Taxonomy - Science topic

Recently there were published many “comment papers” in valid journals such as Palaeoworld, Geological Journal, Carbonates and Evaporites and ... regarding the larger benthic foraminifera where accurate identifications require a high level of experience and knowledge of their taxonomy, this is the main question who are really the cause of these mistakes and problems?

1- Authors

2- Reviewers

3- Editors

1. I suggest to prepare the paper devoted the issues of non-financial reporting (institutional approach; non-financial reporting as a source for decision-making; Taxonomy for non-financial reporting, etc.).

2. If someone has an option to publish an article in such a journal, we can prepare an article together. We can also join forces and conduct joint research in this area.

Waiting for response

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!

This species is encountered in Kokrajhar town of Assam, India. It is thin walled bamboo. As per my knowledge it seems to be Schizostachyum sp. I request the peers to kindly help me identify the same.

I have 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?

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...

I have set of tags per document, and want to create a tree structure of the tags, for example:

Tags:

- Student,

- Instructor,

- Student_profile,

- The_C_Programming_Language_(2nd Edition),

- Head_First_Java

I need to generate a hierarchy as per the attached example image.

Are there Free taxonomy/ontologies which can give Parent words? like

get_parent_word( "Student", "Instructor") = 'People'

get_parent_word("The_C_Programming_Language_(2nd Edition)", "Head_First_Java") = "Book"

is_correct_parent(parent: "Student", child: "Student_profile") = True

I have a corpus of English as well as Technical documents and use Python as the main language. I am exploring WordNet and SUMO Ontology currently, if anyone has used them previously for a similar task or if you know something better I would really appreciate your guidance on this.

I can't find a rigid reference defining which is considered computational and which is not and saw some taxonomies including the regression ( isn't this just statistics?)

I am a bit confused and I feel like the term is loosely defined within the literature (at least what I have looked up)

What are the most influential ontologies or taxonomies in the behavioral/social sciences? How did they make a difference? What does it mean to be an influential ontology or taxonomy? Citations? Use? Saved lives?

While describing or analyzing species taxonomy, we find some taxonomic changes proposed within thesis that we considered appropriate but, since they have never been published in peer reviewed articles they are not officially accepted.

I need help identifying eukaryotic microorganisms found in aquatic samples from a fish farm. Could somebody recommend a source I can use for the taxonomy identification? Or want to take a look at the pictures of my little creatures?

I appreciate any kind of help.

Cheers

I do not understand what do you mean by taxonomy in it? Is it related to 4IR or the roles of management ?

We are trying to better understand the taxonomy of liberica and excelsea to find ways to help farmers taking decisions of how to replant different fields and plots of coffee.

I have asked a question, If baboons appear more like us than any other of our primate relatives, is it sane if I think in reconstructing biological taxonomy on a Cultural basis? Now, I want to ask about the meaning which Culture is supposed to be if this taxonomy wants to go further.

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.

If Ardrey suggested that 'because of its terrestrial life the baboon, as I have suggested, pursues an existence more resembling the human than any other of our primate relatives.' is it sane if I think in reconstruct biological taxonomy on Cultural basis?

Soil profile presents a two-dimensional view of the soil body. According to Hartemink (2009), the first depictions of soil profiles were made in the late 1700 long before soil science was established. The soil profile may also be taken as one side of a pedon, the three-dimensional conceptual soil body used as the basic unit of classification in the Soil Taxonomy of USDA. Simonson and Gardner (1960) who proposed the pedon concept compared it to the cell in biological systems. This comparison, however, has been criticized since cells are functional units with real boundaries (cell walls) while pedons have no boundaries since the soil is a continuum. The French pedologist A. Ruellan, past president of the International Union of Soil Sciences, has summarized the criticisms against the pedon concept, as follows: it is not a natural unit of the soil cover but only an abstraction, its morphological lateral limits are artificial, and its genesis is interpreted vertically without looking at the lateral dynamics and relationships (Ruellan, 2002). What is your opinion on this? Which is a better unit or model to use in the study of soils?

References

Simonson, R.W. and D.R. Gardner. 1960. Concepts and function of the pedon. Trans. 7th Intern. Congr. Soil Sci., Vol. 4, Madison, pp: 127-131.

Hartemink, A.E. 2009. The depiction of soil profiles since the late 1700s. Catena 79: 113–127

Ruellan A. 2002. Classification of pedological systems: a challenge for the future of soil science. Trans. 17th World Congr. Soil Science, Bangkok.

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:

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?

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.

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.

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?

What modern taxonomies are currently used to systematize lichens? I use www.gbif.org and https://inpn.mnhn.fr.

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?

Can anyone help me identify this Orchid?

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?

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

May You recommend me any publications about family business typologies, taxonomies, classifications in countries from Central Eastern Europe?

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.

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

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:

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'!

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...

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?

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.

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?

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?

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.

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.

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!

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.

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

better if includes recent knowledge in physiology taxonomy and diversity .

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

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?

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:

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.

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.

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?

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!

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.

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.

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 :)

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.

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!

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!

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?

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.

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!

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?

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!!!!

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?

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?

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?

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?

How would this appear on a tree if COI only resolved those closely related species and not more distantly related species? Thank you

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! ;)

I am searching for a well accepted taxonomy of resistance to change and in terms of its underlying causes/roots.

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.

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.

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.

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?