[Taxacom] Why character-tracking doesn't happen?

Neil Bell neil.bell at helsinki.fi
Sat Sep 13 08:36:25 CDT 2008


Thomas G. Lammers wrote:

> My opinion is that making assumptions that conflict with reality is 
> not likely to generate much of value.

All methodologies make assumptions that are simplifications of reality 
and thus occasionally conflict with it. The important thing is whether 
the assumptions are reasonable and appropriate for the questions being 
addressed. The working assumptions in higher-level phylogenetics and in 
population genetics are not going to be identical (they can't be), but 
that doesn't mean that they are incompatible. The assumptions of 
phylogenetics don't generally conflict with the reality of the relative 
degrees of relatedness of organisms in different genera, familes and orders.

> Guess you've not worked with angiosperms, huh?

My point was that the more distantly related organisms are, the *more* 
that hierarchical rather than reticulate patterns must be relevant to 
understanding their relationships. Extraordinary events aside, there 
really is no gene flow between extant oaks and palm trees, and yet these 
groups have continued to diversify. Usually the species boundary 
represents a fairly profound shift between the relative dominance of 
these patterns, but obviously in some groups this is less so than in 
others. This just means that in these groups you need to reconsider the 
level at which you apply the various methodologies or apply other 
specialised methodologies within the transition zone. Another factor 
with many groups, including angiosperms, is that there may be a 
considerable mismatch between the described species and the "real" 
species, so that cases of apparent reticulation really just mask 
instances of bad species delimitation (e.g. over-description).

> No.  I do not accept the "reality" of species.  They are an 
> aggregation of convenience.  Even populations can be of dubious 
> reality.  The only reality is the individual.

I'd like to consider this together with something that Richard Pyle wrote:

> I'm not sure I buy that.  It's hard enough characterizing an individual
> multecellular organism as a "discrete unit" (considering turnover of 
> cells,
> let alone molecules, over the lifespan of the organism). I regard it as
> effectively impossible to characterize populations (let alone species) as
> "discrete units", except to define an explicit set of individual 
> organisms
> at a particular moment in time.

Actually, before I read Richard's comment I was going to use the 
arguable "unreality" of the individual to counter Thomas's arguments 
about the unreality of the species! If you accept the reality of the 
individual, I don't see how you can't accept the reality of at least 
*some* species, unless you make a special case for existence within a 
single continuous physical space as being a prerequiste for reality. Or 
do you deny the existence of *any* groups of individuals between which 
there is no gene flow and which are sufficiently differentiated from 
each other such that this situation is permanent for them and for their 
descendents? (again, leaving aside genuinely extraordinary events). 
After that it just becomes a question of "how common are species?". But 
what I find odd in both of these comments is the implication that 
because populations are of dubious reality and dubiously discrete, this 
must be all the more so for species. Isn't the reason that populations 
are difficult to characterise is that they are *not* species? Of course 
I agree with the comments that we may just be quibbling about 
definitions here. "Discrete", "distinct" and "real" are is not very 
discrete or distinct concepts.

> My problem is with those who ascribe FAR too much value and import to 
> their imaginary stick figures, who paint themselves into ridiculous 
> corners because they do not view cladistics as a tool but rather as a 
> religion to be adhered to steadfastly.  The refusal to accept 
> paraphyletic taxa is the most blatant example of a priori philosophy 
> dictating counter-productive results.  I know a reptile or a fish when 
> I see one, and the fact they are defined on the basis of 
> plesiomorphies bothers me not one whit.
>
> Classifications, IMO, should take into account cladistic 
> relationships, but they should not mirror them slavishly.  If a more 
> useful classification obtains through recognition of paraphyletic 
> taxa, or by not giving sister taxa equal rank, so be it.

Seeing past the pejorative terminology here, you are simply stating that 
paraphyletic taxa are acceptable and useful for you. What is a useful 
and productive classification for an ecologist or a physiologist may not 
be for a phylogeneticist. Personally I don't find it particularly useful 
to have taxa that are not natural groups or don't at least represent 
best hypotheses of natural groups. Obviously there is a potential 
conflict here with the value of conservative and transparent 
delimitation of taxa for the majority of users, but if systematists are 
sensitive to this and careful not to make major changes prematurely 
based on limited or poor quality data (as may have happened in the past) 
surely it has to be better to have monophyletic rather than paraphyletic 
taxa? The other alternative is the one taken by many phylogeneticists of 
my generation, which is to disengage entirely from taxonomy. I think 
this is unfortunate because taxa are the main concepts through which 
most people approach biodiversity, and "seeing" diversity through 
classifications that refelct historical relationships can only enhance 
appreciation and understanding.


Neil Bell.


Thomas G. Lammers wrote:
> At 10:34 AM 9/12/2008, Neil Bell wrote:
>  
>> Like any methodology it makes assumptions appropriate to the questions
>> it is trying to answer.
>>     
>
> My opinion is that making assumptions that conflict with reality is 
> not likely to generate much of value.
>
>  
>> Aggregations of individuals and populations (generally and 
>> eventually, if by no means always) become discrete units through the 
>> process of speciation.
>>     
>
> No.  I do not accept the "reality" of species.  They are an 
> aggregation of convenience.  Even populations can be of dubious 
> reality.  The only reality is the individual.
>
>  
>> Incomplete lineage sorting and reticulation occur and should be 
>> identified, but they are not the
>> dominant patterns in the relationships between phylogenetically 
>> distant eukaryotic organisms.
>>     
>
> Guess you've not worked with angiosperms, huh?
>
>  
>> Population genetics can say no more about the relationship between a 
>> frog and a sparrow than cladistics can about the relationship between 
>> individuals within a population (probably a lot
>> less actually).
>>     
>
> I accept that different levels of the hierarchy have different 
> appropriate approaches.  Phenetic approaches are useful for sorting 
> individuals and populations into species and subspecies but are 
> inappropriate at higher levels.  Nonetheless, cladistics purports to 
> represent the *patterns* of evolution; are those patterns not driven 
> by processes at the level of individuals and populations?  If so, 
> should their be such a profound disconnect between them?   If a 
> genealogy purports to show a family tree, would it make sense to have 
> it ignore the processes of marriage and childbearing?
>
>  
>> I always find it odd when people criticise cladistics and/or
>> phylogenetics without suggesting how the questions they ask could be
>> better answered. The implication seems to be that either 1) the
>> questions are unanswerable 2) they are not interesting, or 3) there must
>> be better ways to address them but we don't know what they are...
>>     
>
> I don't think there is a better methodology than cladistics for answer 
> relationship questions above the level of species.  Flawed though it 
> is, it is the best possible.  My problem is with those who ascribe FAR 
> too much value and import to their imaginary stick figures, who paint 
> themselves into ridiculous corners because they do not view cladistics 
> as a tool but rather as a religion to be adhered to steadfastly.  The 
> refusal to accept paraphyletic taxa is the most blatant example of a 
> priori philosophy dictating counter-productive results.  I know a 
> reptile or a fish when I see one, and the fact they are defined on the 
> basis of plesiomorphies bothers me not one whit.
>
> Classifications, IMO, should take into account cladistic 
> relationships, but they should not mirror them slavishly.  If a more 
> useful classification obtains through recognition of paraphyletic 
> taxa, or by not giving sister taxa equal rank, so be it.
>
>
> Thomas G. Lammers, Ph.D.
>
> Associate Professor and Curator of the Herbarium (OSH)
> Department of Biology and Microbiology
> University of Wisconsin Oshkosh
> Oshkosh, Wisconsin 54901-8640 USA
>
> e-mail:       lammers at uwosh.edu
> phone:      920-424-1002
> fax:           920-424-1101
>
> Plant systematics; classification, nomenclature, evolution, and 
> biogeography of the Campanulaceae s. lat.
>
> Webpages:
> http://www.uwosh.edu/departments/biology/Lammers.htm
> http://www.uwosh.edu/departments/biology/herbarium/herbarium.html
> http://www.ratemyprofessors.com/ShowRatings.jsp?tid=297234
> http://www.kewbooks.com/asps/ShowDetails.asp?id=615
> http://www.uwosh.edu/colleges/cols/StaffBooks/lammers.htm
> http://www.geocities.com/TheTropics/Resort/7156/lammers.html
> -----------------------------------------------------------
> "Today's mighty oak is yesterday's nut that stood his ground."
>                                                                -- 
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