[Taxacom] progress on globalnames.org
Peter Stevens
peter.stevens at mobot.org
Mon May 18 14:39:34 CDT 2009
Well, one can always wait for the phylocode to name the clades; if
done cautiously, the names should be stable (although they may have
features which some might think were undesirable).
P.
On May 17, 2009, at 8:24 PM, Michael Heads wrote:
> Hi Pete,
>
> It would be great if species were stable and indivisible but
> molecular work is showing that in many groups some species have not
> been delimited well (e.g. in swifts, owl monkeys). But surely if
> your database is specimen-based (not species-based) you can just
> change the species concept as new data comes in?
> Your point about clades is crucial: many very interesting, well-
> supported molecular (and macromorphological) clades at all levels
> have no name and so don't exist for taxonomy, although for general
> biodiversity, ecology, conservation etc. they are just as 'real' as
> named clades. A taxonomy is just a summary or a framework, not the
> complete picture. Still, even if it doesn't incorporate all the new
> molecular clades it's a great advance to have a major collection
> online, arranged under whatever taxonomy it prefers, rather than
> not available at all.
>
> Michael Heads
>
>
> Wellington, New Zealand.
>
> My papers on biogeography are at: http://tiny.cc/RiUE0
>
> --- On Mon, 5/18/09, Peter DeVries <pete.devries at gmail.com> wrote:
>
>
> From: Peter DeVries <pete.devries at gmail.com>
> Subject: Re: [Taxacom] progress on globalnames.org
> To: "Michael Heads" <michael.heads at yahoo.com>
> Cc: taxacom at mailman.nhm.ku.edu
> Date: Monday, May 18, 2009, 10:51 AM
>
>
> Hi Michael,
>
>
> Yes, I am not saying that the other levels are not important. I
> think what I am proposing still connect to the higher levels.
>
>
> The particular genus something is put into is a statement about
> where it fits in the tree of life. Workers can
> differ on the taxonomic placement of a particular species concept,
> but agree that they are talking about the same
> species concept.
>
>
> Something also needs to be done about how we represent clades, any
> takers?
>
>
> In this example the clades have remained the same, it is just that
> Ochlerotatus was moved from a subgenus
> to a genus. (some accept this, others do not)
>
>
> Yes, there is a difference of opinion on whether species are
> different than the other clades. I think they are.
>
>
> One simple reason is that members of a species are pretty good at
> recognizing each other.
>
>
> The issue of "find ability" would be solved if we had semantic
> identifiers on those pages that would allow you
> to do a search for pages that contain information about the genus
> "Ochlerotatus".
>
>
> The identifier would make it clear that by the string
> "Ochlerotatus" you mean a genus.
>
>
> That specific genus could also have it's own uri hidden in each
> page that would serve a similar purpose.
>
>
> This problem may go away if more people start marking up their web
> pages with semantic identifiers.
> Google just announced they are going to be supporting this, but
> they do not yet have an identifier
> for "genus" or "Ochlerotatus"
>
>
> - Pete
>
>
>
>
>
> On Sun, May 17, 2009 at 4:57 PM, Michael Heads
> <michael.heads at yahoo.com> wrote:
>
>
>
>
>
>
> Hi Peter, Paul et al.,
>
> In theoretical terms, the species is special in the J.Huxley/Mayr
> 'modern synthesis'. But in other syntheses a species difference is
> not regarded as absolute but only relative (e.g. it's a level of
> differentiation between subspecies and subgenera in that group).
>
> In practical terms, many otherwise excellent websites are
> completely species-centric and so, for example, you can't draw a
> genus map. This means that if you want to get an overview of a
> genus with, say, 500 species, you have to look at 500 pages and so
> the site is pretty well useless for this purpose.
> I think the idea should be to look at biodiversity, not just
> species.
>
> Michael Heads
>
> Wellington, New Zealand.
>
> My papers on biogeography are at: http://tiny.cc/RiUE0
>
> --- On Mon, 5/18/09, Peter DeVries <pete.devries at gmail.com> wrote:
>
>
> From: Peter DeVries <pete.devries at gmail.com>
>
> Subject: Re: [Taxacom] progress on globalnames.org
> To: "Paul van Rijckevorsel" <dipteryx at freeler.nl>
>
> Cc: taxacom at mailman.nhm.ku.edu
> Date: Monday, May 18, 2009, 9:05 AM
>
>
>
>
>
> My main goal in this is to try out ways to tie specimens and data
> related to
> specimens to species concepts.
> It is not that the higher clades are not important. I think:
>
> 1) Species are fundamentally different than the higher clades
> (others may
> disagree)
> Following the metapopulation idea.
>
> 2) For the kinds of questions I would like to ask species are the
> priority.
> (many others in the same boat)
>
> 3) From my limited understanding of the EOL approach based on the
> blog post,
> it seems that what they
> are proposing makes sense for the higher taxa. Also the higher
> clades
> org will require a lot more buy in
> from all the interested parties. If someone works to define a
> concept
> for a particular species, others can
> take it or leave it.
>
> I use the *Puma concolor* example because it seemed that scientist
> publishing papers in 2009 about this well known species should be
> using the
> modern nomenclature. It seems to me that the community should not
> be as
> split on this particular species as it is.
>
> There seems to be a bit of a disconnect between how specimens are
> determined
> and labeled and how that label is being perceived.
>
> Most mosquitoes workers use a key. I use Darsie. Most have never
> seen the
> type specimen. They use the key of their choice and assign a name
> to that
> specimen. There is little or no real "mapping" from that keyed
> specimen to
> the typed specimen. Also, not everyone is using the same key.
>
> Assuming that the species concept for each of the specimens in a
> collection
> are defined directly by the type specimen is a little tenuous.
>
> Assuming that every published use of a name can be directly tied to
> the type
> specimen is also a little tenuous.
>
> When someone labels a mosquito specimen, "*Aedes triseriatus*", do
> they mean
> "I believe that this specimen belongs in the genus *Aedes*?"
>
> Or, do most workers really mean "I believe that this specimen maps
> to the
> species concept currently known as "*Aedes triseriatus*"
>
> I think that some of these issues need be be cleared up. If we do
> not, then
> researchers will not be able to get what they
> want once all this data has been digitized.
>
> Put another way, people will realize that what they thought they were
> putting into databases is not what they actually
> did put into the databases.
>
> At a minimum, adding a species concept identifier to a named
> specimen helps
> clarify the intent of the person identifying the specimen.
>
> - Pete
>
>
> On Sun, May 17, 2009 at 1:21 AM, Paul van Rijckevorsel
> <dipteryx at freeler.nl>wrote:
>
>> From: "Geoff Read" <gread at actrix.gen.nz>
>> Sent: Saturday, May 16, 2009 10:01 AM
>>> My point was that both these differences are trivial, they are
>>> not real
>>> "different scientific names", and thus poor examples for your
>>> plan. The
>>> link is the epithet in both, derived from the basionym, and I
>>> betcha the
>>> biologists that work on them happily talk about their 'triseriatus'
>>> experiments and 'concolor' distribution data. Shades of the
>>> LITU. Search
>>> software should be able to pull together the data on them easily.
>>
>> ***
>> Yes, that is not the issue. On the one hand there are scientific
>> names, and
>> on the other hand there are taxon concepts. Any database worth
>> anything
>> will
>> have a 'page' per scientific name, detailing at least the
>> nomenclatural
>> data
>> (publication, typification, etc). However, as such, these data
>> will of very
>> limited use to an end-user.
>>
>> The end-user expects 'taxon pages', and here the trouble starts.
>> It is
>> simple where there are 'good' taxa, with one or more "homotypic" or
>> "objective" synonyms. It is not too bad if there are also
>> "heterotypic" or
>> "subjective" synonyms, when there is consensus about their status.
>>
>> However, in many cases there is less than universal agreement
>> about the
>> taxon. Even if there is consensus at any one time, this may not be
>> the case
>> from a wider historical perspective, and many older taxon concepts
>> will
>> resurface after a few decades. This means that a database will
>> have to deal
>> with family Khgtyryuuaceae sensu author A, Khgtyryuuaceae sensu
>> author B,
>> Khgtyryuuaceae sensu author C, etc. Likely these need separate
>> 'pages'.
>> This
>> is even more confusing when it comes to species: a collection from
>> a tree
>> today may be made under a different name (different basionym,
>> different
>> type) than a collection from that same tree twenty years ago, and in
>> another
>> twenty years it may have reverted. When a taxonomist lumps taxa
>> this may
>> lose information: the literature on taxa G, H, I, K and L can be
>> found by
>> anybody who subscribes to a joint taxon K (comprising G, H, I, K
>> and L),
>> but
>> the reverse is not true. The literature on the joint taxon K may
>> resist
>> being broken down by those who subscribe to separate taxa G, H, I,
>> K and L
>> (even if the end-user is aware of the situation). And yet, this
>> may be of
>> great practical importance to the end-user.
>>
>> And indeed, common names may be of invaluable use in finding
>> information.
>> And, yes, using common names can lead to huge mistakes.
>>
>> Just stating the obvious (yet again)
>> Paul
>>
>>
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>
>
>
> --
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------
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> pipermail/taxacom your search terms here
>
>
>
>
> --
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------
>
>
>
>
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>
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>
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>
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