University of Glasgow

Roderic Page

I\'m adding more charts to the [GBIF Chart
tool](http://bionames.org/~rpage/gbif-stats/), including some to explore
the type status of specimens from the Solomon Islands. There are nearly
500 holotypes from this region, so quite a few new species have been
discovered in this region.  
  
Inspired by the Benoît Fontaine et al. paper on the lag time between a
species being discovered and subsequently described (see [Species wait
21 years to be described - show me the
data](http://iphylo.blogspot.co.uk/2012/11/species-wait-21-years-to-be-described.html))
I thought I would do a quick and dirty plot of the difference between
the year a specimen was collected and the year the name of the taxon it
belongs to was published (from the authorship string for the scientific
name). Plotting the results was \*cough\* interesting:  
![Types](http://lh6.ggpht.com/-9DPEtT38VFc/U5M4p8XbPQI/AAAAAAAADZk/OWonMLcKkuw/types.png?imgmax=800 "types.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="232"}  
In theory, the difference between the two dates should be negative (if
you subtract publication year from collection year), the smaller number
the less the wait for description. But I found some large **positive**
numbers, implying that taxa had been described long before the types
were discovered! Something is clearly wrong. What seems to be happening
here is the GBIF has failed to match the species name for an occurrence,
and so goes up the taxonomic hierarchy and just records the genus. For
example, <http://gbif.org/occurrence/472764211> was collected in 1965
and is the type of *Pandanus guadalcanalius* St.John. GBIF doesn\'t
recognise this name, and so matches the occurrence to the genus
*Pandanus* Linnaeus, 1782. hence it looks like we\'ve used a time
machine to describe a taxon in 1782 based on a specimen from 1965.  
  
At the other end of the spectrum, there are a lot of specimens that seem
to have waited over 200 years for description! Turns out these are
mostly specimens from the MCZ that have their collection date recorded
by GBIF as \"1700-01-01\". This seems an arbitrary date, and turns out
it\'s an artefact. The MCZ records \"unknown\" collection dates as the
range 1700-01-01 - 2100-01-01  
(see <http://mczbase.mcz.harvard.edu/guid/MCZ:IZ:DIPL-4985>).
Unfortunately, when it generates the export for GBIF, these get
truncated to 1700-01-01, and GBIF then (not unreasonably) treats that as
the actual collection date. Somewhere in the middle of the plot of lag
between collection and description is some interesting information, but
it\'s a pity that most of this is obscured by some serious data
errors.  
  
For me the bigger lesson here is the power of visualisation to explore
the data and to expose errors. This is why I was underwhelmed by the
[new charts GBIF is
releasing](http://iphylo.blogspot.com/2014/06/visual-analysis-of-gbif-data.html).
Plots of ever upward trends are ultimately not very useful. They don\'t
give much insight into the data, nor do they help tackle interesting
questions. I think we need a much richer set of visualisations to really
understand the strengths and limitations of the data in GBIF.  
  

### Update

  
Investigating further, there are some other reasons for the \"back to
the future\" types. For example,
<http://www.gbif.org/occurrence/188826624> (CAS 5506 from FishBase) was
collected in 1933 and is recorded as a holotype, with the scientific
name *Cypselurus opisthopus* (Bleeker, 1865). 1933 - 1865 = 68, so the
taxon was named 68 years before it was collected(!).  
  
A bit of investigation using
[BioNames](http://bionames.org/search/Cypselurus+opisthopus),
[BioStor](http://biostor.org/reference/59326), and GBIF
(<http://www.gbif.org/occurrence/473244692>, another record for CAS
5506) reveals that CAS 5506 is the holotype for *Cypselurus crockeri*,
shown below in a plate from it\'s original description (published in
1935):  

> Seale A (1935) The Templeton Crocker Expedition to western Polynesian
> and Melanesian islands, 1933. No. 27. Fishes. Proceedings of the
> California Academy of Sciences 21: 337--378.
> <http://biostor.org/reference/59326>

  
So, in fact this species was described shortly after its collection,
with a lag of 1933 - 1935 = -2 years.  
  
![Proceedingsofcal421193336cali
0397](http://lh3.ggpht.com/-GSC2VJY-KJs/U5RCcuLMBfI/AAAAAAAADZ0/yZNkyJol2_E/proceedingsofcal421193336cali_0397.jpg?imgmax=800 "proceedingsofcal421193336cali_0397.jpg"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="397" height="600"}  
Apart from the duplication issue (FishBase has replicated some of the
CAS dataset, sigh), the other problem is one of modelling the data. The
CAS record has the original taxon name for which CAS 5506 is the type
(*Cypselurus crockeri*), the FishBase record has the currently accepted
name for the taxon (*Cypselurus opisthopus*). These two different
approaches have very different implications for the charts I\'m making,
and simply reinforce my feeling that the GBIF data is both fascinating
and full of \"gotchas!\".  


I'm adding more charts to the GBIF Chart tool, including some to explore the type status of specimens from the Solomon Islands.

Using GBIF to measure the lag between collection and description of a species (oh dear)

![26243 367877492480 367794192480 4194340 6124010
n](http://lh4.ggpht.com/-0yMDlzgSyj8/UuJMx_1a85I/AAAAAAAADQM/o7pmidEzSA0/26243_367877492480_367794192480_4194340_6124010_n.jpg?imgmax=800 "26243_367877492480_367794192480_4194340_6124010_n.jpg"){border="0"
width="128" height="128" style="float:right;"}Scott Federhen told me
about a nice new feature in GenBank that he\'s described in a piece for
[NCBI
News](http://www.ncbi.nlm.nih.gov/news/01-21-2014-sequence-by-type/).
The NCBI taxonomy database now shows a its of type material (where
known), and the GenBank sequence database \"knows: about types. Here\'s
the summary:  
  

> The naming, classification and identification of organisms
> traditionally relies on the concept of type material, which defines
> the representative examples (\"name-bearing\") of a species. For
> larger organisms, the type material is often a preserved specimen in a
> museum drawer, but the type concept also extends to type bacterial
> strains as cultures deposited in a culture collection. Of course,
> modern taxonomy also relies on molecular sequence information to
> define species. In many cases, sequence information is available for
> type specimens and strains. Accordingly, the NCBI has started to
> curate type material from the Taxonomy database, and are using this
> data to label sequences from type specimens or strains in the sequence
> databases. The figure below shows type material as it appears in the
> NCBI taxonomy entry and a sequence record for the recently described
> African monkey species, *Cercopithecus lomamiensis*.

![Cercopithecus](http://lh5.ggpht.com/-bg60I2_M9dE/UuJMwnBAEaI/AAAAAAAADQE/ezlxZXzJ9-8/cercopithecus.png?imgmax=800 "cercopithecus.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="500"}  
  
You can query for sequences from type using the query [\"sequence from
type\"\[filter\]](http://www.ncbi.nlm.nih.gov/nuccore/?term=sequence+from+type%5Bfilter%5D).
This could lead to some nice automated tools. If you had a bunch of
distinct clusters of sequences that were all labelled with the same
species name, and one cluster includes a sequence form the type
specimen, then the other clusters are candidates for being described as
new names.


Scott Federhen told me about a nice new feature in GenBank that he's described in a piece for NCBI News. The NCBI taxonomy database now shows a its of type material (where known), and the GenBank sequence database "knows: about types. Here's the summary:You can query for sequences from type using the query "sequence from type"[filter]. This could lead to some nice automated tools.

Publicaciones de Rogue Scholar

Using GBIF to measure the lag between collection and description of a species (oh dear)

NCBI taxonomy database now shows type material