oeb 181: systematics catalog number: 5459sites.fas.harvard.edu/~bio181/lectures/lecture...

OEB 181: Systematics

Catalog Number: 5459

Tu & Th, 10 - 11:30 am, MCZ 202

Wednesdays, 2 - 4 pm, Science Center 418D

Gonzalo Giribet (Biolabs 1119, ggiribet@oeb.harvard.edu)

Charles Marshall (MCZ 111A, cmarshall@fas.harvard.edu )

Jessica Baker (Biolabs 1119, jessica.baker@post.harvard.edu)

http://www.courses.fas.harvard.edu/~bio181/

Grades

• 4 class assignments (40%)

– First assignment on October 4th, 2weeks per

assignment

• Class participation (10%)

• Final exam (December 16th; 50%)

Recommended books:

Recommended readings:

Graur D, and Li WH (2000). "Fundamentals of Molecular Evolution." Sinauer

Associates, Sunderland. Chapters 1 and 5.

Kitching IJ, Forey PL, Humphries CJ, Williams DM (1998) Cladistics. Theory and

Practice of Parsimony Analysis. The Systematics Association by Oxford University

Press, Oxford.

Page RDM, Holmes EC (1998) Molecular evolution. A phylogenetic approach.

Blackwell Science, Boston.

Schuh RT (2000) Biological systematics. Principles and applications. Cornell University

Press, Ithaca.

Swofford DL, Olsen GJ, Waddell PJ, and Hillis DM (1996). Phylogenetic inference. In:

Hillis DM, Moritz C, Mable BK (eds) “Molecular systematics”. Sinauer Associates,

Sunderland, Massachusetts, pp 407-514.

Felsenstein J (2004). Inferring Phylogenies. Sinauer Associates, Sunderland,

Massachusetts.

Systematic journals/societies

Society of Systematic Biologists: http://systbiol.org/

Willi Hennig Society: http://www.cladistics.org/

Other systematic journals

Phylogenetic softwarehttp://www.courses.fas.harvard.edu/~bio181/programs/programs.html

Systematics […] Discussion Group

http://www.people.fas.harvard.edu/~sramirez/

Fall 2006: Mondays, 1 pm @ Harvard University Herbaria

Motivation for systematics studies

• Biodiversity and its origins

• Relationships (pattern and shape)

• Conservation biology

• Medical applications

“Systematics is the science of biological classification”

Hillis, D. M. & Huelsenbeck J. P. (1994): Support for dental HIV

transmission. Nature 369: 24-25.

Biological Systematics

Biological Systematics is the science that studies relationships among

organisms (living and extant), establishing the patterns that relate those

organisms among each other.

Systematics was an intuitive science from its beginning, and it was not until the

development of modern methodologies that it became a more strict numerical

science.

Empiricism was attempted first from a phenetic point of view, propounding a

taxonomy which simply grouped based on the overall similarity (Sokal and

Sneath, 1963). Simultaneously, phylogenetic systematics (= cladistics)

originated as an approach that would directly reflect information concerning the

results of the evolutionary process, where groupings are based strictly on

special similarity, that is, similarity which arose from common ancestry

(apomorphy) (Hennig, 1950, 1966). The application of the parsimony

principle (minimizing requirements for ad hoc hypotheses of homoplasy:

noise or convergence) to the cladistics methodology gave origin to modern

quantitative cladistics. Probabilistic methods were later incorporated into

systematic research.

Definitions:

• Systematics and taxonomy: methods and practices of

describing, naming, and classifying biological diversity,

at the species level and above.

• Classification: represents the codification of the

results of systematic studies.

• Taxon (plural, taxa): basic units of systematics; group

of organisms at any level in the systematic hierarchy.

• Characters: group of attributes. A unique combination

of such attributes (or states of characters) define a

species or any other supraspecific taxon.

The Linnaean Hierarchy:

Systema Naturae (Linnaeus, 1758)

Kingdom

Class

Order

Genus

Species

Variety

Current classification system

Kingdom

Phylum

Class

Subclass

Order

Suborder

Superfamily

Family

Subfamily

Tribe

Genus

Species

Current classification system

Kingdom Animalia

Phylum Arthropoda

Subphylum Mandibulata

Class Myriapoda

Subclass Chilopoda

Order Lithobiomorpha

Family Henicopidae

Subfamily Henicopinae

Tribe Henicopini

Genus Paralamyctes

Subgenus Thingathinga

Species Paralamyctes (Thingathinga) hornerae

Paralamyctes (Thingathinga) hornerae Edgecombe, 2001

Paralamyctes trailli (Archey, 1917)

Haasiella trailli: Archey, 1917

Pre-darwininan classificationsWilliam Macleay and Quinarianism

• Evolutionary taxonomy: Methods and Principles of Systematic

Zoology, by Ernst Mayr, Gorton Linsley, and Robert Usinger (1953).

McGraw-Hill, New York.

• Phenetic: Principles of Numerical Taxonomy, by R.R. Sokal, and

P.H.A. Sneath (1963). W. H. Freeman, San Francisco.

• Phylogenetic (Cladistic): Grundzüge einer Theorie der

phylogenetischen Systematik, by Willi Hennig (1950); Phylogenetic

Systematics (Hennig, 1966). University of Illinois Press, Urbana.

(Reissued 1999)

Schools of Classification:

Ernst Mayr - 1904-2005MCZ Director 1961-1970

Schools of Classification:

Data type

Grouping method

Diagram type

Hierarchical level

determined by

Sensitive to rate

differences

Evolutionary

taxonomy

Discrete characters

Special similarity

Evolutionary tree

Amount of

difference

Yes

Cladistic

Discrete characters

Special similarity

Cladogram

Sharing of unique

attributes

No

Phenetic

Character data

converted to a

distance matrix

Overall similarity

Phenogram

Amount of

difference

Yes

Musems: where systematics gets done

1859 - 1885

First MCZ director

Louis Agassiz

Museums as sources of morphological

and molecular data for systematics

Traditional specimensFrozen tissues

Where to find more information:

Schuh, R.T. (2000). Biological systematics.

Principles and applications. Cornell University

Press, Ithaca.

Chapter 1 gives a general Introduction to

Systematics