Home / Plant Anatomy & Taxonomy / Cladistic Methods of Phylogenetic Analysis

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.

Y. Asar et al. (2022): Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution. In PDF, bioRxiv.
See also here.
! Note figure 1 (on PDF-page 9): A flowchart of simulation study. About molecular and morphological phylograms, morphological characters and sequence alignments.

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).

! C.D. Bell et al. (2010): The age and diversification of the angiosperms re-revisited. Free access, American Journal of Botany, 97: 1296-1303.

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.

! Jamie Boyer, The New York Botanical Garden:
What is Paleobotany?. Also worth checking out:
Plant Evolution & Paleobotany. An educational resource for students and teachers studying Earth's history, fossils, and evolution.
! Go to: Paleobotany Short-Course. Lecture notes.
Paleobotany Overview; Life moves to land.
Plant classification.
Rise of Seed Plants.
Rise of flowering plants.
Excellent!

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: Evolutionary Theory. Lecture notes. Taxonomic classification and theory of evolution.

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).

J.W. Brown and S.A. Smith (2017): The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates. See also here (in PDF).

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

P.D. Cantino et al. (2007): Towards a phylogenetic nomenclature of Tracheophyta. PDF file, Taxon, 56: 822-846. See also here.

! Catalogue of Life (by Species 2000, Leiden The Netherlands).
The most complete authoritative list of the world's species - maintained by hundreds of global taxonomists.
Go to: Kingdom Plantae.

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.

Cladistics.com: Software for Systematics. Downloadable software, e.g. WinClada, NONA, TNT, Trees.

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

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. 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.

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.

! 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.

! J.A. Cunningham et al. (2016): The origin of animals: can molecular clocks and the fossil record be reconciled? Open access, Bioessays, 39. See also here (in PDF).
Note figure 1: Summary of major Ediacaran and early Cambrian fossil assemblages.
! Figure 2. The mismatch between the fossil and molecular clock records of early animal evolution.
"... Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed.
[...] A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identification in the fossil record.

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.

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

Dave Dobson, Guilford College, Greensboro, NC: SimpleClade. This is is a software program that allows simple cladistic analysis with a graphical user interface.

! M. Dohrmann and G. Wörheide (2017): Dating early animal evolution using phylogenomic data. Open access, Scientific reports, 7.
! Note Figure 4: Time-calibrated phylogeny of animals.

! 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.

! M.J. Donoghue et al. (1989): The importance of fossils in phylogeny reconstruction. In PDF.

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.

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.
See also here.

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.

J.R. Flores (2020): Rooting morphologically divergent taxa–slow-evolving sequence data might help. Free access, bioRxiv preprint, doi: https://doi.org/10.1101/2020.03.15.983684.

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).
This expired link is available through the Internet Archive´s Wayback Machine.

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. See also here.

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).

! J. Hilton and R.M. Bateman (2006): Pteridosperms are the backbone of seed-plant phylogeny. In PDF, Journal of the Torrey Botanical Society, 133: 119-168.
See also here.

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.

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.

! N.M. Koch and L.A. Parry (2020): Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses. Free access, Syst. Biol., 69: 1052–1067.
See also here and there.
"... Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. ..."

! Michel Laurin (2012): Recent progress in paleontological methods for dating the Tree of Life. In PDF, Frontiers in Genetics, 3.

S. Lehtonen et al. (2020): Exploring the phylogeny of the marattialean ferns. Open access, Cladistics.
Note fig. 4: Parsimony-dated phylogeny and Bayesian historical biogeography of the marattialean ferns.
"... We resolved the fossil genera Marattiopsis, Danaeopsis and Qasimia as members of the monophyletic family Marattiaceae, and the Carboniferous genera Sydneia and Radstockia as the monophyletic sister of all other marattialean ferns. ..."

S. Lehtonen (2011): Towards Resolving the Complete Fern Tree of Life. In PDF.

Diana Lipscomb, George Washington University, Washington, DC: Basics of Cladistic Analysis. In PDF. This guide is designed to acquaint students with the basic principles and methods of cladistic analysis.

! R. López-Antoñanzas et al. (2022): Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life. Open access, Biology, 11: 1185. https://doi.org/10.3390/ biology11081185.
"... The statistical techniques mentioned above have only begun to be applied to questions in palaeontology over the past decade but have found extensive applications in phylogenetic comparative analysis, quantitative genetics, and ecology. Complementary methodologies that combine morphological and molecular approaches can provide novel answers to broad evolutionary and deep-time questions ..."

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.

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.

! S. Mathews (2009): Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data. Free access, American Journal of Botany, 96: 228-236.

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.

! J. McNeill et al. (2012): Guidelines for proposals to conserve or reject names. In PDF, Taxon, 61: 248-251.
This expired link is available through 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., 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."

H. Morlon et al. (2011): Reconciling molecular phylogenies with the fossil record. In PDF, PNAS, 108: 16327-16332.

! 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.

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

! K.E. Omland et al. (2008): Tree thinking for all biology: the problem with reading phylogenies as ladders of progress. In PDF, BioEssays, 30: 854–867.
See also here.

! 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.

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.

! 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.

! Phyto Images
Database hosted by the Cornell University Vascular Plant Herbarium. Software deveopment by Kevin C. Nixon and Jan De Laet).
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. Superbly done!

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).

T.B. Quental, C.R. Marshall (2010): Diversity dynamics: molecular phylogenies need the fossil record. In PDF, Trends in Ecology & Evolution, 25: 434-441.
See also here.

! D.L. Rabosky et al. (2017): Is BAMM flawed? Theoretical and practical concerns in the analysis of multi-rate diversification models. In PDF, Syst. Biol., 66: 477–498. See also here.

D.L. Rabosky (2014): Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees. PLoS ONE, 9: e89543. doi:10.1371/journal.pone.0089543

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

! Mark Ridley (2004): Evolution (Third edition). In PDF. 786 pages, Blackwell Publishing company. See likewise here (Google books), or there.
Note especially:
Chapter 1.3, "A short history of evolutionary biology", Start at PDF-page 33.
! Part 5, Macroevolution. Chapter 18, "The History of Life", Start at PDF-page 558.
About plant evolution note:
Chapter 3, "The Evidence for Evolution", Start at PDF-page 43.
Chapter 14, "Speciation", Start at PDF-page 416.
Chapter 19, "Evolutionary Genomics", Start at PDF-page 591.

ScaleNet, Background Information: Glossary. Glossary of terms pertaining to nomenclature.

M. Schmitt (2010): Willi Hennig, the cautious revolutioniser. In PDF, Palaeodiversity, 3, Supplement: 3-9.

M. Schmitt (2003): Willi Hennig and the rise of cladistics. In PDF, The New Panorama of Animal Evolution.
Now provided by the Internet Archive´s Wayback Machine.

Mark E. Siddall, American Museum of Natural History, New York, NY: Phylogenetics: just methods. Various methods in systematics.

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. Provided by the Internet Archive´s Wayback Machine.
Go to: AWTY. A system for graphical exploration of Markov chain Monte Carlo (MCMC) convergence in Bayesian phylogenetic inference. See also:
Beta Documentation (in PDF).

D. Tautz (2006), starting on PDF page 09: Morphologie versus DNA-Sequenzen in der Phylogenie-Rekonstruktion. PDF file, in German. Species, Phylogeny and Evolution 1. Themenheft Phylogenetisches Symposium Göttingen: Der Stellenwert der Morphologie in der heutigen Phylogenetische Systematik.
This expired link is available through the Internet Archive´s Wayback Machine.

TreeView. Tree drawing software for Apple Macintosh and Windows.

! N.J. Wickett et al. (2014): Phylotranscriptomic analysis of the origin and early diversification of land plants. In PDF, PNAS 111, see also here.

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

! 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.

! 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.

Top of page Links for Palaeobotanists

Search in all "Links for Palaeobotanists" Pages! index sitemap advanced site search by freefind This index is compiled and maintained by Klaus-Peter Kelber, Würzburg, e-mail kp-kelber@t-online.de Last updated August 14, 2023