[Taxacom] Describing genera without molecular phyolgies

Sat May 23 17:51:04 CDT 2020

Lynn Raw wrote that a genus is purely an arbitrary concept. No it isn't, that's a sad meme. Those groups of species we intuitively identify in nature are actually clusters of descendants radiating away from some generalized progenitor. I've tested this purely empirical concept of genus, and it works as an explanation. See my recent stuff on ResearchGate.

Richard Pyle wrote " modern technology and biological insights have dramatically improved our ability to infer phylogenetic relationships of organisms; and one could also (rightly) argue that this leads to legitimate rejiggering of prior classifications." Not so. Modern classification should reflect evolutionary relationships. Phylogenetics does not model evolution. It is basically cluster analysis (non-ultrametric, based on state transformations) where data on groups of species "evolve" into data on smaller groups of species. Evolutionary information is maximized only to the extent that dichotomous branching and sets evolving into sets allow.

Molecular studies track molecular strains. There are many molecular strains developed in mature species. Different molecular strains of one species can generate different descendant species, this being molecular paraphyly. Thus, much phylogenetic lineage splitting and generation of cladistic relationships can be and are internal to progenitor species. Molecular paraphyly and extinction of molecular strains mask true relationships.

Molecular paraphyly can be misinterpreted as evidence of cryptic species (molecularly distinguishable). Two exemplars of a single species  need to be quite distant on a cladogram to even be considered as possibly cryptic species. How distant? My recent studies indicate that they should be 13 or more cladogram nodes apart for a 3 sigma (standard deviations) level of distinction before even starting to consider them evolutionarily different species.

Classical taxonomy that recognizes the evolutionary importance of genera as radiating clusters of species is the best way to reflect evolution in classification. I've done this for several genera, see my papers on ResearchGate or Academia.edu.

The present phylogenetic formalism substitutes precision for accuracy, invents unknown ancestors non-parsimoniously, paralyzes the mind with Big Math, and uses a first order Markov chain when the relationship between ancestor and descendant is second-order (nesting without reversals links lineages of ancestor and descendant in a very strong chain easily interpreted as high Bayesian support).

The new very simple protocols and their rationalizations are available online. I am sorry to see classical taxonomists still worrying over the ascendancy and hegemony of phylogenetics. Have faith.
________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Richard Pyle via Taxacom <taxacom at mailman.nhm.ku.edu>
Sent: Saturday, May 23, 2020 1:13 PM
To: 'JF Mate' <aphodiinaemate at gmail.com>
Cc: 'Taxacom' <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] Describing genera without molecular phyolgies

I agree with Jason, except I wouldn't limit the sentiment to supra-specific taxa.

Some people tend to be lumpers, and some tend to be splitters.  My own bias is something like "leave the existing nomenclature/classification alone unless you have a really compelling reason to change it".

I think part of the problem is that, as the proportion of time spent in nature observing organisms vs. time spent analyzing organisms in labs has shifted towards the latter in recent decades*, there seems to be a commensurate increase in confidence that results of phylogenetic analyses represent the best metric for asserting Linnean-style classifications. In many cases I fear that this shift has reduced the overall value of Linnean-style nomenclature and classification -- which has served an extremely practical purpose for two and a half centuries.  One could certainly (and rightly) argue that modern technology and biological insights have dramatically improved our ability to infer phylogenetic relationships of organisms; and one could also (rightly) argue that this leads to legitimate rejiggering of prior classifications.  However, I'm not sure that, on the whole, this trajectory has necessarily favored the notion of "classification as a useful tool for understanding biological diversity".

Aloha,
Rich

*Note: Both obviously are (and always have been) important -- I'm not disparaging the value of time with a microscope or sequencer in producing good taxonomy. But the balance, I think, has shifted strongly toward the latter, and I'm not sure that shift has benefitted the field of taxonomy.

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Database Coordinator
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.

> -----Original Message-----
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of JF
> Mate via Taxacom
> Sent: Friday, May 22, 2020 6:44 PM
> To: Taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] Describing genera without molecular phyolgies
>
> Thanks John. A useful article as I am struggling with the same problems in my
> group but from the other side.  I can't comment on snails but my opinion is
> that without a phylogenetic framework, molecular or morphological,
> taxonomists should be extremely prudent creating supra-specific taxa.
>
> Best
>
> Jason
>
> On Sat, 23 May 2020, 12:52 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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