species group - Dwc interpretations?
Hi all,
Forgive me if this has been discussed already. I am trying to decide how to deal with species groups in our database. Here are some real life examples.
Eg. Terellia sp. (virens group)
option 1: Genus: Terellia SpecificEpithet: virens TaxonCertainty: species group
option 2: Genus: Terellia SpecificEpithet: sp. (virens group)
Eg. Oecetis new sp.? inconspicua group
option 1: Genus: Oecetis SpecificEpithet: new sp. TaxonCertainty: "?" how do I incorporate the group?
option 2: Genus: Oecetis SpecificEpithet: n.sp. (inconspicua group) TaxonCertainty: "?"
--------------------------------------------------- Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/ ---------------------------------------------------
It seems to me there are at least two issues:
(1) what to do with unranked (or awkwardly ranked), informally named, taxonomic groups and (2) whether to put a 'value' into the epithet field -- when the specimen is not identified to the species level.
With regard to the second issue - I'd recommend leaving that field empty (NULL)... in both of your examples, the specimen has not been associated with an available species name. Using 'sp' only confuses things because 'sp' is not an epithet. Is there any information content difference between "Terellia (virens group)" and "Terellia sp. (virens group)". "n.sp" similarly is not an epithet -- although it has 'some' information -- this is something that could be put in a field not associated with nomenclature, but with notes about the specimens (.e.g, that someone thinks it's an undescribed speces).
With regard to the first issue, I'm not sure how an informal rank would best be dealt with. The species groups you mentioned are in some regards "superspecies" and perhaps Article 6.2 of the ICZN is applicable (see below). But I'm pretty certain that superspecies aren't a darwincore rank...or how they'd be dealt with.
-Chris
6.2. Names of aggregates of species or subspecies. A specific name may be added in parentheses after the genus-group name, or be interpolated in parentheses between the genus-group name and the specific name, to denote an aggregate of species within a genus-group taxon; and a subspecific name may be interpolated in parentheses between the specific and subspecific names to denote an aggregate of subspecies within a species; such names, which must always begin with a lower-case letter and be written in full, are not counted in the number of words in a binomen or trinomen. The Principle of Priority applies to such names [Art. 23.3.3]; for their availability see Article 11.9.3.5.
Recommendation 6B. Taxonomic meaning of interpolated names. An author who wishes to denote an aggregate at either of the additional taxonomic levels mentioned in Article 6.2 should place a term to indicate the taxonomic meaning of the aggregate in the same parentheses as its interpolated species-group name on the first occasion that the notation is used in any work.
Example. In the butterfly genus Ornithoptera Boisduval, 1832 the species O. priamus (Linnaeus, 1758) is the earliest-named member of an aggregate of vicarious species that includes also O. lydius Felder, 1865 and O. croesus Wallace, 1865. The taxonomic meaning accorded to the O. priamus aggregate may be expressed in the notation "Ornithoptera (superspecies priamus)", and the members of the aggregate by the notations "O. (priamus) priamus (Linnaeus, 1758)", "O. (priamus) lydius Felder, 1865", and "O. (priamus) croesus Wallace, 1865".
On Mar 27, 2012, at 12:58 AM, Peter Oboyski wrote:
Hi all,
Forgive me if this has been discussed already. I am trying to decide how to deal with species groups in our database. Here are some real life examples.
Eg. Terellia sp. (virens group)
option 1: Genus: Terellia SpecificEpithet: virens TaxonCertainty: species group
option 2: Genus: Terellia SpecificEpithet: sp. (virens group)
Eg. Oecetis new sp.? inconspicua group
option 1: Genus: Oecetis SpecificEpithet: new sp. TaxonCertainty: "?" how do I incorporate the group?
option 2: Genus: Oecetis SpecificEpithet: n.sp. (inconspicua group) TaxonCertainty: "?"
Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
Christopher Marshall Curator & Collections Manager Oregon State Arthropod Collection Zoology - Oregon State University Corvallis OR, 97331-2914 marshach@science.oregonstate.edu
I would also recommend to keep the specificEpithet empty in such a case. The scientificName should contain the full string and taxonRank can indicate its a species - or a species group, aggregate or whatever you consider appropiate even if its a not fully standardized value. For identification uncertainty like cf or aff there is the term identificationQualifier, but for nov.sp. and similar notes I would think taxonRemarks is the best place.
best, Markus
On 27.03.2012, at 19:30, Christopher Marshall wrote:
It seems to me there are at least two issues:
(1) what to do with unranked (or awkwardly ranked), informally named, taxonomic groups and (2) whether to put a 'value' into the epithet field -- when the specimen is not identified to the species level.
With regard to the second issue - I'd recommend leaving that field empty (NULL)... in both of your examples, the specimen has not been associated with an available species name. Using 'sp' only confuses things because 'sp' is not an epithet. Is there any information content difference between "Terellia (virens group)" and "Terellia sp. (virens group)". "n.sp" similarly is not an epithet -- although it has 'some' information -- this is something that could be put in a field not associated with nomenclature, but with notes about the specimens (.e.g, that someone thinks it's an undescribed speces).
With regard to the first issue, I'm not sure how an informal rank would best be dealt with. The species groups you mentioned are in some regards "superspecies" and perhaps Article 6.2 of the ICZN is applicable (see below). But I'm pretty certain that superspecies aren't a darwincore rank...or how they'd be dealt with.
-Chris
6.2. Names of aggregates of species or subspecies. A specific name may be added in parentheses after the genus-group name, or be interpolated in parentheses between the genus-group name and the specific name, to denote an aggregate of species within a genus-group taxon; and a subspecific name may be interpolated in parentheses between the specific and subspecific names to denote an aggregate of subspecies within a species; such names, which must always begin with a lower-case letter and be written in full, are not counted in the number of words in a binomen or trinomen. The Principle of Priority applies to such names [Art. 23.3.3]; for their availability see Article 11.9.3.5.
Recommendation 6B. Taxonomic meaning of interpolated names. An author who wishes to denote an aggregate at either of the additional taxonomic levels mentioned in Article 6.2 should place a term to indicate the taxonomic meaning of the aggregate in the same parentheses as its interpolated species-group name on the first occasion that the notation is used in any work.
Example. In the butterfly genus Ornithoptera Boisduval, 1832 the species O. priamus (Linnaeus, 1758) is the earliest-named member of an aggregate of vicarious species that includes also O. lydius Felder, 1865 and O. croesus Wallace, 1865. The taxonomic meaning accorded to the O. priamus aggregate may be expressed in the notation "Ornithoptera (superspecies priamus)", and the members of the aggregate by the notations "O. (priamus) priamus (Linnaeus, 1758)", "O. (priamus) lydius Felder, 1865", and "O. (priamus) croesus Wallace, 1865".
On Mar 27, 2012, at 12:58 AM, Peter Oboyski wrote:
Hi all,
Forgive me if this has been discussed already. I am trying to decide how to deal with species groups in our database. Here are some real life examples.
Eg. Terellia sp. (virens group)
option 1: Genus: Terellia SpecificEpithet: virens TaxonCertainty: species group
option 2: Genus: Terellia SpecificEpithet: sp. (virens group)
Eg. Oecetis new sp.? inconspicua group
option 1: Genus: Oecetis SpecificEpithet: new sp. TaxonCertainty: "?" how do I incorporate the group?
option 2: Genus: Oecetis SpecificEpithet: n.sp. (inconspicua group) TaxonCertainty: "?"
Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
Christopher Marshall Curator & Collections Manager Oregon State Arthropod Collection Zoology - Oregon State University Corvallis OR, 97331-2914 marshach@science.oregonstate.edu
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
Chris & Markus, et al.,
While it is true that "sp." ("nov.sp.", and other similar conveniences) are not valid available taxon names, there is the practicality of managing a specimen database and the purpose it serves. I have never seen a species list that lists "Bombus" rather than "Bombus sp." for an undetermined specimen. Likewise, I assume the header labels in your museum note either "sp." or "spp." for a tray of undetermined material. It is used as a placeholder, and a very convenient one for a lot of the automation we do in our data capture. We can replace "sp." with (NULL) in our database easily enough and I will consider doing this depending how it will impact data entry, storage, and retrieval for various purposes. But I just queried a number of online specimen databases for "sp." in the species field and each returned results. So I would be far from alone if I continue to enter "sp." in the specificEpithet field.
Regarding species groups, as Chris points out the ICZN suggests how to deal with groupings between Genus and Species (below). I am tempted to use our Subgenus field, since it fills a similar function (and call it Subgenus/Species Group), rather than create yet another database field. But again, the practicality of entering and querying data comes into play. And of course, what to do if a species has both a designated species group and subgenus? Most likely I will put the species group name in parentheses in the specificEpithet field before the species name.
I dislike making arbitrary decisions about database fields (and that's why Darwin Core exists). But for data elements with no DwC recommendations, arbitrary decisions (informed by taxonomic standards) is all we have. That is why I am asking how others have handled this situation. I would like to hear from people who have had to deal with this in their own databases.
Pete
http://essigdb.berkeley.edu/ --------------------------------------------------- Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/ ---------------------------------------------------
Subject: Re: [tdwg] species group - Dwc interpretations? From: mdoering@gbif.org Date: Tue, 27 Mar 2012 22:11:38 +0200 CC: pt_oboyski@HOTMAIL.COM; tdwg@lists.tdwg.org To: marshach@science.oregonstate.edu
I would also recommend to keep the specificEpithet empty in such a case. The scientificName should contain the full string and taxonRank can indicate its a species - or a species group, aggregate or whatever you consider appropiate even if its a not fully standardized value. For identification uncertainty like cf or aff there is the term identificationQualifier, but for nov.sp. and similar notes I would think taxonRemarks is the best place.
best, Markus
On 27.03.2012, at 19:30, Christopher Marshall wrote:
It seems to me there are at least two issues:
(1) what to do with unranked (or awkwardly ranked), informally named, taxonomic groups and (2) whether to put a 'value' into the epithet field -- when the specimen is not identified to the species level.
With regard to the second issue - I'd recommend leaving that field empty (NULL)... in both of your examples, the specimen has not been associated with an available species name. Using 'sp' only confuses things because 'sp' is not an epithet. Is there any information content difference between "Terellia (virens group)" and "Terellia sp. (virens group)". "n.sp" similarly is not an epithet -- although it has 'some' information -- this is something that could be put in a field not associated with nomenclature, but with notes about the specimens (.e.g, that someone thinks it's an undescribed speces).
With regard to the first issue, I'm not sure how an informal rank would best be dealt with. The species groups you mentioned are in some regards "superspecies" and perhaps Article 6.2 of the ICZN is applicable (see below). But I'm pretty certain that superspecies aren't a darwincore rank...or how they'd be dealt with.
-Chris
6.2. Names of aggregates of species or subspecies. A specific name may be added in parentheses after the genus-group name, or be interpolated in parentheses between the genus-group name and the specific name, to denote an aggregate of species within a genus-group taxon; and a subspecific name may be interpolated in parentheses between the specific and subspecific names to denote an aggregate of subspecies within a species; such names, which must always begin with a lower-case letter and be written in full, are not counted in the number of words in a binomen or trinomen. The Principle of Priority applies to such names [Art. 23.3.3]; for their availability see Article 11.9.3.5.
Recommendation 6B. Taxonomic meaning of interpolated names. An author who wishes to denote an aggregate at either of the additional taxonomic levels mentioned in Article 6.2 should place a term to indicate the taxonomic meaning of the aggregate in the same parentheses as its interpolated species-group name on the first occasion that the notation is used in any work.
Example. In the butterfly genus Ornithoptera Boisduval, 1832 the species O. priamus (Linnaeus, 1758) is the earliest-named member of an aggregate of vicarious species that includes also O. lydius Felder, 1865 and O. croesus Wallace, 1865. The taxonomic meaning accorded to the O. priamus aggregate may be expressed in the notation "Ornithoptera (superspecies priamus)", and the members of the aggregate by the notations "O. (priamus) priamus (Linnaeus, 1758)", "O. (priamus) lydius Felder, 1865", and "O. (priamus) croesus Wallace, 1865".
On Mar 27, 2012, at 12:58 AM, Peter Oboyski wrote:
Hi all,
Forgive me if this has been discussed already. I am trying to decide how to deal with species groups in our database. Here are some real life examples.
Eg. Terellia sp. (virens group)
option 1: Genus: Terellia SpecificEpithet: virens TaxonCertainty: species group
option 2: Genus: Terellia SpecificEpithet: sp. (virens group)
Eg. Oecetis new sp.? inconspicua group
option 1: Genus: Oecetis SpecificEpithet: new sp. TaxonCertainty: "?" how do I incorporate the group?
option 2: Genus: Oecetis SpecificEpithet: n.sp. (inconspicua group) TaxonCertainty: "?"
Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
Christopher Marshall Curator & Collections Manager Oregon State Arthropod Collection Zoology - Oregon State University Corvallis OR, 97331-2914 marshach@science.oregonstate.edu
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
Hi Peter, darwin core is not a database standard, so please keep that in mind when term definitions do not always lend themselves easily for a database schema. When we discuss dwc terms it is usually for exchanging data.
The species marker sp surely plays an important role and as suggested before it should therefore exist in the full scientificName. But for the atomised parts of the name I still would not recommend to use it as the species epitheton. It isnt an epitheton after all.
best, Markus
On 01.04.2012, at 01:47, Peter Oboyski wrote:
Chris & Markus, et al.,
While it is true that "sp." ("nov.sp.", and other similar conveniences) are not valid available taxon names, there is the practicality of managing a specimen database and the purpose it serves. I have never seen a species list that lists "Bombus" rather than "Bombus sp." for an undetermined specimen. Likewise, I assume the header labels in your museum note either "sp." or "spp." for a tray of undetermined material. It is used as a placeholder, and a very convenient one for a lot of the automation we do in our data capture. We can replace "sp." with (NULL) in our database easily enough and I will consider doing this depending how it will impact data entry, storage, and retrieval for various purposes. But I just queried a number of online specimen databases for "sp." in the species field and each returned results. So I would be far from alone if I continue to enter "sp." in the specificEpithet field.
Regarding species groups, as Chris points out the ICZN suggests how to deal with groupings between Genus and Species (below). I am tempted to use our Subgenus field, since it fills a similar function (and call it Subgenus/Species Group), rather than create yet another database field. But again, the practicality of entering and querying data comes into play. And of course, what to do if a species has both a designated species group and subgenus? Most likely I will put the species group name in parentheses in the specificEpithet field before the species name.
I dislike making arbitrary decisions about database fields (and that's why Darwin Core exists). But for data elements with no DwC recommendations, arbitrary decisions (informed by taxonomic standards) is all we have. That is why I am asking how others have handled this situation. I would like to hear from people who have had to deal with this in their own databases.
Pete
http://essigdb.berkeley.edu/
Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/
Subject: Re: [tdwg] species group - Dwc interpretations? From: mdoering@gbif.org Date: Tue, 27 Mar 2012 22:11:38 +0200 CC: pt_oboyski@HOTMAIL.COM; tdwg@lists.tdwg.org To: marshach@science.oregonstate.edu
I would also recommend to keep the specificEpithet empty in such a case. The scientificName should contain the full string and taxonRank can indicate its a species - or a species group, aggregate or whatever you consider appropiate even if its a not fully standardized value. For identification uncertainty like cf or aff there is the term identificationQualifier, but for nov.sp. and similar notes I would think taxonRemarks is the best place.
best, Markus
On 27.03.2012, at 19:30, Christopher Marshall wrote:
It seems to me there are at least two issues:
(1) what to do with unranked (or awkwardly ranked), informally named, taxonomic groups and (2) whether to put a 'value' into the epithet field -- when the specimen is not identified to the species level.
With regard to the second issue - I'd recommend leaving that field empty (NULL)... in both of your examples, the specimen has not been associated with an available species name. Using 'sp' only confuses things because 'sp' is not an epithet. Is there any information content difference between "Terellia (virens group)" and "Terellia sp. (virens group)". "n.sp" similarly is not an epithet -- although it has 'some' information -- this is something that could be put in a field not associated with nomenclature, but with notes about the specimens (.e.g, that someone thinks it's an undescribed speces).
With regard to the first issue, I'm not sure how an informal rank would best be dealt with. The species groups you mentioned are in some regards "superspecies" and perhaps Article 6.2 of the ICZN is applicable (see below). But I'm pretty certain that superspecies aren't a darwincore rank...or how they'd be dealt with.
-Chris
6.2. Names of aggregates of species or subspecies. A specific name may be added in parentheses after the genus-group name, or be interpolated in parentheses between the genus-group name and the specific name, to denote an aggregate of species within a genus-group taxon; and a subspecific name may be interpolated in parentheses between the specific and subspecific names to denote an aggregate of subspecies within a species; such names, which must always begin with a lower-case letter and be written in full, are not counted in the number of words in a binomen or trinomen. The Principle of Priority applies to such names [Art. 23.3.3]; for their availability see Article 11.9.3.5.
Recommendation 6B. Taxonomic meaning of interpolated names. An author who wishes to denote an aggregate at either of the additional taxonomic levels mentioned in Article 6.2 should place a term to indicate the taxonomic meaning of the aggregate in the same parentheses as its interpolated species-group name on the first occasion that the notation is used in any work.
Example. In the butterfly genus Ornithoptera Boisduval, 1832 the species O. priamus (Linnaeus, 1758) is the earliest-named member of an aggregate of vicarious species that includes also O. lydius Felder, 1865 and O. croesus Wallace, 1865. The taxonomic meaning accorded to the O. priamus aggregate may be expressed in the notation "Ornithoptera (superspecies priamus)", and the members of the aggregate by the notations "O. (priamus) priamus (Linnaeus, 1758)", "O. (priamus) lydius Felder, 1865", and "O. (priamus) croesus Wallace, 1865".
On Mar 27, 2012, at 12:58 AM, Peter Oboyski wrote:
Hi all,
Forgive me if this has been discussed already. I am trying to decide how to deal with species groups in our database. Here are some real life examples.
Eg. Terellia sp. (virens group)
option 1: Genus: Terellia SpecificEpithet: virens TaxonCertainty: species group
option 2: Genus: Terellia SpecificEpithet: sp. (virens group)
Eg. Oecetis new sp.? inconspicua group
option 1: Genus: Oecetis SpecificEpithet: new sp. TaxonCertainty: "?" how do I incorporate the group?
option 2: Genus: Oecetis SpecificEpithet: n.sp. (inconspicua group) TaxonCertainty: "?"
Peter T Oboyski University of California http://nature.berkeley.edu/~poboyski/
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
Christopher Marshall Curator & Collections Manager Oregon State Arthropod Collection Zoology - Oregon State University Corvallis OR, 97331-2914 marshach@science.oregonstate.edu
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
tdwg mailing list tdwg@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg
participants (3)
-
"Markus Döring (GBIF)" -
Christopher Marshall -
Peter Oboyski