[Taxacom] [iczn-list] GENERAL CALL TO BATTLE

[Stephen Thorpe]

 Carlos,We agree, I think, on the main point, i.e. DNA-only descriptions have no place in taxonomy and threaten to make taxonomy more difficult for no gain. We seem to differ somewhat regarding our preferred methodology for taxonomy based on morphology. I wouldn't say that making some reasonable assumptions amounts to "doing it wrong"! There is no need to consider Neotropical species when describing a new Afrotropical species, I maintain, for example. The consequences of "getting it wrong" (which will be very rare, as such assumptions to hold most of the time) are just a simple synonymy, not a big disaster! So, let's speed up taxonomy and get names on otherwise undescribed species as quickly as possible, just not by way of DNA sequences accompanied or not by inadequate half-arsed photos or descriptions. A good short morphological diagnosis accompanied with a good illustration is fine, we don't actually need the sequence (but chuck it in if you must), but we certainly don't want to require exhaustive morphological descriptions with comparisons to all other described species of the group on a global scale, that would just slow everything down dramatically for no gain. Note also that one must make the reasonable assumption that there are no described species belonging to the genus under revision currently misplaced in other genera (or else one would have to check and compare with all species in all genera!), so there is always going to be a chance of creating a synonym anyway, so making geographical scope assumptions is really no different.Cheers,Stephen
    On Monday, 15 February 2021, 09:14:22 am NZDT, Admin Admin <archilegt at gmail.com> wrote:  
 
 Hi Stephen,As I also wrote, no matter how many times it has been done wrong, it is still illogical and still wrong. Now we have access to literature, access to copying devices, automatic translation for free. Now we can make synthesis and build character matrices. As for the speciose genera, they can be divided into subgenera and species groups. Also, without the need of named subgroups, with character matrices you can differentiate. We can preserve the names done wrong by the old system on the basis of preserving stability. Now, it was done wrong for morphology, in the past. Shall we allow a new parallel system doing it also wrong? Certainly not. Those new names can be declared unavailable without threatening stability, and molecular but unavailable binomials could still be used for purposes other than Zoological Nomenclature. Ah, but if the BIOSCAN project proceeds with this disregard to differentiating from known species across all Earth, we will end up with 80 million new names yes, accompanied by two million new synonyms. 
Cheers,Carlos

On Sun, Feb 14, 2021 at 9:50 PM Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:

 
Carlos said: "Unlike you, I maintain that "purported to differentiate the taxon” cannot be achieved if comparison with all the currently known taxa has not been made"
I strongly disagree! This is simply not the way that taxonomy has been done over the last couple of centuries. Some reasonable assumptions have to be made, due to megadiverse genera (Megaselia, Agrilus, etc.) and the difficulty in obtaining all the literature (esp. from Russia, China, etc. in the past, and taxonomists cannot be expected to read all languages!)
The usual reasonable assumption that is made is for groups which contain species which are expected not to occur in more than one biogeographical area. If you are describing a new species from Africa, for example, then you don't need to compare it to congeners in the Americas. If, by chance, this assumption turns out to be false for a particular case, then it is not a big disaster! Synonymy is the easy solution.
Cheers, Stephen    On Monday, 15 February 2021, 05:51:01 am NZDT, Admin Admin <archilegt at gmail.com> wrote:  
 
 Hi Thomas,Thank you for your reply. Unlike you, I maintain that "purported to differentiate the taxon” cannot be achieved if comparison with all the currently known taxa has not been made. It does not matter how many species are described from maggots or adults only. It does not matter how many times the fallacious claim of "new" was made. What matters is:1) Determining who was the first in making the fallacious novelty claim and expanding the system towards the new set of characters and character states, e.g., a life stage and its characters, detached from the life stage that was previously used as reference. I assume that the author who did this was not the author who first described both life stages, but a later author who decided that lack of logical comparison would not stop him/her from describing a taxon and claiming it as "new". Authors like Meierotto, Sharkey, and van Achtenberg.
2) Determining when the fallacious novelty claim was first made. Stopping and reversing such claims can be done as long as stability and universality are not affected. In the case of "revolutionary methods" which are less than two years old, the fallacious claims of novelty can be stopped without affecting stability and universality, now, today. However, may such a practice be allowed to continue, the current system of names will be overwritten with a multiplicity of synonyms. 
I cannot speak for other communities, but the myriapodological community would not have the capacity to absorb the impact of molecular names and the hit will overwhelm us. We are still mopping the nomenclatural and taxonomic vandalism that Karl Wilhelm Verhoeff and Ralph Vary Chamberlin left behind decades ago. And yes, by now we are quite sure that they were vandals. Cleaning the mess of synonyms takes considerable effort and funds.I remind you that there are quite a few country-level sequencing efforts which could generate thousands of "new" species names within the next five to ten years. Isn't that their stated objective? If the Commission or some commissioners continue to consider fallacious claims of novelty as available under the Code, they will be responsible for the desolation that those new synonyms will cause. And those of us who live today will die before we can mop the dirty trail of the barcoders. It will take several decades, if it ever gets done. The commissioners must also consider the almost immediate decline that widespread adoption of the new methods and fallacious claims will cause in the already reduced and overburdened taxonomic community. Some taxonomists will quit out of frustration. Others will be considered obsolete and their positions closed when they retire. Others may even be forced by their institutions to follow the trend and produce thousands of new molecular names. The Commission is underestimating the seriousness of this problem. You must step back from "the highly pedantic interpretation of the Code" (something along Rich's wording) and bring some common sense in.
The Commission and commissioners may not be able to fix all logical fallacies, especially the old ones based on morphology, but you can certainly prevent new fallacies from happening or expanding, especially the ones based on barcodes. If your concern about consistency is bigger than the upcoming devastation, then split the procedures and limit availability of new molecular names through the use of the Plenary Powers, until we can put an amendment in place, and until we can formalize mandatory diagnoses in the Code 5.
Again, the Code is a scientific standard and as such fallacious illogical claims of novelty have no place under it.Kind regards,Carlos


On Thu, Feb 11, 2021 at 8:17 PM Thomas Pape <tpape at snm.ku.dk> wrote:


Dear Carlos,

 

You mention that you expect a literal answer to your literal question:

>>>if the commissioners understand logic or not.

The literal answer is: Yes, they do.

 

Let me also make clear, that there is no risk that:

(1) “a molecular paper could claim priority over their own published names”

(2) “there won't be a chance for integrative taxonomy under the current Code”

(3) “the Commission allows names to be overwritten”

 

>>>the logic on when a novelty claim is spurious

In a nomenclatural sense, the following is recognized as explicit intent to establish a new nominal taxon:  “Zelomorpha angelsolisi Meierotto, sp. nov.”

 

What is at stake, and what I find both interesting and challenging, is how to interpret Article 13.1.1 when only molecular data is provided. Every new name published after 1930 must be accompanied by (or point to) a description or definition that states in words characters that are purported to differentiate a taxon. Like this one from the paper by Meierotto et al. (2019):

---------------------------

Molecular diagnosis

Nucleotides 43–45 TTA, 54–57 CTTT, 75 G, 136–138 GTG, 165 T, 321 G, 417 G, 462 G, 477 C, 561 G, 684 G.

---------------------------

Given the information also provided by Meierotto et al. (2019), I read this as an explicit listing of attributes (i.e., specific nucleotides at specific positions), which purport to differentiate the taxon from other taxa with which it is likely to be confused.

 

I see attributes, and I see purport to differentiate.

 

I fully understand your concern, that it is meaningless to differentiate a taxon based exclusively on molecular data from a taxon for which we do not have any molecular data. But that does not change the fact that the name was “accompanied by a description or definition that states in words characters that are purported to differentiate the taxon”.

 

When I describe a species of fly from an adult holotype based on morphology, I cannot differentiate this species from those species that are described from maggots only.

 

I am very well aware, that Article 13.1.1 was written with no thoughts of molecular data, but we cannot use that as an argument for non-compliance.

 

All of this is decoupled from my opinion on taxonomic impediment, scientific quality, etc.

It is strict nomenclature as interpreted from the current Code, and whenever we see shortcomings in the way Articles are written, we should discuss possible improvements for the next version.

 

/Thomas

 

 

From: Admin Admin <archilegt at gmail.com>
Sent: 11. februar 2021 14:52
To: Thomas Pape <tpape at snm.ku.dk>
Cc: iczn-list at afriherp.org; Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [iczn-list] GENERAL CALL TO BATTLE

 

Dear Thomas,

My wording is literal and the questions are meant to determine if the commissioners understand the logic on when a novelty claim is spurious. No one can purport to differentiate when available characters, descriptions, specimens, etc., are neglected on purpose, which is what Meierotto et al. (2019) did. I remind you that Sharkey claimed several times that he saw types and had notes, which he also neglected to use. What I see here is a severe author bias in favor of molecular characters, when the same author has expert knowledge on morphology and access to comparative specimens. And before Michael Sharkey can cry on the rock of the "taxonomic impediment", he shall first explain why dozens of species that are very well described and documented since 2006 in a very long thesis remain unpublished. I do not see that he has used all the resources he had at hand to lower the "taxonomic impediment".

 

In the case of your species, if you provide a diagnosis/discussion in which you explain that you are working on another sex or another life stage, you "purported to differentiate". What you cannot do is to use a whole new set of characters and neglect the morphological ones, when you do have the morphological ones at hand. So, no, I assume that you purported to differentiate and that your case does not apply to Meierotto et al. (2019).

 

I still expect a literal answer to my literal question, because it is essential for this community to know if the commissioners understand logic or not.

 

Now I am going to tell you who is lowering the taxonomic impediment: the myriapodological community. All the new taxa of Myriapoda and Onychophora from last year are already databased. We maintain FIVE databases, for years: The Onychophora Website, ChiloBase 2.0, MilliBase (successor of SysMyr), MyriaLit and Myriatrix. We maintain mailing lists, we maintain a Facebook group, we store and share literature, we make good descriptions and good diagnoses, and we do integrative taxonomy as well. Now, if someone expects me to tell my community that a molecular paper could claim priority over their own published names, and that a molecular paper could strip them off from priority over the species that they are working right now, that person is expecting too much. If I tell them that there won't be a chance for integrative taxonomy under the current Code, well, you may rest assured that the community around two branches of the Tree of Life will detach itself from the current Code. Other communities will follow, for sure. We cannot give morphological and integrative taxonomy a chance if the Commission allows names to be overwritten and names to be produced without diagnosing from the previous. Your choice.

 

Cheers,

Carlos

 

On Thu, Feb 11, 2021 at 2:36 PM Thomas Pape <tpape at snm.ku.dk> wrote:


Hi Carlos,

You ask the Commission:

 

>>> Can anyone claim that 15 species in one genus (Zelomorpha) are new

>>> when they know that there are 52 other species

>>> but they only diagnosed the 15 "new" among them and from the type species,

>>> while neglecting other 51 species on purpose?

 

As this is a question to the Commission, I take it to mean:

“Would those 15 new names be available under the ICZN?”

 

This would depend on the exact wording, but if each of those 15 names were “accompanied by a description or definition that states in words characters that are purported to differentiate the taxon”, then the names would be available given that all other requirements were fulfilled.

 

I have myself described new species of the large flesh fly genus Sarcophaga, knowing that there are at least 20 nominal taxa in that genus, which are based on either a female or a maggot, or where the type material is lost and the description useless. I cannot say whether or not my new species are conspecific with any of those. I may have various reasons that conspecificity is ‘unlikely’, but I usually do not make those explicit. But I always provide “a description or definition that states in words characters that are purported to differentiate the taxon”.

 

/Thomas

 

 

 

 

From: Admin Admin <archilegt at gmail.com>
Sent: 11. februar 2021 10:48
To: Richard Pyle <deepreef at bishopmuseum.org>
Cc: Mallet, James <jmallet at oeb.harvard.edu>;iczn-list at afriherp.org; Thomas Pape <tpape at snm.ku.dk>; Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [iczn-list] GENERAL CALL TO BATTLE

 

Hi Rich,

"As you noted in an earlier post, diagnoses are useful for differentiating a new taxon from previously existing taxa."

Read both diagnoses and descriptions, because they are meant to achieve the same, with a different length. And they are not meant to be "useful", they are meant to be methodologically sound, DIFFERENTIAL from the previous, and SUFFICIENT.

 

"They are somewhat less useful with respect to as-yet unnamed taxa."

That depends on how detailed the diagnoses/description is. And they do NOT have to be differential and sufficient (even less "useful") from yet-unnamed taxa, because that does not affect the core Principle of Priority. It is not previous taxa which should be demonstrably different, but new taxa which should be demonstrably new. Additionally, remember that we already have molecular species with equal barcodes that got finally diagnosed and splitted into two on the basis of non-molecular characters. So, barcodes are also not the universal panacea and morphology continues to play a role, especially for authors with apparent "hyperdiversity goals".

 

"One could easily argue that an image or a barcode is vastly more useful than a text diagnosis because both are more likely to contain information about characters that will help distinguish the new species from both previously known *and* as-yet unknown species."

You continue to use "vastly", which is a particular judgement of value from your side. The word "vastly" is mentioned ZERO times in the Code. You continue to use "useful", which is not a qualifier that we are discussing here. The word "useful" is mentioned ONCE in the Code, in the preface to the Fourth Edition, which is NOT part of the Code proper. What we are discussing here is the methodological obligation to diagnose differentially and sufficiently from the previous. That is not achieved by CHARACTERIZING with pictures and barcodes. That is achieved by practicing the methodological exercise of DIAGNOSING, i. e., COMPARING. A methodologically sound comparison contains equal, shared elements among the taxa compared. This is achieved, for two species, by making reference to the genus. A methodologically sound comparison contains differential elements which are not shared among the taxa compared. This is achieved, for two species, by presenting the sufficient diagnostic character state of the new species, or the combination of characters which combined provide a sufficient, differential diagnosis. Regarding "yet-unknown" species, again I remind you that the Code is framed with the Principle of Priority and not with a "Principle of Futurity".

 

"One could easily argue"

As per the explanation above, your easy argument has been easily nullified.

 

"What is more powerful: a text description that my new species has a longer snout than that other species?  Or an image of both snouts, without any text commentary?"

Apply the same reasoning that I applied to "useful". You can use it as a particular judgement of value from your side, but it is mentioned ZERO times in the Code. Apply the rest of my previous argument. This is not about "useful" and "powerful". This is about the methodological obligation to diagnose differentially and sufficiently from the previous.

 

"Or in the case of DNA barcodes, which is more powerful:  a text description that “my new species differs from that other species on the basis of 27 differences in the barcode sequence”; or simply providing the two barcode sequences without any commentary on the differences?"

The former will give you both the barcodes AND the comparison, and it will achieve SUFFICIENCY and DIFFERENTIATION FROM THE PREVIOUS. The latter is inadmissible on methodological grounds, because it fails to exercise COMPARISON and therefore DIAGNOSIS. You continue equate CHARACTERIZING with DIAGNOSING, but it is only the latter which methodologically satisfies the PURPOSE OF DIFFERENTIATING.

 

Now Rich, as I provided the context of Meierotto et al. (2019), and as I have provided profuse methodological explanations, I am going to repeat my direct question to you (and to all the Commissioners): Can anyone claim that 15 species in one genus (Zelomorpha) are new when they know that there are 52 other species but they only diagnosed the 15 "new" among them and from the type species, while neglecting other 51 species on purpose? Can someone claim that those 15 species are new? Do you support that claim? Was letting that claim pass a reviewer and an editorial mistake or not?

Please, do not attempt to dodge my direct question this time. Not you, not the other Commissioners. I am very much looking forward to your answers.

 

I will proceed by explaining what is going to happen if the Commission fails to stop the ongoing nomenclatural vandalism and if it fails to declare the recent fallacious claims of novelty unavailable under article 13.1.1 of the Code.

First, the Commission will be failing in securing an organized transition from one diagnostic character set to another. Second, the Commission will be failing to recognize the necessary role of integrative taxonomy during the transition time, which is meant to secure that 250+ years of morphological knowledge for 10% of the species is integrated into the upcoming, molecularly diagnosed 90% of species.

As the Commission will fail to the broader taxonomic community, those particular taxonomic communities who disagree on having their morphological knowledge overwritten by a parallel molecular nomenclatural system will split apart from the current ZooCode. I will assist those communities myself, and I am sure that many more taxonomists with good knowledge of the Code will respond to the call of duty. Community after community, we will abandon consensus and we will regroup together. The Commission and the molecular taxonomists who want to stay will be left with the "Molecular Code of Zoological Nomenclature", and the rest of us will build consensus about the same Code, the "Integrative Code of Zoological Nomenclature". We will form a new Commission, arbitrarily set the publication date of Meierotto et al. (2019) as 31 December 2019, and arbitrarily set 30 December 2019 as the date of the split of the broader taxonomic community. We will adopt the current Code, we will declare unavailable those molecular works which fail to differentiate from the previous, and we will strengthen Article 13.1.1 and secure a period of integrative taxonomy and a smooth transition to molecular diagnoses. The Integrative Code will rule over 100% of the described species, except for ca. 500 molecular Hymenoptera species.

If the Commission thinks that the broader taxonomic community is going to sit and watch how our names are overwritten and how our corpus of knowledge disregarded, you are very much mistaken.

 

Kind regards,

Carlos

 

 

On Thu, Feb 11, 2021 at 8:14 AM Richard Pyle <deepreef at bishopmuseum.org> wrote:


Hi Carlos,

 

Thank you for the expanded explanation of where you are coming from on this.  What you say makes sense, even though I disagree with some of your positions. Also, I think I was not clear in the point I was trying to make.  I’ll continuing playing the role of devil’s advocate.

 

As you noted in an earlier post, diagnoses are useful for differentiating a new taxon from previously existing taxa. They are somewhat less useful with respect to as-yet unnamed taxa. With something like 90% of biodiversity in the latter category (i.e., as-yet unnamed), we’re kidding ourselves if we think that some sort of textual word-based assertion of character differences with the already-known 10% of taxa someone improves the “robustness” of a new species description.

 

One could easily argue that an image or a barcode is vastly more useful than a text diagnosis because both are more likely to contain information about characters that will help distinguish the new species from both previously known *and* as-yet unknown species.  Sure, the text diagnosis might accidentally include characters or combinations of characters that hep distinguish from future new species.  But there’s a reason I was always taught to examine the types of known species – to make sure that the suite of characters I’m using to distinguish my new species are legit (and not missing from the previous text diagnosis of the previous species, or based on differences in measurement techniques, or whatever).

 

What is more powerful:  a text description that my new species has a longer snout than that other species?  Or an image of both snouts, without any text commentary?  Having only the words tells us only about the relative snout length. Having the images shows us that, in a potentially quantifiable way, and probably shows us a whole bunch of additional characters that might prove useful for distinguishing my new species from future as-yet unknown species.  Or in the case of DNA bar codes, which is more powerful:  a text description that “my new species differs from that other species on the basis of 27 differences in the barcode sequence”; or simply providing the two barcode sequences without any commentary on the differences?  In the latter case, the differences are self-evident from simply comparing the two sequences. And so are he positions of the differences.  And so are all the other positions in the entire barcode for comparing to as-yet unknown future species.

 

Sure, the best thing to do would be to show the pictures *and* point out the differences *and* provide the sequences *and* identify, using words, which positions of the sequence differs.  That’s good (better) taxonomy, of course.  But the point is that, a compelling case can be made that providing the raw data (hence allowing for comparisons with future species) is superior than explicit statements about specific characters that happen to distinguish a new species from previously described species.

 

I hope it’s clear that I’m not trying to say your wrong.  In fact, I personally agree with a lot of what you say (though not all).  I just want to illustrate that a “call to battle” might be a bit overkill on this issue; and instead a reasoned discussion about alternative approaches to establishing new species.

 

Above all, I do not want to discourage these debates – quite the opposite!  Now is *exactly* the time to be having these discussions, because the ICZN very much wants to get input on what the community would like to see in the next (5th Edition) of the Code.  The Code is not for the benefit of the Commission; it is for the benefit of all taxonomy, biology, science, humanity, etc.  It’s important to come up with a Code that both respects historical practice and accommodates trends that apply to the future (and the other ~90% of the world’s species that are yet to be named…)

 

Aloha,

Rich

 

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Director of XCoRE

Bernice Pauahi Bishop Museum

1525 Bernice Street, Honolulu, HI 96817-2704

Office: (808) 848-4115;  Fax: (808) 847-8252

eMail:deepreef at bishopmuseum.org

BishopMuseum.org

Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

 

From: Admin Admin <archilegt at gmail.com>
Sent: Wednesday, February 10, 2021 4:27 PM
To: Richard Pyle <deepreef at bishopmuseum.org>
Cc: Mallet, James <jmallet at oeb.harvard.edu>;iczn-list at afriherp.org; Thomas Pape <tpape at snm.ku.dk>; Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [iczn-list] GENERAL CALL TO BATTLE

 

Uppercase letter used for stylization of text and not for shouting

 

So here came Rich with a "one-line morphological diagnosis":

Rich: “my new taxon differs from that other existing taxon in that mine has a longer snout”

Well, yes, that is a methodologically correct DIFFERENTIAL DIAGNOSIS, which hopefully is also SUFFICIENT to differentiate both taxa in question. And it does fulfill "the requirement that authors must describe in words the characters purported to differentiate the taxon when proposing new names". And it also fulfills the logical requirement of "differentiating from the previous", in this example the previous taxon with the shorter snout.

 

WHAT IS NOT A DIFFERENTIAL DIAGNOSIS:

1) A "high-resolution photograph of the type" per se

2) A "DNA barcode of the type", when there are no barcodes for the vast majority of congeneric species and a comparison with the previous species is not made

 

THIS IS A PROBLEM OF DEFINITION:

<Rich>"the latter two are"</Rich>   NOT   <Rich>"VASTLY more useful in diagnosing the taxon"</Rich>   because CHARACTERIZING IS NOT DIAGNOSING.

 

More about diagnoses:

1) Morphological diagnoses do NOT stand in the air. They stand within a classification, and they inherit the characters of the upper hierarchies. So, Scolopendra morsitans inherits the characters of Arthropoda, Myriapoda, Chilopoda, Scolopendromorpha, Scolopendridae and Scolopendra, unless otherwise stated at the species rank or above. That is ANCHORING.

2) Authors are meant to create a SUFFICIENT diagnosis for a given taxon, shorter or longer, which purports to differentiate that taxon from the closely related taxa. In the case of a species, it can be differentiated from other species in the genus, or subgenus, or from a smaller aggregate of species. That is PURPOSE TO DIFFERENTIATE. Differentiation can be achieved by means of just one character state of one character, the so-called SUFFICIENT CHARACTER STATE, or it can be achieved by CHARACTER STATES WHICH COMBINED ARE SUFFICIENT to differentiate the taxon

 

This is a one-line diagnosis for Scolopendropsis duplicata: With 39 or 43 leg-bearing segments. The binomen provides ANCHORING to a genus in which all known species have 21 or 23 leg-bearing segments and PURPORTS TO DIFFERENTIATE the new species by using the character state “39 or 43 leg-bearing segments”, which is SUFFICIENT for separating the new species from all previously known species in that genus. This can be done because the full set of character states of a character has been scored for all species in the genus.

 

What the enthusiasts of barcoding are trying to do is to use an incomplete set of character states for one character which has not been scored for all species in one genus. And they still pretend to claim priority under the Code over the names of new species proposed using that method, even when they recognize that additional species exist which have not been molecularly surveyed. That means that the purpose of "differentiating from the previous" and Article 13.1.1 cannot be considered as satisfied, unless that we all suddenly become blind to logical fallacies. Something cannot be claimed to be "new" and "differentiated" when a comparison has not been made. Amusing that I have to explain this.

 

If and only if a full set of barcodes is completed for a given group, the logical fallacy will exist no more, as all species would have a full set of barcodes, and new species could be DIFFERENTIALLY AND SUFFICIENTLY DIAGNOSED FROM THE PREVIOUS ONES. Taxa with full sets of barcodes could migrate to barcode diagnoses.

 

Differential barcode diagnoses do not pose a major methodological problem. In Myriapodology, we used the methodology already EIGHTEEN YEARS AGO, for mitochondrial 16S RNA, because yes, not everything in this world is COI. Undoubtedly, this is just one of many options. And I very much encourage everyone to read that paper and see how the diagnostic nucleotide changes for each species were summarized in figure 5, page 520.

-----------------------

Molecular diagnosis of putative Anadenobolus species
Nucleotide substitutions that are diagnostic for each species were determined using the character trace function in the computer program MacClade (Maddison and Maddison 2000). Because we are only interested in three nodes that are found in all recovered trees (see Results), tree choice was unimportant. Therefore one of the most parsimonious trees was chosen at random from the set of all equally parsimonious trees reported in Bond and Sierwald (2002b, fig. 2). All nucleotide substitutions were plotted onto this tree using the ‘Trace All Changes’ function with the ‘Unambiguous Changes Only’ option selected. Only those character-state changes that were non-homoplasious above the node of interest are used to diagnose species.
However, substitutions that appear in other regions of the phylogeny are considered (we differentiate between the two below).
Each species diagnosis lists the character state (nucleotide) followed parenthetically by the nucleotide position number. The position number refers to the nucleotide position in the fully aligned data set used in this study. A reference alignment of all three species is available in electronic form on request from the first author and for download athttp://core.ecu.edu/biol/bondja and is also available as Accessory Material from the journal’s website. We adopt this approach because the region of 16S sequenced is highly variable and is not easily aligned to commonly cited model arthropod genomes (e.g. Drosophila yakuba, Clary and Wolstenholme 1985).

 

Reference: Bond, J. & P. Sierwald. 2003. Molecular taxonomy of the Anadenobolus excisus (Diplopoda:Spirobolida:Rhinocricidae) species-group on the Caribbean island of Jamaica. Invertebrate Systematics 17 (4):515-528.https://www.researchgate.net/publication/253260124

-----------------------

 

And before someone brings up the topic, diagnoses are short descriptions and descriptions are expanded diagnoses. However, given the apparent lack of logic and methodology that has brought us to this historically low point, it would be advisable that SUFFICIENT, DIFFERENTIAL DIAGNOSES are made mandatory as soon as possible, in an Amendment to the Code, to prevent that the purpose of differentiating from the previous continues to be vandalized. It would also be most advisable to set an example by declaring recent fallacious claims of novelty unavailable under article 13.1.1 of the Code.

 

Kind regards,

Carlos

 

 

 

 

On Thu, Feb 11, 2021 at 3:19 AM Admin Admin <archilegt at gmail.com> wrote:


The phrase means nothing else to me than its literal meaning. And as I cannot sleep, I will proceed to explain one of the methodological problems that is causing all this and that is also present in the previous email by Rich.

 

On Thu, Feb 11, 2021 at 3:07 AM Richard Pyle <deepreef at bishopmuseum.org> wrote:


> “Good people on both sides!” Now where have I heard that before?

Yup... hence my comment about it being "a very notorious statement in another context"...

Aloha,
Rich




_______________________________________________
iczn-list mailing list
iczn-list at afriherp.org
http://list.afriherp.org/mailman/listinfo/iczn-list

_______________________________________________
iczn-list mailing list
iczn-list at afriherp.org
http://list.afriherp.org/mailman/listinfo/iczn-list

_______________________________________________
iczn-list mailing list
iczn-list at afriherp.org
http://list.afriherp.org/mailman/listinfo/iczn-list