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Problems of taxonomy and phylogeny

Community and ForumTaxonomy. ClassificationProblems of taxonomy and phylogeny

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03.02.2010 9:46, bora

No, this is not a duel, but an exchange of opinions.
Likes: 4

03.02.2010 9:49, bora

When PCR, etc. these methods will become more accessible , and such suggestions will probably appear.

This is for sure, where you can cut down money, there will definitely be those who want to.

03.02.2010 10:01, swerig

Dmitry, I want it right away

Yes, I, in principle, agree with everything except this:
I consider the possession of a "butterfly with a passport" to be a very dubious and meaningless achievement. When a person is a "specialist", he does not need a" passport " at all, because he knows (for himself) what it is, and this is enough for him. He looked at the signs described in the literature and he is sure. But not for all "outsiders" it will be convincing. Which sounds cooler - "I have "Elena" ex larva from the type locality ", or "I have a CERTIFIED "Elena""? For an outsider, I think the second is" cooler". A butterfly with a passport is necessary for those who want the collection to be cool, SO THAT NO ONE FINDS FAULT.

1. We have specialists - you can count them on your fingers. weep.gif
2. Not many people have the experience, time, energy and capabilities, although, of course, everyone is trying to improve their level. shuffle.gif
3. None of us collect a collection to show off to our neighbors in the stairwell or for a forum.They collect everything for themselves. Therefore, this is not an ambition, but a desire to add to the collection. Everyone wants to have a good collection, and which way is a personal matter. Someone buys, someone changes, someone catches it himself. All options are acceptable.
Does someone buy paratypes??? But no one shouts that they have them. And no one will pin their passports on a pin and shake them too.
EVERYONE WANTS HIS COLLECTION TO BE "COOL". Just the concept of "coolness" is different for everyone.
If there is a demand , there will also be a supply. Both by paratypes and by "genotypes". yes.gif
4. SO THAT NO ONE FINDS FAULT with my collection - "don't tell me what to do-and I won't tell you where to go" umnik.gif

PS; I don't hit the kidneys (I'm not from the internal organs)- ONLY TO THE LIVER lol.gif lol.gif
Likes: 1

03.02.2010 10:21, swerig

Well, I never sell anything from the material at all, but only give it away or, in extreme cases, change it.

subscribe now!!!

By
the way , I've never sold anything either, and I don't sell anything:) .

Sorry. "Your satires in Crimea are delicious.

03.02.2010 10:54, bora

"Your satires in Crimea are delicious.

So maybe a brotherly throw?
Likes: 2

03.02.2010 10:58, swerig

So maybe a brotherly throw?

This is already a provocation that Pavel doesn't like so much!!! lol.gif

03.02.2010 21:24, palvasru4ko

This is already a provocation that Pavel doesn't like so much!!! lol.gif


Provocation provocation discord. By asking a question, we provoke a person to answer. It is ok. Sin - when it is done with malicious intent (to snub, humiliate). I am against SUCH a provocation. And as for satyrs, I wrote a nickname.

03.02.2010 21:34, palvasru4ko

So maybe a brotherly throw?


You can, but not about Phryne. Don't contact me for this type of information. This is the principle. Don't ask me why.

This post was edited by palvasru4ko - 03.02.2010 21: 35
Likes: 1

03.02.2010 21:40, bora

If in the spring I break out to B. Kalitva-I'll catch phryne.
I caught a lot of it in my time in the Orenburg region.

This post was edited by bora - 03.02.2010 21: 41
Likes: 1

03.02.2010 22:18, Yakovlev

Dmitry, I want to warn you right away – this is not a challenge or a provocation. I'm just expressing my opinion. Patsavatoe, rustic, but what is ... By the way, I'm "for peace"! (maybe it will be counted in the next world smile.gif). My colleagues have already suggested that you can't get very far on genetics alone, and there is something in this... Nature usually does not work on "one line of defense" against other people's genes. It is insured - different genitals, pheromones, biotopes, forage plants, phenology, and possibly the time of day when the species is most active (and why not?), etc. etc. etc. The fact that there are species that are most easily distinguished genetically - I agree. But this is FOR NOW! You can put it another way: other signs either haven't been found YET, or they are known, but they don't know how to use them. An example is Polyommatus elena Stradomsky et Arzanov, 1999. What's a bad example? A double of Icarus, but easily genetically different… The taxon was described, but Bolshakov (it seems to be fair) found fault... In addition, they described the genitals in more detail. Then we collected the material, followed the development at the preimaginal stages, and found distinctive criteria. Published it. And "genetics" of course looked... However, even without genetics, if you want, you can figure it out (thanks to the article by Stradomsky and Fomina, I think EVEN I can distinguish between caterpillars and pupae smile.gif). This is despite the fact that Boris Vitalievich himself also distinguishes Elena by her genitals. And he's not an alien! Just a person "stuffed" and that's it. This comes with experience... One hundred, two hundred, three hundred... thousand. We need time! And it's just him who is most often pitied! Therefore, we are going on an easier path - it's easier to pay 200 bucks for the finished analysis and not worry! And it sounds solid ("PASSPORT"!!!!) and you don't need to grow caterpillars, watch your genitals for hours...
Now about "ambition"… You may not agree, though… This is a forum where some people talk, others disagree. This is good and this is correct (I am "for"...). I'll try to explain my position. EVERYONE who knows something well has ambitions, but some of them are "unhealthy"... Ask - what does this have to do with butterflies? I'll explain. I consider the possession of a "butterfly with a passport" to be a very dubious and meaningless achievement. When a person is a "specialist", he does not need a" passport " of a butterfly, because he knows (for himself) that this is, for example, all the same "ELENA" and this is enough for him. He looked at the signs described in the literature and he is sure. But not for all "outsiders" it will be convincing. Which sounds cooler - "I have "Elena" ex larva from the type locality ", or "I have a CERTIFIED "Elena""? For an outsider, I think the second is" cooler". A butterfly with a passport is necessary for those who want the collection to be cool, SO THAT NO ONE FINDS FAULT. That's what I meant when I talked about ambitions, like " my collection is the most correct, all with passports, and you don't know what." NOTHING PERSONAL! I'm not trying to "tease" or denigrate anyone. Having a butterfly with a passport is like having a holotype or paratypes. Holotype (paratype) - COOL!!! After all, then exactly-THIS type (although, there are incidents). Plus, the standard series implies a limited number of instances. A RARITY!!! Why does a collector need a holotype (paratype)? Taxonomists need it. The collector needs a COPY. And you can exchange (or buy) a copy if you can't (or don't want to) go, and sometimes even from a typical area (or near it) - and you don't need a paratype for three hundred years. What does HAVING a paratype DO? Well, if you put your hand on your heart - WHO needs paratypes? TAXONOMISTS! Who is SERIOUSLY involved in taxonomy? After all, there are catastrophically FEW of them!!! It is the same with the "passport"... The possession of a butterfly with a passport is not mandatory, if only because if the taxon cannot be distinguished EXCEPT by genetic data, its validity will STILL be questioned from time to time. It is necessary to look for signs (no matter at what stage of development) by which you can distinguish a species without "genetics", if not by eye, then at least under binoculars... Otherwise, ALL reports, determinants, and articles are worthless. And why are they needed, if only genetics "rolls"? If Mr. Stradomsky distinguishes Elena from Icarus, I think others will also learn IF THEY WANT to. He (Stradomsky) does not make secrets from the signs – everything is described by him and in some detail.
I may have signed my own death warrant, but while I'm still alive, I want to note that those who want to engage in the" passport business "on the contrary, it is profitable to insist on the" mystery " of the species and incredible difficulties in identification. Given the stated price, this is steeper than trading paratypes (they are cheaper) or gynandromorphs (they are few).

P.S. On the kidneys chur not to beat!

If I have a post-graduate program, I invite Mr. Ruchko to take part in a part-time post-graduate program. From myself - I will try to make it work for me

03.02.2010 22:24, palvasru4ko

Herr Reisininger (our colleague with Frost and Ruchko, by the way, is a psychiatrist) I still haven't figured it out...


I think I need to clarify something-Ruchko is not a psychiatrist, but a pediatrician. Here's the confession:
http://molbiol.ru/forums/index.php?showtop...dpost&p=1000663

03.02.2010 23:59, palvasru4ko

If I have a post-graduate program, I invite Mr. Ruchko to take part in a part-time post-graduate program. On my own behalf, I'll try to make sure I have it


I'm very flattered, but I don't think it's necessary...
I am a "lone wolf" smile.gif

04.02.2010 15:43, swerig

  
I'm a "lone wolf" smile.gif

In general,- respect for communication.
Everything is weighed, justified and clearly reasoned. It's nice to communicate. beer.gif

04.02.2010 15:52, Yakovlev

I'm very flattered, but I don't think it's necessary...
I'm a "lone wolf" smile.gif

Postgraduate studies are different.
1. A person is told to do this and that... And it will turn out se...
2. A person is told to do whatever you want, but we will formulate it better and help you in any way we can.
Although you have Yefetov there...
Likes: 1

04.02.2010 16:01, palvasru4ko

In general,- respect for communication.
Everything is weighed, justified and clearly reasoned. It's nice to communicate. beer.gif


Thank you, of course, but do not forget-the forum is a written thing, that is, a person has time to think, come up with it... One biologist, Korolev, worked at our university. The rector once said about him-Vitaly Alexandrovich is a very silent person, but this is only because he has something to say. So - don't exaggerate! Zazanayusya still! smile.gif

04.02.2010 16:48, swerig

Thank you, so don't exaggerate! Zazanayusya still! smile.gif

And this - we will quickly fix lol.gif

11.05.2010 14:24, Dracus

An excellent article on (to put it mildly) problems in modern phylogenetics, which is rapidly moving towards ignoring morphology and the cladistic method in general. It is written, however, by ichthyologists, but the trends are common in all groups.

http://www.mapress.com/zootaxa/2010/f/zt02450p040.pdf

Sure enough, it's time to stop this madness...
Likes: 3

18.06.2010 23:39, Aleksey Adamov

I couldn't read everything here…

Therefore, I just want to express my opinion about the "species" and morpho / genetic criteria of the "species".

In my opinion, in the topic of "species", there is a methodological problem, and not a zoological-botanical-protistological-...-microbiological one.
This is supported by the fact that with each fact obtained by a morphologist or molecular geneticist, the problem of the "species" only gets worse. This is a sure sign of the wrong Concept of "view"!

The second and third concerns the objectivity of the methods of morphologists and geneticists. The former have been talked about a lot for a long time, and the latter have been talked about less... but their time will come.
A few years ago, I asked a young but very good specialist geneticist (our Department of Genetics) about the applicability of these methods in taxonomic studies. In particular, I asked him how they can be used to identify a double species. He replied: "nothing" (as I suspected).
Since then, I have been skeptical about these methods. I admit that they can seriously help morphologists. But to reduce to synonyms, or to describe new taxa, pure molecular genetics...!!!???
Rather early. So far, " they write with pitchforks on water."

26.06.2010 18:47, bora

A few years ago, I asked a young but very good specialist geneticist (our Department of Genetics) about the applicability of these methods in taxonomic studies. In particular, I asked him how they can be used to identify a double species. He replied: "nothing" (as I suspected).

Yes, there is not a single geneticist at Rostov University who is at least somehow engaged in the application of molecular genetic methods in relation to solving taxonomic issues. And what you were told-indicates the incompetence of this young specialist in this matter.
You would rather read Lukhtanov's work, or at least go to the Academy and consult Arzanov - he is aware of the latest scientific achievements.

This post was edited by bora - 26.06.2010 18: 53

26.06.2010 23:03, Aleksey Adamov

Yes, there is not a single geneticist at Rostov University who is at least somehow engaged in the application of molecular genetic methods in relation to solving taxonomic issues. And what you were told-indicates the incompetence of this young specialist in this matter.
You would rather read Lukhtanov's work, or at least go to the Academy and consult Arzanov - he is aware of the latest scientific achievements.


Maybe.

I searched the Web for Lukhtanov's work. I found these links:

1. Lukhtanov V. A. FROM HAECKEL'S PHYLOGENETICS AND GENNIG'S CLADISTICS TO THE MAXIMUM LIKELIHOOD METHOD: OPPORTUNITIES AND LIMITATIONS OF MODERN AND TRADITIONAL APPROACHES TO PHYLOGENETIC RECONSTRUCTION// Entomological review. 2010. Vol. LXXXIX, No. 1, pp. 133-149

2. V. A. Lukhtanov, N. A. Shapoval IDENTIFICATION OF SYMPATRIC TWIN SPECIES OF BUTTERFLIES FROM THE COMPLEX AGRODIAETUS KENDEVANI (LEPIDOPTERA, LYCAENIDAE) USING POPULATION ANALYSIS OF UNCOUPLED GENETIC MARKERS / / Doklady Akademii nauk, 2008, vol. 423, issue 3, pp. 421-426.

3. V. A. Lukhtanov, V. G. Kuznetsova. MOLECULAR GENETIC AND CYTOGENETIC APPROACHES TO THE PROBLEMS OF SPECIES DIAGNOSTICS, TAXONOMY AND PHYLOGENETICS / / ZHOB. 2009, Vol. 70, Issue 5, PP. 415-437.


Are these works enough to understand the essence of the method, or are there other and more accessible ones?

If you have these works in electronic form, I would be very grateful if you would share them.

P.S.
I don't want to bother Arzanov. It's not easy to catch it, and it's usually busy.

27.06.2010 5:05, bora

In these works, everything has already been said. But this is the tip of the iceberg. Another thing is that you may need to delve into concepts of a more general nature, the basics of, say, molecular biology.
It is easier, of course, to explain in words: faster, more accessible, and there is feedback. So if Arzanov is so busy, you can talk to me. Moreover, even though I live in Rostov, but I have a factory in Azov and I visit there from 6 am almost every day. You're based in Chumbur Kos, aren't you?" But only from September, because soon I have to leave for the Teberdinsky reserve.
Likes: 1

09.10.2010 5:27, Proctos

Hehe, here's a fresh review.
It may come in handy, get a drink of water, well, as they say...

Ronquist, F. & A. R. Deans. 2010. Bayesian phylogenetics and its influence on insect systematics. Annual Review of Entomology 55: 189-206
http://www.annualreviews.org/doi/pdf/10.11...4.110807.090529

This post was edited by Proctos - 09.10.2010 05: 33

09.10.2010 10:09, amara

Hehe, here's a fresh review.
It may come in handy, get a drink of water, well, as they say...

Ronquist, F. & A. R. Deans. 2010. Bayesian phylogenetics and its influence on insect systematics. Annual Review of Entomology 55: 189-206
http://www.annualreviews.org/doi/pdf/10.11...4.110807.090529


Is it possible to get the full text?

I'm answering the question smile.gifmyself , right here

http://people.sc.fsu.edu/~fronquis/mrbayes...RevEnt_2010.pdf

This post was edited by amara - 09.10.2010 10: 46
Likes: 3

09.10.2010 15:21, Proctos

It would be nice if someone posted
Lukhtanov V. A. FROM HAECKEL PHYLOGENETICS AND HENNIG CLADISTICS TO THE MAXIMUM LIKELIHOOD METHOD: OPPORTUNITIES AND LIMITATIONS OF MODERN AND TRADITIONAL APPROACHES TO PHYLOGENETIC RECONSTRUCTION// Entomological review. 2010. Vol. LXXXIX. No. 1. pp.
133-149 Thank you in advance!

10.10.2010 5:11, bora

Lukhtanov V. A. FROM HAECKEL PHYLOGENETICS AND HENNIG CLADISTICS TO THE MAXIMUM LIKELIHOOD METHOD: OPPORTUNITIES AND LIMITATIONS OF MODERN AND TRADITIONAL APPROACHES TO PHYLOGENETIC RECONSTRUCTION// Entomological review. 2010. Vol. LXXXIX, No. 1, pp. 133-149

Posting it

This post was edited by bora - 10.10.2010 05: 31

File/s:



download file From_Haeckel_s_Phylogenetics_and_Hennig_s_Cladisticics.pdf

size: 6.19 mb
number of downloads: 1022






Likes: 8

10.10.2010 5:33, plantago

Good article, thank you!

10.10.2010 5:42, plantago

Here in DjVu (with OCR, that is, with the ability to search for text): http://rghost.ru/2869921
Likes: 3

20.01.2011 15:12, lepidopterolog

Of course, a lot of work has been done, but I don't understand how you can conduct taxonomic revisions, and even at the level of higher taxa, completely ignoring morphology and anatomy? It is high time to fix in the Code the inconsistency of nomenclature acts based only on ethics.

20.01.2011 15:22, rhopalocera.com

I will say in one word: a mess.
Likes: 1

20.01.2011 18:58, Vlad Proklov

Of course, a lot of work has been done, but I don't understand how you can conduct taxonomic revisions, and even at the level of higher taxa, completely ignoring morphology and anatomy? It is high time to fix in the Code the inconsistency of nomenclature acts based only on ethics.

You wrote something stupid, Tolya: first, the Code will prescribe that it is impossible to publish nomenclature acts on the basis of habit - and then that on the basis of differences in genitalia (and who said that they are more important than genes?). But, fortunately, our ramsTM are not included in the ICZN.

Science differs from the General Line in that it allows a wide variety of points of view to be heard, and the public decides what will take root and what will not. Pluralism.

This post was edited by kotbegemot - 01/20/2011 18: 59
Likes: 4

21.01.2011 3:03, А.Й.Элез

Vladislav, Anatoly, in my opinion, has the word "only"; even judging by the controversy in another topic, this reservation is quite enough at least to insure against accusations of stupidity, especially if we are for pluralism, and not for general lines.
Likes: 2

21.01.2011 10:56, rhopalocera.com

Let's not confuse the system and the cladogram. They are not equivalent.

21.01.2011 18:52, lepidopterolog

Vlad, reread my message, its main idea is not at all some manipulation of the Code, but the failure of "naked" molecular methods in taxonomy - as in this case, when the data of morphology, zoogeography are denied (which in this case is very important, IMHO), etc. When I mentioned the Code, I only emphasized it, and there is nothing "stupid" here.
By the way, how can the decision of the "public" in general be related to an objective scientific result?

21.01.2011 19:21, AntSkr

In any case, articles of this kind are based on a probabilistic-statistical approach (you can notice words like maximum likelihood, bootstrap algorithm, etc.), so the conclusions are inherently the result of a certain probabilistic approach. There will be some other model, and there may be other results.

21.01.2011 23:42, Vlad Proklov

Vlad, reread my message, its main idea is not at all some manipulation of the Code, but the failure of "naked" molecular methods in taxonomy - as in this case, when the data of morphology, zoogeography are denied (which in this case is very important, IMHO), etc. When I mentioned the Code, I only emphasized it, and there is nothing "stupid" here.
By the way, how can the decision of the "public" in general be related to an objective scientific result?

No, you don't fucking understand.
Do you think "naked" molecular methods are untenable? Because you think they should be banned using the Code?
In order to deny "naked" mechanics, you will first have to scrap all systematic works based on genitalia and other morphology, because there are generally pure improvisations and a personal vision through.
So no-nonsense.

PS. The reaction of the scientific community determines the current paradigm.

This post was edited by kotbegemot - 21.01.2011 23: 48
Likes: 1

22.01.2011 0:07, Vlad Proklov

Unlike morphology, molecular mechanics have a disadvantage (?dignity?) – non-verifiability (yet).
Visual example - http://molbiol.ru/forums/index.php?showtopic=104216&st=350#
After all, no one checked.

Well, I didn't. So what?
How does this affect the search for Phylogenetic Truth in general?

22.01.2011 5:21, bora

Unlike morphology, molecular mechanics have a disadvantage (?dignity?) – non-verifiability (yet).
Visual example - http://molbiol.ru/forums/index.php?showtopic=104216&st=350#
After all, no one checked.

This is in what place of this link is unverifiability?
If about the message of V. A. Lukhtanov about A. pljushtchi, then just this post fully confirms the VERIFIABILITY of the method. M. Vimers checked and informed Lukhtanov about the error (and just purely technical).

This post was edited by bora - 22.01.2011 05: 23
Likes: 3

22.01.2011 11:24, rhopalocera.com

how does molecular taxonomy account for possible mutations?
what is the minimum reliable sample size for a single sequence?
how are transposons and similar structures taken into account (and are they taken into account at all)?
how is optical and any other nucleotide isomerism taken into account?
how is the chemical purity of samples checked (and whether it is checked at all)? what are the standards for this?
why is the protein-coding sequence selected as species-specific? is this the right choice?
why aren't, say, membrane lipids or mRNAs of the same COI selected?

questions are addressed to Vlad Proklov.

22.01.2011 14:48, lepidopterolog

No, you don't fucking understand.
Do you think "naked" molecular methods are untenable? Because you think they should be banned using the Code?
In order to deny "naked" mechanics, you will first have to scrap all systematic works based on genitalia and other morphology, because there are generally pure improvisations and a personal vision through.
So no-nonsense.

PS. The reaction of the scientific community determines the current paradigm.


Well, don't tell me, normally conducted work on the basis of genitals is never improvisation - if the author is aware of what he is doing-he uses a large sample from different points, highlights normal, really working signs, etc. Ideally, the systematic work should generally be a revision of the group - and not an article describing a subspecies based on a pair of battered butterflies.
What are we arguing about anyway? It is good when molecular data coincide with morphological, zoogeographic, and other data (and there may still be a lot of them - ecology, ethology, karyology, etc. - just for some reason no one uses them, but it should be for objectivity). It's bad when you don't - you need to look for an explanation of why this happens (there may be too many of these explanations, see the list is higher - you can still add a lot of things there), and certainly not build a system on them, ESPECIALLY for higher taxa.

From the point of view of the scientific community, molecular methods are very convenient - for example, in the Canadian center for barcoding, all operations are performed by a robot. Much easier than cooking some bellies, sitting and comparing genitals, etc. It seems that this has played a significant role in the dominance of molecular taxonomy in recent times.

Once again, I would like to emphasize that I am not at all opposed to the use of competent and thoughtful use of molecular mechanics in synthesis with other approaches.
Likes: 3

22.01.2011 16:33, rhopalocera.com

No, you don't fucking understand.
Do you think "naked" molecular methods are untenable? Because you think they should be banned using the Code?
In order to deny "naked" mechanics, you will first have to scrap all systematic works based on genitalia and other morphology, because there are generally pure improvisations and a personal vision through.
So no-nonsense.

PS. The reaction of the scientific community determines the current paradigm.



in the West, the response of the scientific community is determined not by the paradigm, but by the funding of a particular project. is the government pumping money into the public purse? everyone will rush there. and it does not matter that the "specialist" "systematizes" what he has never seen in nature. paper can handle anything smile.gif

I am more surprised by HOW people can be zombified by "new revolutionary methods". Vlad, answer the questions I asked you above. I'm curious to know your unbiased opinion :D. And then I'll throw in two more fun questions wink.gif.

there are only three entomologists whose molecular constructs I trust. these are Lukhtanov, Stradomsky and Kandul. they felt their objects in nature, and two of them have experience in " traditional "(but we use the correct term - "evolutionary") taxonomy. and they don't discount morphology, trophism, etc.etc. this is the only correct approach to biological objects: the more parameters are taken into account, the more complete the picture is.

The message was edited rhopalocera.com - 22.01.2011 16: 34
Likes: 3

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