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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
Bla
ck b
ox in
whi
ch ta
xono
mis
ts o
pera
teFlow-through
limitators
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)
Wo
rkin
g h
yp
oth
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is(s
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din
g t
axo
no
my
of
tax
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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
1
Out A B C
1
2
Out A B C
1
23
Out A B C
1
2 34
Out A B C
1
2 345Shared derived characters
determine the classification
Cladistic analysis
1 2 3 4 5 6 7 8 9 10Outgroup 0 0 0 0 0 0 0 0 0 0Alpha 0 0 0 1 1 1 0 0 0 0Beta 0 0 0 1 0 1 0 0 0 0Gamma 0 0 0 0 0 0 1 0 1 0Delta 1 1 1 0 0 0 1 1 1 0Epsilon 1 1 1 0 0 0 1 0 1 1Zeta 1 1 0 0 0 0 1 0 1 1Theta 1 0 0 0 0 0 1 0 1 1
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12 steps12 steps
11 steps11 steps
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
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