[Taxacom] Global counts of accepted genera

[Tony Rees]

Dear Peter, all,

Thank you for the feedback. Before addressing your detailed analysis, let
me first make a few general points:

- First, IRMNG is an "Interim" compilation and that principle was inspired
by colleagues at my former research agency, the marine branch of CSIRO in
Australia, who at one point in the 1990s were asked by the relevant govt
department, if we give you some money, can you produce a biological
regionalisation of Australian seas. (Regionalisation = set of logically
defensible regions differentiated by their distinctive faunal
compositions). The answer was no, the task is too large, it would take 50
years just to gather the required data. So the questioner said, well can
you produce an interim one then, using the data you have? The answer was of
course, no problem, and the task was delivered to everybody's satisfaction,
and went through several versions, each better than the last (e.g. see
https://parksaustralia.gov.au/marine/management/resources/scientific-publications/interim-marine-and-coastal-regionalisation-australia-version-33/
)
- all a matter of expectation management, doing the best job possible with
the data to hand, producing "something" to use now rather than waiting for
ever for a perfect product, and commencing a process ("journey") of ongoing
improvement through time. All of which principles I then "borrowed" for
IRMNG (even in the name), now in its 13th release since 2007.

The take home message being that it is good to start somewhere, and put the
results out there for people to use, and that pointing out areas requiring
improvement is entirely to be expected.

- Second, in the initial start-up phase of IRMNG, I was generously given
some pre-existing lists of genus names, their taxonomic placement, and
accepted name/synonym status, not all of which I have subsequently
re-checked for accuracy; so I know there will be errors there lurking,
waiting to be addressed (some early list compilers made errors as well, or
the data may have formerly been current but is now outdated). In general,
all IRMNG's assertions of taxonomic status come from "somewhere", and I
imagine that now-incorrect ones come from some of these older lists (and
may of course have been upgraded there in the mean time).

- Third, some taxonomic groups in IRMNG have received a more thorough
review against "modern", synoptic compilations for specific groups -
although even that activitiy may be up to 10 years old or so by now. For
example all extant fishes were checked against Eschmeyer's online Catalog
in 2012, Fungi against Index Fungorum around the same time, vascular plants
against GRIN, many orders of insects against Joel Hallan's Biology Catalog,
extant Algae against AlgaeBase, prokaryotes against the List of Prokaryotic
Names with Standing in Prokaryotic Nomenclature, Viruses against the ICTV
database, and so on. Regrettably, Reptila and Aves have not been checked
recently in that manner.

- Fourth, for some groups such as mammals, fishes, etc., there are
excellent print or online resources that included concordances at genus
level, in other words genus A is the current, accepted name, and it has the
synonyms B, C, D, etc. I am not aware of such a source for Reptiles
(preferably covering both extant and fossil names) although it may be out
there - if it is, checking relevant IRMNG content against it for currency
and correctness could be a task for my successors (since I am planning or
hoping to scale back my mainstream involvement with IRMNG following this
release). I am (well) aware of the Reptile Database from when it was
originally at EMBL, but in general it gives such concordances at the
species, not the genus level (Peter will correct me if I am wrong).

OK, now to Peter's analysis, for which I am appreciative of course.

Of the initial 40 example names in Reptilia:

- 22 are listed in IRMNG as accepted, of which 13 are extant and 9 fossil.
Peter comments only on the extant ones, saying that 8 are Ok (we will
disregard the subgenus) and 5 are actually unaccepted names. Presuming that
the fossil ones are OK (not tested), then agreed, 5/22 (23%) of these names
are incorrectly classified, which is higher than I would have hoped, and is
probably reflective of the fact that Reptilia has not be reviewed since the
data arrived in IRMNG, in contrast to some other groups (see above).

- 7 are listed as unaccepted (all are extant names), apparently correctly.
So maybe it is fairer to say that of all the names with a known taxonomic
status, i.e. accepted or unaccepted, 24/29 (83%) are correctly assigned.
Actually that does not sound quite so terrible, and can of course be
improved upon in subsequent releases.

- 11 are listed as "uncertain" - 5 extant, 6 fossil. Peter says (I think)
that the 5 extant ones are all unaccepted; at least one (Abaculabronia) is
a subgenus, which in IRMNG terminology means that it is unaccepted at genus
level. However we do not know about the fossil ones, which are most likely
a mix of accepted and unaccepted names, just not yet investigated. In any
case this means that the IRMNG logic is still OK (in principle) - we give a
range that corresponds to 0 of the "uncertain" names being accepted (low
value) and all of the "uncertain" names being accepted (high value), plus a
mid point, which may then move higher or lower in subsequent versions as
the data are refined further.

So in view of the above, it appears that there is some substance to Peter's
initial reaction (the number of quoted accepted names seems too high), but
maybe not as much as first thought...

Since this type of analysis is not too hard to do, as a comparison/further
dig into the values presented in the "Megataxa" paper, perhaps there are
students out there who would be interested in taking such analyses further
as a classroom excercise, or similar, maybe for some different groups in
IRMNG; certainly some would come out very "clean" i.e. fairly well aligned
with most recent work, others not...

I am happy to receive additional responses from Taxacomers as appropriate.

Regards - Tony


On Thu, 2 Apr 2020 at 17:30, Peter Uetz <peter at uetz.us> wrote:

>
> Tony,
>
> Of the 40, you list …
> — 15 as fossil
> — 11 as unaccepted or uncertain (the latter actually are all not accepted)
> *— 9 as accepted and they are (including 1 subgenus, Abaculabronia, not
> counting), i.e. 22.5% correctly identified as accepted*
> — 5 as accepted while they are actually NOT
>
> The 9 are:
> *Ablepharus*
> *Abronia*
> *Acalyptophis*
> *Acanthocercus*
> *Acanthochelys*
> *Acanthodactylus*
> *Acanthophis*
> *Acanthosaura*
> (Abaculabronia )
>
>
>
> On Apr 2, 2020, at 2:05 PM, Tony Rees <tonyrees49 at gmail.com> wrote:
>
> OK, we can do a small test om the first 40 reptile genera as held in this
> version of IRMNG.
>
> The names look like this (selected fields, as available in the data
> download accompanying the "Megataxa" paper) after re-sorting by
> "taxonomicStatus":
>   (I have made an attempt to preserve the rows and columns as if it were
> the original data table excerpt)
>
> scientificName ... scientificNameAuthorship ... taxonomicStatus ... extant
> status ... acceptedNameUsage ... parentNameUsage ... namePublishedIn
>
> Aardonyx ... Yates, Bonnan, Neveling, Chinsamy & Blackbeard, 2010 ...
> accepted ... fossil (only) ...  ... Anilioidea incertae sedis ... Article
> title: A new transitional sauropodomorph dinosaur from the Early Jurassic
> of South Africa and the evolution of sauropod feeding and quadrupedalism.
> Abajudon ... Angielczyk, Huertas, Smith, Tabor, Sidor, Steyer, Tsuji &
> Gostling, 2014 ... accepted ... fossil (only) ...  ... Anomodontia incertae
> sedis ... Angielczyk, K. D.; Huertas, S.; Smith, R. M. H.; Tabor, N. J.;
> Sidor, C. A.; Steyer, J.-S.; Tsuji, L. A.; Gostling, N. J. (2014). New
> dicynodonts (Therapsida, Anomodontia) and updated tetrapod stratigraphy of
> the Permian Ruhuhu Formation (Songea Group, Ru
> Abastor ... Gray, 1849 ... accepted ... extant ...  ... Colubridae ...
> Cat. Snakes Coll. B. M.
> Abdalodon ... Kammerer, 2016 ... accepted ... fossil (only) ...  ...
> Charassognathidae ... Kammerer, C. F. (2016). A new taxon of cynodont from
> the Tropidostoma Assemblage Zone (upper Permian) of South Africa, and the
> early evolution of Cynodontia. <em>Papers in Palaeontology.</em> 2(3):
> 387-397.
> Abelisaurus ... Bonaparte & Novas, 1985 ... accepted ... fossil (only) ...
>  ... Abelisauridae ... Ameghiniana 21 (2-4)
> Abilenea ... Wells, 2007 ... accepted ... extant ...  ... Pygopodidae ...
> Australian Biodiversity Record 6
> Ablabes ... Duméril, 1853 ... accepted ... extant ...  ... Colubridae ...
> Mém. Acad. Sci. Inst. France, 23
> Ablabophis ... Boulenger, 1893 ... accepted ... extant ...  ... Colubridae
> ... Cat. Snakes Brit. Mus., 1
> Ablepharus ... Fitzinger, 1823 ... accepted ... extant ...  ... Scincidae
> ... Ver. Doubl. Zool. Mus. Berlin
> Abrictosaurus ... Hopson, 1975 ... accepted ... fossil (only) ...  ...
> Heterodontosauridae ... S. Afr. J. Sci. 71
> Abronia ... Gray, 1838 ... accepted ... extant ...  ... Anguidae ... Ann.
> Mag. Nat. Hist., 1 (5)
> Abydosaurus ... Chure, Britt, Whitlock & Wilson, 2010 ... accepted ...
> fossil (only) ...  ... Brachiosauridae ... Article title: First complete
> sauropod dinosaur skull from the Cretaceous of the Americas and the
> evolution of sauropod dentition.
> Abyssomedon ... MacDougall & Reisz, 2014 ... accepted ... fossil (only)
> ...  ... Nyctiphruretidae ... MacDougall, M. J.; Reisz, R. R. (2014). The
> first record of a nyctiphruretid parareptile from the Early Permian of
> North America, with a discussion of parareptilian temporal fenestration.
> <em>Zoological Journal of the Linnean Society.</em> 172(3): 616-630
> Acalyptophis ... Boulenger, 1896 ... accepted ... extant ...  ... Elapidae
> ... Cat. Snakes Brit. Mus., 3
> Acamptonectes ... Fischer, Maisch, Naish, Kosma, Liston, Joger, Krüger,
> Pérez, Tainsh & Appleby, 2012 ... accepted ... fossil (only) ...  ...
> Ophthalmosauridae ... Article title: New ophthalmosaurid ichthyosaurs from
> the European Lower Cretaceous demonstrate extensive ichthyosaur survival
> across the Jurassic-Cretaceous boundary.
> Acanthocercus ... Fitzinger, 1843 ... accepted ... extant ...  ...
> Agamidae ... Syst. Rept., 18
> Acanthochelys ... Gray, 1873 ... accepted ... extant ...  ... Chelidae ...
> Ann. Mag. Nat. Hist., (4) 11
> Acanthodactylus ... Wiegmann, 1834 ... accepted ... extant ...  ...
> Lacertidae ... Herp. Mex.
> Acantholis ... Cocteau, 1836 ... accepted ... extant ...  ...
> Polychrotidae ... C. R. Acad. Sci. (Paris), 3
> Acanthophis ... Daudin in Sonnini, 1803 ... accepted ... extant ...  ...
> Elapidae ... in Sonnini, Suite à Buffon, Hist. Rept., 5
> Acanthopholis ... Huxley, 1867 ... accepted ... fossil (only) ...  ...
> Nodosauridae ... Geol. Mag., 4
> Acanthosaura ... Gray, 1831 ... accepted ... extant ...  ... Agamidae ...
> in Griffith-Cuvier, Anim. Kingd., 9, syn.
> Abas ... Núñez & Yáñez, 1984 ... unaccepted ... extant ... Liolaemus ...
> Tropiduridae ... Mus Nac Hist Nat Bol (Santiago) No. 40
> Ablates ... Beddome, 1862 ... unaccepted ... extant ... Ablates ...
> Colubridae ... Madras Quart. J. Med. Sci., 5, 12
> Ablepharis ... Cocteau, 1832 ... unaccepted ... extant ... Ablepharus ...
> Scincidae ... Magasin de Zool., 2, pl
> Acalyptus ... Duméril, 1853 ... unaccepted ... extant ... Acalyptophis ...
> Hydrophiidae ... Mém. Acad. Sci. Inst., France, 23
> Acanthopis ... Gray, 1825 ... unaccepted ... extant ... Acanthophis ...
> Elapidae ... Ann. Phil., [2] 10
> Acantodactylus ...  ... unaccepted ... extant ... Acanthodactylus ...
> Lacertidae ...
> Acantophis ... Berthold in Latreille, 1827 ... unaccepted ... extant ...
> Acanthophis ... Elapidae ... in Latreille, Nat. Fam. Thierr.
> Abaculabronia ... Campbell & Frost, 1993 ... uncertain ... extant ...  ...
> Anguidae ... Bulletin of the American Museum of Natural History 216,
> September 3
> Abelichnus ... Calvo, 1991 ... uncertain ... fossil (only) ...  ...
> Archosauria (awaiting allocation) ... Ameghiniana 28 (3-4)
> Acadiella ... Sues & Baird, 1998 ... uncertain ... fossil (only) ...  ...
> Procolophonidae ... J Vertebr Paleontol 18 (3), 15 September
> Acaenasuchus ... Long & Murry, 1995 ... uncertain ... fossil (only) ...
>  ... Stagonolepididae ... Bull N M Mus Nat Hist Sci 4
> Acallosuchus ... Long & Murry, 1995 ... uncertain ... fossil (only) ...
>  ... Reptilia (awaiting allocation) ... Bull N M Mus Nat Hist Sci 4
> Acanthocalyx ... Cope, 1895 ... uncertain ... extant ...  ... Reptilia
> (awaiting allocation) ... Trans. Amer. Philos. Soc. (N. S.) 18
> Acanthophallus ... Cope, 1893 ... uncertain ... extant ...  ... Reptilia
> (awaiting allocation) ... Amer. Nat., 27
> Acanthopyga ... Gray, 1838 ... uncertain ... extant ...  ... Reptilia
> (awaiting allocation) ... Ann. Nat. Hist., 1 (4)
> Acanthotoposaurus ... Evans & van den Heever, 1987 ... uncertain ...
> fossil (only) ...  ... Reptilia (awaiting allocation) ... S Afr J Sci 83
> (11)
> Acanthurus ... Daudin, 1803 ... uncertain ... extant ...  ... Reptilia
> (awaiting allocation) ... Mag. Encyclop., An. 8, 5 (20)
> Acerosodontosaurus ... Currie, 1980 ... uncertain ... fossil (only) ...
>  ... Lepidosauria (awaiting allocation) ... Canadian J. Earth Sci. 17 (4)
>
> So of these initial 40 names, we have 22 "accepted", 7 "unaccepted" (known
> synonyms in the main), and 11 "uncertain", which split into 5 extant and 6
> fossil. According to the protocol adopted for the "Megataxa" paper, we
> would report the estimated (mean) total accepted names at 22+5.5 (half of
> the "uncertain" total), rounded up to 28, with an uncertainty range
> of +/-5.5 (rounded up to 6).
>
> So to refine this estimate (effectively of somewhere between 22 and 33
> accepted names), we need additional information on the 11 "uncertain" names
> which I do not have to hand at this time, but may take a look as I have a
> little time - or someone else can :)  The same someone, or another, might
> also care to comment whether the names flagged "accepted" / "unaccepted"
> are correctly so, as well.
>
>  Also of interest to note, of the 22 names listed as "accepted", 9 (41%)
> are fossil, which is not that far from the overall value (48.9%) given for
> all accepted names in Reptilia in the paper (around 4,000 accepted names).
>
> Anyway this shows how the totals are computed for the values given in the
> "Megataxa" paper. Of course some of the IRMNG data may be in error, happy
> to receive any advice of that as well, but hopefully any residual errors
> are not large...
>
> I may post again after further examining the 11 presently "uncertain"
> names in this sample.
>
> Regards - Tony
>
>
>