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Cladistic Methods of Phylogenetic Analysis
J.C. Avise (2009): Timetrees: beyond cladograms, phenograms, and phylograms. PDF file, In: S.B. Hedges and S. Kumar (eds.): The Timetree of Life (see here).
Chris Bell, Department of Geological Sciences, University of Texas, Austin: Life Through Time, Cladistics. Worth checking out: Cladistics Terms.
Michael J. Benton, Department of Earth Sciences, University of Bristol: Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century. PDF file, Proceedings of the Royal Society of London, Series B 268, 2123-2130.
Michael J. Benton, Department of Earth Sciences, University of Bristol: Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead? Biological Reviews, vol. 75; November, 2000 (in press).
The Museum of Paleontology (UCMP), University of California at Berkeley: Why Do Biologists Need Cladistics? and Journey into the World of Cladistics.
Geoffrey C. Bowker (1999): The Game of the Name: Nomenclatural Instability in the History of Botanical Informatics. PDF file, go to page 74 (PDF page 86). Proceedings of the 1998 Conference on the History and Heritage of Science Information Systems.
Palaeontology Research Group, Department of Earth Sciences, University of Bristol: Cladestrat. This data base contains results of tests to compare cladograms with stratigraphy. The data sets have been updated to include the 1000 cladograms and molecular trees assessed for fit to stratigraphy by Benton et al. (2000). Go to: Data on Plant Trees. From the review volume by Kenrick and Crane (1997).
Stuart M. Brown, NYU Medical Center: Cladistic methods, and Introduction to Phylogenetics.
P.D. Cantino et al. (2007): Towards a phylogenetic nomenclature of Tracheophyta. PDF file, Taxon, 56: 822-846.
Philip Cantino et al., Department of Environmental and Plant Biology, Ohio University, Athens, OH: PhyloCode. The PhyloCode is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny.
Cladistics (Elsevier).
Lynne M. Clos, Fossil News: What is Cladistics?
I. Cojocaru (2010): Orientations in Macrotaxonomy. PDF file.
Consortium of European Taxonomic Facilities (CETAF). CETAF is a networked consortium of scientific institutions in Europe formed to promote training, research and understanding of systematic biology and palaeobiology. Go to: Links to taxonomic organisations, programs and initiatives.
Paleobotanical Holdings at the Liberty Hyde Bailey Hortorium at Cornell University, Dept. Plant Biology, Cornell University, Ithaca, NY: Cladistics.
J. Cracraft (1981): Pattern and process in paleobiology: the role of cladistic analysis in systematic paleontology. In PDF, [Paleobiology.
Chris Creevey & James O. McInerney, Bioinformatics Laboratory, Department of Biology, National University of Ireland, Maynooth: Clann. Construction of Supertrees and exploration of phylogenomic information from partially overlapping datasets. This software program is free and it implements the greatest number of phylogenetic supertree methods.
Dave Dobson, Guilford College, Greensboro, NC: SimpleClade. This is is a software program that allows simple cladistic analysis with a graphical user interface.
I.H. Escapa and D. Pol (2011): Dealing with incompleteness: New advances for the use of fossils in phylogenetic analysis. PDF file, Palaios, 26: 121-124.
Joe Felsenstein, Department of Genome Sciences and Department of Biology, University of Washington, Seattle: Phylogeny programs available elsewhere. Links to 383 phylogeny packages (free and non-free ones) and 52 free servers.
Vicki Funk, U.S. National Herbarium, Department of Botany, Smithsonian Institution, Washington D.C.; & Michael Donoghue, University Herbaria, Harvard University, Cambridge, MA: Cladistic Literature. A list of cladistic references.
Pablo Goloboff, Steve Farris and Kevin Nixon: TNT. TNT stands for Tree Analysis Using New Technology a program that can analyse large data sets (i.e. 300-500 taxa) in reasonable times (minutes to find a shortest tree, hours to produce a reliable consensus).
Walton A. Green et al. (2011): Does extinction wield an axe or pruning shears? How interactions between phylogeny and ecology affect patterns of extinction. PDF file, Paleobiology, 37: 72-91.
Guido W. Grimm (2005): Tracing the mode and speed of intrageneric evolution: a phylogenetic case study on genus Acer L. (Aceraceae) and genus Fagus L. (Fagaceae) using fossil, morphological, and molecular data. Doctoral thesis (PDF, 33 MB), University of Tübingen.
Guido Grimm, Department of Palaeobotany, Swedish Museum of Natural History, Stockholm:
Cladistic analyses of fossil and recent Cycadales
based on morphological and molecular data. See also
here (abstract), and
there (in German).
The International Willi Hennig Society.
David E. Joyce, Department of Mathematics and Computer Science, Clark University, Worcester, MA: Phylogeny and Reconstructing Phylogenetic Trees. These few pages describe the problem of reconstructing phylogenetic trees. A demo for two Java applets run on the viewer's browser.
M. Kearney (2002): Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. PDF file, Systematic biology, 51: 369-381.
Jonathan B. Losos and D. Luke Mahler (2010): Chapter 15, Adaptive radiation: the interaction of ecological opportunity, adaptation, and speciation. PDF file.
W. Maddison and D. Maddison, University of Arizona: Mesquite. A modular system for evolutionary analysis. To analyze data for evolutionary patterns, biologists are relying increasingly on specialized software. Mesquite, a Java-based software, allow many programmers to contribute building blocks to a common system with platform independence.
Eugene G. Maurakis and William Woolcott, Science Museum of Virginia, Richmond: Phylogenetic Systematics Video. The video, accompanied by an instructor´s guide, is an educational tool that can be used as an introduction to phylogenectic systematics. With costs.
! Dan Nickrent, Kevin C. Nixon & Dale Vitt (Curatorial Board; website served from Southern Illinois University, Carbondale): Phyto Images. This site includes a wide variety of vascular plant and bryophyte photos of high quality. Phyto Images belongs to DOL (DiversityofLife.org), which is a web interface based on the Encino Software Project. The Encino project is a unified set of software tools for storing, retrieving, and analyzing biodiversity. Search the Cladogramm Database or use the Diagnostic Keys. Superbly done!
! Kevin C. Nixon, L.H. Bailey Hortorium, Cornell University Ithaca, NY: Paleobotany in cladistics and cladistics in paleobotany: enlightenment and uncertainty. Review of Palaeobotany and Palynology, Volume 90, Issues 3-4, February 1996, Pages 361-373.
Robert Nordsieck, Vienna, Austria: The Living World of Molluscs, Begriffe aus der Kladistik (in German).
Rod Page, Division of Ecology and Evolutionary Biology, Faculty of Biomedical and Life Sciences, University of Glasgow: COMPONENT 2.0. Now free of charge! This is a computer program for analysing evolutionary trees.
Jeffrey D. Palmer et al. (2004): The plant tree of life: an overview and some points of view. PDF file, American Journal of Botany, 91: 1437-1445. See also here.
Norman I. Platnick, Division of Invertebrate Zoology, American Museum of Natural History, New York NY: From Cladograms to Classifications: The Road to DePhylocode (PDF file).
! RationalWiki (offering often criticism and satirical articles, a rival website to Conservapedia): Cladistics.
ScaleNet, Background Information: Glossary. Glossary of terms pertaining to nomenclature.
Mark E. Siddall, American Museum of Natural History, New York, NY: Phylogenetics: just methods. Various methods in systematics.
! Society of Australian Systematic Biologists (SASB): Introductory Glossary of Cladistic Terms.
W.E. Stein (1987): Phylogenetic analysis and fossil plants. PDF file, Review of palaeobotany and palynology.
David L. Swofford, Florida State University: PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta. A software package for inference of evolutionary trees, for use in Macintosh, UNIX/VMS, or Windows/DOS-based formats.
TreeView. Tree drawing software for Apple Macintosh and Windows.
! Wikipedia, the free encyclopedia:
Systematics,
Taxonomy,
Cladistics,
Phylogenetics,
Botanical
nomenclature,
Scientific
classification.
The Willi Hennig Society: Education. A link directory. See also: Arnold G. Kluge and Bernd Hennig (The Willi Hennig Society): Willi Hennig.
!
E.O. Wiley, D. Siegel-Causey, D.R. Brooks and V.A. Funk (1991):
The
Compleat Cladist: A Primer of Phylogenetic Procedures.
PDF file, University of Kansas Museum Of Natural History Special Publication 19.
See also
here.
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This index is compiled and maintained by Klaus-Peter Kelber, Würzburg, e-mail kp-kelber@t-online.de Last updated January 11, 2012 
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