A relational database as a tool in ornithological taxonomy and comparative systematics

8 Pages·2003·3.9 MB·English

by  Rémy Bruckert

-
The Ornithological Collection of Emil Werner in the National Museum ofNatural History ofSofia 195
Handbook ofthe Birds ofthe World. Vol. 3. Hoatzin to Leverkühn, p. (1894): Notizen für die Vereinsmitglieder
Auks. Lynx Edicions, Barcelona. 821 pp. Literarisches: No. 15. Werner, Emil. Omithologische
DEL Hoyo, J., Elliott, A. & Sargatal, J. (eds., 1997): Monatsschrift des Deutschen Vereins zum Schutze der
Handbook ofthe Birds ofthe World. Vol. 4. Sandgrouse Vogelwelt 19: 242-243.
to Cuckoos. Lynx Edicions, Barcelona. 679 pp. MouNTFORT, G. (1989): Rare Birds of the World. Lexing-
DEL Hoyo, J., Elliott, A. & Sargatal, J. (eds., 1999): ton, Massachusetts. The Stephen Greene Press, 256 pp.
Handbook ofthe Birds ofthe World. Vol. 5. Bam-Owls Werner, E. (1889): Das Steppenhuhn 1888 bei Kiel.
to Hummingbirds. Lynx Edicions, Barcelona. 759 pp. Monatsschrift des Deutschen Vereins zum Schutze der
DEL HoYO, J., Elliott, A. & Sargatal, J. (eds., 2001): Vogelwelt 13: 122-126.
Handbook ofthe Birds ofthe World. Vol. 6. Mousebirds World Conservation Monitoring Center (1993): World
to Hombills. Lynx Edicions, Barcelona. 589 pp. checklist ofthreatened birds. JointNature Conservation
Gebhardt, L. (1964): Die Ornithologen Mitteleuropas. Ein Committee, Peterborough: 310 pp.
Nachschlagewerk. Brühlscher Verlag Glessen. 403 pp.
Howard, R. & Moore, A. (1991): A complete checklist of
the Birds ofthe World. Oxford Univ. Press, Oxford, 732 Dr. Zlatozar BoEV, National Museum ofNatural His-
pp. toiy, Bulgarian Academy of Sciences, Tsar Osvo-
King, W. (1981): Endangered Birds ofthe World. The ICBP 1,
Bird Red Data Book. Smiths. Inst. Press, Washington. boditel Blv., 1000 Sofia, Bulgaria, e-mail:
boev(^nmnh.bas.bg or boevzazo(^yahoo.co.uk
Bonner zoologische Beiträge Band 51 (2002) Heft 2/3 Seite 196 Bonn, September 2003
The Whereabouts of Salvadori's Bird Collections
&
Carlo G. Violani Fausto Barbagli
Dipartimento di Biologia Animale deH'Universitá di Pavia
and Centro Interdipartimentale di Servizi „Musei Universitari", Pavia, Italy
SUMMARY
The richness in exotic birds preserved in Genoa
Among the Italian naturalists ofthe 19^'^ century who Museum is due to the activity ofits founder and direc-
tor Marquis Giacomo Doria who financed several
studied local and exotic avifaunas. Count Tommaso
naturalistic expeditions in which ornithological series
Salvador! (1835-1923) stands out as one ofthe most
were particularly sought after Salvadori as deputy
celebrated ornithologists in Italy and abroad. Owing director of the Zoological Museum of Turin Univer-
to his vast knowledge ofornithology and to his untir-
sity was the only one entrusted with the study of all
ing activity in the study ofmuseum material, the pro- the birds brought back to Genoa Museum and his
duction of Salvadori as a scientific author is indeed work was rewarded with duplicates ofthe skins, also
remarkable: approximately 350 publications, includ-
including some syntypes, for the Turin Museum.
ing the famous „Ornitologia della Papuasia e delle
After the relevant papers were published, part of the
Molucche" in three volumes and three supplements.
studied collections was often broken up by the owners
Many Museums of Natural History and private col- and part of them was sold or exchanged with other
lectors entrusted him with series of birds, obtained institutions. Some important material was unfortu-
from the exploration of little known countries, to be nately destroyed (e.g. most ofthe Turati collection in
described. Therefore he soon became an expert on the Milan Museum, some specimens in Lisbon and Dres-
birds ofNew Guinea, Moluccas, Indonesia, East Asia, den Museums), while several series were actually dis-
Korea, Central and East Africa, Bolivia, Ecuador, persed and scattered as single specimens in other
Argentina, the North Pole, as well as Italy. A consid- Museums (Palermo, Parma, Pavia, Pisa, Rome,
erable achievement was also the compilation ofthree Verona, Leiden, Rothschild collection, now in New
volumes of the „Catalogue of Birds in the collection York).
of the British Museum" (dealing with Parrots,
Pigeons, Ducks, Flamingos, Tinamous and Ratites),
with accurate descriptions ofthe rich collections then e.G. ViOLANi, Dipartimento di Biologia Animale del-
preserved in London, and now at Tring. The finest rUniversitá di Pavia, Piazza Botta 9 - 1-27100 Pavia,
specimens in the series studied in Italy by Salvadori Italy.
are still preserved in the Museums of Genoa, Turin F. Barbagli, Centro Interdipartimentale di Servizi
and, at a lesser extent, Milan and Florence, including „Musei Universitari", Piazza Botta 9 - 1-27100 Pavia,
the majority ofthe types ofhis new taxa.
Italy.
Bonner zoologische Beiträge Band 51 (2002) Heft 2/3 Seiten 197-204 Bonn, September 2003
A Relational Database as a Tool in Ornithological Taxonomy
and Comparative Systematics
Rémy Bruckert
Muséum National d'Histoire Naturelle, Paris, France
Abstract. Computer programs that store information on historical and current taxa names are called 'taxonomic referen-
tials'. I created such a taxonomic referential forthe class ofbirds (Aves) in the form ofa relational database using the soft-
ware 4D (www.4d.fr).
About 40,000 original designations ofspecies and subspecies ofbirds, which were supposed new to science at the time of
publishing, havebeen entered into the database so far The designationsofapprox 2,000authors were compiled usingabout
c. 1,400 different books orjournals. All these Linnean bi- or tri-nomina are combined with approx 7,000 genera names,
which are themselves published with their own descriptions and, however not always, with a proper designation oftheir
type species.
All genera, species and subspecies namesretained bythe three main classifications used in modem ornithology, i.e. Peters
et al. (1931-1987), Sibley & Monroe (1990-1993) and Howard & Moore (1980-1994), are also defined in the database
and linked with the original names. Additionally, suprageneric categories and many synonyms ofdifferent taxonomic lev-
els were included in the database. English and French common names and geographical distributions are also recorded
therein.
In conclusion I show how a taxonomic referential can be used to computerize a collection and how it plays a vital part in
assembling type data.
Keywords. Taxonomic referential, avian types, comparative systematic, ornithological collections, collection management
1. INTRODUCTION 3. THE DATABASE AS A TOOL IN
ORNITHOLOGICAL TAXONOMY
The base line of any taxonomy is the 10th edition of
Systema Naturae by Linne (1758). The publishing The taxonomic referential consists of three main
year ofthis work, 1758, or even more accurately, 1st traits. Firstly, there are three tables for names ofgen-
January 1758, is considered to be the point „zero" of era (genus by original designation), species and sub-
zoological nomenclature by article 3.1. ofthe Interna- species (top of fig. secondly tables for the refer-
1 ),
tional Code of Zoological Nomenclature (ICZN ences ofeach taxon (bottom row) and lastly tables for
1999). From then onwards, any new name of a bird the author(s) ofeach taxon (middle row).
species or subspecies published in a book orjournal in Each species or subspecies in the table TAXA is
the standard form of a Linnean binomen or trinomen
brought in relation by an identifier ('pointer')joining
is regarded as a valid contribution to nomenclature.
the following tables: (1) its current genus stored in a
A collection ofsuch published scientific names asso- table of GENERA NAMES and (2) its current species
ciated with their references is called a 'taxonomic ref- name and, if existing, its subspecies name (might be
erential'. Meanwhile, the number of animals known the same name(s) as in the table 'TAXA', if the taxon
to science has become very large and hence there is a is not considered to be a synonym), both stored in a
demand to manage the huge set of names and biblio- table SPECIES & SUBSPECIES NAMES. It is further
graphic references with computers. have commen- connected (3) with a table for its first and subsequent
I
ced the task of creating such a taxonomic referential authors stored in a table ofauthors (AUTHORS TAXA)
for the class ofbirds (Aves) in form ofa database. and lastly with its references in a table of references
of taxa (REFERENCES TAXA). There might be more
2. MATERIAL AND METHOD than one reference linked as a taxon that may have
My been described or discussed in several different publi-
computerized taxonomic referential is based on a rela-
tional database invented in the 1970s (Codd 1970). The key cations even though only the first, the oldest refer-
structural element ofa relational database is that any infor- ence, is important in terms ofpriority.
mation is storedonlyonce inthewhole system. Avoidingany The same scheme has been followed for generic
duplications minimizesthe sizeofsuchadatabaseandallows
quickand easyadjustments inthe caseoferrors ortaxonomic names. Each genus name ofthe table GENERANAMES
revisions. In doing this, links among data follow the logical is related to the tables AUTHORS and REFERENCES by
structure ofthe scientific approach. I used the database man- the table AUTHORS GENERA and the table REFER-
agement system 4D (www.4d.fr/) on MAC OS 9. ENCES GENERA.
198 Rémy Bruckert
TAXA
GENERANAMES H" E
H» E Genus Name N° E
SPECIES&SUBSPECIESNAMES;
A20 Species Name N** E
E
D Subspecies Name N** E
Name A20
Type SpeciesH" E D AUTHORS
Nomennuduni B Nomonnudum B N° E
Norni^nnovum B Nomonnovumi B Name A20 f
Preoccupied Genus H" E Preoccupied Taxon H" E FirstName A20
1
Conflict Genus H" E Conflict Taxon H" E Birth c
Synonyme Taxon H" E Death D
AUTHORSGENERA AUTHORSTAXA AUTHORS ARTICLES AUTHORSWORKS
Genus H" E Taxon N° E Author N" E Author N° E
Author N° E Author N° E Article N" E Vork H" E
N" E N'^ E N^ E E
REFERENCESGENERA REFERENCESTAXA
Genus H" E Taxon N" E REFERENCES
Reference H" E Reference N° E N» E v/ORKS
N' E N° E Vork N" E H" E
Article H" E ARTICLES DateBeg. D
[•äto D H" E DateEnd D
Details T Vork H" E Title T
Page E Date D Details T
Plate E Title T
Details T
PageBeg. E
PageEnd E
Fig. 1: Structure ofthe taxonomic referential with three major traits: upper row: names ofgenera, species and subspecies,
middle row: authors ofgenera, species and subspecies, lower row: references.
Each reference is listed in context to the medium it For all genus names the type species (ifknown) may
was published in. Books are entered in the table be stored in the table TAXA.
WORKS related to all their authors and editors (table
AUTHORS) by the table AUTHORS WORKS. Ifthe pub-
lication medium is a journal, a full quotation of the 4. THE DATABASE AS A TOOL IN
reference also includes an article stored in the table COMPARATIVE SYSTEMATICS
ARTICLES related to its own authors through the table
AUTHORS ARTICLES. Due to the continuous growth of ornithological
knowledge, avian names have changed significantly
Thirteen tables are needed to store the taxonomic ref- in different classifications over time. Furthermore,
erential. This can be seen as a look-up table of avian some of the original descriptions were considered to
names, consisting so far of approx 40,000 original be of no relevance to modern systematics and their
designations of avian species and subspecies which
names subsequently became synonyms.
were supposed new to science, published in approx
10,000 scientific papers by about 2,000 authors in Nowadays, three main classifications are commonly
about 1,400 different books and journals. All these used by ornithologists. The classification of James
Linnean bi- or tri-nomina include about 17,000 Lee Peters et al. (193 1-1986, JLP) has been generally
species or/and subspecies and 7,000 generic names. adopted by museums for arranging their collections.
DNA
The first classification partially based on analy-
aOcbcvoiuonuts.lyT,healrleftoarxeontohmeidcaatlabraulseesdhiasvtienbgueiesnhetsakneonmiinntao sis, the work ofSibley & Monroe (1990-1993, SM),
nuda and nomina nova. In the latter case, where a although often criticized, has become a major refer-
newly established name replaces a preoccupied name, ence, mostly in biomolecular studies. Finally, the
the database has to use two identifiers ('pointers') check-list of Howard & Moore (1980-1994, HM)
connecting the old with the new name. provides a modem update ofPeters' classification.
A Relational Database as a Tool in Ornithological Taxonomy and Comparative Systematics 199
^j±) 1 TAXA if±
FAMILIESNAMES ±j GENERANAMES |t] w" E
1
N" E N" E Genus Name N° E SPECIESSUBSPECIESNAMES
Name A20 Name A20 Species Name H" E
N° E
Date D Subspecies Name H" E
Name A20
Date D
JLPTAXA
N" E
r JLPSPECIES
JLPGENERA Taxon N** E
N" E
E < Genus N° E
Name H" E
JLPFAMILIES Genus Name N" E Species H" E
E Family H" E Subspecies N° E
JLPSUBSPECIES
Family Name N° E Synonyme B
Order N" E Date D
Name N"
Volume E
Page E
SMTAXA SMSUPERSPECIES
N° E
SMGENERA Taxon H° E Name N°
E Genus N<> E
SMFAMILIES Genus Name N° E Superspecies N" E SMSPECIES
Family N° E Species N*" E
Family Name N° Subspecies E Name N"
Order H" Synonyme B
Date D SMSUBSPECIES
Volume E E
Page E Name H" E
Fig. 2: Structure of the table comparing the classifications of Sibley & Monroe (bottom row) with Peters' Checklist
(middle row).
Any classification reflects the personal knowledge cific names, are fed into the database in the same way.
and views of its author(s), thus changing names from All higher taxonomical levels ofSM, i.e. subfamilies,
one classification to the other. Therefore 1 have cre- tribes, families, orders, etc., are also entered as shown
ated a table comparing the same taxon (species or on the left of fig. 2 (here for families). Last but not
subspecies) among the tree major classifications men- least, Howard & Moore (HM) is combined with the
tioned above. same links to the rest of the database. In future, fur-
Fig.2 shows the basic structure which enables my ther classifications like Wolters (1975-1982) and
Sharpe et al. (1874-1898) can be added in the same
database to compare different classifications. At the
way.
top right comer, one finds again the previously
defined table TAXA with its two companion tables Table 1 gives a summary ofthe contents entered into
GENERA NAMES and SPECIES & SUBSPECIES NAMES. the database so far. The specific qualities ofeach clas-
In the middle row follow the corresponding tables of sification are shown in bold. The numbers of genera
names used in Peters' classification (JLP). Each and subgenera given in parentheses include syn-
name of a species/subspecies of JLP is brought in onyms.. The two numbers given in parentheses in the
relation with a name of the original table of subspecies category are the totals of nominal sub-
species/subspecies as well as with JLP's generic species and non-nominal subspecies, respectively.
names. The latter must be present in the table GEN- Wolters' classification is left in the table with some
ERA NAMES. question marks, as this information has not been
obtained yet.
This „Standard sef can be seen as the taxonomic ref-
erential's dictionary of names. The classification of In this taxonomic referential, common English names
Sibley & Monroe (SM), tables shown at the bottom and geographical distributions follow Sibley & Mon-
offig. 2, with a supplementary table for the superspe- roe (1990). French names are from The International
200 Rémy Bruckert
CLASSIFICATION J. L. Peters et al. H. E. Wolters SiBLEY & Monroe Howard & Moore
Dates 1931-1986 1975-1982 1990-1993 1990-1994
Authors & Date ofTaxa YES YES YES NO
References YES NO NO NO
Orders ZD 31 ¿D L
1
TT
ramilies 164 23o 147 1172
^1iKfnrni]ií=*q 173 17S 81 81
Tribes 7 59 0 0
Genera 2,129 (4,434) 2,669 (4,228) 2,064 2,018
Subgenera 149 (164) 1,757 (2,691) 0 0
Superspecies 0 0 1,451 0
Species 8,897 ? 9,702 9,359
Subspecies 22,217 7 2,115 22,589
Synonymes 8,714 ? 67 0
Type localities YES NO NO NO
Distribution YES YES YES YES
Common names NO German+English English English
Genera nova 1 15 0 0
Nomina nova 38 2 0 0
Table 1: The number ofgenera, species, subspecies and other peculiarities in the main classifications.
Commission on French Names ofBirds (Devillers & 5. TAXONOMIC REFERENTIAL FOR
Quellet 1993). MANAGING COLLECTIONS AND TYPES
A query interface offers the following query options: The dictionary of names, which is built up from the
-name or part ofa name ofany taxonomical category, different publications entered, helps to find the names
- name or part ofa name ofauthors, used in different publications, on specimen labels and
in type lists and may also help to computerize avian
- year or time interval ofpublications,
collections.
- name ofpublishing organ (book orjournal)
Fig. 4 indicates a possible use ofmy taxonomic refer-
Queries can be made in a specified classification or ential to computerize a collection. For illustrative pur-
across all classifications. Synonyms of names can poses, all tables introduced above are merged into one
also be requested. table (TAXONOMIC REFERENTIAL) shown at centre
Fig. 3 shows an example ofthe database's output after left of fig. 4. The table SPECIMENS on the right side
represents the collection of the Muséum National
a query for the following information on all classifi-
cations: generic name begins with „an" and species d'Histoire Naturelle de Paris (MNHN).
name with „rubr". Each record ofthe table SPECIMENS stands for a spec-
The output table is entitled by the total account for the imen ofany kind (skin, skeleton, tissue, ...) registered
particular quei^. In the above mentioned case seven under a collection number and collected at a given
date and place (table LOCALITIES) by one or several
possibilities of41,373 entries fit the criteria (five are
presented). Each taxon fulfilling the search criteria is collectors. Each specimen is brought in relation with
given under its original designation as well as under a name found in any ofthe classifications ofmy data-
its corresponding name in each classification, includ- base by the table IDENTIFICATIONS. This table is nec-
essary to store the successive identifications made by
ing its publication reference.
further ornithologists who have been working on the
particular specimen at different times. One additional
table is linked into the identification table: that ofthe
A Relational Database as a Tool in Ornithological Taxonomy and Comparative Systematics 201
;
202 Rémy Bruckert
IDENTIFICATIONS
r
E
ReamenN* E lOEHTIFICATORSSPECIMENS
TaxonÑameIT E SpedmenN*
[lité 0 Identífiatorir
COLLECTORSSPECIMENS
TÄ3CÖfioMrCREFERENTIAL SpedmenIT E
laxonH* ColledM>rir E
N' E
TYPES
mmms
r
E
1
E E
TaxonHameIT E ObjectKind E
MkiseufflIT E (Museum E
CatalogK* A20 CatalogIT AZO
IfpeLocalityK* E A2
LOCALITIES
Age E
r
E
REk'ISIOHS CollectingObte D
L Name A20
Typeir E Localit)'
LocalityMother E
ReferenceH* E
Latitudiä A2
N" E
Longitude A2
^ MUSÉES ' REFERENCES AUTHORS
r
E ir E
Acroriyme A5 Workr E Name A20
Name A20i Aftider E FirstName A20
j
lown A20
:
Country A20
Fig. 4: Taxonomic referential: managing collections and types.
names of scientists identifying the specimen (table papers might also be cross-linked to the former table
IDENTIFICATORS). Collectors of specimens and per- (REVISIONS).
sons that identified specimens are stored in separate About 500 types from the MNHN, and more than
AUTHORS.
tables linked to the table
7,000 types from the Natural History Museum, Tring,
I have added another table to my database, the table NHM, are already listed in my database. The unique
TYPES. Each record ofthis table isjoined - by defini- combination of register/catalogue numbers of each
tion - with a taxon name (table TAXA), which obvi- specimen with the internationally accepted acronym
ously should exist in the taxonomic referential. Fur- ofeach museum forms a code which would facilitate
ther information, which would be wanted for each any connections between single specimens ofnumer-
type, is the correct type status (neo-, lecto-, syn- and ous museums' databases world-wide. This uniqueness
holotype, perhaps also para-, paralectotype), the ofeach entry ofmy database, combined with possible
LOCALITY where it was collected (terra typica), the digital photos, would make it possible in the near
name ofthe type-holding institution (MUSHES) and a future to construct a virtual, international, ornitholog-
catalogue/register number, if additional papers quote ical museum via the internet. Each institution sharing
further information on a type and if these papers are their databases with my database would have free
already entered in the 'REFERENCES' table, then these access to this resource.