Fundamentals in Systematics

Thu Mar 9 09:03:57 CST 2006

Hi Lyn et al.

I don't specifically raise the issue of new species rendering their
parent species paraphyletic with the third year students.

One thing is that rather than seeing the "parent" species as a
paraphyletic group of individuals, those individuals should have the
potential to interbreed, and consequently their continued
reticulations are _within_ the branch of the imaginary cladogram, and
aren't really a paraphyletic "group" at all.  In that case I see that
it makes the whole species paraphyly "problem" one of an artefact
caused by confusing species with individuals, as terminal taxa, and
forgetting that individuals within species are reticulate.

As for drawing a ruled line across a cladogram - do people really do
that?  I know it is done with phenetic analyses to show a level of
dissimilarity across all groups, but not for cladograms. I am quite
happy to delimit species by phenetic methods, and to reconstruct
their relationships with phylogenetic methods.

Cheers, David.

On 08/03/2006, at 11:45 AM, <Lyn.Craven at csiro.au>
<Lyn.Craven at csiro.au> wrote:

>
> David,
>
> What do you teach about some of the really hard points involved in
> classifying evolutionary products (e.g. species), such as paraphyly?
> The theoretical (and hence perfect) view of total monophyly for
> classifications, as exemplified by the more extreme cladists, comes
> apart when faced with the realities of evolution.
>
> Really bright students might anticipate the question, but it usually
> takes some years of studying a group before the penny drops that
> classifications made by drawing a ruled line across the phylogeny are
> often about as useful as a ruled line across a blank sheet of paper.
>
> Lyn
>
>
> -----Original Message-----
> From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
> Behalf Of David Orlovich
> Sent: Wednesday, March 08, 2006 7:22 AM
> To: TAXACOM at LISTSERV.NHM.KU.EDU
> Subject: Re: [TAXACOM] Fundamentals in Systematics
>
>
> Actually I'll follow up my own post here.  The papers I included
> below are for an undergraduate class, but I don't really see much
> difference since we don't have too much graduate coursework here.
>
> Also, the papers I listed aren't necessarily classic papers - in fact
> maybe none of them are.  One of the hardest things is to get the
> students interested in systematics.  I try to do a good job - one
> student told me that I was really good at making really boring things
> sound like fun!  I'm not sure how much of a compliment that was
> though!  I try to get them engaged in controversy.  Hence discussions
> on things like the balance between nomenclatural stability and
> achieving a phylogenetic classification, and things like that.
>
> Cheers, David Orlovich.
>
>
> On 08/03/2006, at 9:11 AM, David Orlovich wrote:
>
>> On 8/03/2006, at 4:56 AM, Susan B. Farmer wrote:
>>
>>> If you were going to teach a Fundamentals of Systematics class, what
>>> papers would you include?
>>>
>>> Susan
>>>
>>
>> Well these are the ones I've just put together for this semester.
>> I also include a selection of my own papers, that I haven't listed
>> here.  I admit it is an eclectic mix.  The students get a few
>> lectures from me on each topic, and we dedicate at least a lecture
>> per topic to discussing the literature.
>>
>> Cheers, David Orlovich
>>
>> Classification
>>
>> Mayr E 1998. Perspective. Two empires or three. Proceedings of the
>> National Academy of Sciences USA 95, 9720-9723.
>>
>> Woese CR 1998. Perspective. Default taxonomy: Ernst Mayr's view of
>> the microbial world. Proceedings of the National Academy of
>> Sciences USA 95, 11043-11046.
>>
>> Nomenclature
>>
>> Entwisle TJ, Weston PH 2005. Majority rules, when systematists
>> disagree. Australian Systematic Botany 18, 1-6.
>>
>> Phylogenetics
>>
>> Funk VA 2001. SSZ 1970-1989: A view of the years of conflict.
>> Systematic Biology 50, 153-155.
>>
>> Felsenstein J 2001. The troubled growth of statistical
>> phylogenetics. Systematic Biology 50, 465-467.
>>
>> Hibbett DS, Gilbert L-B, Donoghue MJ 2000. Evolutionary instability
>> of ectomycorrhizal symbioses in basidiomycetes. Nature 407,
>> 506-508. (example of use of phylogenetic trees)
>>
>> Barkman TJ, Lim S-H, Salleh KM, Nais J 2004. Mitochondrial DNA
>> sequences reveal the photosynthetic relatives Rafflesia, the
>> world's largest flower. Proceedings of the National Academy of
>> Sciences USA 101, 787-792.
>>
>> Barkman TJ, Chenery G, McNeal JR, Lyons-Weiler J, Ellisens WJ,
>> Moore G, Wolfe AD, dePamphilis CW 2000. Independent and combined
>> analyses of sequences from all three genomic compartments converge
>> on the root of flowering plantphylogeny. Proceedings of the
>> National Academy of Sciences USA 97, 13116-13171.
>>
>> I try to get a debate going about the current focus on molecular
>> systematics, and give the students the following papers.
>>
>> Isley D 1972. The disappearance. Taxon 21, 3-12.
>>
>> Lammers TG 1999. Commentary. Plant systematics today: All our eggs
>> in one basket? Systematic Botany 24, 494-496.
>>
>> Stace CA 2005. Plant taxonomy and biosystematics - does DNA provide
>> all the answers? Taxon 54, 999-1007.
>>
>> Cresci JV 2006. Commentary. One-dimensional systematist: Perils in
>> a time of steady progress. Systematic Botany 31, 217-221.
>>
>> Hebert PDN, Cywinska A, Ball SL 2002. Biological identifications
>> through DNA barcodes. Proceedings of the Royal Society of London,
>> Series B DOI10.1098/rspb.2002.2218.
>>
>> Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM 2004. Identification
>> of birds through DNA barcodes. PLoS Biology 2, e312.
>>
>> Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W 2004. Ten
>> species in one; DNA barcoding reveals cryptic species in the
>> neotropical skipper butterfly Astraptes fulgerator. Proceedings of
>> the National Academy of Sciences USA101, 14812-14817.
>>
>> Moritz C, Cicero C 2004. Correspondence: DNA barcoding: Promise and
>> pitfalls. PLoS Biology 2, e354.
>>
>>
>>
>>> And on a similar note to the Phylogenetics text question ...
>>>
>>> In our department, there are several "Fundamentals" classes that all
>>> graduate students are required to take wherein they read the classic
>>> papers of the particular topic -- "Fundamentals in Evolution" and
>>> "Fundamentals of Ecology" for 2 of them.
>>>
>>> If you were going to teach a Fundamentals of Systematics class, what
>>> papers would you include?
>>>
>>> Susan
>>> -----
>>> Susan Farmer
>>> sfarmer at goldsword.com
>>> University of Tennessee
>>> Department of Ecology and Evolutionary Biology
>>> http://www.goldsword.com/sfarmer/Trillium/
>>>
>> Dr David Orlovich,
>> Senior Lecturer in Botany.
>>
>> Department of Botany,
>> University of Otago,
>> P.O. Box 56,
>> (Courier: 464 Great King Street)
>> Dunedin,
>> New Zealand.
>>
>> Phone: +643 479 9060
>> Fax: +643 479 7583
>> Mobile: +6421 122 7230
>>
>> Web: http://www.botany.otago.ac.nz/
>>
>> Ecology, Conservation and Biodiversity Research Group: http://
>> www.otago.ac.nz/erg/
>>
>> Botanical Society of Otago: http://www.botany.otago.ac.nz/bso/
>
> Dr David Orlovich,
> Senior Lecturer in Botany.
>
> Department of Botany,
> University of Otago,
> P.O. Box 56,
> (Courier: 464 Great King Street)
> Dunedin,
> New Zealand.
>
> Phone: +643 479 9060
> Fax: +643 479 7583
> Mobile: +6421 122 7230
>
> Web: http://www.botany.otago.ac.nz/
> Ecology, Conservation and Biodiversity Research Group: http://
> www.otago.ac.nz/erg/
> Botanical Society of Otago: http://www.botany.otago.ac.nz/bso/
> Fungal Network of New Zealand: http://www.funnz.org.nz/

Dr David Orlovich,
Senior Lecturer in Botany.

Department of Botany,
University of Otago,
P.O. Box 56,
(Courier: 464 Great King Street)
Dunedin,
New Zealand.

Phone: +643 479 9060
Fax: +643 479 7583
Mobile: +6421 122 7230

Web: http://www.botany.otago.ac.nz/
Ecology, Conservation and Biodiversity Research Group: http://
www.otago.ac.nz/erg/
Botanical Society of Otago: http://www.botany.otago.ac.nz/bso/
Fungal Network of New Zealand: http://www.funnz.org.nz/