[Taxacom] Collections and APG

Alina Freire-Fierro freirefierro at acnatsci.org
Mon Nov 12 13:04:46 CST 2007


Hi,


In our case (PH herbarium, ~ 1,5 million specimens) and in other cases
(other large herbaria in the US and Latin America) have followed the more
than 100-year old Englerian system (in which angiosperms and gymnosperms
numbered 1 through 280).

We try to update our collection as much as we can with the one from the APG.
But it can not be so easy, because sometimes I do not know to which APG
family assign a particular genus (so far we have been using the 1997 edition
of Mabberley's Plant Book).

On the other hand, there is this publication that came in the February's
issue of Taxon: 

Haston, Elspeth; Richardson, James E.; Stevens, Peter F.; Chase, Mark W.;
Harris, David J. 2007. A linear sequence of Angiosperm Phylogeny Group II
families. Taxon 56 (1): 7-12, E12-E6(6).

In it, the authors present the 479 families (only angiosperms) in a linear
fashion, but closely reflecting the APG II.


So, it would also be interesting to know which herbaria have completely
switched from an alphabetical to a systematic system, and which herbaria
have switched the other way around? And how much time/people was involved
into that?

Best,

Alina.


******  
Alina Freire-Fierro
Collection Manager
PH Herbarium, Botany Department
Academy of Natural Sciences
Philadelphia, PA 19103-1151
U.S.A.
*
freirefierro at ansp.org
Tel: 1-215-299-1157; Fax: 1-215-299-1051
http://www.ansp.org/research/biodiv/botany/index.php
http://www.mbgpress.info/index.php?task=id&id=90148
http://espanol.groups.yahoo.com/group/Anunciosbotanicos/



> From: "taxacom-request at mailman.nhm.ku.edu"
> <taxacom-request at mailman.nhm.ku.edu>
> Reply-To: <taxacom at mailman.nhm.ku.edu>
> Date: Mon, 12 Nov 2007 12:00:02 -0600
> To: <taxacom at mailman.nhm.ku.edu>
> Subject: Taxacom Digest, Vol 20, Issue 11
> 
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> Today's Topics:
> 
>    1. Postdoctoral Fellowship on Cape Plants (Terry Hedderson)
>    2. Re: Practical Taxon Concept Software (Anthony Pigott)
>    3. Re: Practical Taxon Concept Software (Anthony Pigott)
>    4. COllections and APG (Tati Konno)
>    5. Re: COllections and APG (Thomas G. Lammers)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 12 Nov 2007 10:26:43 +0200
> From: Terry Hedderson <thedders at egs.uct.ac.za>
> Subject: [Taxacom] Postdoctoral Fellowship on Cape Plants
> To: Taxacom at mailman.nhm.ku.edu, HERBARIA at NACSE.ORG
> Cc: bryonet-l at mtu.edu
> Message-ID: <E72C2F98-042A-47EC-937E-65CA9357411B at egs.uct.ac.za>
> Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes;
> format=flowed
> 
> Please note the following advert and kindly pass it on to potentially
> interested/suitable individuals.
> 
>  From outside South Africa, the stipend might seem small.  However,
> it is tax free and actually constitutes a reasonable wage given
> living costs in South Africa.  The Smuts Fellowship has been very
> productive for most people who have held it over the years, with the
> most recent fellow getting his work into NATURE.
> 
> Please contact me for any further clarification that you might require.
> 
> 
> 
> SMUTS MEMORIAL BOTANICAL FELLOWSHIP: 2008/9
> 
> 
> 
> VALUE UP TO R115 000 PA
> 
> 
> Applications are invited from suitably qualified persons for this
> prestigious Fellowship which commemorates General Smuts? interest in
> South African Botany.
> 
> The object of the Fellowship is to enable a person who has exhibited
> proficiency in independent research to undertake study and research
> in systematic botany and geographical distribution of South African
> flora, these being the branches of Botany in which General Smuts was
> most keenly interested.  The possibility of work on other aspects of
> the South African flora is not excluded.
> 
> The fellowship is open to any person, South African or otherwise, who
> is capable of carrying out its objective and materially advancing the
> knowledge of the South African flora.  Possession of a PhD degree is
> a minimum requirement.
> 
> The work of the Fellow will be under the general supervision of the
> Director of Research, South African National Botanical Institute,
> Kirstenbosch, and the Head of Botany at the University of Cape Town.
> The Fellow will also be offered the opportunity to participate in the
> teaching and supervision of senior students in Botany.
> 
> The Fellowship will be awarded for one year in the first instance and
> may be renewed for an additional year subject to satisfactory
> progress.  An extension for a third year will be considered only in
> exceptional cases.
> 
> Please complete the PDOC01 application Form.  This is available from
> the Postgraduate Centre and Funding Office and electronically on
> www.pgfo.uct.ac.za
> 
> Applications must include the following:
> 
> -The completed PDOC01 Application form including all required
> information and attachments.
> 
> -The applicant?s full curriculum vitae and list of publications.
> 
> -Three reports from referees, which must be submitted in sealed
> envelopes.
> 
> -Certified copies of all academic transcripts and degree certificates.
> 
> Applications should be to the Head of Department  of Botany;
> Information on faculty structure and academic departments may be
> found on the UCT website at http://www.uct.ac.za
> 
> All applicants are subject to the policies surrounding the
> postdoctoral sector at the University of Cape Town
> 
> 
> 
> The closing date for receipt of applications is 30 November 2007.
> Please note that late and/or incomplete applications will not be
> accepted.
> 
> 
> 
> The University of Cape Town reserves the right to make no awards at
> all; to cancel the award if the conditions are not met, and to effect
> changes to the conditions of award.
> 
> 
> 
> Prof. T.A.  Hedderson
> Dept. of Botany
> University of Cape Town
> thedders at egs.uct.ac.za
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 12 Nov 2007 10:36:55 -0000
> From: "Anthony Pigott" <Anthony.Pigott at btinternet.com>
> Subject: Re: [Taxacom] Practical Taxon Concept Software
> To: "Adorian Ardelean" <ardelean at aquaecology.de>, "Gael Lancelot"
> <lancelot at mnhn.fr>
> Cc: Taxacom <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <DCEFIBBAOPBHLHBNBDGHAEEMKCAA.Anthony.Pigott at btinternet.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Thanks To Gael and Adorian for your help / advice.
> 
> Adorian - I think you've very accurately described what I'm looking for and
> what many of the issues are.
> 
> Regards
> 
> Anthony
>   -----Original Message-----
>   From: Adorian Ardelean [mailto:ardelean at aquaecology.de]
>   Sent: 29 October 2007 10:39
>   To: Gael Lancelot; Anthony Pigott
>   Cc: Taxacom
>   Subject: Re: [Taxacom] Practical Taxon Concept Software
> 
> 
>   Dear Lancelot,
> 
>   From my interpretation, Anthony needs to build/explore several custom and
> concurrent (perhaps even ad-hoc) scenarios on what is Dryopteris affinis (in
> a neutral fashion). This is highly related with published record (e.g.
> monographies, revisional work, in general taxonomic literature) .
> 
>   Indeed the results in the search suggested by you may include several
> taxonomic concepts, but tracing what taxonomic concept was used when
> labeling specimens stops at data source specimen/its label/ or in the best
> case its citation in literature. It does not return a whole taxon concept
> with lists of related names and relations among them. I guess, for some of
> the records the use of LSIDs, RDF and semantic web may be useful for tracing
> the applied taxon concept, but I am not sure how much development is
> currently put into this.
> 
>   As I see things now, there are two directions on how this may be
> approached: simple synonymy lists and laborious chresonymy. In first
> instance, it would be wonderful if GBIF for example or other similar
> projects will produce filters for selecting occurrence data allowing
> alternative views (taxon concepts in form of synonym lists) or, why not,
> even user suggested views. I guess this is  easily achievable if a standard
> is developed and various international resources serve their synonym lists
> for further use. However, this may not solve Anthony's issue because
> although all labels on specimens say D. affinis behind may be different
> taxon concepts (we could have specimens collected in at least 200 years!)
> and this can be solved mainly by tracing literature and citation of
> specimens in literature (more related to chresonymy). This is a quite
> difficult and laborious task that can be actually passed partially to user
> side (if we speak about a limited number of records), or to taxon focused
> projects. In myNature project (http://mybiosis.org) for example we will ask
> users to specify what guide, key, publication was used when ID was given -
> this included in metadata of record may help later deciding on what taxon
> concept was applied. Aside from this discussion, I see regional biodiversity
> focused projects enormously benefiting from such developments.
> 
>   All the best,
>   Adorian
> 
> 
>   At 09:59 29.10.2007, Gael Lancelot wrote:
> 
>     This might not be exactly what you're looking for, but GBIF (Global
>     Biodiversity Information Facility) connects together a large number of
>     specimen and observation databases, and keeps record of the taxonomy
>     used in each. You can consult these taxonomies for Dryopteris affinis
>     at this link:
> 
> http://data.gbif.org/species/search.htm?c[0].s=0&c[0].p=0&c[0].o=Dryopteris%
> 20affinis&c[1].s=9&c[1].p=0&c[1].o=7000
> 
>     More general information to be had at http://data.gbif.org .
> 
>     Cheers,
> 
>     G. Lancelot
> 
>> Thanks for the responses. I'll try to be a bit more specific. I'd like
> to be
>> able to record and organise the various names that taxa have been
> given in
>> different treatments so that I can in due course produce a 'preferred
>> taxonomy with synonymy, etc., as traditionally done in a monograph, I
>> suppose, but also to be able to compare and demonstrate alternative
>> treatments in a neutral way.  The immediate target is the Dryopteris
> affinis
>> complex in the ferns, which is a  particularly nomenclaturally-tangled
>> asexual species complex in which most taxa have been given a wealth of
> names
>> at various levels and with various circumscriptions. I thought it
> would be
>> useful way to approach it especially as I'm interested in the idea of
>> databases holding multiple taxonomies (alternative treatments) rather
> than
>> the more traditional method of just holding one preferred view with
>> synonymy.
>> 
>> Regards
>> 
>> Anthony
>> 
>>> -----Original Message-----
>>> From: taxacom-bounces at mailman.nhm.ku.edu
>>> [ mailto:taxacom-bounces at mailman.nhm.ku.edu]On Behalf Of Roger Hyam
>>> Sent: 28 October 2007 20:52
>>> To: taxacom at mailman.nhm.ku.edu
>>> Subject: [Taxacom] Practical Taxon Concept Software
>>> 
>>> 
>>> 
>>> Anthony,
>>> 
>>> I'd be interested to know your requirements a little better. Why do
>>> you want to track the taxonomies? Are you creating a monograph or
>>> flora/fauna or do you need it to accurately integrate ecological or
>>> other studies?
>>> 
>>> The chances are you don't just want Taxon Concept software but want
>>> software to do something "useful" that just happens to handle Taxon
>>> Concepts data correctly.
>>> 
>>> Thanks,
>>> 
>>> Roger
>>> 
>>> 
>>> 
>>> 
>>> On 28 Oct 2007, at 17:00, taxacom-request at mailman.nhm.ku.edu wrote:
>>> 
>>>> Date: Sun, 28 Oct 2007 10:03:14 -0000
>>>> From: "Anthony Pigott" <Anthony.Pigott at btinternet.com>
>>>> Subject: [Taxacom] Practical Taxon Concept Software
>>>> To: "Taxacom" <taxacom at mailman.nhm.ku.edu>
>>>> Message-ID:
>>>>     <DCEFIBBAOPBHLHBNBDGHGEKAKAAA.Anthony.Pigott at btinternet.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>> 
>>>> Does anyone have experience of the practical use of software
>>>> supporting the
>>>> creation and use of a database for recording multiple taxonomies,
>>>> i.e. taxon
>>>> concepts, publication-based, etc.?  I've tried a few of the
>>>> examples that
>>>> various people have built and made available for download but so
>>>> far I've
>>>> not found anything that works sufficiently well (or at all,
>>>> sometimes) for
>>>> practical use. Thanks.
>>>> 
>>>> Anthony
>>> 
>>> 
>>> _______________________________________________
>>> Taxacom mailing list
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>> 
>> 
>> 
>> _______________________________________________
>> Taxacom mailing list
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>> 
> 
> 
> 
>     Ga?l Lancelot
>     Communication Officier
>     EDIT - WP1
>     (0033)1 40 79 80 19
> 
> 
> 
>     _______________________________________________
>     Taxacom mailing list
>     Taxacom at mailman.nhm.ku.edu
>     http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>   Dr. Adorian Ardelean
> 
> 
> 
> ----------------------------------------------------------------------------
> --
>   AquaEcology
>   Stresemanstr. 46
>   27570 Bremerhaven
>   Germany
> 
>   Phone: 0471-140-475
> 
> ----------------------------------------------------------------------------
> --
>   coordinator of myNature Project
> 
>   proiectul myNature
>   str. Rascoala din 1907 nr 12
>   Timisoara 300325
>   Romania
> 
>   http://mybiosis.org/nature/portal.php?pagename=firstpage [a Romanian
> biodiversity-database]
>   http://mybiosis.org/nature/portal.php?pagename=adorian [CV]
>   http://mybiosis.org/romanianorchids/ [Romanian Orchids]
>   http://greendorf.com [botanical illustration]
>   http://planktonnet.awi.de/ [planktonNet]
> 
>   Projects in which I was involved:
>   http://hercules.kgs.ku.edu/Hexacoral/Anemone2/ [Hexacorallians of the
> World]
>   http://www.ubio.org [uBio Project]
>   http://portal.ubio.org [uBio Portal]
>   http://microscope.mbl.edu [micro*scope Project]
>   http://starcentral.mbl.edu/biopedia [BioPedia]
>   http://starcentral.mbl.edu/custar [CU*STAR]
> 
>   Yahoo messenger: transylvaniasan
> 
>   Ne vom ?ntoarce ?ntr-o zi...
>   Si cei de azi cu pasii grei
>   Nu ne-or vedea, nu ne-or simti,
>   Cum vom intra ?ncet ?n ei.
>   Radu Gyr
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 12 Nov 2007 10:41:57 -0000
> From: "Anthony Pigott" <Anthony.Pigott at btinternet.com>
> Subject: Re: [Taxacom] Practical Taxon Concept Software
> To: "Taxacom" <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <DCEFIBBAOPBHLHBNBDGHMEENKCAA.Anthony.Pigott at btinternet.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Thanks to everyone for all the responses, both on and off this list. I think
> I've responded to everyone but if not , apologies and thanks again.
> 
> I've got a number of new leads to follow.
> 
> Regards
> 
> Anthony
> 
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu
>> [mailto:taxacom-bounces at mailman.nhm.ku.edu]On Behalf Of Anthony Pigott
>> Sent: 28 October 2007 10:03
>> To: Taxacom
>> Subject: [Taxacom] Practical Taxon Concept Software
>> 
>> 
>> Does anyone have experience of the practical use of software
>> supporting the
>> creation and use of a database for recording multiple taxonomies,
>> i.e. taxon
>> concepts, publication-based, etc.?  I've tried a few of the examples that
>> various people have built and made available for download but so far I've
>> not found anything that works sufficiently well (or at all, sometimes) for
>> practical use. Thanks.
>> 
>> Anthony
>> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Mon, 12 Nov 2007 15:12:56 -0300
> From: "Tati Konno" <tkonno at uol.com.br>
> Subject: [Taxacom] COllections and APG
> To: <taxacom at mailman.nhm.ku.edu>
> Message-ID: <20071112171421.9BDBD457 at socom1.uol.com.br>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear Taxacomers
> 
> I?m organizing a botanical collection for local reference and I came across
> an interesting issue. What classification system should I use? APG is in
> constant move and seems to be not so practical to manage.
> 
> So I would like to ask, especially to curators:
> 
> What system do you apply in your collection?
> 
> Do you think that a collection should be organized in order to reflect a
> system?
> 
>  
> 
> Thanks in advance
> 
>  
> 
> TK
> 
>  
> 
> ****************************************************************************
> ***
> 
> TATIANA UNGARETTI PALEO KONNO
> 
> N?cleo em Ecologia e Desenvolvimento S?cio-Ambiental de Maca? (NUPEM/UFRJ)
> 
> Rua Rotary Club s/n (atr?s do Parque de Exposi??es) S?o Jos? do Barreto --
> Maca? -- RJ
> 
> Cx. Postal 119331   CEP 27910-970
> 
> tel.: 22 27629313  ramal 209
> 
> VoIP: 11006976
> 
>  
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Mon, 12 Nov 2007 12:36:05 -0500
> From: "Thomas G. Lammers" <lammers at uwosh.edu>
> Subject: Re: [Taxacom] COllections and APG
> To: Tati Konno <tkonno at uol.com.br>, taxacom at mailman.nhm.ku.edu
> Message-ID: <6.1.0.6.2.20071112123304.01be6ec0 at mail.uwosh.edu>
> Content-Type: text/plain; format=flowed; charset=us-ascii
> 
> At 01:12 PM 11/12/2007, Tati Konno wrote:
>> Do you think that a collection should be organized in order to reflect a
>> system?
> 
> No.  Two reasons:
> 
> (1) Practicality.  Nothing beats the alphabet, especially if your filers
> aren't Ph.D. systematists.  An alphabetical arrangement disposes of the
> need for guide sheets, numbering the families, etc.
> 
> (2) Misleading about evolution.  We know that evolution is a branching (and
> reticulating) process; it is misleading to distort that reality into a
> linear sequence.  Conjures up bad misconceptions about the
> "progressiveness" of evolution, Scala Naturae, etc.
> 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.geocities.com/TheTropics/Resort/7156/lammers.html
> -----------------------------------------------------------
> "Today's mighty oak is yesterday's nut that stood his ground."
>                                                                -- Anonymous
> 
> 
> ------------------------------
> 
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