The Phylogeny Toolbox

This bibliography gives you an entry to phylogeny, its philosophical background, techniques, and applications. Note it is biased towards cladisitics, English language and US schools of thought. There is ample literature in German and French, as well. '*' indicates personal favourites.

Philosophical background

Daniel R. Brooks & Deborah A. McLennan. 1991. Phylogeny, Ecology, and Behavior. The University of Chicago Press, Chicago & London, XII+434 pp.

Donald H. Colless. An examination of certain concepts in phenetic taxonomy. Systematic Zoology. 6-27

James S. Farris. The meaning of relationship and taxonomic procedure. Systematic Zoology. 44-51

Brian K. Hall (ed.). Homology. The hierarchical basis of comparative biology. Academic Press (New York), XVI+483 pp.

Willi Hennig. 1950. Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag, Berlin.

Willi Hennig. 1963. Phylogenetic Systematics. University of Illinois Press, Urbana.

David L. Hull. 1967. Certainty and circularity in evolutionary taxonomy. Evolution. 21, 174-189

Arnold G. Kluge. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among epicrates (Boidae, Serpentes). Systematic Zoology. 38(1), 7-25

* John G. Lundberg & Lucinda A. McDade. 1990. Systematics. in Carl B. Schreck & Peter B. Moyle (eds.), Methods for Fish Biology, American Fisheries Society, Bethesda, XIX+684 pp. 65-108

Brent D. Mishler & Efrain De Luna. 1991. The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology. 4, 121-167

* Kevin C. Nixon & Quentin D. Wheeler. 1990. An amplification of the phylogenetic species concept. Cladistics. 1990(6), 221-223

* Robert J. O´Hara. 1988. Homage to Clio, or, toward an historical philosophy for evolutionary biology. Systematic Zoology. 37(2), 142-155

* Robert J. O´Hara. 1992. Telling the tree: Narrative representation and the study of evolutionary history. Biology and Philosophy. 7, 135-160

Alan de Queiroz, Michael J. Donoghue, Junhyong Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Annual review of Ecology and Systematics. 26, 657-681

Kevin de Queiroz. 1985. The ontogenetic method for determining character polarity and its relevance to phylogenetic systematics. Systematic Zoology. 34(3), 280-299

* Kevin de Queiroz. 1992. Phylogenetic taxonomy. Ann. Review of Ecology and Systematics. 23, 449-480

N.R. Scott-Ram. 1989. Transformed cladistics, taxonomy and evolution. Cambridge University Press, Cambridge, XII+238 pp.

Elliot Sober. 1988. Reconstructing the past. Parsimony, evolution, and inference. MIT Press, Cambridge, XVIII+265 pp.

 

Phylogenetic methods & techniques

Lois A. Abbott, Frank A. Bisby & David J. Rogers. 1985. Taxonomic analysis in Biology. Computers, Models, and Databases. Columbia Universoty Press, New York. 336 pp.

* Peter Ax. 1987. The phylogenetic system. John Wiley & Sons, Chichester, XIV+340 pp.

* Kåre Bremer. 1994. Branch support and tree stability. Cladistics. 1994(10), 295-304

Daniel R. Brooks & Deborah A. McLennan. 1991. Phylogeny, Ecology, and Behavior. The University of Chicago Press, Chicago & London, XII+434 pp.

James S. Farris. The meaning of relationship and taxonomic procedure. Systematic Zoology. 44-51

Brian K. Hall (ed.). Homology. The hierarchical basis of comparative biology. Academic Press (New York), XVI+483 pp.

Willi Hennig. 1950. Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag, Berlin.

Willi Hennig. 1963. Phylogenetic Systematics. University of Illinois Press, Urbana.

David L. Hull. 1967. Certainty and circularity in evolutionary taxonomy. Evolution. 21, 174-189

* John G. Lundberg & Lucinda A. McDade. 1990. Systematics. in Carl B. Schreck & Peter B. Moyle (eds.), Methods for Fish Biology, American Fisheries Society, Bethesda, XIX+684 pp. 65-108

* W.P. Maddison & D.R. Maddison 1992: MacClade. Analysis of phylogeny and character evolution. Sinauer Associates, Inc., Sunderland, USA.

Alan de Queiroz, Michael J. Donoghue, Junhyong Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Annual review of Ecology and Systematics. 26, 657-681

Naruya Saitou & Masatoshi Nei. 1987. The Neigbor-joining method: a new method for reconstructing trees. Molecular Biology and Evolution. 4(4), 406-425

Michael J. Sanderson. 1995. Objections to bootstrapping phylogenies: a critique. Systematic Biology. 44(3), 299-320

N.R. Scott-Ram. 1989. Transformed cladistics, taxonomy and evolution. Cambridge University Press, Cambridge, XII+238 pp.

Elliot Sober. 1988. Reconstructing the past. Parsimony, evolution, and inference. MIT Press, Cambridge, XVIII+265 pp.

D.L. Swofford & D.P. Begle 1993. PAUP, Phylogenetic Analysis Using Parsimony, Version 3.1. Users Manual, Laboratory of molecular systematics, Smithsonian Institution, Washington DC, USA

Mark Wilkinson. 1994. Three taxon statements: when is parsimony analysis also a clique analysis ?. Cladistics. 1994(10), 221-223

Quentin D. Wheeler. 1986. Character weighting and cladistic analysis. Systematic Zoology. 35, 102-109

 

Interpretation of phylogenies

Lois A. Abbott, Frank A. Bisby & David J. Rogers. 1985. Taxonomic analysis in Biology. Computers, Models, and Databases. Columbia Universoty Press, New York. 336 pp.

Sara S. Bretsky. 1970. Phenetic and phylogenetic classifications of the Lucinidae (Mollusca, Bivalvia). Bull. geol. Instn. Univ. Upsala N.S. 2(2), 5-23

Donald H. Colless. An examination of certain concepts in phenetic taxonomy. Systematic Zoology. 6-27

Brian K. Hall (ed.). Homology. The hierarchical basis of comparative biology. Academic Press (New York), XVI+483 pp.

Arnold G. Kluge. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among epicrates (Boidae, Serpentes). Systematic Zoology. 38(1), 7-25

* John G. Lundberg & Lucinda A. McDade. 1990. Systematics. in Carl B. Schreck & Peter B. Moyle (eds.), Methods for Fish Biology, American Fisheries Society, Bethesda, XIX+684 pp. 65-108

* W.P. Maddison & D.R. Maddison 1992: MacClade. Analysis of phylogeny and character evolution. Sinauer Associates, Inc., Sunderland, USA.

Brent D. Mishler & Efrain De Luna. 1991. The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology. 4, 121-167

Brent D. Mishler. 1989. Review of D.L. Hull ‘Science as a Process’. Systematic Botany. 14(2), 266-268

* Robert J. O´Hara. 1988. Homage to Clio, or, toward an historical philosophy for evolutionary biology. Systematic Zoology. 37(2), 142-155

* Robert J. O´Hara. 1992. Telling the tree: Narrative representation and the study of evolutionary history. Biology and Philosophy. 7, 135-160

* Alan de Queiroz, Michael J. Donoghue, Junhyong Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Annual review of Ecology and Systematics. 26, 657-681

Kevin de Queiroz. 1985. The ontogenetic method for determining character polarity and its relevance to phylogenetic systematics. Systematic Zoology. 34(3), 280-299

* Kevin de Queiroz. 1992. Phylogenetic taxonomy. Ann. Review of Ecology and Systematics. 23, 449-480

N.R. Scott-Ram. 1989. Transformed cladistics, taxonomy and evolution. Cambridge University Press, Cambridge, XII+238 pp.

Elliot Sober. 1988. Reconstructing the past. Parsimony, evolution, and inference. MIT Press, Cambridge, XVIII+265 pp.

P.F. Stevens. 1980. Evolutionary polarity of character states. Annual review of Ecology and Systematics. 11, 333-358

 

Phylogeny of certain groups

Sara S. Bretsky. 1970. Phenetic and phylogenetic classifications of the Lucinidae (Mollusca, Bivalvia). Bull. geol. Instn. Univ. Upsala N.S. 2(2), 5-23

Arnold G. Kluge. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among epicrates (Boidae, Serpentes). Systematic Zoology. 38(1), 7-25

* Brent D. Mishler & Efrain De Luna. 1991. The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology. 4, 121-167

Claus Nielsen. 1995. Animal evolution. Oxford University Press, Oxford, VI+467 pp.

* Winston F. Ponder & David R. Lindberg. 1997. Towards a phylogeny of gastropod molluscs: an analysis using morphological characters. Zoological Journal of the Linnean Society, 119, 83-265

Thomas R. Waller. 1998. Origin of the molluscan class Bivalvia and a phylogeny of major groups. pp. 1-47 in Paul A. Johnston & James W. Huggart (eds.): Bivalves: an eon of evolution - paleobiological studies honoring Norman D. Newell.

 

Teaching resources

Geological Society of America. The evolution-creation controversy: perspectives on religion, science, and education - a handbook. Special Publication 1 of Geological Society of America

* J. Scotchmoor & Dale A. Springer (eds.). 1999. Evolution: investigating the evidence. Special Publication 2 of Geological Society of America, 357 pp.

* J. Scotchmoor & F.K. McKinney (eds.). 1996. Learning from the Fossil Record, Paleontological Society Paper no. 2, 348 pp. - also on WWW: http://www.ucmp.berkeley.edu/fosrec/

P.H. Kelley, J.R. Bryan, T.A. Hansen (eds.). 1999. The evolution-creation controversy II: perspectives on science, religion, and geological education , Paleontological Society Paper no. 5, 241 pp.

Paleontological Society of America, Publication Sales

c/o Carnegie Museum of Natural History

4400 Forbes Ave., Pittsburgh, PA 15213-4080, USA

Most of the following comes from the educational resource links from University of California Museum of Paleontology:

The Active Learning Club (http://www.dkonline.com/kids/). A Guide to the internet which catalogues a small number of high-quality sites. Includes science, nature, history, etc.

Association for Biology Laboratory Education (http://www.zoo.toronto.edu:80/able/). ABLE is an organization promoting information exchange for biology teaching at the undergraduate level. Their site includes proceedings and selected articles, as well as workshop information.

ENSIWEB. (http://www.indiana.edu/~ensiweb/) Lessons for Teaching Evolution and the Nature of Science. Gathered, created, developed, and classroom tested by many biology teachers from across the nation during nine years of NSF-funded summer institutes, these lessons were designed to help teach basic concepts in the areas of evolution and the nature of science more realistically.

AskERIC Virtual Library (http://ericir.sunsite.syr.edu/). Curriculum materials and education research, with links to additional resources. Search for 'evolution'

EP-GED (http://wbar.uta.edu/): Evolution and Population Genetics Educational Database. This site includes links to labs around the world that are involved in evolution and genetics research, plus links to educational aids and software for teachers and students in these fields (mostly high school and above).

National Center for Science Education (http://www.natcenscied.org/). The NCSE works to promote the teaching of evolutionary science, to counter creationist claims, and to increase public understanding of evolution.

Introduction to Evolutionary Biology (http://www.talkorigins.org/faqs/faq-intro-to-biology.html). Evolution summarised in a few pages.

The Museum of Paleontology in Berkeley just gave a short-course on evolution and is gradually building a web site with teaching resources (http://www.ucmp.berkeley.edu/education/evoforum/index.html) - this is quite new, and is certain to grow!