Teaching Documents, Lecture Notes and Tutorials /
Teaching Documents about Cladistics
Teaching Documents about Palaeobotany
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What is Palaeontology or Palaeobiology?
Teaching Documents about Palaeontology and Palaeoecology
Teaching Documents about Ichnology
Teaching Documents about Ecology
Teaching Documents about Taphonomy
Teaching Documents about Plant Anatomy
Teaching Documents about Wood Anatomy and Tree-Ring Research
Teaching Documents about Botany
Teaching Documents about Biology
Teaching Documents about Evolution
Teaching Documents about Mass Extinction
Teaching Documents about Classification and Nomenclature
Teaching Documents about Palaeogeography
Teaching Documents about Palaeoclimate
Teaching Documents about Stratigraphy and Historical Geology
Teaching Documents about Geochronological Methods
Introductions to Statistics
Meta Indexes of Online Education
Virtual Field Trips
Cladistic Methods of Phylogenetic Analysis@
! Focused on the Evolution of Plants@
! Taxonomy, Systematics, Plant Classification@
Botanical Nomenclature and Taxonomy Databases@
Evolution Sciences versus Doctrines of Creationism and Intelligent Design@
Introductions to both Fossil and Recent Plant Taxa@
Glossaries, Dictionaries and Encyclopedias: Palaeontology@
Glossaries, Dictionaries and Encyclopedias: Biology@
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). Go to: Evolution and Phylogenetics (in PDF).
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.
Jamie Boyer, The New York Botanical Garden:
The Paleoplant Website.
An educational resource for students and teachers studying Earth's history, fossils, and evolution.
! Cladistics. Methodology to deciphering true evolutionary groupings.
Stuart M. Brown, NYU Medical Center:
Cladistic methods, and
These expired links are available through the Internet Archive´s Wayback Machine.
! Cantino, P.D. and K. de Queiroz, Ohio University, Athens, Ohio: The PhyloCode. 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.
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.
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.
Lynne M. Clos, Fossil News: What is Cladistics?
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.
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).
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.
! 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.
J.A. Doyle, and M.D. Donoghue: Seed plant phylogeny and the origin of angiosperms: An experimental cladistic approach. Abstract, Bot. Rev. 52: 321-431.
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. PDF file, 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).
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.
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.
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. ^
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.,
"... 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. Review of Palaeobotany and Palynology, Volume 90, Issues 3-4, February 1996, Pages 361-373.
! 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).
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.
! 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).
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).
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.
! 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:
Systematics. Scientific classification.
E.O. Wiley, D. Siegel-Causey, D.R. Brooks and V.A. Funk (1991):
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.
Paul Wolf, Utah State University:
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:
Lecture notes about plant taxonomy and systematics,
history of plant taxonomy, identification keys used to identify plants,
plant nomenclature, etc.
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