[Taxacom] progress on globalnames.org

Sun May 17 20:24:18 CDT 2009

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

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

-- 
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
------------------------------------------------------------