Home / Teaching Documents, Lecture Notes and Tutorials / Teaching Documents about Cladistics

American Museum of Natural History, New York.
Resources for Learning. Resources for anyone interested in teaching or learning about science. Go to:
Tree of Life Cladogram.
Find out "What is a cladogramm" or "How to read a cladogram". Easy to understand information.

American Museum of Natural History, New York: Understanding Cladistics (PDF files). Background information about cladistics.

Annenberg Learner (media and telecommunications to advance excellent teaching in American schools):
Rediscovering Biology. An online textbook, written by multiple authors (UMass Amherst, University of Missouri-St. Louis, Portland Community College).
The link is to a version archived by the Internet Archive´s Wayback Machine.

J.C. Avise (2009): Timetrees: beyond cladograms, phenograms, and phylograms. PDF file, In: S.B. Hedges and S. Kumar (eds.): The Timetree of Life.

Günter Bechly, SMNS, Stuttgart: Glossary of Phylogenetic Systematics with a critic of mainstream cladism.

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).

! University of California Museum of Paleontology, Berkeley (with support provided by the National Science Foundation and the Howard Hughes Medical Institute): Understanding Evolution. Understanding Evolution is a non-commercial, education website, teaching the science and history of evolutionary biology. Go to: Phylogenetic systematics, a.k.a. evolutionary trees. This tutorial gives information about how to read, reconstruct and use an evolutionary tree and how to classify organisms based on evolutionary trees. Superbly done!

! The Museum of Paleontology (UCMP), University of California at Berkeley: Journey into the World of Phylogenetic Systematics. Introduction to cladistics, their methodology and implications and about the need for cladistics. Excellent!
See especially: An Introduction to Cladistics. Cladistics in brief.

Department of Integrative Biology, University of California, Berkeley: Plant Biology - Evolution - Ecology. Go to: Online Archived Lectures, General Biology. Video lectures (RealMedia Format).

Biology-Nation. This website provides resources for anyone with an interest in biology. (see also Biology-Nation.com Whois Record). Many links lead to Wikipedia. Go to: Introduction to Taxonomy and Introduction to Cladistics.

Department of Geological Sciences, University of Colorado, Boulder, CO: Web-based instruction. Annotated links to information on using the web to teach. Go to: CzPaleobotany. Go to: Cenozoic Elevation of the Rocky Mountains, Paleobotanical Methods. About fossil classification (nearest living relative, physiognomy and CLAMP) and climate and elevation analysis.
These expired links are now available through the Internet Archive´s Wayback Machine.
Go to: Cenozoic Elevation of the Rocky Mountains, Paleobotanical Methods. About fossil classification (nearest living relative, physiognomy and CLAMP) and climate and elevation analysis.

Jamie Boyer, The New York Botanical Garden: The Paleoplant Website. An educational resource for students and teachers studying Earth's history, fossils, and evolution. Go to:
! Cladistics. Methodology to deciphering true evolutionary groupings.

Stuart M. Brown, NYU Medical Center: Cladistic methods, and Introduction to Phylogenetics.
These expired links are available through the Internet Archive´s Wayback Machine.

Steven M. Carr, Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, # Memorial University of Newfoundland, St. John's, Canada: Principles of Systematics. Lecture notes with links.

Gregory T. Chandler, The Australian National University:
Introduction to Taxonomy.

Cladistics (Wiley-Blackwell). The International Journal of the Willi Hennig Society. Cladistics publishes high quality research papers on systematics, especially in biogeography, coevolution, conservation biology, ontogeny, genomics and palaeontology.

! CLAMP Online (Climate Leaf Analysis Multivarite Program). This site is the result of an ongoing collaboration between the Institute of Botany, Chinese Academy of Sciences, Beijing, and the Open University UK.
How you can use foliar physiognomy (leaf architecture) to determine ancient climates from fossil leaves or explore the relationship that exists between leaf form and climate. CLAMP is a multivariate statistical technique that decodes the climatic signal inherent in the physiognomy of leaves of woody dicotyledonous plants. See especially:
! Teaching Materials.
Older CLAMP websites are available through the Internet Archive´s Wayback Machine:
Robert A. Spicer, The Warm Earth Environmental Systems Research Group: Plant Fossils as Climatic Indicators. Go to: Climate Leaf Analysis Multivariate Programe (CLAMP). An introduction to the use of leaf architecture for determining past climatic conditions.

! C.J. Cleal and B.A. Thomas (2021): Naming of parts: the use of fossil-taxa in palaeobotany. In PDF, Fossil Imprint, 77: 166–186.
See also here.

Lynne M. Clos, Fossil News: What is Cladistics?
This expired link is still available through the Internet Archive´s Wayback Machine.

Paleobotanical Holdings at the Liberty Hyde Bailey Hortorium at Cornell University, Dept. Plant Biology, Cornell University, Ithaca, NY: Cladistics. Provided by the Internet Archive´s Wayback Machine.

J. Cracraft (1981): Pattern and process in paleobiology: the role of cladistic analysis in systematic paleontology. In PDF, Paleobiology.

! M.D. Crisp, Division of Botany and Zoology Australian National University Canberra: Introductory Glossary of Cladistic Terms. Invited contribution of the Society of Australian Systematic Biologists (SASB).
Website outdated. The link is to a version archived by the Internet Archive´s Wayback Machine.

Cyberinfrastructure for Phylogenetic Research (CIPRES).
Building the Tree of Life: A National Resource for Phyloinformatics and Computational Phylogenetics. CIPRES is a collaboration of many american museums and institutions. Go to:
What is Phylogeny? An introduction to phylogenetic trees and what they represent. See also:
What can phylogenies be used for?
and about the practical importance of the Tree of Life (a brochure from the National Science Foundation, in PDF).
Still available via Internet Archive Wayback Machine.

Deep Green - Green Plant Phylogeny Research Coordination Group (supported by National Science Foundation). The "Tree of Life" for plants. Two interactive versions are given: one is for reasearch and one is for teaching.

! M.C.C. de Pinna (1991): Concepts and tests of homology in the cladistic paradigm. Free access, Cladistics, 7 :367-394.

! P.C.J. Donoghue and M.J. Benton (2007): Rocks and clocks: calibrating the Tree of Life using fossils and molecules. In PDF, Trends in Ecology and Evolution.
See also here.
! Note figure 2: Concordance of palaeontological data, phylogenetic hypotheses, macroevolutionary events and molecular clock.

J.A. Doyle, and M.D. Donoghue: Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach. In PDF, Botanical Review, 52: 321-431.
See likewise here.

Alexander Edens, Hartnell College, Salinas, CA: Biology Tutorials. Tutorials on several important biology topics. Powerpoint presentations. Go to: Taxonomy and Phylogeny.

Niles Eldredge, American Museum of Natural History: Spectrum of Life. 28 major groups of organisms organized into basic divisions of life, explained in a nutshell.

P.K. Endress and J.A. Doyle (2009): Reconstructing the ancestral angiosperm flower and its initial specializations. Free access, American Journal of Botany, 96: 22-66.

! Joe Felsenstein, Department of Genome Sciences and Department of Biology, University of Washington, Seattle: PHYLIP. PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. Go to: Phylogeny Programs. The programs listed here include both free and non-free ones.

Peter Forey, Natural History Museum, London: Cladistics for Palaeontologists (PalAss Newsletter).

! F. Forrest (2009): Calibrating the Tree of Life: fossils, molecules and evolutionary timescales. Free access, Annals of Botany, 104: 789–794.
"... New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record.
[...] ! "...the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account. ..."

J. Gravendyck et al. (2023): (142–148) Proposals to improve the definition, utility, and curation of (type) specimens of fossil algae, fungi, and plants. Open access, Taxon, 71: 705–706.

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.

! T.R. Gregory (2008): Understanding evolutionary trees. Abstract, Evolution: Education and Outreach, 1: 121–137. See also here (in PDF).

Kent E. Holsinger, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT: Reproductive systems and evolution in vascular plants (PDF file).

! W.S. Judd, C.S. Campbell, E.A. Kellogg, and P.F. Stevens: A Phylogenetic Approach, Chapter 2: Plant Systematics. PDF file, 2nd Edition, 2002. Sinauer Associates, Inc.

Keith Karoly, Biology Department, Reed College, Portland, OR: Vascular Plant Diversity. An internet guide. Go to: Introduction to Plant Taxonomy.

Nikita Julievich Kluge, Department of Entomology, S.-Petersburg State University. Russia: General Principles of Biological Systematics. Chapter 1 from the book "Modern Systematics of Insects".
Website outdated. The link is to a version archived by the Internet Archive´s Wayback Machine.

M. Koopman and E. Hoffmann, Department of Botany, University of Wisconsin, Madison, WI: Temporal Sequences. Powerpoint presentation.

! Diana Lipscomb (1998), Department of Biological Sciences, George Washington University, Washington D.C.: Basics of Cladistic Analysis (PDF file). This tutorial briefly reviews basic cladistic methods and the various options of character analysis and dealing with multiple trees. Each of these topics has worked examples.

! G.Q. Liu et al. (2022): The Molecular Phylogeny of Land Plants: Progress and Future Prospects. Open access, Diversity, 14 (from the Special Issue Ecology, Evolution and Diversity of Plants).
Note figure 1: Summary of phylogenetic relationships among major clades of land plants.

Jonathan B. Losos and D. Luke Mahler (2010): Chapter 15, Adaptive radiation: the interaction of ecological opportunity, adaptation, and speciation. PDF file. Provided by the Internet Archive´s Wayback Machine.

S.G. Lucas (2023): Cladistics and Stratigraphy. Open access, Geosciences, 13.

! B.R. Moore et al. (2016): Critically evaluating the theory and performance of Bayesian analysis of macroevolutionarymixtures. In PDF, Proc. Natl. Acad. Sci. U.S.A., 113: 9569–9574.
"... the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM."

! Kevin C. Nixon, L.H. Bailey Hortorium, Cornell University Ithaca, NY: Paleobotany in cladistics and cladistics in paleobotany: enlightenment and uncertainty. In PDF, Review of Palaeobotany and Palynology, 90: 361-373. See also here.

! Norman MacLeod, Natural History Museum, London: PalaeoMath. Aspects of quantitative analysis in paleontological contexts. Each essay (from the Palaeontological Association Newsletter since 2004) is written for the novice data analyst, especially those who always wanted to gain knowledge of this subject, but never had the opportunity to do so and haven´t managed to make much progress through self-education. Including some MS Excel spreadsheets providing examples and data.

Department of Geoscience, University of Wisconsin, Madison: Paleontological Experiences for Science Teachers (funded by the Howard Hughes Medical Institute). Hands-on training in vertebrate paleontology, using fieldwork and laboratory work. Go to: Cladistics and diagrams.

Robert Nordsieck, Vienna, Austria: The Living World of Molluscs, Begriffe aus der Kladistik (in German).

Peter Ommundsen, Selkirk College, Canada: Pronunciation of Biological Latin. Including taxonomic names of plants and animals. See also here (PDF file).

! Dennis O´Neil, Behavioral Sciences Department, Palomar College, San Marcos, California:
Classification of Living Things.
An introduction to the principles of taxonomy with a focus on human classification categories. In this tutorial you will be learning about the Linnaean system of classification used in the biological sciences to describe and categorize all living things.
Websites still available via Internet Archive Wayback Machine.

! K. Padian et al. (1994): Cladistics and the fossil record: the uses of history. In PDF, Annual Review of Earth and Planetary Sciences, 22: 63-89.
See also here.

! J.D. Palmer et al. (2004): The plant tree of life: an overview and some points of view. Free access, American Journal of Botany, 91: 1437-1445.

! J.F. Parham et al. (2012): Best Practices for Justifying Fossil Calibrations. In PDF, Syst Biol., 61: 346-359. See also here

The PhyloCode Website

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).

The PhyloCode (hosted by Ohio University, Athens, Ohio). A phylogenetic code of biological nomenclature. The development of the PhyloCode grew out of a recognition that the current Linnaean system of nomenclature, as embodied in the preexisting botanical, zoological, and bacteriological codes, is not well suited to govern the naming of clades and species.
See also here (Wikipedia).

Quizlet.com study tools:
! Search for Phylogeny.
! Search for Cladistics.

! RationalWiki (offering often criticism and satirical articles, a rival website to Conservapedia): Cladistics.

John Rushin, Missouri Western State University:
History of Plant Taxonomy.
Plant Taxonomy (Systematics).
Powerpoint presentations.

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.

Michael G. Simpson: Plant Nomenclature. Powerpoint presentation.

! P.F. Stevens and Hilary Davis, University of Missouri, St Louis, and Missouri Botanical Garden, St. Louis: Angiosperm Phylogeny Website. Descriptive characterization of all angiosperm orders and families, including images, phylogenetic trees, the description of characters used complete family and order synonymies, a link directory and a bibliography.

Alycia L. Stigall, Department of Geological Sciences and OHIO Center for Ecology and Evolutionary Studies (website hosted by the Paleontological Society, Boulder): Tracking Species in Space and Time: Assessing the relationships between paleobiogeography, paleoecology, and macroevolution. In PDF, lecture notes, PS Centennial Short Course. See also here.

! Wikipedia, the free encyclopedia:
Biological classification.
Systematics. Scientific classification.
Taxonomy.
Cladistics.
Phylogenetics,
Botanical nomenclature.

! 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.

! The Willi Hennig Society. The Hennig Society was founded with the expressed purpose of promoting the field of Phylogenetic Systematics.
Go to: Education. A link directory, still available via Internet Archive Wayback Machine.
See also: Bernd Hennig and Arnold G. Kluge: Willi Hennig.

The Willi Hennig Society.
The Willi Hennig Society is a forum for advancing the science of phylogenetic systematics. Go to: Education. A link directory.
Still available via Internet Archive Wayback Machine.

Paul Wolf, Utah State University: Introduction to Phylogenetics. Powerpoint presentation.
This expired link is available through the Internet Archive´s Wayback Machine.

Steven J. Wolf, Department of Biological Sciences, California State University, Stanislaus: Flowering Plants. Lecture notes about plant taxonomy and systematics, history of plant taxonomy, identification keys used to identify plants, plant nomenclature, etc. Go to: History of Plant Taxonomy.
These expired links are now available through the Internet Archive´s Wayback Machine.

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