Taxonomy and systematics: generators of prime

biodiversity data

Yves Samyn1 & Hendrik Segers2

1Belgian Focal Point to the Global Taxonomy Initiative2Belgian Biodiversity Platform

Royal Belgian Institute of Natural Sciences

Vautierstraat 29, B-1000 Brussels

Taxonomy, a multilayered science

< Greek: Taxis = order; nomos = law => taxinomie (French); taxonomy (English) (concept from A.P. de

Candolle, 1813)

Simpson (1961): ‘The theory and practice of delimiting kinds of organisms and of classifying them

Wilson (1992): ‘ Science and art ...’ ICZN: theory and practice of classifying organisms.

Taxonomy, a multilayered science

Steps in taxonomy:

Microtaxonomy: the demarcation of speciesWhat is a species ? What species concept is best? Pluralism seems to be the key! Link

Macrotaxonomy: the classification of speciesHow do we classify organisms ? According to genealogy or to degree of similarity... or both?

Steps in taxonomy...:-taxonomy: recognition and description of species &

first classification

-taxonomy: classification of species in hierarchical system

-taxonomy: understanding the evolutionary factors

Micro-taxonomy

Macro-taxonomy

Roles of taxonomy:

Proximate:

Establish universal, unique and unambiguous tags: necessary for interdisciplinary communication

Provide an heuristic information retrieval system (identification, comparative research)

Ultimate: Comprehension of the living world (ordering; prediction)

Consequences of taxonomy:

Scientific names are critical keys that unlock biosystematic information

Scientific names also represent hypotheses; they place information in a hierarchical system that allows prediction

Taxonomy, roles and consequences

Recognition & description of taxonomic units

Product development: taxonomic tools

Amalgam of raw biodiversity dataOrganismal

diversityEcological

diversityGenetic diversity

Detection Temporal, spatial, methodological, infrastructural &

financial resources

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Variation,incipient and cryptic

nature of life

Voucher collections, literature (including

grey), character recognition

Character analysis

Overall similarity clustering,

shared derived character clustering

Classification: information storage and retrieval + prediction

Understanding of clock estimators,

assembly of physical & biological

parameters

Observational phase

Redescription phase

Similarity scrutinizing phase

Homology scrutinizing phase

Phenogram

Cladogram

Phylogeny Integrative phase

Nomenclature

Communication & information retrieval

Identification (e.g. keys, bar codes)

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Organismaldiversity

Ecological diversity

Genetic diversity

Refined biodiversity data

But how does taxonomy operate?

Biological Classification - what is it?

Classifying has always been a favorite human occupation

Every classification system has two functions: facillitation of information retrieval (incl. communication)

serve as the basis for comparative research

Biological classification is concerned with the hierarchical ordering of organisms into objective (principled) hierarchical groups

Approach to biological classifications has changed through history (e.g. classifications existed two millenia before evolutionary theory entered the scene)

Two kinds of answers have been offered :

- phenetic hierachy based upon similarity of form of the groups being classified - numerical taxonomy- phylogenetic hierarchy based on the pattern of evolutionary descent, that is according to recency of common ancestry - cladism

The result of these 2 approaches may agree or disagree

What supplies the principle for hierarchical classification?

Agreement between the two if:• rate of evolution is approximately constant• Direction of evolution is divergent

Disagreement between the two if:• differential rate• convergence

Some examples

Deciding on the approach implies agreeing on the

principle

Phenetics (numerical taxonomy)

Starting point:Starting point:

Phylogeny is unknown and most probably cannot be known and thus classification according to genealogy is not an option

Development of methodologies (basically multivariate

cluster analysis) to reveal the differences and similarities between OTU

In order to be successful:Consideration of as many characters as possible (+ 100) Equal character weighting Similarity-index expresses relatedness between OTU

Phenetics in practice

• Determination of the distance between the units being classifiede.g. trait 1 thorax length: sp. A (6 cm); sp. B (4 cm) => distance =2 units;

trait 2, digit length: sp. A (0.9 cm); sp. B (0.6 cm) => distance 0.3 units

Average distance for both (mean trait distance) (2+0.3)/2 = 1.15 units

• cluster statistic forms groups by successively aggregating the units with the shortest distances to each other• classification equals the hierarchical output of the statistic

Phenetics claims

Thus obtained classifications are: • objective• repeatable

Are these claims justified?

No!

Thus phenetics successfully removed subjectivity from the choice of traits, but subjectivity re-entered in the choice of cluster statistic

(From Ridley 1985)

Fylogenetic classification (cladistics)

Cladistic analysis

Characters are•Autapomorph = when unique to a taxon (A & D in species X) •Synapomorph = when derived from the nearest common ancestor (B& C in species x & y)•Symplesiomorph = when derived from an older common ancestor (a & d in species z & y)

Clades are•Monophyletic = when sharing synapomorphies (X & Y sharing characters B&C)

•Non-monophyletic= when sharing symplesiomorphies (Z & Y sharing characeters a & d); when convergent characters determine relationship (E in Z & Y)

Determination of condition: outgroup comparison, ontogeny, paleontology

Starting point:Starting point:

Phylogeny should be retrievable and thus classification according to genealogy is the best option (Hennig)

Relationship according to common decent (≈Darwin, Wallace, …, Haeckel,…)

Methodology to arrive at cladograms

1 2 3 4 5Outgroup 0 0 0 0 0A 1 0 0 0 1B 1 1 0 1 0C 1 0 1 1 0

CharactersOut A B C

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determine the classification

Cladistic analysis

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What cladograms say about relationships

Cladistics is:• only a relative statement of relationship• hypothesizes on a sister-group hierarchy (sharing of a more recent common ancestor)

• expressed as branching diagrams: cladograms

Cladistics does not:• explicitely hypothesize ancestor-descendant relationships

Species J

Species N

Species O

Species K

Species PSpecies OSpecies P

Species A

Species E

Species G

Species C Species DSpecies C Species D

Species B

Monophyletic taxon Paraphyletic taxon

Polyphyletic taxon

Paraphyletic taxon

Classification & phylogeny

Same methodology as cladists (search for monophyletic groups)

But classification does not necessarily reflect phylogeny

Weighting of number of synapomorphies in relation to taxonomic rank

e.g. Aves merits class of itsown due to abundant

synapomorphies

Valuation of certain paraphyletic taxa

Evolutionary taxonomy (eclectic taxonomy)

Tools to the aid of taxonomic research

Taxonomy, an information-rich science For specialists only?

Ultimate difficultiesComplexity

EvolutionRecognitionIdentification

Concepts & Language, , taxonomyBiogeographyNomenclature

CharactersHomology - anologyVariationOntogeny

Proximate difficultiesAccess to information storage system

Literature (original + derived)Collections (types + other representatives)Data (geographical, ecological: databases)

Access to information retrieval systemIdentification keysClassificationsNomenclature

OperabilityInfrastructureKnow-howFunding

Traditional tools for the taxonomist

• Zoological Record• Nomenclator zoologicus• List of available names in zoology• Index Nominum Genericorum• Approved list of Botanical Names• Other, more general, abstracting services (Biological abstracts; BIOSIS Previews,…)

How to get to the tools?

Some traditional entry points

General guides to zoological, biological and botanical literature

Bell, G.H. and Rhodes D.B. 1994. A Guide to the Zoological Literature: The Animal Kingdom. Englewood, Colo., Libraries Unlimited

Sims, R.W. 1980. Animal Identification: A Reference Guide. New York, Wiley. 3 vols

Books and textbooks

Rupert, E.E. and Barnes, R.D. 1994. Invertebrate Zoology, Sixth edition. New York, Saunders College Publishing

Nichols, D. 1969. Echinoderms, Fourth edition.Hutchinson University Library, London.

Field Guides

Hickman, C.P. 1998. A Field Guide to Sea Stars and other Echinoderms of Galapagos. Galapagis Marine Life Series, Sugar Spring Press, Lexington, USA.

Some traditional entry points

Specialised literature (revisions, monographs,…)

Rour, E., Ghahlaoui A., Van Goethem, J. 2002. Etat actuel des connaisances de la malacofaune terrestre du Maroc. Bull IRSNB, Biologie 72: 189-198

Abstract and indexes

Zoological Record: from 1864 onwards, from biodiversity and the environment to taxonomy and veterinary sciences, covers 4,500 serials

Biological Abstracts: braoder than Zoological Records, covers every life sciences discipline, covers some 3,700 serials

…

The present-day taxonomist

Has access to digitalised informationOn CD ROM On the internet

Knows where to start his search wisely

Is aware of the pitfalls of non peer-reviewed information

The present-day taxonomist

Also has access to digitalised information

On CD ROM On the internet

Some websites that provide data on species distributions (from Graham et al. 2004)

The present-day taxonomist

Some noteworthy entry points: Non-specialist:

Wikipedia; Google scholar; SciDev.Net, Public library of Science

Specialist:The Natural History Portal of the Natural History Museum in L

ondonSpecies 2000uBio, GBIF, ITIS, GTI, IPNI, Index FungorumICZN, ICBN, E-type initiative

Journals:Journal of Natural History, Systematics and Biodiversity; Zootaxa;…(previews!)Zoological Studies

And many more…

Thank you for your attention

Thank you for your attention