taxonomy is inaccessible.
It's a bleak picture. Best regards, Jim Des Lauriers