Hi Kirk,
There are always compromises made when one is constructing papers.
Otherwise we would never publish anything; endlessly waiting until we
had assembled all the data that is deemed necessary by purists.
Phylogenetics is an iterative process and we all felt that the
sequence data analysis, which incidentally will swamp any
morphological dataset when its finished, was worth putting out as
short note for a broad audience. A more complete detailed analysis and
assessment, for digestion by the true friends of annelids, will appear
in an appropriate journal in due course, and will no doubt pass
unmentioned in this forum.
The methods we used produced congruent results with reference to the
establishment and position of Swima, and so should satisfy
phylogeneticists of various philosophies, with the exception of you of
course. If we had published only the parsimony analysis, we would have
expected similar disparaging rants from those who prefer model-based
approaches. Being pluralistic does not diminish rigor or concern for
evidence.
best,
greg
On Aug 23, 2009, at 9:41 AM, J. Kirk Fitzhugh wrote:
> Thanks Greg. No matter what method is used, be it 'parsimony,' quasi-
> Bayesianism, etc., I would never accept the results when I know
> there are other relevant data that need to be considered. In lieu of
> even publishing a cladogram using the sequence data, it would have
> been appropriate to wait on the formal phylogenetics until the
> relevant data are compiled. There is no such thing as 'total
> evidence' analyses - an inference either considers one's available
> relevant evidence for the sake of maximizing rationality of
> explanation, or they opt for accepting that the results are going to
> be more irrational.
>> But since you mention it, I'm also deeply concerned at the fact that
> systematists routinely publish phylogenetic hypotheses using a
> variety of different methods, often with contradictory results,
> regardless of what data are used. Why do it? We can't compare the
> results because they're inferred from very different assumptions
> regarding theories, and no one has ever provided any good empirical
> arguments for the practice. It seems we've lost sight (or maybe
> never had it) of why those trees are produced in the first place,
> and are too enamored with the fact that computers can produce
> branching diagrams whenever we want 'em.
>> I'm sorry for coming across so critically, but, we have to face the
> fact that a critical attitude toward phylogenetics is just plain
> absent. It's a dangerous situation when a field of science becomes
> so complacent that any sort of method is acceptable and in fact
> condoned.
>> Kirk
>> Greg Rouse wrote:
>>>> Kirk,
>> Please consult the Supplement for details on a maximum parsimony
>> analysis that I assume you would not find dubious. A total evidence
>> analysis (i.e., a "limited set of sequence data", plus what must
>> also be called a "limited set" of morphological data) will appear
>> in due course that may alleviate your other concern.
>> greg
>>>> On Aug 23, 2009, at 7:15 AM, J. Kirk Fitzhugh wrote:
>>>>> The phylogenetic hypotheses are only 'solid' insofar as they
>>> explain a limited set of sequence data. Given that the authors
>>> must know they are actively avoiding considering all sorts of
>>> other relevant data that are in need of being explained in the
>>> same context, e.g. the setae as Jim Blake noted, and the use of
>>> Bayes Theorem is not meant for the inference of hypotheses, then
>>> Torsten's endorsement is ill-founded at best.
>>>>>> But then, let's not quibble with the fine points of doing good
>>> science - it's more important to impose blind acceptance of
>>> methods by even more blind endorsement.
>>>>>> Kirk
>>>>>> Struck, Torsten wrote:
>>>>>>>> Indeed, it is a nice discovery and very interesting. Moreover, the
>>>> phylogenetic hypotheses are very solid (not at all "dubios at
>>>> best") and
>>>> good in comparison to several other analyses out there.
>>>>>>>> Nice work Karen,
>>>>>>>> Torsten.
>>>>>>>>>>>> On 8/22/09 10:30 AM, "Kirk Fitzhugh" <kfitzhug from nhm.org> wrote:
>>>>>>>>>>>>> Nice discoveries indeed. It's unfortunate that the scientific
>>>>> merits of the
>>>>> phylogenetic hypotheses are dubious at best. But then, it *is*
>>>>> published in
>>>>> Science. ;-)
>>>>>>>>>> Kirk
>>>>>>>>>>>>>>>>>>>> -----Original Message-----
>>>>> From: annelida-bounces from oat.bio.indiana.edu on behalf of Geoff Read
>>>>> Sent: Sat 8/22/2009 12:54 AM
>>>>> To: <Annelida list
>>>>> Subject: [Annelida] Swima the swimmer
>>>>>>>>>> FYI
>>>>>>>>>> Osborn KJ, Haddock SHD, Pleijel F, Madin LP, Rouse GW 2009. Deep-
>>>>> Sea, Swimming
>>>>> Worms with Luminescent "Bombs". Science 325: 964 (and online
>>>>> 'supplement').
>>>>>>>>>>http://www.sciencemag.org/cgi/citmgr?gca=sci;325/5943/964>>>>>>>>>> Swima bombiviridis named (new genus, new species of acrocirrid)
>>>>>>>>>> Abstract: "By using remotely operated vehicles, we found seven
>>>>> previously
>>>>> unknown species of swimming annelid worms below 1800 meters.
>>>>> Specimens were
>>>>> large and bore a variety of elaborate head appendages. In
>>>>> addition, five
>>>>> species have pairs of ellipsoidal organs homologous to branchiae
>>>>> that produce
>>>>> brilliant green bioluminescence when autotomized. Five genes
>>>>> were used to
>>>>> determine the evolutionary relationships of these worms within
>>>>> Cirratuliformia. These species form a clade within Acrocirridae
>>>>> and were not
>>>>> closely related to either of the two known pelagic
>>>>> cirratuliforms. Thus, this
>>>>> clade represents a third invasion of the pelagic realm from
>>>>> Cirratuliformia.
>>>>> This finding emphasizes the wealth of discoveries to be made in
>>>>> pelagic and
>>>>> deep demersal habitats."
>>>>>>>>>>>>>>> Nice discovery. I want to know what they feed on, and how.
>>>>>>>>>> Geoff
>>>>>>>>>>>>>>> --
>>>>>>>>>> Geoff Read <g.read from niwa.co.nz>
>>>>>http://www.annelida.net/>>>>>http://www.niwa.co.nz/about-niwa>>>>> ***************************
>>>>>>>>>>>>>>> NIWA is the trading name of the National Institute of Water &
>>>>> Atmospheric
>>>>> Research Ltd.
>>>>>>>>>> _______________________________________________
>>>>> Annelida mailing list
>>>>> Post: Annelida from net.bio.net>>>>> Help/archive: http://www.bio.net/biomail/listinfo/annelida>>>>> Resources: http://www.annelida.net>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>> Annelida mailing list
>>>>> Post: Annelida from net.bio.net>>>>> Help/archive: http://www.bio.net/biomail/listinfo/annelida>>>>> Resources: http://www.annelida.net>>>>>>>>>>>>>>>>> ------ CONTACT INFORMATION ------
>>>> PD Dr. habil. Torsten H. Struck
>>>> University of Osnabrück
>>>> Department of Biology/Chemistry
>>>> Zoology
>>>> Barbarastrasse 11
>>>> D-49069 Osnabrück
>>>> Germany
>>>>>>>> Phone: +49-541-9693450
>>>> Fax: +49-541-9692587
>>>> e-mail: struck from biologie.uni-osnabrueck.de>>>>>> <ATT00001.txt>
>>>> Greg Rouse
>> Scripps Institution of Oceanography, UCSD
>> 9500 Gilman Drive
>> La Jolla CA, 92093-0202
>> USA
>>>>http://spineless.ucsd.edu/>>>> e-mail: grouse from ucsd.edu>> Office Ph: +1 858 534 7973
>> Lab Ph: +1 858 534 9941
>> Fax: +1 858 534 7313
>>>> Courier delivery address:
>> Scripps Institution of Oceanography
>> 8750 Biological Grade
>> 2170 Hubbs Hall
>> La Jolla, CA 92037
>> USA
>> .............................................................................
>>>>>>>>>> _______________________________________________
>> Annelida mailing list
>> Post: Annelida from net.bio.net>> Help/archive: http://www.bio.net/biomail/listinfo/annelida>> Resources: http://www.annelida.net>> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> J. Kirk Fitzhugh, Ph.D.
> Curator of Polychaetes
> Invertebrate Zoology Section
> Research & Collections Branch
> Natural History Museum of Los Angeles County
> 900 Exposition Blvd
> Los Angeles CA 90007
> Phone: 213-763-3233
> FAX: 213-746-2999
> e-mail: kfitzhug from nhm.org>http://www.nhm.org/research/annelida/staff.html>http://www.nhm.org/research/annelida/index.html> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> <ATT00001.txt>
Greg Rouse
Scripps Institution of Oceanography, UCSD
9500 Gilman Drive
La Jolla CA, 92093-0202
USA
http://spineless.ucsd.edu/
e-mail: grouse from ucsd.edu
Office Ph: +1 858 534 7973
Lab Ph: +1 858 534 9941
Fax: +1 858 534 7313
Courier delivery address:
Scripps Institution of Oceanography
8750 Biological Grade
2170 Hubbs Hall
La Jolla, CA 92037
USA
.............................................................................
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