[Taxacom] ZooBank Progress

[Tony.Rees at csiro.au]

RE fossil flags in ZooBank: maybe for animals they make no difference, but in the botanical Code, now ICNafp there are some nomenclatural consequences according to whether the type is fossil or extant, some examples given below. Insofar as ZooBank is an instantiation of the GNUB model, and GNUB (which accommodates all Codes) will therefore need to know whether types of taxa are fossil or non-fossil, retaining this concept in ZooBank at no cost (and the benefit of some associated information to the enquirer) seems useful in my view.

Also some of the protistan / algae groups cited below under the "botanical" Code may also be treated under the zoological Code either now or in the past.

Regarding a comment of Rich's, there are some examples (Spiniferites Mantell, 1850 vs. Gonyaulax Diesing, 1866 comes to mind) of dinoflagellate cysts described first as fossils which turn out to be the resting stages of extant species names later and placed in a junior genus. I am not sure how these are currently resolved but maybe someone on this list will tell us.

Regards - Tony

---

Excerpts from ICNafp (Melbourne Code, 2012), see http://www.iapt-taxon.org/nomen/main.php: 

Article 13

13.1. Valid publication of names for organisms of different groups is treated as beginning at the following dates (for each group a work is mentioned that is treated as having been published on the date given for that group):
Non-fossil organisms:

(a). Spermatophyta and Pteridophyta, names at ranks of genus and below, 1 May 1753 (Linnaeus, Species plantarum, ed. 1); suprageneric names, 4 August 1789 (Jussieu, Genera plantarum).
(b). Musci (except Sphagnaceae), 1 January 1801 (Hedwig, Species muscorum).
(c). Sphagnaceae and Hepaticae (including Anthocerotae), names at ranks of genus and below, 1 May 1753 (Linnaeus, Species plantarum, ed. 1); suprageneric names, 4 August 1789 (Jussieu, Genera plantarum).
(d). Fungi (Pre. 8), 1 May 1753 (Linnaeus, Species plantarum, ed. 1). Names in Uredinales, Ustilaginales, and Gasteromycetes (s. l.) adopted by Persoon (Synopsis methodica fungorum, 31 December 1801) and names of other fungi (excluding slime moulds) adopted by Fries (Systema mycologicum, vol. 1 (1 January 1821) to 3, with additional Index (1832); and Elenchus fungorum, vol. 1-2), are sanctioned (see Art. 15). For nomenclatural purposes names given to lichens apply to their fungal component. Names of Microsporidia are governed by the International Code of Zoological Nomenclature (see Pre. 8).
(e). Algae, 1 May 1753 (Linnaeus, Species plantarum, ed. 1). Exceptions:
Nostocaceae homocysteae, 1 January 1892 (Gomont, "Monographie des Oscillariées", in Ann. Sci. Nat., Bot., ser. 7, 15: 263-368; 16: 91-264). The two parts of Gomont's "Monographie", which appeared in 1892 and 1893, respectively, are treated as having been published simultaneously on 1 January 1892.

Nostocaceae heterocysteae, 1 January 1886 (Bornet & Flahault, "Révision des Nostocacées hétérocystées", in Ann. Sci. Nat., Bot., ser. 7, 3: 323-381; 4: 343-373; 5: 51-129; 7: 177-262). The four parts of the "Révision", which appeared in 1886, 1886, 1887, and 1888, respectively, are treated as having been published simultaneously on 1 January 1886.

Desmidiaceae (s. l.), 1 January 1848 (Ralfs, British Desmidieae).

Oedogoniaceae, 1 January 1900 (Hirn, "Monographie und Iconographie der Oedogoniaceen", in Acta Soc. Sci. Fenn. 27(1)).

Fossil organisms (diatoms excepted):

(f). All groups, 31 December 1820 (Sternberg, Flora der Vorwelt, Versuch 1: 1-24, t. 1-13). Schlotheim's Petrefactenkunde (1820) is regarded as published before 31 December 1820.
13.2. The group to which a name is assigned for the purposes of Art. 13.1 is determined by the accepted taxonomic position of the type of the name.
Ex. 1. The genus Porella and its single species, P. pinnata, were referred by Linnaeus (1753) to the Musci; since the type specimen of P. pinnata is now accepted as belonging to the Hepaticae, the names were validly published in 1753.
Ex. 2. The designated type of Lycopodium L. (1753) is L. clavatum L. (1753), the type specimen of which is currently accepted as a pteridophyte. Accordingly, although the genus is listed by Linnaeus among the Musci, the generic name and the names of the pteridophyte species included by Linnaeus under it were validly published in 1753.
13.3. For nomenclatural purposes, a name is treated as pertaining to a non-fossil taxon unless its type is fossil in origin (Art. 1.2). Fossil material is distinguished from non-fossil material by stratigraphic relations at the site of original occurrence. In cases of doubtful stratigraphic relations, and for all diatoms, provisions for non-fossil taxa apply.
13.4. Generic names that appear in Linnaeus's Species plantarum, ed. 1 (1753) and ed. 2 (1762-1763), are associated with the first subsequent description given under those names in Linnaeus's Genera plantarum, ed. 5 (1754) and ed. 6 (1764). The spelling of the generic names included in Species plantarum, ed. 1, is not to be altered because a different spelling has been used in Genera plantarum, ed. 5.
Note 1. The two volumes of Linnaeus's Species plantarum, ed. 1 (1753), which appeared in May and August, 1753, respectively, are treated as having been published simultaneously on 1 May 1753 (Art. 13.1).
Ex. 3. The generic names Thea L. (Sp. Pl.: 515. 24 Mai 1753; Gen. Pl., ed. 5: 232. 1754), and Camellia L. (Sp. Pl.: 698. 16 Aug 1753; Gen. Pl., ed. 5: 311. 1754), are treated as having been published simultaneously on 1 May 1753. Under Art. 11.5 the combined genus bears the name Camellia, since Sweet (Hort. Suburb. Lond.: 157. 1818), who was the first to unite the two genera, chose that name, and cited Thea as a synonym.
Ex. 4. Sideroxylon L. (1753) is not to be altered because Linnaeus spelled it "Sideroxylum" in Genera plantarum, ed. 5 (1754) usage of Brunfelsia L. (1753, orth. cons., 'Brunsfelsia'), which Linnaeus adopted in 1754, has been made possible only through conservation (see App. III).

Article 43

43.1. In order to be validly published, a name of a new fossil-taxon published on or after 1 January 1996 must be accompanied by a Latin or English description or diagnosis or by a reference (Art. 38.13) to a previously and effectively published Latin or English description or diagnosis.
Note 1. As Art. 39.1 does not apply to names of fossil-taxa, a validating description or diagnosis (see Art. 38) in any language is acceptable for them prior to 1996.
43.2. A name of a new fossil-genus or lower ranked fossil-taxon published on or after 1 January 1912 is not validly published unless it is accompanied by an illustration or figure showing the essential characters or by a reference to a previously and effectively published such illustration or figure. For this purpose, in the case of a name of a fossil-genus or subdivision of a fossil-genus, citation of, or reference (direct or indirect) to, a name of a fossil-species validly published on or after 1 January 1912 will suffice.
Ex. 1. "Laconiella" when published by Krasser (in Akad. Wiss. Wien Sitzungsber., Math.-Naturwiss. Kl. Abt. 1, 129: 16. 1920) included only one species, the intended name of which, "Laconiella sardinica", was not validly published as no illustration or figure or reference to a previously and effectively published illustration or figure was provided. "Laconiella" is not, therefore, a validly published generic name.
Ex. 2. Batodendron Chachlov (in Izv. Sibirsk. Otd. Geol. Komiteta 2(5): 9, fig. 23-25. 1921) was published with a description and illustrations. Even though the new fossil-genus did not include any named species, its name (an illegitimate later homonym of Batodendron Nutt. 1843) is validly published.
43.3. A name of a new fossil-species or infraspecific fossil-taxon published on or after 1 January 2001 is not validly published unless at least one of the validating illustrations is identified as representing the type specimen (see also Art. 9.15).


Article 44

44.1. In order to be validly published, a name of a new taxon of non-fossil algae published between 1 January 1958 and 31 December 2011, inclusive, must be accompanied by a Latin description or diagnosis or by a reference (Art. 38.13) to a previously and effectively published Latin description or diagnosis.
Note 1. As Art. 39.1 does not apply to names of algal taxa, a validating description or diagnosis (see Art. 38) in any language is acceptable for them prior to 1958.
Ex. 1. Although Neoptilota Kylin (Gatt. Rhodophyc.: 392. 1956) was accompanied only by a description in German, it is a validly published name since it applies to an alga and was published before 1958.
44.2. A name of a new taxon of non-fossil algae of specific or lower rank published on or after 1 January 1958 is not validly published unless it is accompanied by an illustration or figure showing the distinctive morphological features, or by a reference to a previously and effectively published such illustration or figure.




Tony Rees
Manager, Divisional Data Centre,
CSIRO Marine and Atmospheric Research,
GPO Box 1538,
Hobart, Tasmania 7001, Australia
Ph: 0362 325318 (Int: +61 362 325318)
Fax: 0362 325000 (Int: +61 362 325000)
e-mail: Tony.Rees at csiro.au
Manager, OBIS Australia regional node, http://www.obis.org.au/
Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm
Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566
LinkedIn profile: http://www.linkedin.com/pub/tony-rees/18/770/36

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Francisco Welter-Schultes
> Sent: Monday, 29 April 2013 8:14 AM
> To: Richard Pyle
> Cc: 'Taxacom'
> Subject: Re: [Taxacom] ZooBank Progress
> 
> Just some thoughts on two issues you brought up.
> 
> "Fossil: No": I would still remove it. The example I gave you was not a
> result of a systematic search but I just saw it coincidentally when
> passing by. Linnaeus 1758 described many fossil species, so finding
> such a
> case would probably not be such a rare event.
> 
> You know in AnimalBase we display a field concerning the gender
> treatment,
> a specific name is either marked as changeable or unchangeable. Shortly
> after we began doing this around 2005 we obtained angry feedback from
> users who discovered wrong information. Our team members had selected
> the
> wrong item. We initially answered "thanks, I corrected it, took me 10
> seconds", but this did not help.
> So we quickly modified our strategy and instructed our team members
> very
> strictly to give this information only if they were absolutely sure
> about
> what they wrote. If they were not sure we demanded them to select the
> option "I don't know". We had obtained feedback that saying "I don't
> know"
> was much better than giving incorrect information.
> I would compare this experience with the fossil information. Only
> display
> it if you have verified it. Otherwise, write "I don't know" or "not
> verified".
> 
> 
> 
> The long s. I had discussions with others and the same arguments came
> up,
> and we also had this problem in AnimalBase. We discussed it intensively
> and came to a different conclusion.
> Let me summarize the arguments, maybe you find them interesting.
> Perhaps
> you already know them, but these things are rarely discussed.
> 
> (1) the long s is a rare letter and many non-insiders do not know this
> letter and when they see it, they cite it as f. The result is that we
> observe a number of Latin names spelled with f instead of s. Many
> people
> do not know Latin and do not know a word refinella or resinella. If
> ZooBank (which is deveoping into a very important database) decides
> displaying the long s and will be consulted by many people, these
> errors
> will increase and we will have to search for names like Musca and
> Mufca,
> Ostrea and Oftrea, pusio and pufio, refinella and resinella, and so on,
> a
> never ending list. Citing the long s would create more problems than
> benefit.
> We repeatedly had to teach AnimalBase team members to pay very much
> attention on the f and long s problem, and also, if they did not find a
> name with f, for example in Sherborn, we instructed them to look for it
> spelled with s.
> This had the funny result that in the weekly lectures when they
> reported
> their problems with names they had not found in the literature, they
> always knew where they had to add the sentence "I also looked for the
> name
> with f and did not find it either".
> 
> (2) The long s and other special characters have never been cited as
> such
> by taxonomists. We quickly said, let's avoid introducing a totally new
> standard, we can only make mistakes and we don't help people. This was
> probably the most important argument: we intended to present a service
> for
> the community, to facilitate people's work, and not to complicate it.
> The ae and oe ligatures have been cited in the past, so these
> characters
> are well known and we decided to cite them.
> 
> (3) the argument "let's display all the UTF-8 characters as in the
> original source" seemed weak to us. In UTF-8 you can display almost
> anything. We would have needed to teach our team members a whole new
> world
> of Latin script characters. Would have been like teaching Chinese...
> In ZooBank you now have the problem of being inconsistent, in that some
> UTF-8 characters were ignored and automatically corrected, others were
> incorrectly cited. For example the ct ligature seems to have been
> consistently ignored, or the Linnean u with tilde (ũ) at the end
> of a
> name ending in -um is incorrectly displayed.
> 
> http://zoobank.org/NomenclaturalActs/6FCAAF6C-3DAE-4237-B61E-
> 6CAABCE1AAD3
> Alcyonium arboreú Linnæus, 1758 - ú was the incorrect UTF-8 character,
> correct would be u with tilde.
> This seems to be a systematic error, incorrectly cited at all
> instances.
> http://zoobank.org/NomenclaturalActs/41F4F85A-33EC-49BF-AA41-
> 872E0D8F1294
> Alcyonium digitatú Linnæus, 1758, same problem.
> 
> However, only extremely skilled experts know this u tilde spelling mode
> at
> all, so for not making zoology more sophisticated than it needs to be,
> there seems to be a general convention to cite such a name as arboreum,
> and to ignore the u with tilde.
> 
> Looking for a name Alcyonium digitatum in the ZooBank search box does
> not
> return a result, you have to search for digitatu.
> 
> Sometimes I also saw m with tilde, this stands for mm.
> 
> Name with ligatures in the original sources which also have UTF-8
> characters:
> 
> http://zoobank.org/NomenclaturalActs/F3685154-FA47-4085-BFAE-
> 5CF4CF0445DA
> Tubipora muſica Linnæus, 1758, with long s - i ligature
> 
> http://zoobank.org/NomenclaturalActs/0BD4B2B0-E5E6-4161-BD5B-
> 63678A694474
> Dermestes pectinicornis Linnæus, 1758, originally with ct ligature
> 
> http://zoobank.org/NomenclaturalActs/4F7B08AD-13A7-4C58-94FD-
> FEFCFF188399
> Gadus aeglefinus Linnæus, 1758, originally with fi ligature (and
> moreover,
> originally spelled Æglefinus, with AE ligature, in Zoobank cited as
> aeglefinus, probably unintended)
> 
> I guess there are half a dozen more of such ligatures, about 10 % of
> the
> Linnean names are involved and we would have become crazy. A whole hell
> of
> devils in the details.
> 
> Never hesitate if you have more questions and ideas
> Francisco
> 
> 
> >
> >> If it's done manually it might be worth to correct some other names
> that
> >> were linked by ZooBank to the Linnean 1758 work.
> >
> > Yes, exactly!  Part of the process of cross-linking is to compare
> > discrepancies.  We've found that in most datasets that we cross-link
> > against, there are a relatively small fraction of discrepancies.  For
> > example, out of 50,000 names, there might be only a few hundred
> > discrepancies -- usually involving the date of publication, correct
> > authorship, or the exact orthography of the name.  This means that
> it's a
> > very manageable task to investigate each one of the discrepancies.
> Also,
> > I've found that no database is perfect.  Some are better than others,
> to
> > be sure -- but one can never assume that one database is always
> correct --
> > which means that it's important to examine the discrepancies
> individually.
> >  Indeed, this is one of the main reasons why we wanted to establish
> this
> > link with BHL -- to make it easier to resolve discrepancies.
> >
> >> My understanding is that ZooBank is a data resource where available
> >> names
> >> are contained. Unavailable names should probably not be contained at
> >> all,
> >> and if yes, they should clearly be marked as such.
> >> I am not sure how names should be treated which were initially made
> >> available and later suppressed.
> >
> > This is an issue that has been debated since ZooBank was first
> conceived.
> > In 2008, at a Commissioners meeting in Paris, it was determined that
> > ZooBank *would* include unavailable names, and that those names would
> be
> > clearly marked not only as unavailable, but also give the reason(s)
> why
> > the name is unavailable.  We already have a very robust data model to
> deal
> > with this (which I'd be happy to describe, if anyone is interested).
> But
> > as with most aspects of ZooBank development, the tricky part is how
> to
> > implement it (devil is always in the details).  One of the things in
> the
> > works is a policy on data verification in ZooBank.  Right now, the
> focus
> > is on building the core infrastructure of ZooBank, populating it with
> > restrospective content, and building tools to streamline the capture
> of
> > prospective content.  However, what people *really* want from ZooBank
> is a
> > definitive declaration of whether or not any particular name is
> available
> > under the Code.  This is the entire process of content verification.
> So
> > far, we focused only on registration (these are two very different
> > things).
> >
> >> Example:
> >> http://zoobank.org/NomenclaturalActs/1E691819-76A8-492D-8AE1-
> DA84F9103CF8
> >> Acarus telarius Linnæus, 1758 - this name should somehow be marked
> as
> >> suppressed (ICZN Op. 968).
> >> There were many other such names established in the 1758 work, which
> >> were totally or partly suppressed by the Commission.
> >
> > Yes, indeed!  In fact, one of the projects we've been working on
> (with
> > LARGE thanks to Charles Hussey, and also to Rod Page who defined the
> > article boundaries of historical BZN volumes in BHL) is a complete
> > database of Opinions.  This is effectively complete (still needs some
> > verification, though), and will be one of the new features added to
> > ZooBank this summer.  But again, we need to sort out exactly how this
> sort
> > of thing will be implemented on the ZooBank website, and what the
> policy
> > is for editing these sorts of things, etc.
> >
> > Many thanks for pointing out the individual issues related to
> Linneaus
> > names.  This sort of thing is EXTREMELY helpful!  I will definitely
> use
> > these as test cases when we implement the next set of features
> involving
> > ZooBank record verification/validation.  But again, it probably can't
> be
> > implemented until later this summer (northern hemisphere summer, that
> is).
> >
> >> Maybe some other systematic things could be fixed.
> >>
> >> - Remove the long s throughout the original spellings, and replace
> it at
> >> all
> >> instances by the short s.
> >
> > In this case, we want to maintain the precise orthography as it
> originally
> > appeared on the printed page -- in al respects.  Basically, if a UTF-
> 8
> > character exists for a particular glyph, we want to capture it as
> such.
> > The main exceptions are that all-caps words are not faithfully
> captured as
> > such, and other stylistic attributes (e.g., boldface, small-caps,
> when
> > original names were not italicized, etc.) will not be captured.  But
> > characters such as the long s and dipthong "æ" will be captured as
> > originally printed on the page.
> >
> > The next step is to build the correct algorithm to transform these
> things,
> > so that the Code-corrected "original spelling" can be generated
> > automatically.  In most cases, this is easy to do -- but there are
> some
> > tricky ones (e.g., see Art. 32.5.2.1. -- which would require us to
> know
> > whether the root word is German or not; or some of Art. 32.5.2.4.).
> This
> > is one more example of features currently in the works, that will be
> > introduced over time as they rise up the priority list, and as
> appropriate
> > policies are drafted and ratified.
> >
> >
> >> Example Musca Linnæus, 1758, this name was
> >> spelled Musca with long s at some occasions and MUSCA at others,
> MUSCA
> >> is
> >> usually converted to Musca with short s. So all specific names
> should
> >> correctly be combined with Musca with short s.
> >
> > This is a slightly separate issue (multiple spellings of the same
> genus
> > name, and how they map to the species they are combined with).  The
> new
> > GNUB data model (not yet implemented) deals with this by capturing
> > separately the verbatim name-string, and the separate name
> components.  At
> > the moment, this sort of issue is rare enough that it has not risen
> up the
> > priority "to-do" list.  But it's definitely on the list.
> >
> >> Also, the long s is not cited consistently. Example:
> >> http://zoobank.org/NomenclaturalActs/D2B4DA70-35AE-4D87-9E34-
> E219FC8E3DA0
> >> Ostrea Puſio Linnæus, 1758 - here Pusio with long s and Ostrea
> >> with
> >> short s, both had the long s in the original source.
> >
> > This is another example of the previous.  The genus was rendered as
> OSTREA
> > on p. 696 (http://www.biodiversitylibrary.org/pagethumb/727611), so
> the
> > genus is captured as such in the database (minus the all-caps).  I
> only
> > see "OÅ¿trea" in the page header.  Is it rendered this way somewhere
> else?
> >
> >> - Consider presenting a field "original spelling" and another field
> >> "correct
> >> spelling". This would probably reduce confusion. In the correct
> spelling
> >> field
> >> the species would not appear capitalised, and diacritics would be
> >> removed.
> >
> > Yes!  This is already part of the plan.  It just needs to rise up the
> > priority list for implementation.
> >
> >> - I am confused by the statement "Fossil: No" in the ZooBank data
> result
> >> set.
> >> Is this nomenclaturally relevant?
> >
> > It's not a Code-relevant issue, but it is a useful piece of
> information
> > (just like type locality, figures, and page number).
> >
> >> Is there an exact definition for the term "fossil"? Since when does
> a
> >> taxon
> >> need to be extinct for obtaining the attribute "fossil"?
> >
> > If you read the help section for this particular field (click on the
> blue
> > icon when registering a new name, or editing an existing name), it
> > explains it thusly:
> >
> > "If this new name is based on fossil material, select this checkbox.
> > Otherwise, leave the checkbox unselected."
> >
> > In other words, it only applies to species-group names, and it is a
> > specific indication of the nature of the name-bearing type material.
> > Technically, if the type specimen of Latimeria chalumnae had been a
> > fossil, and then it was later discovered alive, this would be
> "Fossil:
> > Yes".  However, I am not aware of any case where a name is
> established
> > based on a fossilized type, and then later discovered (at the species
> > level) to be extant.  Generally such cases are described as separate
> > species.
> >
> >> Can we be sure that all molluscs and brachiopods named in the early
> >> Linnean
> >> works were recent?
> >
> > Nope.  Neither can we be sure that all the page numbers are correct,
> or
> > all the type localities are correct -- or any number of other things.
> > That doesn't mean the data field should be eliminated.  It just means
> we
> > have to deal with cases that prove to be inaccurate (or unknown).
> >
> >> Would it not be better to remove the statement, to avoid running the
> >> risk to
> >> give an incorrect information?
> >
> > I don't think so, but I'd be interested in hearing opinions from
> others on
> > this.  As I already said, there is no such thing as a perfect
> database.
> > One of the things Rob Whitton constantly reminds me of is not to let
> the
> > "perfect" be the enemy of the "good".  I tend to be a perfectionist
> on
> > thses sorts of things (as many database managers are).  But sometimes
> it's
> > better to just get what you have out there, and then provide a
> > crowd-sourcing mechanism to get it corrected.
> >
> >> Example:
> >> http://zoobank.org/NomenclaturalActs/04B5D5F4-648A-489F-ADE9-
> 2C13971F8A69
> >> Anomia Gryphus Linnæus, 1758. Here a fossil species was described,
> and
> >> in
> >> Zoobank it was marked as "Fossil: No".
> >
> > Many thanks for the correction!  I have already implemented it on
> ZooBank
> > (it took me 7 seconds to correct this -- but you did the hard part of
> > finding the error, and made it extremely easy for me by providing the
> > link).
> >
> > I want to thank you again for providing all of these VERY VALUABLE
> > corrections to names in ZooBank.  I will study them in more detail
> (along
> > with your other recent messages), and will likely come back to you
> with
> > follow-up questions.
> >
> > Aloha,
> > Rich
> >
> >
> 
> 
> Francisco Welter-Schultes
> Zoologisches Institut, Berliner Str. 28, D-37073 Goettingen
> Phone +49 551 395536
> http://www.animalbase.org
> 
> 
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