[Taxacom] New systematics book

[Pierre Deleporte]

OOooops...

I just wrote
"I agree that species are the result
of an evolutionary process"

so I am myself using a somewhat ambiguous formulation
regarding my own recommendations

the problem is with "are"
(and different acceptions and implicatons of this term)

our (rough) knowledge of the evolutionary process
is the theoretical context
in which a historical clade makes evolutionary sense

so I better write :
"I agree that species are historically meaningful
because of the evolutionary process"

while "are the result of" is a very evasive shortcut to say this

reification and anthropomorphism are very frequent in ordinary language
(fossils tell us that... cladistics imposes... ideas evolve...)

scientific specialized jargon is not ordinary language,
and philosophy matters (ontology and logics)

sloppy vocabulary is no problem
when everybody agree on what words refer to,
which is obviously not the case for the ongoing systematics debates

Pierre


Le 09/09/2013 06:04, Curtis Clark a écrit :
> First I want to say that, from all the agreement on this list that
> species are not entities in nature, it seems that pattern cladistics has
> won, and those of us who studied (and perhaps still study) speciation
> could have done no worse by studying unicorns. All the rest of what I
> write is based on the assumption that species are the result of an
> evolutionary process, and to that extent (at least) are real. I surmise
> that you agree.
>
> I accept paraphyletic species, and in fact my own studies suggested
> several examples. What I have never understood is how the existence of
> paraphyletic species provides a general justification for paraphyletic
> higher taxa. If the pattern of character distribution in extant lineages
> showed, say, four lineages that share a synapomorphy, three of them have
> distinct autapomorphies, and the fourth has no autapomorphies, that
> could be suggestive of ancient peripatric speciation. And it would be a
> clear case for a polytomy in a cladogram. But paraphyletic taxa like
> Reptilia (sensu antiquo)  and Dicotyledonae are most often the result of
> gaps in knowledge; it's hard for me to imagine the existence of
> peripatric speciation justifying them.
>
> On 2013-09-08 1:35 PM, Richard Zander wrote:
>> " ... parsimony and other optimality analyses only work with accuracy
>> with pseudoextinction (dying ancestor, two new species). The correct
>> optimality for branching analysis is that which makes the shortest (most
>> likely, most credible) tree given identified surviving ancestors and
>> their daughter taxa based on other information. This is merely, MERELY
>> less precise, correctly less precise and therefore with more uncertainty
>> about evolutionary relationships.
> This is a methodological issue, not a conceptual one. There are many
> other problems with parsimony as well (including long branch attraction
> for molecular data). I don't see how this supports recognition of
> paraphyletic groups.
>
> One of the reasons that the results of the Angiosperm Phylogeny Group
> are so widely accepted is that the groups are things we were considering
> anyway, but didn't quite have the evidence for. In a previous post, I
> gave some examples from Scrophulariaceae s.l.; plant taxonomists have
> known for years that the family was heterogeneous, and now we have a few
> more lines of evidence to convince us of that. Just because some people
> make classifications from bootstrapped molecular parsimony trees with no
> other input doesn't invalidate cladistics.
>
>> "...  molecular "lineages" are molecular strains, and ancestral taxa in
>> stasis generate lots of molecular strains before and after generation of
>> one or more daughter species. The DNA continues to mutate in isolation
>> while expressed traits remain in stasis for millions of years. Molecular
>> phylogenetics gives precise sister group analyses of extant strains, not
>> taxa. Evidence? Molecular paraphyly. What about extinct or unsampled
>> strains? They could have diverged molecularly long before or after any
>> extant strain."
> This is again methodological. The lack of congruence of many gene trees
> is well-known, as are the evolutionary processes resulting in the lack
> of congruence. Again, no basis here for general recognition of
> paraphyletic higher taxa.
>
> Within the eukaryotes, the general pattern of groups within groups is
> pervasive. Peripatric speciation, hybrid speciation, and lateral gene
> transfer are all fascinating processes that certainly muddy the waters,
> but there are a lot of "just-so stories" lurking in Bessey's Cactus and
> its descendents. Perhaps your book has a methodological framework to
> address that (I presented a method for defining grades a year or two
> ago, but you neither challenged nor agreed).
>
> And as far as "phylogenetic jargon has taken a life of its own," it's
> perhaps not a good idea to redefine terms like monophyly yet again.
>


-- 
Pierre DELEPORTE
UMR6552 EthoS
Université Rennes 1
CNRS
Station Biologique
35380 PAIMPONT
tél (+33) 02 99 61 81 63
fax (+33) 02 99 61 81 88