Allow provisional names

[RoDuth]

e.g. these 2 exist in our database Gen. (Aq520454) sp. Shute Harbour (D.A.Halford Q811) Argyrodendron sp. Whitsundays (W.J.McDonald+ 5831)

from ITF2: C.11 Species Epithet Rules of Information:

1. If the Infraspecific Rank/Hybrid Flag is not included in the current record, this field must contain a validly published, non-hybrid specific epithet under the International Code for Botanical Nomenclature (ICBN), except in the following special cases:

   1.2 If the plant represents a new species which has not been formally described, sp. nov, sp. A, sp. 1 (or other acceptable codes c.f. Greuter et al 1994) should be entered, if possible followed by a unique identifier, such as the collector's name and number or the locality.

from the International Code of Nomenclature for algae, fungi, and plants provisional name. A designation proposed in anticipation of the future acceptance of the taxon concerned, or of a particular circumscription, position, or rank of the taxon (Art. 36.1)

see the following wikipedia articles also: Undescribed taxon - provisional names in botany Phrase name Naming Conventions (flora) - ...provisional names particularly:

Several conventions exist for naming unpublished taxa, all of which are complicated, and none standardised. In the rare case where an unpublished taxon is notable enough to warrant a Wikipedia article, the article title should use the provisional name exactly as given in reliable sources; e.g. Grevillea sp. Mt Burrowa.

For example (re: "the provisional name exactly as given in reliable sources") In the examples I gave above from the Atlas of Living Australia we use a slightly different format as our "reliable source" is Queensland Herbarium and we use their format verbatim.

(of course this is only currently possible with changes I have made here)

Another example in common usage but not so well documented is where the species is believed to be known but it is significantly different to be separately identified e.g. Acacia fimbriata (dwarf form) may become a forma, cultivar, variety, etc. (or may not) This is particularly common in cultivated plants in the nursery trade.

[RoDuth]

Stumbled upon this, may be of interest also.

I notice they say "Taxonomists have routinely used provisional names, but their practices have not been standardized or consistent." and then provide several dissimilar examples from GenBank and describe 2 completely differing standards that have been or are used. I would think it folly to use anything other than free text entry for this.

how about a check box to allow free text entry into the epithet? Call it "informal name". As that seems to be the over arching term used for all examples like this.

[mfrasca]

please have a look at the unit tests for the Taxonomy plugin in ghini-3.2-dev.

asterales = Taxon(rank=self.ordo, parent=self.plantae, epithet='Asterales')
asteraceae = Taxon(rank=self.familia, parent=asterales, epithet='Asteraceae')
gen_nov = Taxon(rank=self.genus, parent=asteraceae, nov_code='Aq520454')
sp_nov = Taxon(rank=self.species, parent=gen_nov, nov_code='D.A.Halford Q811', nov_name='Shute Harbour')
cv = Taxon(rank=self.cultivar, parent=sp_nov, epithet='Due di Denari')
self.assertEquals(sp_nov.show(), 'Gen. (Aq520454) sp. Shute Harbour (D.A.Halford Q811)')
self.assertEquals(gen_nov.show(), 'Gen. (Aq520454) sp.')
self.assertEquals(cv.show(), "Gen. (Aq520454) sp. Shute Harbour (D.A.Halford Q811) 'Due di Denari'")

further, if want to describe here what would happen to, say … one such informally named species taxon1, referred to by two accessions, when its new hypothetical method taxon1.gets_published_as(taxon2) is invoked.

[RoDuth]

this doesn't seem to allow free text or am I wrong?

some other examples: a species informally collected from the wild with little records that is obviously Rubiaceae and believed to be new RUB sp. nov a plant in the nursery trade, this may be an example where it is believed to be a wild collected new species, proper records do not exist so it has not been identified as a species yet because no other properly recorded examples have turned up yet. (we see these a lot, nursery growers often collect but keep no records) Melaleuca ​sp. (Eungella) see here for this one (last few paragraphs explains how they often used these sorts of names, this is not a true cultivar name, we currently store it as such but it gets in the way when searching for cultivars. I would prefer to store it as a informal name.) Neoregelia 'Fireball' then Argyrodendron sp. (Whitsunday W.J.McDonald+ 5831) Acacia fimbriata (dwarf form)

all of the above are in our database

and then there are these from the 'Examples of Taxon Labels' from here (not necessarily botanic) Ocyptamus sp. MZH S143_2004_ Xenopus_ (Silurana) sp. new tetraploid __Astraptes LOHAMP Patelloa xanthuraDHJ02

the point being they are informal names with no formal rules. You seem to be dealing only with Phrase names but as can be seen by Qld Herbarium's records for Argyrodendron sp. (Whitsunday W.J.McDonald+ 5831) these rules aren't used uni-formally even for members of CHAH.

[mfrasca]

this doesn't seem to allow free text or am I wrong?

I am working at giving users the freedom to define their own rules, but I expect that you to agree with the rules you dictated.

so you define yourself your ranks, and how they show up.

as of now, each taxon has the standard epithet-authorship-year, plus the two alternative extra fields nov_name and nov_code, taken from your "Shute Harbour / D.A.Halford Q811" example.

these rules, you can check them in the plugins/taxonomy/defaults/rank.txt, in branch 3.2.

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your ›RUB sp. nov‹ could fit: do not specify the code, and only give nov as name. without changing the rules, you would get Rubiaceae sp. nov.

I should adapt the code so that it also handles the "name but no code" case, which I had not included.

in my opinion this makes more sense if you intend to identify the species at some later time. if it's just an accession from a further unspecified species, meaning it's an accession identified at rank family and waiting for identification, then I would probably suggest that the 'nov' be specified in the accession, not in the taxon. can be done, as everything else.

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›Melaleuca ​sp. (Eungella)‹

also fitting, with nov_cod='Eungella'

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›Neoregelia 'Fireball'‹

why are you using quotes around the name? and why you do not want the sp.? let me understand the point. I find this confusing.

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›Acacia fimbriata (dwarf form)‹

I guess you have an Acacia fimbriata, too. then a dwarf form. and "dwarf form" does not look like a code to me, or is it?

it is not possible with the current rules, but easy to write a rule for it:

17,"informal","",99,".complete (.nov_name)",""

I would not use the 'epithet' field because it's not an epithet and I would rather enforce the standard rules checking on epithets. also not 'nov_code' because it's not a code …

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I don't think I can support multiple rules within the same garden, nor do I think that it is a good idea for a garden to follow too many different naming patterns. try to convince me otherwise if you think so. I guess I can also add a variable or a large but fixed amount of fields, maybe 8 text fields. then it's your problem how you want to use them, in the ranks definition. I do not think this would make the software more appealing, just a lot more complex to configure properly, very easy to break, and very good at helping gardens produce a naming mess.

reading the http://baloun.entu.cas.cz/png/SchindelMiller2009.pdf document, I see that the rules I had written implement the proposed standard CHAH format.

[RoDuth]

›Neoregelia 'Fireball'‹

because that is the way the original collector decided to name it (see the full story). Note the last few paragraphs. This is an unnamed species that from what I have heard will likely never get a species name as the area it came from has since been logged and no other plant exists. (all living examples are from this one poorly documented wild collection)

›Acacia fimbriata (dwarf form)‹

Because this is the how they were named when we received them. This could be a new forma (most likely), subsp., var. or even just a cv. that has yet to receive a name.

The only rule we follow is that it should be exactly as the plant was supplied or recorded when original collected, etc.. (in the nursery trade it is not uncommon to have several variations for the one plant, we may record these as synonyms at times.) This makes it possible to link it with any other records or documents in the future and records the history of a its taxonomy (using the accessions vouchers and verifications tabs - love these features!). A plant may even have several names during its time (e.g. if our RUB sp. nov then goes to the herbarium and they assign another more detailed provisional name we will rename it to that in our records and keep the RUB sp. nov as a synonym. so it may have several variations before it is formally named - and it could even end up being renamed to a known species of course.).

The Phrase names rules that CHAH has advocated are common but not universal. This is why I have no need for rules just free text. All the systems I commonly use (ALA, Qld Herbarium's API) return this as the species epithet which makes sense to me. This is why I suggested a check box to allow free text in that field (or like the infraspecific parts rank drop down the ability to select what 'type' of name)