Questions related to Systematics
Submit your abstract for the Symposium organised by Ivana Rešetnik and me at the XX International Botanical Congress in Madrid (21-27 July 2024)!
The deadline for abstract submission is November, 30 for oral presentations and February 1, 2024, for posters.
Here you can find the submission guidelines: https://ibcmadrid2024.com/index.php?seccion=scientificArea&subSeccion=abstractGuidelines
Link for abstract submission: https://ibcmadrid2024.com/index.php?seccion=scientificArea&subSeccion=abstractSubmission1
The general link to the congress: https://ibcmadrid2024.com/
Our symposium is the n. 13
I have sequenced and identified a new bacteria species, and a phylogenetic tree of it and other type strains in the same genus has been built. I have also annotated the Go term of all species in this tree. I wonder if I can assess enriched gene functions in my new species by doing a go term enrichment analysis.
I tried in R using TopGo package, by setting genes in my species as significant, others not significant, as if it's differential expression data, using the options: algorithm = "weight01", statistic = "fisher". It works and the result looks good because it shows some pattern that I also noticed before.
I wonder if there's any pitfalls doing this. One problem is: in DF dataset, the gene universe is the same for each treatment, however in my dataset the gene universe is different between species. I want to know how this might affect the internal fisher test.
Also, there could be bias in the species selection. If the majority of species I picked are distantly related to my species, false positives are expected. I tried to address this by doing the same test in various clades. Starting from all species as a clade, then to more closely related species as a clade, finally to the sister group, the significance goes down as expected, while the rank of significance of each go term is relatively stable. This provides some evidence that the top go terms are not biased by the background species I picked.
Thank you if anyone can contribute some idea on this.
I would like to add a data matrix of morphological data, assembled in the software Mesquite, to a manuscript. I would either add an electronic supplement (MS Excel format) or a table as *.txt or *.dic file. Anyone with experience around? I find Mesquite to be a bit user-unfriendly with this regard.
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?
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?
A "nursing theory" is a description or explanation of an area of professional nursing. This description or explanation is proposed in a systematic way in order to provide the broadest and most practical information for use in nursing practice and research. They are useful. OK, but it appears that many of them are not practical in a real environment like a hospital or a clinic.
What is your opinion about the obstacles that prevent nursing theories to be practicable?
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.
Can you share any interesting photo concerning insects you'd met in nature in your region, country or during your voyages?
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 the other participants about the specy name, instead.
During one of my holidays in Dolomiti I've spot the above Panorpa sp. (Mecoptera: Panorpidae) at wild flower of lily in Cortina d"Ampezzo Valley.
The recent official publication of PhyloCode has caught my attention, not for new arguments being presented for a system that has already been extensively discussed and, as I see it, whose downsides and problems surpass the envisioned advantages, but surprisingly because of the mediatic coverage it is currently receiving. So many of the major newspapers, which are generally regarded as part of the "mainstream media", are publishing articles and stories praising the "new" PhyloCode as a much-welcome, even necessary, advance to the "terribly outdated" taxonomic classification system currently in use, which "ignores decades of advances in molecular phylogenetics and does not reflect evolutive relationships of organisms". Anyone familiar with the current practices in Systematics is aware that this is malicious disinformation.
In talking with colleagues some have resonated with my impression that, instead of an academic debate, the PhyloCode is becoming a mediatic thing, so that systematists in disagreement with its adoption are branded as "reactionary" and "outdated", not only by the colleagues with whom they disagree but also by the "mainstream media" and possibly the public influenced by it. This type of political interference is negative to Science, and certainly very much unwanted by those endeavouring to advance, improve and refine human understanding of Earth's biodiversity and Natural History.
I think this debate should be kept academic, free as much as possible from this type of political interference. Your thoughts on this topic are very much welcome.
In energy and relaxation calculations, I do a convergence test to determine the best number of K points. I do this by varying the k points number N x N x 1 and getting the energy. When the energy difference between the N x N x 1 and (N-1) x (N-1) x 1 is no longer greater than 0.001 eV, I take (N-1) x (N-1) x 1 as the K points settings.
My question is this: Is there a systematic method similar above in order to determine the best number of k points for DOS calculations? I read in the VASP manual that it should require more k points, but how should I know how many is enough?
Thank you very much.
"Taxonomy and Systematics of Molluscs"
or "Systematics of Molluscs"
（1）Denying the essential differences of infinite set elements’ “special nature, special existing condition, special manifestation and special relationship among each other”, so, elements in all different infinite sets are only heaps of infinite “indiscriminative, nonquantitative, abstract points” and it is unnecessary and impossibale to have any quantitative studying and cognizing on “infinite elements (points) in infinite sets”, the number of elements in all infinite sets are the same and it is just infinite. For example, elements in many infinite mother sets and their sub-sets are in fact all the same stuff of infinite “indiscriminative, nonquantitative, abstract points” without any differences of “nature, existing condition, manifestation and relationship among each other”. The typical cases are “the element numbers in Rational Numbers Set and Natural Numbers Set are equal, the element numbers in Natural Numbers Set and Even Numbers Set are equal and they are just all infinite”. The conclution is: any infinite set has limitless, endlees, infinite elements, so their “one-to-one coresponding operations” of quantitative studying and cognizing on “infinite elements (points) in infinite sets”
can be carried on for ever and their element numbers are all “equally infinite”.
（2）Affirming the essential differences of infinite set elements’ “special nature, special existing condition, special manifestation and special relationship among each other”, so, elements in all different infinite sets can be “discriminative, quantitative visible and tangible mathematical things” and it is necessary and possibale to have all kinds of quantitative studying and cognizing on “infinite elements in infinite sets”. For example, there are different “special nature, special existing condition, special manifestation and special relationship among each other” betwee elements in Real Numbers Set and Natural Numbers Set, so, these two infinite sets have different element numbers. The typical cases are “the element numbers in Real Numbers Set are more than that of Natural Numbers Set, the element numbers in Power Set are more than that of its original set and they are all inequal”. The conclution is: Different infinite sets may have different element numbers. So, in the “one-to-one coresponding operations” of quantitative studying and cognizing on infinite elements of two different infinite sets, the elements in smaller set with fewer elements are consumed and finished soon, it means the element numbers in such an infinite set are not endlees and limitless at all (fake infinite); but in the begger set, infinite many elements are left during this operations, this means its elements are endlees and limitless (real infinite), never be consumed and finished at all, the “one-to-one coresponding operations” here can never be carried on for ever at all.
（3）The above different operating ideas and results of quantitative studying and cognizing on “elements in infinite sets” in present classical infinite set theory are affirmed scientific and both aceptable. The one-to-one coresponding operation idea and result of quantitative studying and cognizing on Rational Numbers Set and Natural Numbers Set is the most typical example. In present classical infinite set theory, on the one hand, we can prove the general acepted conclution of “Rational Numbers Set has exactly same elements as Natural Numbers Set, so it is countable” by the above first operating idea and result; on the other hand, we can also prove “Rational Numbers Set has infinite more elements than Natural Numbers Set, so it is uncountable” by the above second operating idea and result, because just a tiny portion of rational numbers from Rational Number Set (such as 1, 1/2, 1/3, 1/4, 1/5, 1/6, …, 1/n …) can map and use up (bijective) all the numbers in Natural Number Set. This is the newly discoved “’Countable-uncountable’ Paradox of Rational Number Set”. The conclution is: the quantitative studying and cognizing theories and operations in present classical infinite set theory are lack of scientificity.
It is because of the fundermental defects of the absence of “infinite carrier theory” and the unscientific concepts of “potential infinite--actual infinite” in present classical infinite set theory that have been making people unable to know which of the above threedifferent operating ideas and results is scientific and why, unable to know scientifically and systematically the relationship between “elements in infinite set” and “infinite set” , unable to know scientifically and systematically the “nature, existing condition, manifestation and relationship among each other” of sets through their elements, ... This situation has been making people unable to know clearly since antiquity how to carry on quantitative studying and cognizing on elements in infinite set scientifically and systematically, resulting in the production and suspending of all kinds of “infinite things’ quantitative cognizing paradox families” in present classical infinite set theory.
At this very moment (2 September; 22h00, local time), the National Museum (MN, Rio de Janeiro, Brazil), one of the most important museums of natural history in the world, is burning in flames.
In addition to the exhibitions open to the public, the MN housed some of the largest and most important scientific collections existing in Brazil. The collections of biological items included thousands of types (insects, reptiles, birds, mammals, plants, etc.).
To the taxonomists (and other colleagues): You could say how many specimens (mainly types) collected or described by you were deposited in MN? And to what taxonomic groups (family or above) these specimens belonged?
[In 2016, a coup d’état turned Brazil in a country with no future. Now, in his final months at the head of the Government, the President Michel Temer wants also to ensure that the country erase its own past.]
First of all decide what are the equipment, chemicals etc.. required for the project. procure them, design the work well and systematically carry out the work. The success is yours.
I am doing some research on typifying a plant species and have encountered the following situation.
- The description is very old and no specimens were cited in the protologue.
- No extant specimens survive that would constitute "original material" as defined by article 9.3 of the IUCN.
- The protologue contains an illustration that could be selected as a lectotype , but it is not very detailed and could be variously interpreted as any of several species.
- There are also herbarium specimens of this species collected by the author himself, but years after the description was published, and thus could only be selected as neotypes because they cannot be considered "original material".
My options are the following:
1) Designate the drawing as a lectotype
2) Designate the specimen as a neotype
3) Simultaneously designate the drawing as a lectotype and the specimen as an epitype
I would prefer to select an actual specimen over an illustration which is more ambiguous, but the fact that the extant surviving specimen was collected after the species was published is problematic, and I am not sure if in all cases one should select "original material" over other alternatives that may otherwise be easier to interpret. There appears to be some precedence for option 3 above, but I am wondering what others would suggest in a situation such as the above.
The question stated above is the title of a book review (see http://www.journals.uchicago.edu/doi/pdfplus/10.1086/694936?utm_content=bufferaebfd&utm_medium=social&utm_source=linkedin.com&utm_campaign=buffer ). I thought it would be interesting to read both opinions about the book reviewed ("The Future of Phylogenetic Systematics: The Legacy of Willi Hennig.") and colleagues' own answers to the questions: "Does the Future of Systematics Really Rest on the Legacy of One Mid-20th-Century German Entomologist?"
I am searching for any possible fellowship to complete my study on Molecular phylogeny and systematic of Sphodristocarabus (Coleoptera; Carabidae; Carabini) species of Iran.
Several species and subspecies of this subgenus described from north of Iran but most of these described species or subspecies synomyzed or their taxonomic status changed, during the time, but the relationship between the species and subspecies of this subgenus in north of Iran, is still unclear.
For example: The subspecies esfandiarii Heinz, 1973, esperanzae Heinz, 1970 and morvani Morvan, 1976, first time placed under species adamsi Adams, 1817, but later Lassel (2001), put these subspecies under species bohemani Ménétriés, 1832.
So it is my pleasure if any body can suggest any possible fellowship to complete this study.
What do you consider the most important developments in the fields of Systematic Conservation Planning and/or Integrated Spatial Planning over the last 5 years?
Additionally, are there techniques/tools/technologies that facilitate the application of these newer developments? What are your favorites? What works well? What doesn't?
References/citations welcome :-)
One of the statistical analysis that usually is done on DNA barcoding sequences is calculating CG-content. I read in some papers that this sequence (COI or cox1) is usually AT rich in insects. But I didn't read about the importance of this observation in discussion part on the article.
I'm aware of the application of CG-content in systematics of bacteria, but what about Eukaryota like insects?
I found that Weiyong Lu (China University of Mining Technology) systematically steal papers from me and many others.
My research topic is plasma based acceleration, and this guy steal many of my highly cited papers ( including Nature papers). how can I deal with this kind of cheater more efficiently?
I am finishing a paper about Knowledge management and I would like to describe Brazilian context in a systematic way. Looking for ideas.
It would be better if the article mentioned the properties of acids
The ABAT Accreditation and ACM Computer Science Curriculum is systematically evolving and adapting to make sure that current and future Computer Science Graduates are well trained and qualified to enter the job market with proper skills and competencies. Is the current or future ABAT Accreditation adopting the new developments in Bio-Computing, and to what extend will both the undergraduate and graduate higher education change in next five years?
I would like to know who is the author of this definition and these 6 theory analysis steps ?
"Theory analysis is the systematic examination of the
theory for meaning, logical adequacy, usefulness,
generality, parsimony, and testability."
SIX STEPS IN THEORY ANALYSIS
identify the origins of the theory
examine the meaning of the theory
analyze the logical adequacy of the theory
determine the usefulness of the theory
define the degree of generalizability and the parsimony of
determine the testability of the theory.
If you have to chose between two sampling methods, Consecutive sampling or systematic random sampling for your study, from the hospital OPD, which method is better. As in fixed duration say from Jan 17 to Dec 17, if we do by systematic random sampling ie we chose one patient from first five and then chose every fifth patient then the systematic random sampling is only representative of consecutive samples, hence I feel that the consecutive samples should be better. Need advice and clarification from researcher
Accounting for core gain and loss after every run offers a reliable basis for sample evaluation thus strict core quality standards need to be maintained at all times. How then can one account for core loss or gain ? Is there a systematic manner to tackle this ?
How do a computer main board start up?
When you press the start button on a computer what procedures happen to turn on the CPU.
In another way, a CPU has a DC-DC converter to supply own variable power needs. But what things I want to know are a systematic procedure of turning on a CPU.
Thank you in advance for whom giving me guidance.
What do you think about the revision of the GUM? Do you know if we will soon have another version of the Guide and what, according to your knowledge/experience, will change or should be changed?
Do you think that the concepts of random and systematic uncertainties will be used again? What then about Type A and Type B uncertainties?
Since cladistics and then cladism were born in Western Germany and then developped in English-speaking Western countries, I am interested in the perception of this classificatory philosophy in the former Soviet Union before 1991 and then in its successor states.
I make a carefull distinction between the methodology of tree reconstruction called cladistics, and the dogma that all taxa must be holophyletic called cladism. I do not want to discuss whether cladism is right or wrong here, I am only interested in the perception of scientists in these countries (now and historically).
I am interested in your own testimonies, but I am also interested in historical papers I could read since I didn't find anything myself.
For example the study is conducted through the interview and systematic observation. Can I use just interview part in my systematic review?
Tardigrada and Bdelloidea research in México is very limited, so I would like to identify researchers or grups on these topics to make a network. I work mainly on systematics of Tardigrada and Bdelloidea groups.
Thanks for your answers
Identification requested to experts. Currently i am working in high altitude plant ecology at Great Himalayan National Park, Kullu, India. i want to identify these four plant species from the above mentioned study area from an elevation upto 3400m above sea level.
Lately I have studied Toyota Manufacturing System, but it seems I go in circles, because the tools are so intertwined, sometimes so overlapped, that I cannot let go one tool while studying another one. I go round and round, it gets me boring. I think that the System as a whole is a masterpiece, but when it comes to be studied under systematic methods, it seems so redundant. I feel like wasting tons of times, and I get in the same place of the beginning. Because you need to link the dots between and among tools to make sense of this whole thing. So, my question is: how can one study Toyota System tools, as a self-learner, harnessing the study time as best as possible? (I consider that this study lacks practice, so in this sense I rise my question, as a newbie in this subject.)
Where there are slight differences it often becomes very difficult in traditional/classical taxonomy to separate varieties (forms), subspecies, sister species or cryptic species especially where reproductive isolation or behavioural or other differences are difficult or impossible to see.I am in the habit of separating geographic variants as subspecies and sympatric variants as varieities/forma. However, I have read some comments on Researchgate that all geographic variants should be regarded as separate species while I believe that such differences if minor should be looked at as incipient speciation. Orshould it be left to the specialist to decide whether a taxon should be treated as a variety/subspecies/different species as Darwin suggested?
We currently working on wolffish larvae hatched from wild-caught eggs and at ca 180 dph we're still not sure to which species they belong. Hopefully, we'll see this later in the juvenile/adult phase.
However, for similar, future work it would be extremely valuable if we can determine at the onset of the experiment, to which species the larvae belong.
Any information on genotyping/bar-coding procedures appreciated.
I have not come across any paper where it is systematically stated about how to calculate life cycle impact of a product manufactured using any process. if any one has idea or paper, kindly let me help in this regards,
Thanks with regards,
I request brethren from the research and academic community to answer the following question. What is the procedure of writing a manuscript (article/ note/ short communication, whatever it be!) dealing with rediscovery/ new report or extended geographical report of any taxa, be it plant, animal, fungal or lichen?
The aims are to know relationships among individuals in one species and to classify into two groups: good and bad individual which will be used to increase a population and to control it.
We found this mantis and ootheca during a herpetology expedition this spring in eastern/central part of Kyrgyzstan (Naryn region). Unfortunately we have a problem with determination. Any suggestions are welcome. Any tip for papers engaged in distribution data of Mantodea in Central Asia would be also very appreciated.
Politically skilled but otherwise incompetent people might sometimes climb up the ladders of an organization better than people high on substance know-how but low on politics. This, of course, likely results in non-optimal management performance. It would be interesting to know if there's a systematic bias involved here.
Anyone know of this type of research?
Olfactometers allow for the systematic administration of odorants to humans. I'm looking for something similar (preferably commercially-available and computer-controlled) for tastes/liquids. I've looked around, but so far, I haven't found anything. I'm trying to avoid making my own if possible! :-)
I have generated category summarized taxonomy tables, alpha and beta diversity metrics in Qiime and want to present the data in good publication quality graphical images. Are there any alternatives to Qiime generated output?
hello everyone ! I got a question about trait evolution analysis.
I have COI (Cytochrome oxidase I) DNA sequences for all species, and I have excel sheet for all morphological characters for all species eg. (thorax volume, proboscis length, wings and legs length, Max. width of tergite and sternite, mature egg length and number of mature eggs in ovary.........ect.). I need to use R software (ape and caper package).
Now, I want to analysis these data to study trait evolution history (Mapping these traits on the tree, the evolution relationships between these species). So, how could I achieve that goal ?
thank you all ! Any comments would be appreciated !
actually, I am a beginner in this field, I didn't have a lot experience. I need to now that:
1- I should build the tree from different software (like MEGA) and then import this tree to R.
2- Can I import the sequences to R and build the tree from it with out use other software?
3- In which kind of format I should save the sequences to import it to R?
4- how can I link this morphological data to the tree?
Thank you for all.
I am trying to use Polysat to perform calculate pair-wise distances and determine Principal analysis (PCA) on a polyploid (hexaploid) group. To do this in polysat we use the command code "> plot(pca[, 1], pca[, 2], col = rep(c("red", "green", + "blue"), each = 100), main = "PCA with Bruvo distance")" is used. In this code the term "each = 100" specifies the number of samples in each population (group). The assumption here is that populations have equal number of samples. My question is how can this term be modified in order to accommodate populations with different sample numbers? I would appreciate any suggestion that would help me address this issue?
Hi, i'm studying about divergence time estimation in Piscis using Beast. But i'm only a beginner, so it's too confused.
In my last question, some kind people told me several tips. And i have additional question.
In calibration to divergence time using fossil data, i only know minimum and maximun age of the fossil, but for log-normal distribution, extinction rate (μ) and standard deviation parameter (σ) are necessary.
The problem is that i can't find the way to calculate parameters mentioned above.
Anyone knows the protocol or website about that, please help.
Estimation of ageing errors while determining precise age from different ageing structures. How errors are calculated while estimating precise age in fishes.
It seems that the taxonomic ranks subfamily and tribe are not commonly used in current bacterial systematics. Here are some of my findings. The LSPN (List of Prokaryotic Names) website does not include names at the subfamily or tribe rank. The NCBI bacterial taxonomy also does not have these ranks. Tindall et al. (2006) specifically remarked that "The ranks of subfamily, tribe, subtribe and subgenus are not widely used at present." I did a quick Google Scholar search for the tribe name "Pseudomonadeae" and only found 76 results, of which only 13 since the year 2000. See the attached links for the relevant info.
This is quite curious to me. The International Code of Nomenclature of Bacteria actually specifies rules for forming subfamily and tribe names, among other ranks such as family and order.
In my view intermediate ranks such as subfamily and tribes increase the resolution and informativeness of a classification and should be used. These ranks are very commonly used in zoology and botany.
What do you think are the reasons subfamily and tribe are not used and what is the relevant history?
Attached is a pretty picture of what our current understanding of species looks like at the genome level (ie the big complete picture)
Generally the darker the colour the better the match between isolates.
This particular picture is of all the currently known genome sequenced isolates of S. epidermidis.
As you can see there is a lot of white space indicating genes outside a core genome and almost no black (close to 100% match).
This could be due to:
1) Misidentified isolates being called S. epidermidis by the authors of the sequence
2) Sequencing errors
3) Plasmids being forced into alignments inappropriately
4) There really is this much genetic variation at the species level.
Assuming 4) is true, there are a number of interesting consequential ideas:
a) All previous ideas regarding the concept of clonality need to be completely re-evaluated with all non-genomic previous papers claiming clonality disregarded in this aspect.
b) PCR tests and PCR sequencing tests, MMLVA, MLST of genes like rRNA, cytochrome oxidase and other housekeeping genes can be used to group isolates but these groupings only relate to evolutionary history and say very little about what a bacterial isolate currently is.
c) In terms of pathobiology, the term species is almost meaningless. A single base pair mutation in one regulatory gene can fundamentally change how a isolate interacts with a host and how easily it is triggered to cause disease. Given the huge number of differences between isolates of the same species, it is invalid logic to make any pathobiologic statements or assumptions at the species level.
d) Given the genomic differences at the species level, it is completely invalid logic to expect to make a single vaccine or antimicrobial to protect against an entire species of bacteria that do not burn down the house to keep warm (obligately virulent). At best we could hope to make a vaccine against a single isolate, or tight group of closely related, recently diverged isolates.
Methods based on functional decomposition and morphology belong to the so called systematic design methodology. They are widely taught in accademia, but their diffusion in industry has not reached the same success. Some hypothesis have been formulated by literature, but it is still not possible to identify concrete reasons.
What do you think about that?
In a case control study, systematic sampling design for case (with disease) and purposive sampling design for control (without disease non -case healthy individual) can both design be used?
What is the raison d'être of uninformative priors? Isn't one of the Bayesian goals that of allowing to systematically incorporate prior information into inference?
I am seeking quotes definition of the term taxonomy and systematics. I am looking for definition by Myer and Ashlock 1991.
Between CTAB and QIAGEN DNeasy Mini Kit extraction methods which will produce the cleanest and largest amount of DNA for Araliaceae? I am specifically working with leaf material from Polyscias (Tetraplasandra).
I have found only some of the information and - as I am not familiar with the latest taxonomy - these are quite incomprehensible for me.