[Taxacom] Chameleons, GBIF, and the Red List

Roderic Page Roderic.Page at glasgow.ac.uk
Fri Aug 22 22:39:32 CDT 2014


Hi Jason,

+1. Yes, if people identified specimens unambiguously ("identified" in the sense of using a specimen code) and explicitly assigned them to taxa then we could track a lot of this stuff without having to make inferences based on trying guess what someone meant by a name.

The analogy with GenBank is apt, because a lot if recent changes in chameleons (and many other taxa) are driven by phylogenetic analysis of sequences. We could track taxa across trees by tracking GenBank accession numbers, and if those sequences are linked to museum specimens, we could map those taxa to concepts used prior to sequencing. But all if this requires a level of reporting of data that is not always found in taxonomic and systematic publications.

Regards

Rod

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On Fri, Aug 22, 2014 at 4:44 PM -0700, "JF Mate" <aphodiinaemate at gmail.com<mailto:aphodiinaemate at gmail.com>> wrote:

As a total ignoramus on the subject, couldn't we just track the records by
assigning unique identifiers to the actual specimens in the same way as we
already do with Genebank?

Jason
On 23/08/2014 1:37 AM, "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz> wrote:

> And what happens when an old name is now split into two or more taxa? For
> example, "cryptic species". What value/status does data have which is
> associated with pre-split concepts? A name, Aus bus, could refer either to
> a species complex before a split. or to one and only one of the cryptic
> species after the split. What if some modern workers reject the split?
>
> Stephen
>
> --------------------------------------------
> On Sat, 23/8/14, Richard Pyle <deepreef at bishopmuseum.org> wrote:
>
>  Subject: Re: [Taxacom] Chameleons, GBIF, and the Red List
>  To: "'TAXACOM'" <taxacom at mailman.nhm.ku.edu>
>  Received: Saturday, 23 August, 2014, 5:06 AM
>
>  I have not followed this
>  thread closely, but it seems to me that the main problems
>  people complain about regarding data harvested by
>  aggregators like GBIF fall into two broad categories:
>  1) The indicated geographic location is bad
>  2) The indicated taxon is bad
>
>  Bad geography comes in two
>  basic forms:
>  a) The stated geographic place
>  is not correct.  This could be due to bad original data or
>  bad digitization, but there is generally no way to fix this
>  other than fixing it at the source.
>
>  b) The stated geographic place is correct, but
>  the associated lat/long coordinates are either missing or
>  wrong.  This one could be improved through various
>  georeferencing algorithms and tools and/or
>  crowd-sourcing.
>
>  Bad
>  taxonomy also comes in two basic forms:
>  a)
>  The organism was misidentified. Again, there is no real way
>  to fix this other than to fix it at the source.  Sometimes
>  a reasonable inference can be made by a good taxonomist, but
>  that always comes with risks.
>
>  b) The name used to represent the organism was
>  "correct" in the context in which the organism was
>  identified, but the name is not consistent with
>  "modern" representations of "accepted"
>  taxonomy.  There are many reasons for this, such as
>  abbreviated or misspelled names, names that are objectively
>  unavailable via the relevant Code (e.g., not validly
>  published), names that are now widely regarded as
>  heterotypic synonyms of other names, names that are
>  classified in a different genus from what modern taxonomists
>  follow, and text-strings that are really not representative
>  of Linnean-style scientific names at all.
>
>  Of these various categories of
>  problems, I suspect it's the last one that represents
>  the largest portion of the "mess".  The good news
>  is that help is on the way.
>
>  If you've got some time, and have an
>  interest in this sort of thing, grab a cup of coffee and
>  read on. Otherwise, hit "delete" now.
>
>  -------------------
>
>  Still here?  Cool.
>
>  OK, so one of the prototype
>  services Rob Whitton and I developed through NSF funding of
>  the Global Names Architecture is a service we call
>  "real-time taxonomic translation".  Basically,
>  this is a service that "translates" taxon names
>  into the "modern" equivalent. The best way to
>  demonstrate the power of this service is through a specific
>  example.
>
>  When Rob and I are
>  wearing our fish-nerd hats instead of our database-nerd
>  hats, we are collaborating with colleagues at NOAA to
>  develop a comprehensive checklist of the fishes of the
>  Northwestern Hawaiian Islands that is
>  "evidence-based" (i.e., occurrence-based with
>  explicit evidence supporting each occurrence).  When this
>  is published later this year (or possibly early next year),
>  I think it will represent a very cool model for how all
>  regional organism checklists should be done in the future.
>  But for this Taxacom post, I want to focus on just one small
>  component of it:  how real-time taxonomic translation
>  works.
>
>  So, the
>  "evidence" behind the occurrences we are using to
>  develop this checklist come from various sources: Museum
>  specimens, recorded observations, photos and videos, and, of
>  course, historical literature reports.  On the literature
>  reports, so far we have captured 2,856 Occurrence records
>  based on reports in 24 publications going back 114 years.
>  If we only look at the raw taxon names as they appeared in
>  these 24 publications, we get a list of 675 distinct
>  scientific names.  Obviously, the prevailing taxonomy has
>  changed over these 114 years, so many of those names are not
>  consistent with the "modern" interpretation of the
>  relevant taxonomy.  It would take many hours of time from
>  multiple experts to review all of those 675 names and figure
>  out all the corrected spellings, etc.  However, using the
>  real-time taxonomic translation service Rob and I developed,
>  we can convert these 675 historical names into the 506
>  "accepted" names as we would use them today.  And
>  it does so in a few seconds (i.e., in "real
>  time").
>
>  A short
>  explanation of how it works is as follows:
>
>  All 2,856 literature-based
>  occurrence records are tied to a "Taxon Name
>  Usage" (TNU) instance (i.e., the usage of a taxon name
>  within a publication). These represent how the original
>  publication recorded the name.  For example, what we now
>  call Acanthurus triostegus had been variously recorded in
>  these literature citations by the following names:
>  Acanthurus triostegus (Linnaeus, 1758)
>  Hepatus triostegus (Linnaeus, 1758)
>  Acanthurus triostegus sandvicensis Streets,
>  1877
>  Hepatus sandvicensis (Streets, 1877)
>  Teuthis sandvicensis (Streets, 1877)
>
>  Similarly, what we now call
>  Coris flavovittata has been recorded variously as:
>  Coris flavovittata (Bennett, 1828)
>  Coris lepomis Jenkins, 1901
>  Julis eydouxii Valenciennes in Cuvier &
>  Valenciennes, 1839
>  Julis flavovittata
>  Bennett, 1828
>
>  ...and so on
>  for all the different names.
>
>  Every TNU is linked to what we call the
>  "Protonym" of the name.  This is essentially
>  equivalent to the botanical "basionym", but
>  essentially represents the original description of the name.
>  Taking the second example above, there are three distinct
>  Protonyms represented among the four names used for Coris
>  flavovittata:
>  flavovittata Bennett, 1828
>  eydouxii Valenciennes in Cuvier &
>  Valenciennes, 1839
>  lepomis Jenkins, 1901
>
>  The taxonomic translation
>  service is built around the "Meta-Authority"
>  (Authority of Authorities) concept.  A Meta-Authority is
>  any organization or individual who wants to assert an
>  "accepted" taxonomy.  For example, ITIS, CoL,
>  WoRMS, etc. are all Meta-Authorities, because they assert an
>  "accepted" usage for each taxon name.  For our
>  checklist paper, we have established our own Meta-Authority
>  (technically now recorded as the "Rob Whitton
>  Meta-Authority, but functionally it is the Bishop Museum
>  Meta-Authority). Each Meta-Authority has a specific scope of
>  interest -- which might be very large (ITIS, CoL, WoRMS,
>  etc.), or might be very small (e.g., a single family or
>  geographic region).
>
>  In any
>  case, what a Meta-Authority does is, for each name within
>  the scope of interest, it makes a statement along the lines
>  "For Protonym A, I/We follow the Treatment of Reference
>  X"
>
>  In this case, The
>  Rob Whitton/Bishop Museum Meta-Authority has made these
>  assertions:
>  - For the protonym
>  "flavovittata Bennett, 1828", we follow the
>  treatment of Randall 2007 [who treats it as a valid species
>  within the genus Coris].
>  - For the protonym
>  "eydouxii Valenciennes in Cuvier & Valenciennes,
>  1839", we follow the treatment of Eschmeyer 2004 [who
>  treats it as a junior synonym of flavovittata Bennett,
>  1828].
>  - For the protonym "lepomis
>  Jenkins, 1901", we follow the treatment of Eschmeyer
>  2004 [who treats it as a junior synonym of flavovittata
>  Bennett, 1828].
>
>  This is how
>  we are able to collapse those messy 675 names spanning 114
>  years of taxonomic history into the 506 names that we (the
>  experts of the fishes of the Northwestern Hawaiian Islands)
>  regard as "accepted" in a few seconds.
>
>  If anyone wants more details
>  on how it works, I'd be happy to explain further.
>
>  The main limitations of this
>  services are:
>  1) It's limited to the
>  names within the Global Names Usage Bank (GNUB; currently
>  543,989 TNUs linked to 195,369 Protonyms); and
>  2) There is currently only one Meta-Authority
>  implemented
>
>  We already have
>  funding from NSF to address limitation #1, by developing a
>  workflow to capture millions of protonyms and tens of
>  millions of TNUs through integrating GNUB, GNI, BHL, and
>  multiple other taxonomic data sources.  We also plan to
>  expand the Meta-Authority list to include the
>  "big" ones (e.g., IT IS/CoL, WoRMS, NCBI), and
>  develop tools to make it easy for any individual or
>  organization to create their own personal Meta-Authority.
>  And, we just submitted a proposal to NSF to (among other
>  things) develop this real-time taxonomic translation service
>  into a set of tools that can be very easily applied to any
>  list of taxon names.
>
>  If we
>  are successful, users of GBIF data will have the option of
>  selecting any Meta-Authority they want (one of the big ones,
>  or their own), and then be able to translate (in real time)
>  all the taxon names as they appear in the GBIF dataset into
>  the "accepted" modern/clean equivalent names
>  according to the selected Meta-Authority.  And the
>  Meta-Authorities aren't just for species-level names --
>  they also provide full "accepted" classifications
>  all the way up to Kingdom.
>
>  Obviously this won't solve all the problems
>  with aggregated data, but it will help solve a lot of it.
>
>  OK, enough for now....
>
>  Aloha,
>  Rich
>
>
>  Richard L.
>  Pyle, PhD
>  Database Coordinator for Natural
>  Sciences
>  Associate Zoologist in
>  Ichthyology
>  Dive Safety Officer
>  Department of Natural Sciences, Bishop
>  Museum
>  1525 Bernice St., Honolulu, HI
>  96817
>  Ph: (808)848-4115, Fax:
>  (808)847-8252
>  email: deepreef at bishopmuseum.org
>  http://hbs.bishopmuseum.org/staff/pylerichard.html
>
>  Note: This disclaimer formally
>  apologizes for the disclaimer below, over which I have no
>  control.
>
>
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