[Taxacom] Describing genera without molecular phyolgies

[Kenneth Kinman]

Hi Richard,
        I definitely agree that adhering to strict phylogenetic monophyly has created a lot of problems (in its attempt to totally eliminate paraphyly), including nomenclatural instability (which, as you point out, negatively affects biodiversity studies and actions).
        As for describing taxa without molecular phylogenies or based solely on them, the results vary depending on the kind of organism being studied and at what taxonomic level.  Molecular phylogenies have greatly clarified the relationships of bird Orders, such as Falconiformes (sensu stricto) being unrelated to other raptors.  So many convergences in morphology and behavior.   Order Cathartiformes (New World vultures) unfortunately got thrown in with Ciconiformes for many years due to some poor molecular data, but that mess was finally resolved by better molecular data.
      I suspect that molecular data would also provide some surprises for more speciose taxa, such as those beetles in Aphodiinae.  And extinction has done far less pruning of many insect taxa than it has in a lot of vertebrate taxa.  So the successes of strict cladists and molecularists for vertebrates at higher taxonomic levels don't always have as much success at the lowest taxonomic levels (especially speciose taxa).  So, yes, I am worried too.
      Premature nomenclatural changes are too often done based on limited data.  A total evidence approach by a team of workers (evaluating different data) would be preferable in most cases.
                                     ----------------Ken

________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Richard Zander via Taxacom <taxacom at mailman.nhm.ku.edu>
Sent: Monday, May 25, 2020 5:09 PM
To: 'Richard Pyle' <deepreef at bishopmuseum.org>; 'JF Mate' <aphodiinaemate at gmail.com>
Cc: 'Taxacom' <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] Describing genera without molecular phyolgies

I appreciate the comments of Lynn Raw and Richard Pyle. They mention important concerns.

Richard Pyle wrote:
I consider myself a classical taxonomist, and I'm not worried.  Who is worried?  Are you worried?

Well, yes, I am worried.

 For two reasons: (1). Biodiversity analysis requires decent classifications. Nowadays, environmental protection of molecularly cryptic species gets more attention in the news than protection of whole ecosystems. Following strict phylogenetic monophyly, species, genera, and even families are commonly either sunk to synonymy or invented without reasonable evolutionary evaluation. Making predictions for the expected vast changes in floral and faunal composition is now difficult because of the sea of rapidly changing nomenclature that lumps disparate taxa or splits taxa into unmanageable units.

And (2): Systematics is supposed to be a science. But it has always been vulnerable because mathematics and statistics are not reputed to be a strength of taxonomists. I think "innumerate" is the term often used for us. Phylogenetics is replete with bad statistics. Sampling is a joke, with say 5 or 10 exemplars of a species being considered a lot. Evolutionary scenarios from different data sets (morphology and DNA) are compared with Bayes Formula, instead of Bayes Factors. Accuracy is rejected in favor of precision. Dichotomous trees of cluster analysis are accepted as models for analysis. Molecular studies substitute clades of molecular strains of species for actual species, when (or perhaps because)  the last might require much additional sampling, assuming many information-bearing strains are not extinct. "Shared ancestors" are considered by some cladists to be interspersed in a cladogram without actually modeling these (e.g. where are their autapomorphies? Do they reverse and disappear?).

I am worried for biodiversity analysis in an era of climate crisis and for any remaining respect for systematics as a science. I do not say that phylogenetics is a shuck and a scam, or that it is a 30-year Lysenko-level perversion of science. If true, then that would be more than just worrisome.

Richard Zander

-----Original Message-----
From: Richard Pyle <deepreef at bishopmuseum.org>
Sent: Saturday, May 23, 2020 7:44 PM
To: Richard Zander <Richard.Zander at mobot.org>; 'JF Mate' <aphodiinaemate at gmail.com>
Cc: 'Taxacom' <taxacom at mailman.nhm.ku.edu>
Subject: RE: [Taxacom] Describing genera without molecular phyolgies

Hi Richard,

> 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."

So, your primary point of disagreement is that I used the expression "phylogenetic relationships", instead of "phylogenies"???  If so, then sure -- consider my sentence amended to:

"modern technology and biological insights have dramatically improved our ability to infer phylogenies of organisms"

Note that I never said or even intended to imply that we're in any way closer to inferring evolutionary relationships.  Although I think a pretty powerful case can be made for that assertion as well.

I'm pretty-much in agreement with everything else you wrote.  I just tend to be a little less grumpy (and less self-confident) about it.

> I am sorry to see classical taxonomists still worrying over the
> ascendancy and hegemony of phylogenetics.

I consider myself a classical taxonomist, and I'm not worried.  Who is worried?  Are you worried?

Aloha,
Rich

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