[Taxacom] Describing genera without molecular phyolgies

Sat May 23 12:10:06 CDT 2020

Always corrections to be made - I think that is the essence. I've seen that
in both molecular and macro morphology. Just hope journal editors
appreciate that and that science benefits from a multi-perspective approach.

John Grehan

On Sat, May 23, 2020 at 12:17 PM Robert Zuparko <rz at berkeley.edu> wrote:

> I agree 100% with that article. Yes, not using molecular data MAY lead to
> faulty results, but using it doesn't guarantee correct results either. In
> this day and age of reduced funding for taxonomy, and fewer and fewer
> people around who can confidently identify the fauna of a region, we do NOT
> need more impediments for people who can publish decently researched
> papers, even if (heaven forfend!) they are based solely on morphology. Let
> us get the knowledge out to our peers WHILE WE STILL CAN. If mistakes later
> become evident, fine, they can be corrected then  - there will ALWAYS be
> corrections to be made in the future as our knowledge progresses,
> regardless of morphological or molecular basis.
>
> -Bob Zuparko
>
> On Fri, May 22, 2020 at 6:38 PM John Grehan via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
>> Since I do that all the time I am in some sympathy with the extracted text
>> below of a fairly recent article. Thought it might be of interest to
>> others
>> who may not be aware of it.
>>
>> John Grehan
>>
>> BARNA PÁLL-GERGELY 2017 Should we describe genera without molecular
>> phylogenies? Zootaxa 4232 (4): 593–596
>>
>> For nearly a decade I have published species descriptions and revisions of
>> land snails in peer- reviewed journals. As a systematist, it is often
>> requisite to reclassify species into other, sometimes unnamed genera.
>> Although in most cases editors and reviewers have not commented on the
>> taxonomic changes I have made and the new taxa I described, I sometimes
>> received negative critiques when I described new genera unaided by
>> molecular phylogenetic support. I feel these critiques have become
>> increasingly more frequent, and am convinced that many fellow taxonomists
>> share this experience. Addressing this problem is particularly difficult
>> due to three reasons. First, it is impossible to support these
>> observations
>> with statistical data (i.e. the frequency of similar reviews increasing or
>> not); second, the increasing number of published phylogenetic works
>> reveals
>> more and more cases of polyphyletic genera, which might suggest that
>> morphology-based generic grouping is unreliable, and thus, should be
>> avoided; and third, no publications exist suggesting not to describe
>> genera
>> using (still) reliable morphological foundations. Subsequently, the
>> unsatisfactory review process of taxonomic works is often exacerbated by
>> the biases of reviewers and their inobservance of valuable historic
>> convention in light of the current wave of molecular phylogenies.
>> Moreover,
>> the future value of morphological descriptions for biodiversity
>> assessments
>> (i.e. IUCN) is not even addressed. Here, I argue against prohibiting
>> descriptions of genera without phylogenetic support, and make suggestions
>> how editors and reviewers should handle "phylogeny-free" genus
>> descriptions. To illustrate my experience, I quote some text from previous
>> reviews and editorial comments that I have received: Editor of a taxonomic
>> journal, (07.02.2012). "(...) In particular, I need you to provide much
>> more information regarding your decision to erect new genera; as of now
>> you
>> provide no rationale, and you must fully defend this approach. I frankly
>> would feel much more comfortable if you had corroborating DNA sequence
>> analyses to demonstrate that these are not simply subgenera or even simple
>> groups within already existing genera -- and you have not even minimally
>> done this. There is a strong burden of poof to undertake such splitting,
>> and I expect these decisions to be clearly reasoned and proved with
>> empirical data. If you cannot do this, then I strongly suggest that you
>> place your new taxa into already existing generic entities." Anonymous
>> reviewer (02.11.2016). "(...) As for the description of a new subgenus, I
>> am strongly opposed to this taxonomic proposal. Taxonomy serves three
>> possible purposes: (1) the ego of the author, (2) the human desire to
>> classify things, (3) the scientific purpose to conceptualize ideas about
>> the evolutionary relationships amongst organisms. The only purpose this
>> new
>> subgenus serves is 1. (...) As for purpose 3, attempting to conceptualize
>> the evolutionary relationships of species, this decision is even worse.
>> Inevitably, you are making a statement about the evolution of this group
>> and you imply that one species is the sister group of all other species
>> combined based on one character. You have a one in six chance that you are
>> right because your treatment is not backed up by any phylogenetic
>> analysis." Anonymous reviewer (23.11.2016) "(...) The taxonomic
>> description
>> of the new species is also good. However, in the absence of molecular
>> sequence data, I consider that there are insufficient grounds for erecting
>> a new genus. (...) As taxonomists living in the 21st century we have a
>> responsibility to investigate the phylogenetic basis of
>> historically-erected genera and sub-genera by the combined study of
>> morphological and molecular data. This is often not possible because of
>> limited funding, and so the best course when describing species new to
>> science is to work with existing generic and sub-generic names and to
>> avoid
>> contributing to taxonomic instability by creating new generic level taxa
>> purely on the basis of a few shell characters." 594 · Zootaxa 4232 (4) ©
>> 2017 Magnolia Press PÁLL-GERGELY In the first case, my proposal to erect
>> new pulmonate land snail genera was based on shell and genital anatomical
>> characters, whereas in the latter two cases, I attempted to describe new
>> (sub)genera based on differences of the breathing tubes, a traditional
>> approach used in the respective land snail groups (Kobelt, 1902). In other
>> words, 30–200 years ago the scientific community would not have questioned
>> the establishment of these new genera based on morphology. Naturally,
>> without knowing the background of the above examples, it is not possible
>> to
>> form an opinion whether I was right or wrong when I tried to erect new
>> genera, although this is not my point here. Instead, I aim to show that
>> the
>> preference of existing generic names over erecting new genera is strong.
>> Are the reviewers right? Strictly speaking, the reviewers, who disapprove
>> and forbid morphology-based genera may be right. "How do I know that they
>> are really monophyletic?" We cannot know whether a taxon is monophyletic
>> without a proper phylogeny. To investigate this question we have to go
>> back
>> to the definition of the genus. If we define a genus as "a group of
>> species
>> that are more closely related to one another than they are to any species
>> assigned to another genus" (Wood & Collard 1999: 201), then only an
>> appropriate phylogeny would provide satisfactory evidence, although a
>> hypothesis of monophyly based on morphology should be also acceptable. If
>> we define a genus as a group of species defined by apomorphic character
>> states, morphology is sufficient. Regardless of generic definitions or
>> criteria, which are usually not given in genus descriptions, monophyly of
>> genera is, or at least should be assumed (Ebach et al. 2006) (although
>> species are not necessarily monophyletic; Schluter & Nagel 1995, Nosil et
>> al. 2002). The level of provided supporting evidence should be up to the
>> journal's policy and the taxonomists' personal preference. In the vast
>> majority of species descriptions, no species criteria are specified.
>> Unlike
>> genera, describing species without molecular support appears acceptable.
>> Species criteria (e.g. presence of reproductive barriers) are mostly
>> assumed rather than tested in species descriptions. On the contrary,
>> assuming monophyly is deemed to be insufficient by some members of the
>> taxonomic community. The reason for this double standard is puzzling.
>> Especially since one might encounter larger difficulties handling synonyms
>> of species than those of genera. Reviewers suggesting not to describe
>> phylogeny-free genera supposedly aim to minimize the subjectivity of
>> taxonomy caused by the never-ending battle of lumpers and splitters. This
>> goal is admirable. However, taxonomy is a science, and all new taxa that
>> are proposed are hypotheses that can be refuted and falsified (Evenhuis
>> 2008). Not always a matter of money Although molecular phylogeny becomes
>> an
>> everyday tool for some proportion of professional taxonomists, it is not
>> available for many researchers due to the lack of funds. Moreover, in
>> Europe, 60 % of new taxa are described by nonprofessionals (Fontaine et
>> al.
>> 2012), who have nearly no chance to support their taxonomic decisions with
>> molecular phylogeny. However, the lack of funds and limited access to
>> molecular laboratories explain only a fragment of cases when molecular
>> phylogeny could not be performed. In many cases it is not possible to
>> perform phylogenetic analysis due to a number of other reasons. For
>> example, the absence of specimens in museum collections potentially
>> containing DNA (e.g. empty mollusc shells and wrongly preserved historical
>> specimens; see Jaksch et al. 2016); type localities of species described
>> centuries ago are not precise enough to allow revisiting the original
>> sites; the original sites are destroyed and the targeted species might be
>> extinct in the wild; not to mention fossil taxa, which also need to be
>> placed in the system obviously without molecular support. Furthermore,
>> molecular studies that propose new taxa should also return to
>> morphological
>> characters in light of the molecular phylogenetic trees. More
>> repercussions
>> than merits Genera, irrespective of the fact that they are "old" or "new",
>> are testable hypotheses of monophyletic groups that predict the
>> distribution of characters (Platnick 1979; Wheeler 2004). In the absence
>> of
>> molecular support, I cannot see a good scientific reason to prefer
>> existing
>> genera over new genera. The action of placing a species into a genus
>> irrespective of being named or not, is a hypothesis of the species'
>> evolutionary history. Describing new, morphologically well-defined genera
>> is not "unnecessary splitting", but small steps towards understanding
>> evolutionary relationships of organisms. Forcing classification of new
>> species into already named genera could have more repercussions than
>> merits. It would, for example, result in unnecessarily "dumping" of
>> species
>> into well-defined genera, the reduction of diagnostic apomorphic
>> characters
>> in morphologically defined groups. Such practice will turn a well-defined
>> genus into a wastebasket taxon, which may, for instance, create artificial
>> biogeographic "connections" between areas. Taxonomy and systematics faces
>> several challenges in the 21st Century, and the naming of new genera
>> without phylogeny is certainly not the biggest of these. For instance,
>> incorrect identification of specimens used for molecular studies (Nilsson
>> et al. 2006; Groenenberg et al. 2011), taxonomic inflation (Isaac et al.
>> 2004; Harris & Froufe 2005), and DESCRIBE GENERA WITHOUT MOLECULAR
>> PHYLOGENIES? Zootaxa 4232 (4) © 2017 Magnolia Press · 595 the increasing
>> gap between phylogeny and classification (Franz 2005) are much more
>> serious
>> problems. On one hand, phylogeny provides us with a powerful tool to
>> hypothesise evolutionary relationships. On the other hand, since the
>> world's biodiversity is largely unknown (some 86% of non-marine eukaryotic
>> species are unknown; Mora et al. 2011) and the number of taxonomists is
>> decreasing (Bebber et al. 2014; Wheeler 2014), it is not yet the time to
>> regulate morphology-based grouping of species. Instead of criticising
>> their
>> well-trained, professional expertise (gleaned through years of intense
>> study), we should invest more trust in the taxonomic evaluations of the
>> decreasing number of taxonomists as well as allow more freedom for
>> morphology-based grouping. Especially, given that if someone wants to
>> describe something, he/she can find a way to do so in local, small non
>> peer-reviewed journals or self-published books. One-sided critiques
>> emphasising only the taxonomic value of molecular assessment could well
>> result in the weakening trust of taxonomists (mostly the ones not
>> dependent
>> on impact factors) in peer-reviewed journals, which is already a major
>> problem in today's taxonomy. Morphology is still what makes the organism a
>> tangible entity beyond its DNA. Necessary changes in the review process
>> What we need, is better editorial practice. To overcome this recent trend,
>> I suggest considering the following points: (1) Authors have to justify
>> their conclusions clearly with their data. Also, if the reason is other
>> than no access to molecular laboratory and funds, they should state the
>> reason why molecular phylogeny is not performed. (2) Editors need to
>> understand the hypothesis-driven nature of taxonomy, systematics and
>> phylogeny, and need to be able to ignore reviewers who do not engage the
>> subject. (3) Reviewers should refrain from rejecting the description of
>> new
>> genera on the basis of the lack of molecular data. Instead, they should be
>> critical of poorly defined genera, no clear gaps in the morphological
>> continuum, overlapping character states across genus-group taxa, and
>> genera
>> awaiting descriptions based on non-conventional morphological characters.
>> (4) Taxonomic journals could state whether they allow, discourage or
>> prohibit descriptions of taxa above species level without molecular
>> phylogenetic support. On one hand, this would allow the authors to prepare
>> to the nature of reviews, and choose journals where the lack of sequence
>> data will not result in changing the proposed taxonomic decisions. On the
>> other hand, this would create a rather harmful division in how journals
>> deal with taxonomic submissions.
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>
>
> --
> Robert Zuparko
> Essig Museum of Entomology
> 1101 Valley Life Sciences Building, #4780
> University of California
> Berkeley, CA 94720-3112
> (510) 643-0804
>
>