[Taxacom] Seeking for a technician - Systematics of Caribbean cycads

Javier Ortega ortegaj at fiu.edu
Mon Jan 10 14:36:41 CST 2011


Dear Systematists,

We (FIU-Fairchild, USDA, Montgomery Botanical Center, and New York Botanic Garden) were fortunate to have a NSF proposal (focusing on molecular systematics and population genetics of Caribbean cycads) funded this go round, and we are looking to fill a 2-year technical position who will be working primarily in USDA (Alan Meerow's lab).  Our target would be an advanced undergraduate student or MS with the molecular biology skills.  If you know anyone who might be interested or anyone else who should see the description, please forward to Alan (Alan.Meerow at ars.usda.gov) or to me.
 
With best,


===============
Javier Francisco-Ortega,
Associate Professor,
Department of Biological Sciences,
Florida International University,
OE167 - University Park,
Miami, FL 33199
USA
Phone: 305-348-2080
Fax: 305-348-1986

Center for Tropical Plant Conservation,
Fairchild Tropical Botanic Garden,
11935 Old Cutler Road,
Coral Gables (Miami),
FL 33156
USA
Phone: 305-665-2844 Ext 3423 or Ext 3432
________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] on behalf of taxacom-request at mailman.nhm.ku.edu [taxacom-request at mailman.nhm.ku.edu]
Sent: Sunday, December 12, 2010 1:00 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Taxacom Digest, Vol 57, Issue 11

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Today's Topics:

   1. Re: [Taxacom Digest] Phylogenetic Game (Simon Mayo)
   2. Phylogenetic Game (Richard Zander)
   3. Re: Phylogenetic Game (Curtis Clark)
   4. Re: Phylogenetic Game (Richard Zander)
   5. Re: Phylogenetic Game (Curtis Clark)
   6. Re: Phylogenetic Game (John Grehan)


----------------------------------------------------------------------

Message: 1
Date: Sat, 11 Dec 2010 19:31:12 +0000
From: Simon Mayo <simonjosephmayo at hotmail.co.uk>
Subject: Re: [Taxacom] [Taxacom Digest] Phylogenetic Game
To: taxacom <taxacom at mailman.nhm.ku.edu>
Message-ID: <SNT120-W5EB720940D355438651D0F5100 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"


"Classification rather than systematization. Demarcating groups rather
than causal explanations."

Well...not rather than, just as well as and prior to causal explanations. All cladograms are based on patterns surely?


> From: taxacom-request at mailman.nhm.ku.edu
> Subject: Taxacom Digest, Vol 57, Issue 10
> To: taxacom at mailman.nhm.ku.edu
> Date: Sat, 11 Dec 2010 12:00:02 -0600
>
> Send Taxacom mailing list submissions to
>       taxacom at mailman.nhm.ku.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>       http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> or, via email, send a message with subject or body 'help' to
>       taxacom-request at mailman.nhm.ku.edu
>
> You can reach the person managing the list at
>       taxacom-owner at mailman.nhm.ku.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Taxacom digest..."
>
>
> Today's Topics:
>
>    1. Re: Phylogenetic Game (Simon Mayo)
>    2. Re: Phylogenetic Game (J. Kirk Fitzhugh)
>    3. Re: Phylogenetic Game (John Grehan)
>    4. Re: Phylogenetic Game (J. Kirk Fitzhugh)
>    5. Database of Vascular Plants of Canada (VASCAN) released
>       (Peter Desmet)
>    6. Re: Checklist of World Grasses [URL fixed] (Erik Rijkers)
>    7. Zootaxa 2713-2719 on Wikispecies (Stephen Thorpe)
>    8. Interciencia journal from Caracas (Geoff Read)
>    9. Re: Phylogenetic Game (Jim Croft)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 10 Dec 2010 18:12:39 +0000
> From: Simon Mayo <simonjosephmayo at hotmail.co.uk>
> Subject: Re: [Taxacom] Phylogenetic Game
> To: <taxacom at mailman.nhm.ku.edu>
> Message-ID: <SNT120-W23A6B1BCDF898D2260D34BF52F0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Peter,
>
> Idealistic morphology rears its head again in a new guise! Phylogeny is only interpretation of patterns ....
>
> Simon Mayo
>
> > From: taxacom-request at mailman.nhm.ku.edu
> > Subject: Taxacom Digest, Vol 57, Issue 9
> > To: taxacom at mailman.nhm.ku.edu
> > Date: Fri, 10 Dec 2010 12:00:01 -0600
> >
> > Send Taxacom mailing list submissions to
> >     taxacom at mailman.nhm.ku.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >     http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> > or, via email, send a message with subject or body 'help' to
> >     taxacom-request at mailman.nhm.ku.edu
> >
> > You can reach the person managing the list at
> >     taxacom-owner at mailman.nhm.ku.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Taxacom digest..."
> >
> >
> > Today's Topics:
> >
> >    1. protection of specimens (Vlastimil Mikolas)
> >    2. Re: protection of specimens (Hans Henderickx)
> >    3. Checklist of World Grasses (Simon Bryan)
> >    4. Phylogenetic Game (Peter Stevens)
> >    5. Re: Phylogenetic Game (John Grehan)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 9 Dec 2010 20:26:10 +0100
> > From: Vlastimil Mikolas <dolomiticola at gmail.com>
> > Subject: [Taxacom] protection of specimens
> > To: taxacom at mailman.nhm.ku.edu
> > Message-ID:
> >     <AANLkTi=vjwtyGpoFeFGjWxmknbzbe_hFoWNu9ByaLZHQ at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Dear Taxacomers,
> > I have many herb. specimens from Slovakia and adjacent Europe, including
> > many tax. critical taxa (all determined), however I have not enough of money
> > fo payment of rents of rooms with specimens. If you have interest in
> > specimens and can slightly to help me, write me. Many thanks !
> > Cordial best,
> > Vlastimil
> >
> > --
> > Vlastimil MIKOLAS
> > Hanojska 4
> > SK-040 13 KOSICE
> > Slovakia
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 9 Dec 2010 20:56:58 +0100
> > From: "Hans Henderickx" <cavexplorer at gmail.com>
> > Subject: Re: [Taxacom] protection of specimens
> > To: "Vlastimil Mikolas" <dolomiticola at gmail.com>,
> >     <taxacom at mailman.nhm.ku.edu>
> > Message-ID: <4F8B815CC2AB491C975F77C0DF7D47F5 at cavex76040a5ab>
> > Content-Type: text/plain; format=flowed; charset="iso-8859-1";
> >     reply-type=original
> >
> > That is interesting, Vlastimil. Than why did you collect them?
> > Hans
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Fri, 10 Dec 2010 13:13:22 +1000
> > From: "Simon Bryan" <bryan.simon at derm.qld.gov.au>
> > Subject: [Taxacom] Checklist of World Grasses
> > To: <taxacom at mailman.nhm.ku.edu>
> > Message-ID:
> >     <FA14B37EFE33F647B409C8B24F40D169019CDA18 at MINMAIL4.lands.resnet.qg>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > A check-list of currently accepted species of grasses of the world can
> > be found at the GrassWorld Scratchpad
> > http://grassworld.myspecies.info/content/check-list-world-grasses
> > The first list includes authors,  place of publication and TDWG Level 1
> > distributions  (Europe, Africa, Temperate Asia, Tropical Asia,
> > Australasia, Pacific, North America, South America, Antarctic.) and
> > classification, where subfamilies, tribes and genera follow GPWG and
> > subsequent grass taxonomic literature.
> > Lists of each Continental Region follow, with TDWG Level 3 distributions
> > indicated. Distributional information has been gleaned from the
> > agrostological literature, the Kew SYNON access database and TROPICOS.
> > Feedback from users would be much appreciated in cases where information
> > is noted to be incorrect or where different distributional information
> > from that given in this check-list is known. Exchange of such
> > information can be placed in the Forums section of the GrassWorld
> > Scratchpad.
> > It is possible to provide a list of grasses to interested parties of any
> > country of the world or region of larger countries (Russia, China,
> > India, USA, Canada, Brazil, Argentina, Chile, Mexico, Australia, South
> > Africa) where this information is available.
> > Bryan Simon
> > Principal Botanist
> > Queensland Herbarium
> > DERM, Brisbane Botanic Gardens
> > Mt Coot-tha, Toowong, Qld 4066
> > Australia
> >
> >
> >
> >
> > +----------------------------------------------------------------+
> > Think B4U Print
> > 1 ream of paper = 6% of a tree and 5.4kg CO2 in the atmosphere
> > 3 sheets of A4 paper = 1 litre of water
> > +----------------------------------------------------------------+
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Fri, 10 Dec 2010 11:02:09 -0600
> > From: Peter Stevens <peter.stevens at mobot.org>
> > Subject: [Taxacom] Phylogenetic Game
> > To: TAXACOM <taxacom at mailman.nhm.ku.edu>
> > Message-ID: <C8CF6F50-1BB9-4DBD-836D-8A0FB85468D7 at mobot.org>
> > Content-Type: text/plain;   charset=WINDOWS-1252;   delsp=yes;
> >     format=flowed
> >
> > Note that "Players don't need to understand (or even care about)
> > phylogenetics."
> >
> > P.
> >
> > Subject: Phylogenetics game
> >
> > December 2, 2010 | A pattern-matching puzzle created by
> > bioinformaticians at McGill University lets players sort genetic
> > code. The game, called Phylo, takes advantage of the human brain's
> > efficiency at recognizing and sorting patterns to tackle multiple
> > sequence alignments.
> >
> > Aligning genetic sequences is traditionally done computationally, but
> > what is a huge computational problem, is a bit easier for the human
> > brain. ?There are some calculations that the human brain does more
> > efficiently than any computer can, such as recognizing a face,?
> > explained lead researcher J?r?me Waldispuhl of the School of Computer
> > Science in a McGill press release. ?Recognizing and sorting the
> > patterns in the human genetic code falls in that category."
> >
> > Players don't start from scratch, but instead refine data that has
> > already been aligned. "By taking data which has already been aligned
> > by a heuristic algorithm, we allow the user to optimize where the
> > algorithm may have failed," the game creators explain on the site.
> >
> > All alignments were made available through UCSC Genome Browser and
> > contain sections of human DNA which have been speculated to be linked
> > to various genetic disorders, such as breast cancer. Every alignment
> > is received, analyzed, and stored in a database, where it will
> > eventually be re-introduced back into the global alignment as an
> > optimization. Players can choose which disease they'd like to work
> > on, or be assigned to a random level.
> >
> > Players don't need to understand (or even care about) phylogenetics
> > though. Rather than strings of As, Ts, Cs, and Gs, players align four
> > colored squares on a grid. Each row of colors represents a sequence
> > from a certain species. Sequences can be moved horizontally and
> > spaced out, but not rearranged or deleted. The goal is to line up
> > columns of colors that represent alignments between the two or more
> > sequences. There will, of course, be gaps in sequences and spots
> > where the two rows don't match. The goal is to find the best tradeoff
> > between aligning color and creating gaps. Players try to manually
> > find the best alignment and beat the computer's original alignment
> > score. The first level aligns two sequences, and sequences are added
> > as players advance.
> >
> > Researchers released the game on Monday after testing. They hope the
> > create a Facebook, iPhone, and Android application versions of the
> > game. Until then, Phylo can be played at http://phylo.cs.mcgill.ca
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Fri, 10 Dec 2010 12:20:33 -0500
> > From: "John Grehan" <jgrehan at sciencebuff.org>
> > Subject: Re: [Taxacom] Phylogenetic Game
> > To: "TAXACOM" <taxacom at mailman.nhm.ku.edu>
> > Message-ID:
> >     <26DA12164B238549B6D89A2F2A8EE7990200F0CB at bmsmail.sciencebuff.org>
> > Content-Type: text/plain;   charset="iso-8859-1"
> >
> > This just goes to show that molecular phylogenetics is nothing more than a 'game'. Something I have suspected for a long time.
> >
> > John Grehan
> >
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Peter Stevens
> > Sent: Friday, December 10, 2010 12:02 PM
> > To: TAXACOM
> > Subject: [Taxacom] Phylogenetic Game
> >
> > Note that "Players don't need to understand (or even care about)
> > phylogenetics."
> >
> > P.
> >
> > Subject: Phylogenetics game
> >
> > December 2, 2010 | A pattern-matching puzzle created by
> > bioinformaticians at McGill University lets players sort genetic
> > code. The game, called Phylo, takes advantage of the human brain's
> > efficiency at recognizing and sorting patterns to tackle multiple
> > sequence alignments.
> >
> > Aligning genetic sequences is traditionally done computationally, but
> > what is a huge computational problem, is a bit easier for the human
> > brain. "There are some calculations that the human brain does more
> > efficiently than any computer can, such as recognizing a face,"
> > explained lead researcher J?r?me Waldispuhl of the School of Computer
> > Science in a McGill press release. "Recognizing and sorting the
> > patterns in the human genetic code falls in that category."
> >
> > Players don't start from scratch, but instead refine data that has
> > already been aligned. "By taking data which has already been aligned
> > by a heuristic algorithm, we allow the user to optimize where the
> > algorithm may have failed," the game creators explain on the site.
> >
> > All alignments were made available through UCSC Genome Browser and
> > contain sections of human DNA which have been speculated to be linked
> > to various genetic disorders, such as breast cancer. Every alignment
> > is received, analyzed, and stored in a database, where it will
> > eventually be re-introduced back into the global alignment as an
> > optimization. Players can choose which disease they'd like to work
> > on, or be assigned to a random level.
> >
> > Players don't need to understand (or even care about) phylogenetics
> > though. Rather than strings of As, Ts, Cs, and Gs, players align four
> > colored squares on a grid. Each row of colors represents a sequence
> > from a certain species. Sequences can be moved horizontally and
> > spaced out, but not rearranged or deleted. The goal is to line up
> > columns of colors that represent alignments between the two or more
> > sequences. There will, of course, be gaps in sequences and spots
> > where the two rows don't match. The goal is to find the best tradeoff
> > between aligning color and creating gaps. Players try to manually
> > find the best alignment and beat the computer's original alignment
> > score. The first level aligns two sequences, and sequences are added
> > as players advance.
> >
> > Researchers released the game on Monday after testing. They hope the
> > create a Facebook, iPhone, and Android application versions of the
> > game. Until then, Phylo can be played at http://phylo.cs.mcgill.ca
> >
> >
> > _______________________________________________
> >
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > The Taxacom archive going back to 1992 may be searched with either of these methods:
> >
> > (1) http://taxacom.markmail.org
> >
> > Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> >
> > Taxacom Mailing List
> >
> > Taxacom at mailman.nhm.ku.edu
> >
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > The entire Taxacom Archive back to 1992 can be searched with either of these methods:
> >
> > http://taxacom.markmail.org
> >
> > Or use a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> >
> > End of Taxacom Digest, Vol 57, Issue 9
> > **************************************
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 10 Dec 2010 10:21:55 -0800
> From: "J. Kirk Fitzhugh" <kfitzhugh at nhm.org>
> Subject: Re: [Taxacom] Phylogenetic Game
> To: taxacom at mailman.nhm.ku.edu
> Message-ID: <4D026FC3.6040509 at nhm.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> "Pattern" cladists will love it, as it has nothing at all to do with
> phylogenetics, much less science.
>
> On 12/10/2010 9:02 AM, Peter Stevens wrote:
> > Note that "Players don't need to understand (or even care about)
> > phylogenetics."
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 10 Dec 2010 13:28:31 -0500
> From: "John Grehan" <jgrehan at sciencebuff.org>
> Subject: Re: [Taxacom] Phylogenetic Game
> To: <taxacom at mailman.nhm.ku.edu>
> Message-ID:
>       <26DA12164B238549B6D89A2F2A8EE7990200F0F1 at bmsmail.sciencebuff.org>
> Content-Type: text/plain;     charset="us-ascii"
>
> What is the criterion being presented here for a "pattern" cladist.
>
> John Grehan
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of J. Kirk
> Fitzhugh
> Sent: Friday, December 10, 2010 1:22 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Phylogenetic Game
>
> "Pattern" cladists will love it, as it has nothing at all to do with
> phylogenetics, much less science.
>
> On 12/10/2010 9:02 AM, Peter Stevens wrote:
> > Note that "Players don't need to understand (or even care about)
> > phylogenetics."
>
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of
> these methods:
>
> (1) http://taxacom.markmail.org
>
> Or (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 10 Dec 2010 10:38:55 -0800
> From: "J. Kirk Fitzhugh" <kfitzhugh at nhm.org>
> Subject: Re: [Taxacom] Phylogenetic Game
> To: taxacom at mailman.nhm.ku.edu
> Message-ID: <4D0273BF.60908 at nhm.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Classification rather than systematization. Demarcating groups rather
> than causal explanations.
>
> On 12/10/2010 10:28 AM, John Grehan wrote:
> > What is the criterion being presented here for a "pattern" cladist.
> >
> > John Grehan
> >
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu
> > [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of J. Kirk
> > Fitzhugh
> > Sent: Friday, December 10, 2010 1:22 PM
> > To: taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] Phylogenetic Game
> >
> > "Pattern" cladists will love it, as it has nothing at all to do with
> > phylogenetics, much less science.
> >
> > On 12/10/2010 9:02 AM, Peter Stevens wrote:
> >> Note that "Players don't need to understand (or even care about)
> >> phylogenetics."
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 10 Dec 2010 16:11:05 -0500
> From: Peter Desmet <peter.desmet at umontreal.ca>
> Subject: [Taxacom] Database of Vascular Plants of Canada (VASCAN)
>       released
> To: Taxacom mailing list <taxacom at mailman.nhm.ku.edu>
> Message-ID:
>       <AANLkTikcYQAVbD3jETyjC0KvaGmab2ok8CoLEA7nWYuX at mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> *Database of Vascular Plants of Canada (VASCAN) released* (Fran?ais
> ci-apr?s)
>
> Canadensys announces the release of VASCAN, the Database of Vascular Plants
> of Canada, a comprehensive list of all vascular plants reported in Canada,
> Greenland (Denmark) and Saint Pierre and Miquelon (France).
>
> http://data.canadensys.net/vascan/
>
> Canadensys is a Canada-wide effort to unlock the biodiversity information
> held in biological collections. The network currently includes biological
> collections from 11 participating universities, five botanical gardens, and
> two museums, covering insects, fungi and plants. The network is operated
> from the Biodiversity Centre, Universit? de Montr?al.
>
> The goal of VASCAN is to provide an up-to-date, documented source of the
> names of vascular plants in Canada, Greenland, and Saint Pierre and
> Miquelon, both scientific and vernacular. For every species, subspecies and
> variety, VASCAN provides the accepted scientific name (Latin), the accepted
> French and English vernacular names, and their synonyms/alternatives in
> Canada. The distribution status (native, introduced, etc.) of the plant for
> each province or territory, and the habit (tree, shrub, herb or vine) of the
> plant in Canada are given. Maps at the provincial/territorial level are
> provided with an indication of status. For reported hybrids (nothotaxa or
> hybrid formulas), the parents also are provided. A source is given for each
> name, classification and distribution information (still being completed).
>  All taxa are linked to a classification. The following were used: Smith et
> al. (2006) for ferns, APG III (2009) for flowering plants, and Chase and
> Reveal (2009) for the higher taxonomy.
>
> It is possible to generate lists in VASCAN using the Checklist builder tool.
> Data can be downloaded from VASCAN under the Creative Commons (BY-NC)
> license.
>
> Brouillet, L., F. Coursol, M. Favreau & M. Anions (compilers). 2010+ VASCAN,
> the Database of Vascular Plants of Canada.
> http://data.canadensys.net/vascan/
>
> For information: http://data.canadensys.net/vascan/about
>
> ---
>
> *Publication de la Base de donn?es des Plantes Vasculaires du Canada
> (VASCAN)*
>
> Canadensys annonce la publication de VASCAN, la Base de donn?es des Plantes
> Vasculaires du Canada, une liste compl?te des plantes vasculaires
> identifi?es au Canada, au Gro?nland (Danemark) et ? Saint-Pierre-et-Miquelon
> (France).
>
> http://data.canadensys.net/vascan/?lang=fr
>
> Canadensys est un projet pancanadien visant ? rendre l?information contenue
> dans les collections biologiques accessible ? tous.  Pour l?instant le
> r?seau comprend les collections biologiques de 11 universit?s participantes,
> cinq jardins botaniques et deux mus?es, comprenant les insectes, les
> champignons et les plantes.  Le r?seau est g?r? par le Centre sur la
> biodiversit?, Universit? de Montr?al.
>
> Le but de VASCAN est de fournir une source ? jour, document?e des noms des
> plantes vasculaires du Canada, du Gro?nland, et de Saint-Pierre-et-Miquelon,
> tant scientifiques que vernaculaires. Pour chaque esp?ce, sous-esp?ce ou
> vari?t?, VASCAN fournit le nom scientifique accept? (latin), les noms
> vernaculaires fran?ais et anglais accept?s, et les synonymes/noms
> alternatifs au Canada. Nous donnons le statut de r?partition (indig?ne,
> introduit, etc.) de la plante dans chaque province ou territoire, et le port
> (arbre, arbuste, herbac?e ou vigne) de la plante au Canada. Nous fournissons
> une carte de r?partition par province/territoire avec indication du statut
> pour chaque taxon. Pour les hybrides (nothotaxons ou formules hybrides),
> nous donnons les parents. Nous fournissons une source pour tous les noms et
> les informations concernant la classification et la r?partition (en
> compl?tion). Tous les taxons sont li?s ? une classification. Nous suivons
> Smith et al. (2006) (2006) pour les foug?res et plantes alli?es, APG III
> (2009) pour les plantes ? fleur et Chase et Reveal (2009) pour la taxonomie
> sup?rieure.
>
> VASCAN permet de g?n?rer des listes de taxons selon divers crit?res
> (r?partition, port, etc.). Il est possible de t?l?charger les donn?es de
> VASCAN sous licence Creative Commons (BY-NC).
>
> Brouillet, L., F. Coursol, M. Favreau & M. Anions (compilateurs). 2010+.
> VASCAN, la Base de donn?es des Plantes Vasculaires du Canada.
> http://data.canadensys.net/vascan/
>
> Pour information: http://data.canadensys.net/vascan/about?lang=fr
>
>
> --
> Peter Desmet
> Biodiversity Informatics Manager / Directeur de l'informatique de la
> biodiversit?
> Biodiversity Centre / Centre sur la biodiversit?
> Canadensys - www.canadensys.net
>
> Institut de recherche en biologie v?g?tale
> Universit? de Montr?al
> 4101 rue Sherbrooke est
> Montr?al, Qu?bec, H1X2B2
> Canada
>
> T?l? / Phone: 514-343-6111 #82354
> T?l?copie / Fax: 514-872-9406
> Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 10 Dec 2010 22:30:45 +0100
> From: "Erik Rijkers" <er at xs4all.nl>
> Subject: Re: [Taxacom] Checklist of World Grasses [URL fixed]
> To: "Simon Bryan" <bryan.simon at derm.qld.gov.au>
> Cc: taxacom at mailman.nhm.ku.edu
> Message-ID:
>       <805fbfb890a58648fa1c7e492afa0240.squirrel at webmail.xs4all.nl>
> Content-Type: text/plain;charset=iso-8859-1
>
> On Fri, December 10, 2010 04:13, Simon Bryan wrote:
> > A check-list of currently accepted species of grasses of the world can
> > be found at the GrassWorld Scratchpad
> > http://grassworld.myspecies.info/content/check-list-world-grasses
>
>
> "Page not found
> The requested page could not be found. "
>
> The above url didn't work for me; this one does:
> http://grassworld.myspecies.info/content/check-list-world-grasses-december-2010
>
> or even just:
> http://grassworld.myspecies.info/
>
>
> Nice site - thanks,
>
>
> Erik Rijkers
>
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 10 Dec 2010 14:02:10 -0800 (PST)
> From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Subject: [Taxacom] Zootaxa 2713-2719 on Wikispecies
> To: taxacom at mailman.nhm.ku.edu
> Message-ID: <328904.83738.qm at web114218.mail.gq1.yahoo.com>
> Content-Type: text/plain; charset=utf-8
>
> Zootaxa 2713-2719 on Wikispecies:
> http://species.wikimedia.org/w/index.php?title=User:Stho002/notepad&oldid=1051174
>
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Sat, 11 Dec 2010 20:25:36 +1300 (NZDT)
> From: "Geoff Read" <gread at actrix.gen.nz>
> Subject: [Taxacom] Interciencia journal from Caracas
> To: taxacom at mailman.nhm.ku.edu
> Message-ID:
>       <ffbebbe4f6126c3a6b3689e92742a050.squirrel at my.actrix.co.nz>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi,
>
> I'm uncertain if Interciencia (ISSN 0378-1844) is now solely electronic
> publication, as their web pages are unclear on whether hard copy is still
> produced. Can anyone help? I can ask them directly but hopefully someone
> on the list will know.
>
> http://www.worldcat.org/title/interciencia/oclc/55102200
>
> http://www.interciencia.org
>
> Thanks,
>
> Geoff Read
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Sat, 11 Dec 2010 22:56:48 +1100
> From: Jim Croft <jim.croft at gmail.com>
> Subject: Re: [Taxacom] Phylogenetic Game
> To: Peter Stevens <peter.stevens at mobot.org>
> Cc: TAXACOM <taxacom at mailman.nhm.ku.edu>
> Message-ID:
>       <AANLkTimLpH-Rzt4f2rF7+sF=7BBW9qdP6sOR_aUVQ9am at mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> Neither do taxonomists, nor TaxaCom  ;)
>
> Jim
>
> On Saturday, December 11, 2010, Peter Stevens <peter.stevens at mobot.org> wrote:
> > Note that "Players don't need to understand (or even care about)
> > phylogenetics."
> >
> > P.
> >
> > Subject: Phylogenetics game
> >
> > December 2, 2010 | A pattern-matching puzzle created by
> > bioinformaticians at McGill University lets players sort genetic
> > code. The game, called Phylo, takes advantage of the human brain's
> > efficiency at recognizing and sorting patterns to tackle multiple
> > sequence alignments.
> >
> > Aligning genetic sequences is traditionally done computationally, but
> > what is a huge computational problem, is a bit easier for the human
> > brain. ?There are some calculations that the human brain does more
> > efficiently than any computer can, such as recognizing a face,?
> > explained lead researcher J?r?me Waldispuhl of the School of Computer
> > Science in a McGill press release. ?Recognizing and sorting the
> > patterns in the human genetic code falls in that category."
> >
> > Players don't start from scratch, but instead refine data that has
> > already been aligned. "By taking data which has already been aligned
> > by a heuristic algorithm, we allow the user to optimize where the
> > algorithm may have failed," the game creators explain on the site.
> >
> > All alignments were made available through UCSC Genome Browser and
> > contain sections of human DNA which have been speculated to be linked
> > to various genetic disorders, such as breast cancer. Every alignment
> > is received, analyzed, and stored in a database, where it will
> > eventually be re-introduced back into the global alignment as an
> > optimization. Players can choose which disease they'd like to work
> > on, or be assigned to a random level.
> >
> > Players don't need to understand (or even care about) phylogenetics
> > though. Rather than strings of As, Ts, Cs, and Gs, players align four
> > colored squares on a grid. Each row of colors represents a sequence
> > from a certain species. Sequences can be moved horizontally and
> > spaced out, but not rearranged or deleted. The goal is to line up
> > columns of colors that represent alignments between the two or more
> > sequences. There will, of course, be gaps in sequences and spots
> > where the two rows don't match. The goal is to find the best tradeoff
> > between aligning color and creating gaps. Players try to manually
> > find the best alignment and beat the computer's original alignment
> > score. The first level aligns two sequences, and sequences are added
> > as players advance.
> >
> > Researchers released the game on Monday after testing. They hope the
> > create a Facebook, iPhone, and Android application versions of the
> > game. Until then, Phylo can be played at http://phylo.cs.mcgill.ca
> >
> >
> > _______________________________________________
> >
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > The Taxacom archive going back to 1992 may be searched with either of these methods:
> >
> > (1) http://taxacom.markmail.org
> >
> > Or (2) a Google search specified as: ?site:mailman.nhm.ku.edu/pipermail/taxacom ?your search terms here
> >
>
> --
> _________________
> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
> http://www.google.com/profiles/jim.croft
> 'A civilized society is one which tolerates eccentricity to the point
> of doubtful sanity.'
>  - Robert Frost, poet (1874-1963)
>
> Please send URIs, not attachments:
> http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> ------------------------------
>
> _______________________________________________
>
> Taxacom Mailing List
>
> Taxacom at mailman.nhm.ku.edu
>
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The entire Taxacom Archive back to 1992 can be searched with either of these methods:
>
> http://taxacom.markmail.org
>
> Or use a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>
> End of Taxacom Digest, Vol 57, Issue 10
> ***************************************


------------------------------

Message: 2
Date: Sat, 11 Dec 2010 17:11:07 -0600
From: "Richard Zander" <Richard.Zander at mobot.org>
Subject: [Taxacom] Phylogenetic Game
To: "taxacom" <taxacom at mailman.nhm.ku.edu>
Message-ID:
        <F96F97BCBD9C1C46A99B1FDBD2644C2F0B73DA at MBGMail01.mobot.org>
Content-Type: text/plain;       charset="us-ascii"

Fitzhugh is right about causality. Cladograms are parenthetically nested
sets of extant specimens, the nesting being a pattern apparently due to
shared ancestry. This is a pattern of evidence of descent with
modification of taxa, yet cladistics provides no theory of the evolution
of the groups involved. Only offered by cladistics is the pattern of
nesting of the result of evolution. We are supposed to classify all
organisms by the pattern of nesting of extant taxa due to shared
ancestry.

Seems okay on the face of it, doesn't it? Don't we all search for
patterns? Well, the pattern of evidence is never used by cladists to
create a theory of evolution of the groups involved. The pattern IS
evolution, and there is no theory. All mapping of trait changes,
biogeography, and so on are theorems, not theories, because all
deductions from an axiom or first principle must be correct (apodictic).
No theory, no science.

Only extant specimens are used in creating cladograms. Thus, the pattern
reflects no theory of extinct lines that may affect interpretation of
evolution. E.g. what is the chance that there is an extinct line of
polar bears below the splitting of the two molecular lines of brown
bears in the cladogram ((polarbear, brownbear1) brownbear2) . . .?
Small, because the autapomorphies of the polar bear are unique and
highly specialized. So it is probable that the polar bear evolved from
one line of brown bears. But one is not allowed to use discursive
reasoning or induction or any theorization in phylogenetics.
Phylogenetics is not science.

An evolutionary systematist, on the other hand, can use induction to
infer macroevolutionary changes and their direction, that is, one taxon
changing into another through descent with modification. Paraphyly on a
molecular tree is one indication of such a progenitor-descendant
relationship, and it can be further analyzed with reasonable application
of Dollo's rule using biogeography, cytology, chemistry, and other
directional changes to gauge the probability of taxon A evolving into
taxon B, or did it happen vice versa? But that additional information is
not as certain as the patterns of evidence comprising the cladogram, and
the "rocket science" statistical certainty of the (molecular) cladogram
would collapse if such additional evidence were to be used.

It is the self-serving saving of apparent "rocket science" that animates
cladists of both morphological and molecular stripe into enforcing the
principle of strict phylogenetic monophyly. Abandoning empiricism for
structuralism (look it up) is the bane of present systematics, and
adversely affects our stewardship of biodiversity by epistemological
extinction of taxa that render other taxa paraphyletic (if something has
no scientific name, then biodiversity stewardship is crippled). There is
also a scrambling of nomenclature and proliferation of "cryptic"
molecular variants that dilute appreciation of significant
macroevolutionary entities when perceiving patterns of evidence as
evolution itself rather than using induction to create robust and
responsible theories. Phylogenetic analysis does use powerful tools that
might prove helpful in devising an evolutionarily based classification,
but the results of their use to date is, in my opinion, a disaster.

It is time to stop pussyfooting around and begging phylogeneticists to
allow recognition of paraphyletic taxa. Paraphyly is when nomenclature
does not agree with unanalyzed patterns of evidence of macroevolution in
the theory-free context of structuralism. Phylogenetics is not science.

* * * * * * * * * * * *
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
Web sites: http://www.mobot.org/plantscience/resbot/ and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm


-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Simon Mayo
Sent: Saturday, December 11, 2010 1:31 PM
To: taxacom
Subject: Re: [Taxacom] [Taxacom Digest] Phylogenetic Game


"Classification rather than systematization. Demarcating groups rather
than causal explanations." - (J. Kirk Fitzhugh)

Well...not rather than, just as well as and prior to causal
explanations. All cladograms are based on patterns surely?




------------------------------

Message: 3
Date: Sat, 11 Dec 2010 15:50:20 -0800
From: Curtis Clark <lists at curtisclark.org>
Subject: Re: [Taxacom] Phylogenetic Game
To: taxacom at mailman.nhm.ku.edu
Message-ID: <4D040E3C.4030508 at curtisclark.org>
Content-Type: text/plain; charset=UTF-8; format=flowed

On 12/11/2010 3:11 PM, Richard Zander wrote:
[A bunch of stuff along the same lines that he has written before]

There are two kinds of people in the world, those who divide people into
two kinds and those who don't. Richard is evidently in the former group.

--
Curtis Clark                  http://www.csupomona.edu/~jcclark/
Director, I&IT Web Development                   +1 909 979 6371
University Web Coordinator, Cal Poly Pomona




------------------------------

Message: 4
Date: Sat, 11 Dec 2010 17:57:57 -0600
From: "Richard Zander" <Richard.Zander at mobot.org>
Subject: Re: [Taxacom] Phylogenetic Game
To: "Curtis Clark" <lists at curtisclark.org>,
        <taxacom at mailman.nhm.ku.edu>
Message-ID:
        <F96F97BCBD9C1C46A99B1FDBD2644C2F0B73DB at MBGMail01.mobot.org>
Content-Type: text/plain;       charset="iso-8859-1"

Curtis, if you say there are two kinds of people in the world, one of which divides people into two kinds, then you must be a member of the same group as me since you say I do so. I am uncomfortable with this.

Or have I committed uncalled for discursive reasoning? Or was this a risible comment by you, for which I missed the point? Or is everyone supposed to agree about something? That WOULD be nice.


???
* * * * * * * * * * * *
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
Web sites: http://www.mobot.org/plantscience/resbot/ and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm


-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Curtis Clark
Sent: Saturday, December 11, 2010 5:50 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Phylogenetic Game

On 12/11/2010 3:11 PM, Richard Zander wrote:
[A bunch of stuff along the same lines that he has written before]

There are two kinds of people in the world, those who divide people into two kinds and those who don't. Richard is evidently in the former group.

--
Curtis Clark                  http://www.csupomona.edu/~jcclark/
Director, I&IT Web Development                   +1 909 979 6371
University Web Coordinator, Cal Poly Pomona




------------------------------

Message: 5
Date: Sat, 11 Dec 2010 16:36:08 -0800
From: Curtis Clark <lists at curtisclark.org>
Subject: Re: [Taxacom] Phylogenetic Game
To: taxacom at mailman.nhm.ku.edu
Message-ID: <4D0418F8.8050300 at curtisclark.org>
Content-Type: text/plain; charset=UTF-8; format=flowed

On 12/11/2010 3:57 PM, Richard Zander wrote:
> Curtis, if you say there are two kinds of people in the world, one of which divides people into two kinds, then you must be a member of the same group as me since you say I do so. I am uncomfortable with this.
We can agree that there are two kinds of people without agreeing on what
those kinds are. Better? :-)

--
Curtis Clark                  http://www.csupomona.edu/~jcclark/
Director, I&IT Web Development                   +1 909 979 6371
University Web Coordinator, Cal Poly Pomona




------------------------------

Message: 6
Date: Sun, 12 Dec 2010 08:43:43 -0500
From: "John Grehan" <jgrehan at sciencebuff.org>
Subject: Re: [Taxacom] Phylogenetic Game
To: "taxacom" <taxacom at mailman.nhm.ku.edu>
Message-ID:
        <26DA12164B238549B6D89A2F2A8EE79901AACB24 at bmsmail.sciencebuff.org>
Content-Type: text/plain;       charset="us-ascii"

I'm confused by the restriction of cladistics to extant specimens. Does
the inclusion of fossils mean that the method is no longer cladistic?

I'm also confused by the absence 'of a theory of evolution of the groups
involved' Hennig (and Rosa I think) postulated an unequal divergence
from the ancestor. One can implement cladistics without caring either
way, but that would seem to be true of phenetics or any other clustering
method.

"the pattern of evidence is never used by sadists to create a theory of
evolution of the groups involved." Meaning what? Please give an example
of a non-cladistic method of systematics that does this.

On the bear speculations - it would seem that could be applied to any
theory of relationship, cladistic or not.

On paraphyly - I respectfully disagree. Some people are ok with
paraphyletic groups, others are not. So why lose sleep over it? Heck,
only a handful think that morphological evidence can potentially falsify
molecular evidence. But there's no point in castigating anyone for that.

John Grehan (a cladist according to some, an extreme cladist according
to some, a Hennigian cladists according to some, a non-cladist according
to some).



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard Zander
Sent: Saturday, December 11, 2010 6:11 PM
To: taxacom
Subject: [Taxacom] Phylogenetic Game

Fitzhugh is right about causality. Cladograms are parenthetically nested
sets of extant specimens, the nesting being a pattern apparently due to
shared ancestry. This is a pattern of evidence of descent with
modification of taxa, yet cladistics provides no theory of the evolution
of the groups involved. Only offered by cladistics is the pattern of
nesting of the result of evolution. We are supposed to classify all
organisms by the pattern of nesting of extant taxa due to shared
ancestry.

Seems okay on the face of it, doesn't it? Don't we all search for
patterns? Well, the pattern of evidence is never used by cladists to
create a theory of evolution of the groups involved. The pattern IS
evolution, and there is no theory. All mapping of trait changes,
biogeography, and so on are theorems, not theories, because all
deductions from an axiom or first principle must be correct (apodictic).
No theory, no science.

Only extant specimens are used in creating cladograms. Thus, the pattern
reflects no theory of extinct lines that may affect interpretation of
evolution. E.g. what is the chance that there is an extinct line of
polar bears below the splitting of the two molecular lines of brown
bears in the cladogram ((polarbear, brownbear1) brownbear2) . . .?
Small, because the autapomorphies of the polar bear are unique and
highly specialized. So it is probable that the polar bear evolved from
one line of brown bears. But one is not allowed to use discursive
reasoning or induction or any theorization in phylogenetics.
Phylogenetics is not science.

An evolutionary systematist, on the other hand, can use induction to
infer macroevolutionary changes and their direction, that is, one taxon
changing into another through descent with modification. Paraphyly on a
molecular tree is one indication of such a progenitor-descendant
relationship, and it can be further analyzed with reasonable application
of Dollo's rule using biogeography, cytology, chemistry, and other
directional changes to gauge the probability of taxon A evolving into
taxon B, or did it happen vice versa? But that additional information is
not as certain as the patterns of evidence comprising the cladogram, and
the "rocket science" statistical certainty of the (molecular) cladogram
would collapse if such additional evidence were to be used.

It is the self-serving saving of apparent "rocket science" that animates
cladists of both morphological and molecular stripe into enforcing the
principle of strict phylogenetic monophyly. Abandoning empiricism for
structuralism (look it up) is the bane of present systematics, and
adversely affects our stewardship of biodiversity by epistemological
extinction of taxa that render other taxa paraphyletic (if something has
no scientific name, then biodiversity stewardship is crippled). There is
also a scrambling of nomenclature and proliferation of "cryptic"
molecular variants that dilute appreciation of significant
macroevolutionary entities when perceiving patterns of evidence as
evolution itself rather than using induction to create robust and
responsible theories. Phylogenetic analysis does use powerful tools that
might prove helpful in devising an evolutionarily based classification,
but the results of their use to date is, in my opinion, a disaster.

It is time to stop pussyfooting around and begging phylogeneticists to
allow recognition of paraphyletic taxa. Paraphyly is when nomenclature
does not agree with unanalyzed patterns of evidence of macroevolution in
the theory-free context of structuralism. Phylogenetics is not science.

* * * * * * * * * * * *
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA Web
sites: http://www.mobot.org/plantscience/resbot/ and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm


-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Simon Mayo
Sent: Saturday, December 11, 2010 1:31 PM
To: taxacom
Subject: Re: [Taxacom] [Taxacom Digest] Phylogenetic Game


"Classification rather than systematization. Demarcating groups rather
than causal explanations." - (J. Kirk Fitzhugh)

Well...not rather than, just as well as and prior to causal
explanations. All cladograms are based on patterns surely?


_______________________________________________

Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom

The Taxacom archive going back to 1992 may be searched with either of
these methods:

(1) http://taxacom.markmail.org

Or (2) a Google search specified as:
site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here



------------------------------

_______________________________________________

Taxacom Mailing List

Taxacom at mailman.nhm.ku.edu

http://mailman.nhm.ku.edu/mailman/listinfo/taxacom

The entire Taxacom Archive back to 1992 can be searched with either of these methods:

http://taxacom.markmail.org

Or use a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here

End of Taxacom Digest, Vol 57, Issue 11
***************************************


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