[Taxacom] Diagnosing species

Mon Jun 25 20:52:37 CDT 2007

     More about species below, but I suppose the Banyon tree analogy could 
be extended to some very old (high ranking) taxa.  But for them, periodic 
extinctions tend to severely prune away most of that reticulation.  
Therefore although evolution is largely a paraphyletic process, major 
extinctions allow us to simplify our classifications in a dichotomous 
fashion in a majority of cases.  Obviously I am not arguing against the use 
of paraphyletic taxa, but it needs to be done selectively and judiciously if 
we are to optimize and stabilize our classifications.  That dichotomies are 
probably more apparent than real does not detract from their usefulness (the 
rarity of fossilization will always make them so).  Unfortunately, 
phylocodists think dichotomies are the ONLY game in town, and that is way 
too much of a good thing.  Moderation and a more balanced approach is sorely 
needed.

     As for the ancestral eukaryote, I would regard the ancestral 
prokaryotic host cell (presumably a metabacterium, a.k.a. archaebacterium) 
as the major constituent and primary ancestor.  That is why I suggest 
placing a {{Eukaryota}} exgroup marker within Metabacteria, and this is the 
main branch I would use to follow the tree of life (in terms of evolution 
and classification in tracing that continuum as it crosses the eukaryotic 
threshold).  Organelles are significant, but comparably minor additions that 
apparently were sequentially "engulfed" over time (mitochondria first, and 
chloroplasts and peroxisomes later).  Therefore, I place exgroup markers for 
these organelles within their ancestral prokaryotic groups, but there was 
presumably only one ancestral eukaryote species (also the ancestral 
protist), and the only major question that seems to still be somewhat 
controversial is  whether the nucleus itself was the result of a mere 
membrane extension into the interior of the ancestral eukaryote or an 
organelle-type endosymbiosis.

    One can take the same approach with species of prokaryotes, the main 
("vertical") tree being mostly dichotomous, but with some kind of 
{{markers}} for genes that have been transferred horizontally between 
clades.  Of course, a complete classification of Eubacteria (with all the 
markers for horizontal transfers) would be extremely complex and used mainly 
by a subset of microbiologists, but the rest of us would just use the main 
(vertical) classification with outgroup markers only for mass horizontal 
transfers (via organelles).  Therefore I have never seen a big problem using 
mainly dichotomous classifications as long as you also allow occasional 
paraphyletic breaks that store useful divergence information and also keeps 
our classifications from becoming PURELY dichotomous chains of 
legalistically defined clades that will only be understood by the 
phylocodists who create them.  Would strict cladists even use phylogenetic 
software if it allowed formal paraphyly?  Many might actually do so in the 
future, but I certainly wouldn't hold my breath when it comes to diehard 
phylocodists.

    As for Richard's fishes, I think he may well be moving toward regarding 
some of these so-called separate species as actually being subspecies (or 
just populations in a more continual spectrum of populations) within a 
larger species.  Speciation simply hasn't been achieved and sampling is 
finally showing that reproductive isolation has not taken place.  Whether it 
is geographically more linear across the ocean or circular around an ocean 
where the outlying subspecies obviously can't interbreed when they come back 
into contact, genetic flow through intermediate populations can show that 
speciation has not occurred, and lumping of species is in order.  Most of 
that "Banyon"-like reticulation would be shifted to the population level 
where formal taxonomic names are not normally used.  For some organisms, 
documenting gene flow may be so labor intensive as to be largely futile at 
the present time, but a generation from now (with whole genome barcoders and 
the like), it will become easier, cheaper, and less labor intensive.  It may 
also lead to a general consensus how low gene flow needs to become to 
indicate speciation has occurred (although it would be different for 
different groups of organisms).

    And I don't know a great deal about species hybridization in plants, but 
botanists obviously have a lot more experience than zoologists in storing 
that kind of information in their classifications.  However, wouldn't it be 
extremely rare for such hybrids to give rise to higher taxa, like families 
and orders.  I would think even "hybrid" genera are probably pretty rare 
(even though hybridization between species in different genera may be 
relatively common in plants).

     --------Ken Kinman

**********************************
>From: "Richard Pyle" <deepreef at bishopmuseum.org>
>To: "'TAXACOM'" <taxacom at mailman.nhm.ku.edu>
>Subject: Re: [Taxacom] Diagnosing species
>Date: Sat, 23 Jun 2007 22:38:53 -1000
>
>
>Thank you, Bob Mesibov, for capturing so effectively in one email the core
>essence of a fundamental point I have tried again and again to make on this
>forum in recent years.  And, for doing so much more effectively than I ever
>have.
>
>First, a short soapbox commentary, followed by directly addressing one of
>the points/questions in Bob's post.
>
><Rant>
>This history of life on earth seems, for the most part, to represent a
>single unbroken continuum spanning some 4 billion years (give or take).  
>The
>resolution of that continuum is individual reproduction events, giving a
>granularity of "smoothness" to of something on the order of 10^-7 to 10^-9.
>If the timeline were printed at a resoultion of 4000dpi (a high-resolution
>scanned image, ten times higher resolution than a typical image in a 
>typical
>publication), it would be something like sixteen miles long (give or take a
>couple of orders of magnitude).  Everything we now consider to be a
>"species" parted company through historical time from its nearest sibling
>"species" somewhere along that very high-resolution gradation.  It is that
>smoothness of historical transition -- that high resolution -- that utterly
>defies attempts to objectivly identify where a "species" begins.
>
>The smoothness of the continuum further increases, and the objective
>demarcation of "species" from one another is rendered ever more futile, in
>consideration of the patterns of assortative
>mating/introgression/hybridization/reticulate evolution that are already
>very evident in organisms like plants and corals; and perhaps increasingly
>so elsewhere in the Eukaryotic realm.
></Rant>
>
>Which brings me to my direct response to Bob's question regarding these
>sorts of patterns in the animal world.
>
>For the past 15 years or so, I have gradually begun to see more and more
>anecdotal/cirumstantial evidence within my animal group (coral-reef fishes)
>for a prevelance of reticulate patterns of evolution at the "species" level
>(i.e., at the level at which modern ichthyologists typically tend to draw
>species lines).  These patterns were further illustrated to me during a
>month-long cruise across part of the western Pacific, where we saw clear
>examples of species "A" in the central Pacific being traditionally
>unambiguously different from species "B" in the western Pacific, in fact
>being represented by a continuum of forms along intervening areas.  I'm
>gradually collecting examples of this sort of thing, and hope to start
>looking at it through molecular techiques in time.  I may be totally wrong
>about this, but if I'm not wrong, then at least within the realm of
>coral-reef fishes, the historical pattern may in many cases look less like
>the branches of a maple tree, than the "trunk" of a Banyon tree.
>
>Aloha,
>Rich
>
>Richard L. Pyle, PhD
>Database Coordinator for Natural Sciences
>   and Associate Zoologist in Ichthyology
>Department of Natural Sciences, Bishop Museum
>1525 Bernice St., Honolulu, HI 96817
>Ph: (808)848-4115, Fax: (808)847-8252
>email: deepreef at bishopmuseum.org
>http://hbs.bishopmuseum.org/staff/pylerichard.html
>
>
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu
> > [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Bob Mesibov
> > Sent: Saturday, June 23, 2007 6:07 PM
> > To: TAXACOM
> > Subject: [Taxacom] Diagnosing species
> >
> > Richard Zander's recent TAXACOM posts have pointed to
> > regarding species as diagnosable entities for taxonomic
> > purposes, rather than as historical entities. By "historical"
> > I mean "phylogenetic" as understood by most TAXACOM readers:
> > a species as a single branch on a dichotomous tree of life.
> > Zander's diagnosis would include a range of characters not
> > commonly thought of as species-defining.
> >
> > At first glance this suggestion seems to be an abandonment of
> > the Darwinian goal of a taxonomic system which accurately
> > reflects the genealogical history of life.
> >
> > At second glance, it does no such thing. Botanists like
> > Zander are aware that a very large proportion of plants have
> > hybrid origins, and they have no reason to think that
> > hybridisation hasn't been going on for a very long time. Even
> > if hybridisation was less frequent among the ancestors of
> > today's plants than it was in recent times, the multitude of
> > hybrid ancestors that must have existed should encourage
> > botanists to throw strictly dichotomous trees on the No
> > Longer Useful heap. The genealogical history of plants is a
> > network, and "reconciling" incongruent gene trees into a
> > dichotomous structure is not unlike a Ptolemian trying to
> > "save the circles" to keep the Earth at the centre of the
> > Universe. It perpetuates a falsehood.
> >
> > Defining genera as historical entities makes just as little
> > sense. The reality is that depending on which gene tree you
> > look at, a plant species could logically belong to several
> > historical genera at one and the same time. Genera also need
> > diagnosing.
> >
> > Microbiologists are very comfortable with this approach to
> > taxonomy, even if many botanists are still not. Most
> > zoologists don't want to think this way at all, even though
> > they would admit they come from a hybrid ancestor, i.e.
> > the first eukaryotic cell. They prefer to think that animal
> > evolution has been largely dichotomous since the earliest
> > metazoans appeared, and if gene exchange happens at all, it
> > occurs mainly during slow sympatric or parapatric speciation,
> > and less frequently afterwards, as reproductive isolation
> > gradually becomes a no-exception policy. (I'm thinking here
> > of speciation not driven by chromosomal rearrangements. These
> > isolate animal lineages immediately.)
> >
> > However, I wonder how many zoologists actually test their
> > molecular phylogenies for evidence of hybridisation or
> > introgression, as botanists do more and more? If you don't
> > look for signs of hybridisation you won't find it, and a
> > successful hybrid species looks just like a (excuse me!) real one.
> >
> > Getting back to seeing species as diagnosable entities, that
> > seems an eminently sensible approach to dealing with a
> > Network of Life. Arguments about adhering to strict monophyly
> > vs. allowing some paraphyly could be restricted to those bits
> > of the Network where they have some logical relevance. (I'm
> > thinking here of higher taxonomic divisions, although I read
> > that monophyly has run into serious trouble at the Domain
> > level in recent
> > years.)
> >
> > As for the argument that phylogenetic software doesn't (yet)
> > deal adequately with reticulate evolution, so until it does
> > we should continue to believe that animal evolution is
> > strictly dichotomous... Hmmmm. Hey, Procrustes, maybe you
> > should learn more about your guests before settling them down
> > in that bed of yours?
> > ---
> > Dr Robert Mesibov
> > Honorary Research Associate, Queen Victoria Museum and Art
> > Gallery and School of Zoology, University of Tasmania Home
> > contact: PO Box 101, Penguin, Tasmania, Australia 7316
> > (03) 64371195; 61 3 64371195
> >
> > Australian Millipedes Checklist
> > http://www.qvmag.tas.gov.au/zoology/millipedes/index.html
> > Tasmanian Multipedes
> > http://www.qvmag.tas.gov.au/zoology/multipedes/mulintro.html
> > Spatial data basics for Tasmania
> > http://www.utas.edu.au/spatial/locations/index.html
> > Biodiversity salvage blog
> > http://biodiversitysalvage.blogspot.com/
> > ---
> >
> >

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