[Taxacom] On genera

JF Mate aphodiinaemate at gmail.com
Tue Jul 23 15:34:39 CDT 2013


Thanks Richard, sorry for the delay. I realised that I employed rather
colloquial (and confusing) choice of words in my previous post, so I will
rephrase: ancestors in a tree are assumed. They are real in as far as the
daughter lineages originated from a common ancestor, but lacking said
ancestor its phenotype is assumed based on the characters of the sister
lineages. As such, the ancestral condition is a hypothesis based on the
character distribution of the daughter lineages. I hope this makes my
position clear. In regards to the other points.

"Related, in phylogenetics, means distance on a cladogram."

Both sister taxa are equally related to their most recent ancestor. You may
choose to argue that according to your metrics of choice one changed less
than the other ('less evolved', different branch lengths), but this doesn´t
mean it is more or less related.

"The only way that one might postulate an extinct shared ancestor is if
there were data supporting such, for instance, a group of specialized taxa
in isolated recent environments that share some distinctive set of traits
that might be ascribed to a more generalized and widespread but now extinct
ancestral taxon."

This statement presuposes that:

a)you KNOW the ancestor in all aspects and can compare it to the descendant
lineages. Outside microorganisms I don't know of any case were you can
compare all features of the ancestor to its descendants.
b) your metrics (aspects of the pheno/genotype you have coded) are unbiased
and representative of the evolutionary rate of the whole organism. There
are only a handful of organisms for which we have this information but
actually coding it in a meaningful way is very subjective. Is a longer neck
more important evolutionary than a 3 aa insertion in a digestive enzyme?

"Do not put your trust in anagenetic change. Always look for stasis first,
because if it is there (and fits theory by biogeography, relative age of
habitat, relatively generalized morphology, maybe even fossils), then
postulating unknown, unnamed, and ad hoc shared taxa is not parsimonious"

I am unsure how you look for stasis a prori. Surely you are making
assumptions with some sort of data (a mental tree)?

"You indicate that my "hunch" may be countered by demonstrable phylogenetic
relationships. Piffle. My "scientific hypothesis" can never be countered by
imaginary shared ancestors. "

I wasn´t talking specifically about ancestors or even about your specific
ideas that was just another colloquialism. My view is that phylogenies
allow you to arrange characters in such a way as to exclude certain
hypothesis. So in this way they are a test, albeit an imperfect one as they
(the cladograms) rely on bits of data to reconstruct the past so they too
are fallible and subject to constant retesting.

"The stochastic element generating the shared ancestral node is provided by
the false idea that characters themselves evolve (as opposed to an
organism).

I would say genes evolve, albeit mostly in an indirect way as they are
acted upon through the phenotype (I am not getting into the wonderful world
of genomic evolution). Similarly the organism evolves indirectly. It is
this indirectness, and the difference in rates, that makes speciation
fuzzy. It is a gradual process, beginning with some sort of gene-flow
disruption  (at which point we are still talking about the same species,
even if from the point of view of the genes the split has begun) and ending
in distinct species (whatever they may be). Between both ends you will find
the full gamut of species concepts. At the beginning a cladistic concept
and at the end probably the typological SC. I am quite comfortable with a
juxtaposition of states but building a phylogeny (in the most lose term of
the word) involves extracting one thread and like with Schrondinger´s cat,
simply by looking through your data of choice will determine where the line
will fall in that fuzzy edge.

Best

Jason


On 21 July 2013 23:04, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:

> Maybe part of the difficulty here arises from the fact that phylogenetic
> relationships are between taxa, but decent is a relationship between
> individuals (e.g., like a family tree)?
>
> Stephen
>
>   *From:* Richard Zander <Richard.Zander at mobot.org>
> *To:* JF Mate <aphodiinaemate at gmail.com>; Taxacom <
> taxacom at mailman.nhm.ku.edu>
> *Sent:* Monday, 22 July 2013 5:33 AM
>
> *Subject:* Re: [Taxacom] On genera
>
> Jason:
>
> Let's focus on one thing at a time: "The ancestor in a phylogeny is
> hypothetical." No, it isn't a hypothesis. A hypothesis has some data or
> observations of some sort to support it. A shared ancestor is there by
> cladistic definition, as in "There must be a shared ancestor, since of any
> three taxa two are more closely related." Related, in phylogenetics, means
> distance on a cladogram.
>
> Shared ancestral nodes are contrivances, not hypotheses. They are put
> there to make sure all cladograms have the potential to be fully resolved.
> If an ancestral taxon has, say, two daughter taxa, then one of those taxa
> will be more closely "related" in a cladogram to the ancestral taxon (as
> sister groups) by chance alone. The only way that one might postulate an
> extinct shared ancestor is if there were data supporting such, for
> instance, a group of specialized taxa in isolated recent environments that
> share some distinctive set of traits that might be ascribed to a more
> generalized and widespread but now extinct ancestral taxon.
>
> Do not put your trust in anagenetic change. Always look for stasis first,
> because if it is there (and fits theory by biogeography, relative age of
> habitat, relatively generalized morphology, maybe even fossils), then
> postulating unknown, unnamed, and ad hoc shared taxa is not parsimonious.
>
> You indicate that my "hunch" may be countered by demonstrable phylogenetic
> relationships. Piffle. My "scientific hypothesis" can never be countered by
> imaginary shared ancestors. The stochastic element generating the shared
> ancestral node is provided by the false idea that characters themselves
> evolve (as opposed to an organism). Thus, any two of three taxa that share
> traits must have "evolved" through those traits away from the third. Proof,
> of course, is that the cladogram shows "phylogenetic distance."
>
> Richard
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:
> taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of JF Mate
> Sent: Thursday, July 18, 2013 2:06 PM
> To: Taxacom
> Subject: Re: [Taxacom] On genera
>
> Thanks Richard, sorry for the delay. It´s not very clear what you mean by:
>
> "... cladistics, because it will not name shared ancestors, cannot infer
> monophyly?..."
>
> The ancestor in a phylogeny is hypothetical. With the exception of
> incipient species you will never encounter the ancestor. It is gone,
> evolved into the other sister taxon. Is this what you mean?
>
> "Suppose we have a bunch of taxa terminal on a clade. Two are most terminal
> with shared synapomorphies. The next taxon down, however, clearly, derived
> from the same ancestral taxon as the two most terminal taxa. Asserting that
> the two most terminal taxa are monophletic splits the ancestral taxon...
> Lots of subgenera commonly have some one wide-ranging species of
> generalized morphology with some closely related species specialized into
> more recent habitats. A theory could be developed if one was not a cladist
> that these are all daughter species of the more generalized species."
>
> You appear to suggest that phylogenetics doesn´t make use of plesiomorphic
> characters and that it is a bad thing. But lack of change is hardly
> informative about relationships isn´t it. Stasis cannot record anything by
> definition since it is unchanging. Sure, it can tell you something about
> the selective pressures on the taxa but nothing about relationships at that
> level. In any case not useing plesiomorphies doesn´t impede I have to be
> clear that all data has a phylogenetic signal, the problem is if it is at
> the level of interest. On the other hand a phylogeny would not be very
> useful if you imposed a given direction on the character state changes.
> After all you analyze the data to build a cladogram and in the process test
> your hunch. If your hunch is part of the analysis why bother?
>
> "In the first place, I advance a scientific theory, descent with
> modification from a species at hand with a clear and known evolutionary
> process, specialization into particular habitats. Otherwise, inventing ad
> hoc, unnamed and unnameable, invisible explanations for a natural
> phenomenon is a step back. The only reason to advance an unidentified
> ancestral species is when all the taxa involved are specialized into
> particular habitats."
>
> A phylogeny narrows the possibilities in regards to evolutionary direction
> but it is hardly ad hoc. You may have a hunch as to how evolution in a
> certain group has proceeded (generalized to specialized for example) but if
> the relationships are at odds with this scenario you can´t simply dismiss
> it or the method as someone´s invention. Either the phylogeny is wrong
> (why, do you have outside data that support this) or your hunch is wrong.
> Either way you need more data.
>
> Best
>
> Jason
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