Introductory lecture for the "Evolution, Biodiversity, and Conservation" orientation course, Leiden University

1. History and Future
of
Taxonomy
Jeremy Miller
Leiden, 31 August 2015

2. , Natural History Museum, London, U.K.
iczn@nhm.ac.uk www.iczn.org
Ellinor Michel
International Commission
on Zoological Nomenclature(ICZN)
Zoological Nomenclature
The Garden of Eden with the Fall of Man
Jan Brueghel the Elder and
Pieter Paul Rubens
and whatsoever Adam called every living creature,
that was the name thereof. Genesis 2:19

3. Shen Nong
ca. 3,000 B.C.
Author of early pharmacopoeia
• Hundreds of medicines derived from
minerals, plants, and animals
Advanced agriculture
• Credited with invention of hoe plow,
axe, and irrigation
Emperor Shen Nung is said to have tasted
hundreds of herbs to test their medicinal value

4. First to classify all living things
Empiricism
• General principals derived from
specific observations
Aristotle
(384-322 BC)
The School of Athens (detail)
Raffaello Sanzio

5. The Baptism of Constantine (detail)
Giulio Romano
Decline of the
Roman Empire
Empire partitioned
• 293 by Emperor Diocletian
Byzantine Empire
• Survived nearly 1000 years
• Ancient texts
• Centers of learning
Western Roman Empire
• Disintegrated by late 5th century
• Lost contact with much of its past
• Knowledge concentrated in monasteries

6. The duty of the man who investigates the
writings of scientists, if learning the truth is his
goal, is to make himself an enemy of all that he
reads, and,.. attack it from every side. He
should also suspect himself as he performs his
critical examination of it, so that he may avoid
falling into either prejudice or leniency.
Alhazen (Ibn al-Haytham)
(Fatimid Caliphate, 965-1040)
Father of modern optics
First to test hypotheses with
verifiable experiments
Latin translation of major work probably made in late 12th century,
influenced community of scholars in Catholic Europe
Alhazen (Ibn al-Haytham)

7. Scholasticism
By 1200, reasonably accurate Latin
translations of most major classical
scholars were available
Rediscovery of Aristotle,
combined with Christian
philosophy, led to development
of Scholasticism
• Repeated cycles of observation,
hypothesis, experimentation
• Need for independent verification
• Experimental methods precisely
documented to facilitate
independent test
Medieval Universities developed
in 12th and 13th centuries
14th-century image of a university lecture

8. Ockham’s Razor
No more things should be presumed
to exist than are absolutely
necessary, i.e., the fewer
assumptions an explanation of a
phenomenon depends on, the better
the explanation
William of Ockham, stained glass church window,
Surrey
Everything should be made as
simple as possible, but not simpler
Albert Einstein
William of Ockham
(Franciscan friar, 1287-1347)

9. Black Death
(1346-1353)
Pandemic in Europe
75-200 million deaths
(30-60% of Europe)
Religious, social, and
economic upheaval
Followed by lull in
scientific activity
The Black Death depicted in the Toggenburg Bible, 1411

10. Scientific revolution (1543)
Nicolaus Copernicus
De revolutionibus orbium coelestium
(On the Revolutions of the Celestial Spheres)
Andreas Vesalius
De humani corporis fabrica
(On the Fabric of the Human Body)

11. Nicolaus Copernicus
(Royal Prussia, 1473-1543)
Copernicus’ heliocentric model of the
universe described in De revolutionibus
orbium coelestium
Geocentric model
• Aristotle
• Church authority
Heliocentric model
• Based on astronomical observations
• Explained apparent retrograde
motion of planets as due to
movement of Earth
• Only mild initial controversy
• Church opposition 73 years later
Galileo Galilei
• Champion of heliocentrism
• Judged by Roman Inquisition

12. Andreas Vesalius
(Brabançon physician, 1514-1564)
Author of On the Fabric of the Human Body
influential book series on human anatomy
Performed own dissections
• Previously performed by barber surgeon
• Corrected errors of the ancient Greeks
Vesalius was going up against the towering authority
of a tradition stretching back to the ancients — here
specifically the work of Galen — with only his
experience on his side. He knew what his eyes saw
and his hands felt, and he knew therefore that
traditional belief was wrong.
Anatomical illustration from De
humani corporis fabrica

13. Contemporary revolutionaries
Questioning religious doctrine in the early 1500s
Martin Luther (1483-1546)
German priest
Protestant Reformation challenged
authority of Pope
John Calvin (1509-1564)
French Theologian
Broke with Catholic Church 1530

14. “What marks out modern science … is not the
conduct of experiments ... but the formation
of a critical community capable of assessing
discoveries and replicating results”. Science
needed to be reported openly and debated by
peers, as it was (after a fashion) in the Royal
Society's Philosophical Transactions, the first
true scientific journal, launched in 1665.
Philosophical Transactions of the Royal Society
(1665-present)
First journal devoted to science
Longest running scientific journal
Divided into separate physical and
life sciences publications in 1887
Philosophical Transactions, volume 1

15. The earliest known artistic representation of eyeglasses
Cardinal Hugh de Provence reading in a scriptorium
Tommaso da Modena, 1352
Lenses
Came into widespread use in
Europe with invention of
spectacles, Italy, 1280s
Improved lenses led to
compound optical microscope,
refracting telescope
• Compound microscope, 1595
• Refracting telescope, 1608
Impact on taxonomy
• More detail visible
• Classical scholars surpassed
• Specimen collections

16. Carl Linnaeus
(Swedish naturalist, 1707-1778)
Start of modern taxonomy
• Nature organized as nested hierarchy of
ranks
• Binary species names replaced phrase
names
• Based plant classification on sexual
characters
Carl von Linné
Alexander Roslin, 1775
Linnaean Ranks
Kingdom
(Phylum)
Class
Order
Family
Genus
Species

17. Phrase names
Phrase name
• Plantago foliis ovato-lanceolatis
pubescentibus, spica cylindrica, scapo
tereti
Linnaean name
• Plantago media
The phrase names included a description of the
species that distinguished it from other known
species in the genus. With an expanded
knowledge of the global fauna and flora
through 17th and 18th century scientific
expeditions, a large number of new species
were found and named, and more terms had to
be added to each phrase name.

18. Charles Darwin
(English naturalist, 1809-1882)
Linnaean taxonomy
• Intended for ease of identification
• Expression of classification in the
form of a tree-like diagram was
formulated by late 18th century
With Darwin’s theory
• Agreement that classification should
reflect evolution
Excerpt from Darwin’s notebook. First known
illustration of a phylogenetic tree

19. Suitability
Name should reflect characteristics
“If it is decided that none of the synonyms is really suitable for the
plant, then necessity compels us to make up a new one.”
(Linnaeus 1737:259; tr. Hort 1938:209)
Stability
Recent, widely used names preferred over older forgotten names
Priority
Oldest name preferred
Linnaean Taxonomic Nomenclature
Implementation issues
• How to resolve nomenclatural conflict?
• Synonymy: more than one name available for a taxon
• Homonym: more than one taxon given the same name
• Under what conditions should names be changed?

20. “the goal of nomenclature of natural
history is to be universal, common to
scientists of all nations”
Candolle (1813:227, tr.)
Augustin Pyramus de Candolle
(Swiss botanist, 1778-1841)
Rules
• The first name given to a species must remain
unchanged
• Names must be in Latin and follow grammatical rules
Exceptions
• Name already in use (homonyms)
• Mix Greek and Latin roots
• Names that contradict characteristics of the taxon

22. Strickland’s Rules, 1837
• The Principle of Priority with
exceptions similar to Candolle’s
It would (…) be highly desirable if an
authorized body could be constituted, to
frame a code of laws for naturalists, instead
of the present anarchical state of things in
which every one does that which is right in
his own eyes.
Strickland, 1835
Strickland Code, 1843
• Starts with 12th edition of Systema
Naturae
• British initiative with international
input
• French and Italian translations
Toward the Strickland Code
Strickland’s Rules for Zoological
nomenclature, published in this issue
of the Magazine of Natural History

23. Names must be accompanied by a description.
But what determines whether a description is acceptable?
Can the species be recognized based on the description?
“…when can it be said that a species has been
described? Even the most fanatical advocate of the
law of priority will not pretend that a species has been
described, concerning which utterly false notices, or
erroneous or unimportant indications, are given, which
so completely fail in characterizing the species that no
one is able to recognize it.”
Schaum, 1862:323
• Type specimens (specimens examined by the author for
the description) can permit identification when
description is inadequate
• Such specimens cannot always be unambiguously
identified
Most taxonomists would agree today that using type
specimens to determine the application of a species
name is a rigorous approach.
Description versus Specimen
Original description of Adonea parva
Tucker, 1920, excerpt
Type specimen of Adonea parva,
deposited in Iziko South African
Museum, Cape Town

24. Règles Internationales de la
Nomenclature Zoologique (1905)
• Intended to apply to all of Zoology
• Set starting point as 10th edition of
Systema Naturae, 1758
• Recommendation: Designated type
specimen, museum depository and
accession number stated in description
International Rules of Botanical
Nomenclature (1906)
• Intended to apply to all plants,
algae, and fungi
• Set starting point Species Plantarum,
1753
International Codes of Taxonomic Nomenclature

25. • Computers has their most visible impact on
classification
• Tables of characteristics by taxon used to cluster
most similar taxa together
• Replace taxonomic names with numbers?
• Provided mechanism to evaluate alternative classifications
• Optimality criteria shifted
Overall-similarity
Shared derived character states
Evolutionary models, mostly applied to DNA sequence data
…to “avoid Linnaeus’s error of incorporating into
the designation of the organism information
about its classification which is subject to change
with improved knowledge or changing ideas.”
(Michener 1963:166)
The 1960s: Early Computers
and Numerical Taxonomy
Programmers using IBM 026
keypunches, 1970

26. • Use numbers as well as names for
all taxa
• Nomenclatural system must
become completely logical
• Names will become less important
• Priority will become less important
and may eventually be discarded
• These changes will irritate most
taxonomists
• Taxonomists will rise to fight the
machines
• The machines will win
Man versus Machine
Jahn’s 1961 article on taxonomy in an
increasingly computerized world

27. 500,000,000+ printed pages
1,900,000 species described
20,000,000+ species treatments
17,000 new species per year
Biodiversity Knowledge
Incomplete digitization
Publications are not
semantically enhanced
Collections are incomplete
Data is not linked
Most data are not open
BUT: The data are hidden

28. Average Annual New Species 2000-2009
Chordata (666)
Insecta (8860)
Arachnida (1275)
Crustacea (707)
Mollusca (595)
Plantae (2410)
Fungi (1198)
Chromista (83)
Protozoa (265)
Bacteria (427)
17,000 new species per year

29. Taxonomic Literature
Valid name
Taxonomic name usages for this species
Treatment citations
Author, year Identifier

30. Taxonomic Literature
Valid name
Taxonomic name usages for this species
Treatment citations
Author, year Identifier
C.L. Koch, 1837a
Original description Eresus fumosus

31. Taxonomic Literature
Valid name
Taxonomic name usages for this species
Treatment citations
Author, year Identifier
L. Koch, 1865
Original description Eresus budo

32. Taxonomic Literature
Valid name
Taxonomic name usages for this species
Treatment citations
Author, year Identifier
L. Koch, 1878a
Redescription Eresus budo
Citation: earlier description
L. Koch, 1865

33. Taxonomic Literature
Valid name
Taxonomic name usages for this species
Treatment citations
Author, year Identifier
Tucker, 1920
Eresus budo L. Koch, 1865
recognized as junior synonym of
Eresus fumosus C.L. Koch, 1837

34. Taxonomic Literature
Valid name
Taxonomic name usages for this species
Treatment citations
Author, year Identifier
Lehtinen, 1967
Eresus fumosus C.L. Koch, 1837
transferred to new genus
Gandanameno

35. Taxonomic Name Resolution
Valid name
Taxonomic name usages for this species
Treatment citations
Author, year Identifier
Eresus fumosus C. L. Koch, 1837a
Eresus fumosus C. L. Koch, 1837
Eresus fumosus
E. fumosus
Eresus bubo L. Koch, 1865
Eresus bubo Koch
Eresus bubo
Eresus fumosus Tucker, 1920
Gandanameno fumosa (C.L. Koch, 1837)
Gandanameno fumosa
G. fumosa
Gandanameno fumosa (C.L. Koch, 1837)
“Dirty Bucket”
Raw text strings
“Clean Bucket”
Curated taxon names
urn:lsid:nmbe.ch:spidersp:005856
Identifier

36. Names
Characteristics
Publications
GenesCollections
Specimens
Distribution
Names as Information Tags in Life Sciences

38. Publication PDF
XML: TaxPub

39. Publication PDF
XML: TaxPub

40. Publication PDF
XML: TaxPub

41. Publication PDF
XML: TaxPub

42. XML: TaxPub
Encyclopedia
of Life

47. Legacy Taxonomic Literature

48. Legacy Taxonomic Literature

49. Legacy Taxonomic Literature

50. Legacy Taxonomic Literature

51. Cybertaxonomic
Publication Venue
Drawings: slavenapeneva.com
Primary Data
Thanks: Lyubomir Penev
Data Want to be Free

52. Drawings: slavenapeneva.com
Primary Data
Traditional
Publication VenuePDF Prison
GoldenGATE XML Markup Editor
TaxonX XML Schema
Thanks: Lyubomir Penev
Data Want to be Free

53. Drawings: slavenapeneva.com
Primary Data
Traditional
Publication Venue
Thanks: Lyubomir Penev
Data Want to be Free

54. Dark Taxa: Biodiversity without Names

55. Acknowledgments
Images
• The garden of Eden with the fall of man. Jan Brueghel the Elder and Pieter Paul Rubens (1816). Wikimedia Commons.
• Shen Nong. Li Ung Bing (1914). Outline of Chinese History, Shanghai. Wikimedia Commons. Public domain.
• The school of Athens (detail). Raffaelo Sanzio (1509). Museos Vaticanos. Public domain.
• Baptism of Constantine. Giulio Romano (1520-1524). Wikimedia Commons. Public domain.
• Alhazen. Famous Inventors.
• Fourteenth-century university lecture. Laurentius de Voltolina. http://people.uwplatt.edu/~turnern/classroomFull.html
• William of Ockham. Moscarlop (2007). Wikimedia Commons. Creative Commons Attribution-Share Alike 3.0 Unported license.
• The Black Death. Toggenburg Bible (1411) History Today.
• Nicolaus Copernicus. Wilimedia Commons. Public domain.
• Heliocentric model. Nicolai Copernici (1543) De revolutionibus orbium coelestium. Wikimedia Commons. Public domain.
• Andreas Vesalius. Jan van Calcar (1543) De humani corporis fabrica. Wikimedia Commons. Public domain.
• Image from Andreas Vesalius's De humani corporis fabrica (1543), page 174. Wikimedia Commons. Public domain.
• Martin Luther. Lucan Cranach the Elder (1529). Wikimedia Commons. Public domain.
• John Calvin. Hans Holbien (1550). Wikimedia Commons. Public domain.
• Philosophical Transactions (1665) Wikimedia Commons. Public domain.
• Portrait of the cardinal Hugh de Provence reading in a scriptorium. Tommaso da Moden (1352) Wikimedia Commons. Public domain.
• Carl von Linné. Alexander Roslin (1775). Wikimedia Commons. Public domain.
• Plantago media. C. A. M. Lindman. Bilder ur Nordens Flora.
• Darwin’s notebook (excerpt) (1937). The Guardian.
• Augustin Pyramus de Candolle. Museum of Geneva.
• Hercules beetle. Wikimedia Commons. Creative Commons Attribution-Share Alike 4.0 International license.
• Magazine of Natural History (1837). Archive.org.
• Systema Naturae. Wikimedia Commons. Public domain.
• Species Plantarum. Wikimedia Commons. Public domain.
• Aachen, Technische Hochschule, Rechenzentrum (1970). Wikimedia Commons. Creative Commons Attribution-Share Alike 3.0 Germany license.
• Taxonomic research life cycle. Illustration by Slavena Peneva slavenapeneva.com. Thanks to Lyubomir Penev.
Literature
• Ball, P. (2015) History of science: The crucible of change. Nature524, 412–413.
• Dayrat, B. (2010) Celebrating 250 Dynamic Years of Nomenclatural Debates. Systema Naturae 250 - The Linnaean Ark, 185–240.
• Fontaine, B., , Perrard, A., , Bouchet, P. (2012) 21 years of shelf life between discovery and description of new species. Current Biology 22, R943–R944.
• IISE (2011). Retro SOS 2000-2009: A Decade of Species Discovery in Review. Tempe, AZ. International Institute for Species Exploration.
http://www.esf.edu/species/documents/sosretro.pdf
• Jahn, T.L. (1961) Man Versus Machine: A Future Problem in Protozoan Taxonomy. Systematic Zoology 10, 179.
• Ledford, J., , Griswold, C., , Audisio, T. (2012) An extraordinary new family of spiders from caves in the Pacific Northwest (Araneae, Trogloraptoridae, new family). ZooKeys 215,
77–102.
• Lin, Y., , Li, S. (2012) Three new spider species of Anapidae (Araneae) from China. Journal of Arachnology 40, 159–166.
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• Miller, J., , Griswold, C., , Scharff, N., , Rezac, M., , Szuts, T., , Marhabaie, M. (2012) The velvet spiders: an atlas of the Eresidae (Arachnida, Araneae). ZooKeys 195, 1–144.
• Miller, J.A., , Miller, J.H., , Pham, D.-S., , Beentjes, K.K. (2014) Cyberdiversity: Improving the Informatic Value of Diverse Tropical Arthropod Inventories. PLoS ONE 9, e115750.
• Sautter G (2013) GoldenGATE Document Editor. Version 3. Plazi. URL: http://www.plazi.org/wiki/GoldenGATE_Editor.
• Westwood, J. (1837) On generic nomenclature. Magazine of Natural History 1, 169-173
• World Spider Catalog (2015). World Spider Catalog. Natural History Museum Bern, online at http://wsc.nmbe.ch.