History and Future of

Taxonomy

Jeremy Miller Leiden, 31 August 2015

, 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

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

First to classify all living things

Empiricism • General principals derived from

specific observations

Aristotle (384-322 BC)

The School of Athens (detail) Raffaello Sanzio

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

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)

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

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)

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

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)

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

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

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

“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

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

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

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.

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

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?

“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

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

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

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

• 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

• 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

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

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

Taxonomic Literature

Valid name

Taxonomic name usages for this species

Treatment citations

Author, year Identifier

Taxonomic Literature

Valid name

Taxonomic name usages for this species

Treatment citations

Author, year Identifier

C.L. Koch, 1837a Original description Eresus fumosus

Taxonomic Literature

Valid name

Taxonomic name usages for this species

Treatment citations

Author, year Identifier

L. Koch, 1865 Original description Eresus budo

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

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

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

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

Names

Characteristics

Publications

Genes Collections

Specimens

Distribution

Names as Information Tags in Life Sciences

Publication PDF

XML: TaxPub

Publication PDF

XML: TaxPub

Publication PDF

XML: TaxPub

Publication PDF

XML: TaxPub

XML: TaxPub

Encyclopedia

of Life

Legacy Taxonomic Literature

Legacy Taxonomic Literature

Legacy Taxonomic Literature

Legacy Taxonomic Literature

Cybertaxonomic Publication Venue

Drawings: slavenapeneva.com

Primary Data

Thanks: Lyubomir Penev

Data Want to be Free

Drawings: slavenapeneva.com

Primary Data

Traditional Publication Venue PDF Prison

GoldenGATE XML Markup Editor

TaxonX XML Schema

Thanks: Lyubomir Penev

Data Want to be Free

Drawings: slavenapeneva.com

Primary Data

Traditional Publication Venue

Thanks: Lyubomir Penev

Data Want to be Free

Dark Taxa: Biodiversity without Names

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. • Manktelow, M. History of Taxonomy. Uppsala University . • 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.