Systematics, Taxonomy, and Phylogeny: References

J. David Archibald (2009) 'Edward Hitchcock's Pre-Darwinian (1840) 'Tree of Life'.', Journal of the History of Biology (2009) 42:561-592
Early trees

Ashlock, P.D. (1971). "Monophyly and associated terms". Systematic Zoology 20 (1): 63–69. doi:10.2307/2412223.
monophyletic

Ashlock, P D (1974) The Uses of Cladistics. Annual Review of Ecology and Systematics Vol. 5: 81-99 (November 1974) DOI: 10.1146/annurev.es.05.110174.000501
monophyletic

Fausto Barbagli (2009) 'In Retrospect: The earliest picture of evolution?', Nature 19 November 2009
Early trees

Benton, MJ (2000), Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead? Biol. Rev. 75: 633-648
"Evolutionary phylogeny" - Supraspecific Taxa

Benton, M.J. 2004, Vertebrate Paleontology, 3rd ed. Blackwell Science Ltd;
Romerogram, "Evolutionary phylogeny" - Stratigraphic sequence

Benton, M.J. 2007 The Phylocode: Beating a dead horse? Acta Palaeontol. Pol. 52 (3): 651–655, 2007
History of Taxonomy, Phylogenetic classification

Bininda-Emonds, O.R.P., 2004, The evolution of supertrees, Trends in Ecology and Phylogeny Vol.19 No.6 June 2004
Adams consensus, Majority rule consensus, supertree, total evidence

Brian E. Bodenbender and Daniel C. Fisher, 2001, Stratocladistic analysis of blastoid phylogeny, Journal of Paleontology (March 2001), 75(2):351-369
"Evolutionary phylogeny" - Stratocladistics

Peter J. Bowler (2003) Evolution. The History of an Idea, third edition, p.90-91.
Early trees

Brochu, C.A.; Sumrall, C.D. (2001). "Phylogenetic nomenclature and paleontology". Journal of Paleontology 75 (4): 754–757. doi:10.1666/0022-3360(2001)075.
Cladistics

Budd, G.E. (1996). "The morphology of Opabinia regalis and the reconstruction of the arthropod stem-group". Lethaia 29 (1): 1–14. doi:10.1111/j.1502-3931.1996.tb01831.x.
Stem group

Budd, G. E. (2001). Tardigrades as "stem-group arthropods": the evidence from the Cambrian fauna. Zoologischer Anzeiger, 240, 265–279. pdf
Stem group

Joe Cain (2009), "Mayr, Ernst Walter", in Michael Ruse and Joseph Travis ed. Evolution: the first four billion years, Belkna Press of Harvard University Press, Cambridge & London, pp.724-7
Evolutionary Systematics - Methodology

Carlson, Sandra J, 2001. "Ghosts of the past, present, and future in brachiopod systematics". Journal of Paleontology, 75 (6), 2001, pp.1109-1118.
Phylogenetic classification

Coyne, J.A. & Orr, H.A. 2004. Speciation. Sunderland, Massachusetts: Sinauer.
"Evolutionary phylogeny" - cladogenesis

Darwin, Charles (1859), On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (1st ed.), London: John Murray, ISBN 1-4353-9386-4
Darwin's tree

Darwin, Charles (1872), The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (6th ed.), London: John Murray, ISBN 1-4353-9386-4
Darwin's tree

Delsuc, F., Brinkmann, H., & Philippe, H. 2005, Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics 6, 5 (2005) 361-75 pdf
"Garbage in, garbage out", heterotachy, Long branch attraction, phylogenomics, root

Donoghue P.C.J. & Benton M.J. (2007) Rocks and clocks: Calibrating the Tree of Life using fossils and molecules. Trends Ecol Evol 22:424-431 pdf
molecular clock, "Evolutionary phylogeny" - Rocks and clocks, Stratigraphy and phylogeny

Malte C. Ebach, Juan J. Morrone and David M. Williams 2008 A new cladistics of cladists. Biology and Philosophy 23 (1). 153-156, DOI: 10.1007/s10539-007-9069-7
Cladistics, Gradists, Numerical cladistics Pattern cladistics

Edgecombe, G.D. 2009, Palaeontological and molecular evidence linking arthropods, onychophorans and other Ecdysozoa. Evolution: Education and Outreach 2: 178-190. 10.1007/s12052-009-0118-3 pdf
Long branch attraction

Ereshefsky, M. (2000). The Poverty of the Linnaean Hierarchy: A Philosophical Study of Biological Taxonomy. Cambridge: Cambridge University Press.
Taxonomy

Felsenstein, J. 2003. Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts. review
Gradists

Fisher, D.C. , 1994, Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. in Interpreting the hierarchy of nature (Grande, L. & Rieppel, O. eds) 133-171 (Academic Press, San Diego).
"Evolutionary phylogeny" - Stratocladistics

Fisher, D.C. 2008, Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference Annual Review of Ecology, Evolution, and Systematics Vol. 39: 365-385 DOI: 10.1146/annurev.ecolsys.38.091206.095752 Daniel C. Fisher
Stratocladistics (glossary), "Evolutionary phylogeny" - Stratocladistics

Peter L. Forey, Christopher J. Humphries, Ian J. Kitching, Robert W. Scotland, D. J. Siebert, D. M. Williams, 1992, Cladistics: a practical course in systematics, Oxford University Press
Adams consensus, Strict consensus

Gauthier, J. 1986. Saurischian monophyly and the origin of birds. In: K. Padian, ed. The Origin of Birds and the Evolution of Flight. Memoirs California Academy of Sciences 8. pp. 1–55
Cladistics

Marius Dan Georgescu, 2009, Taxonomic revision and evolutionary classification of the biserial Cretaceous planktic foraminiferal genus Laeviheterohelix Nederbragt, 1991, Rev. mex. cienc. geol v.26 n.2 México ago. Online
Stratigraphy and phylogeny - Diagram

Grant, V. 2003, Incongruence between cladistic and taxonomic systems American Journal of Botany 90(9): 1263–1270. 2003.
monophyletic, "Evolutionary phylogeny" - ancestors

Gribaldo, S. & Philippe, H. 2002, Ancient Phylogenetic Relationships. Theoretical Population Biology 61, 391–408 (2002) doi:10.1006/tpbi.2002.1593 pdf
Long branch attraction

Haeckel, E. 1866. Generelle Morphologie der Organismen. Georg Reiner, Berlin, Germany.
monophyletic

Hedges, B and Kumar S. Eds. 2009. The Timetree of Life. Oxford University Press.
"Evolutionary phylogeny" - Stratigraphic sequence

Hennig, W. 1966, Phylogenetic Systematics. (tr. D. Davis and R. Zangerl), Univ. of Illinois Press, Urbana 1966, reprinted 1979,
monophyly, paraphyly

Susan Holmes. 2003. Bootstrapping Phylogenetic Trees: Theory and Methods. Statistical Science, Vol. 18, No. 2, 241–255 pdf
Bootstrap

Hörandl, E, 2010. Beyond cladistics: Extending evolutionary classifications into deeper time levels. Taxon 59 (2) April 2010: 345–350 pdf

Hörandl, E. & Stuessy, T.F., 2010 Paraphyletic groups as natural units of biological classification, Taxon 59 (6) December 2010: 1641-1653 on line
"Evolutionary phylogeny" - cladogenesis, budding, paraphyly

Keeling, P.J. & Palmer J.D. 2008, Horizontal gene transfer in eukaryotic evolution
horizontal gene transfer, polytomy

Kröger B, Vinther J, Fuchs D. 2011, Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules: Extant cephalopods are younger than previously realised and were under major selection to become agile, shell-less predators. Bioessays. 33(8):602-13. doi: 10.1002/bies.201100001.
Total Evidence approach

Kühl, G.; Briggs, D.E.G., and Rust, J. (February 2009). "A Great-Appendage Arthropod with a Radial Mouth from the Lower Devonian Hunsrück Slate, Germany". Science 323 (5915): 771–773. doi:10.1126/science.1166586. PMID 19197061.
Lazarus taxon

Lane, A & MJ Benton (2003), Taxonomic level as a determinant of the shape of the Phanerozoic marine biodiversity curve. Amer. Naturalist 162: 265-276 pdf
"Evolutionary phylogeny" - Supraspecific Taxa

Levinton, J.S. 2001, Genetics, Paleontology, and Macroevolution, 2nd ed. Cambridge University Press
Ghost lineage, Stratigraphic congruence

Lipscomb, D. 1998. Basics of Cladistic Analysis. George Washington University, Washington D.C. pdf
Length, Phylogenetic systematics.

Liu, J. et al.(2011). Jianni Liu, Michael Steiner, Jason A. Dunlop, Helmut Keupp, Degan Shu, Qiang Ou, Jian Han, Zhifei Zhang & Xingliang Zhang. (2011). Liu et al. reply. Nature 476, 526–530
Gap codings

Mayr, E. 1963, Animal Species and Evolution, Cambridge, MA: Harvard University Press,
species

Mayr, E., & P. D. Ashlock. 1991. Principles of systematic zoology, 2nd ed. McGraw-Hill, New York, New York, USA.
monophyletic, phenetics

Mayr, E., & W. Bock. 2002. Classifications and other ordering systems. Zeitschrift für zoologische Systematik und Phylogenysforschung 40: 169–194. pdf
monophyletic, phenetics, "Evolutionary phylogeny" - ancestors, "Evolutionary phylogeny" - budding

Mounce, R. C. P. & Wills, M. (2011). Phylogeny of Diania challenged. Nature 476, doi:10.1038/nature10266
Gap codings

O'Keefe, F. R. and P. M. Sander (1999) Paleontological paradigms and inferences of phylogenetic pattern: a case study. Paleobiology 25: 518-533 abstract
"Evolutionary phylogeny" - Anagenesis, ASCII Phylogenetic Tree, Total evidence

O'Leary, M.A., et al. 2013. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 339:662-667.
Phylogenetics

Pearson, C.H., 2010. Pattern Cladism, Homology, and Theory-Neutrality. History and Philosophy of the Life Sciences - Vol. 32, no. 4 (2010) abstract

Pattern cladistics

Pisani, D., Yates, A. M., Langer, M., and Benton, M. J. 2002. A genus-level supertree of the Dinosauria. Proceedings of the Royal Society, Series B, 269, 915-921. PDF
Supertree

de Queiroz, A. & Gatesy, J., 2007, The supermatrix approach to systematics, Trends in Ecology and Phylogeny Vol.22 No.1 pdf
supermatrix

Rieseberg, L. & Brouillet, L. 1994. Are many plant species paraphyletic? Taxon 43: 21–32.
"Evolutionary phylogeny" - budding

Rieppel, O. 1993 in The Conceptual Relationship of Ontogeny, Phylogeny, and Classification: the Taxic Approach, Phylogenyary Biology vol. 27, edited by Max K. Hecht et al., Plenum Press, New York, pp.1-32,
homology

Scott D. Sampson, Mark A. Loewen, Andrew A. Farke, Eric M. Roberts, Catherine A. Forster, Joshua A. Smith, and Alan L. Titus (2010). "New Horned Dinosaurs from Utah Provide Evidence for Intracontinental Dinosaur Endemism". PLoS ONE 5 (9): e12292. DOI:10.1371/journal.pone.0012292. Online
Speciation - Dendrogram

Searls, D.B. 2003. Pharmacophylogenomics: genes, evolution and drug targets. Nature Reviews Drug Discovery 2, 613-623 (August 2003) | doi:10.1038/nrd1152. online
molecular clock, phylogenomics

Sereno, P.C., 2007. Logical basis for morphological characters in phylogenetics. Cladistics 23 (2007) 565–587 (pdf)
Character

Schram, F. R. and C. H. J. Hof (1998), Fossi ls and the interrelationships of major crustacean groups, 233-302. In G. D. Edgecombe (ed.), Arthropod Fossils and Phylogeny. Columbia University Press. New York
Vraagteken effect

Simpson, George G. "The Principles of Classification and a Classification of Mammals." Bulletin of the AMNH, vol. 85, p. 23. 1945. American Museum of Natural History, New York.
Splitters versus lumpers

Siveter, Derek J.; Fortey, R.A., Sutton, M.D., Briggs, D.E.G., and Siveter, David J. (2007). "A Silurian "marrellomorph" arthropod". Proceedings of the Royal Society: B 274 (1623): 2223–2229. doi:10.1098/rspb.2007.0712. PMC 2287322. PMID 17646139.
Lazarus taxon

Michelle Spaulding, Maureen A. O'Leary, John Gatesy, (2009). "Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution". In Farke, Andrew Allen. PLoS ONE 4 (9): e7062, doi:10.1371/journal.pone.0007062 pdf
Cladogram

Stetter, K. O. 1996. Hyperthermophiles in the history of life, Ciba Found. Symp. 202, 1–10.
Long branch attraction

Stuessy, T.F. Paradigms in biological classification Taxon 58 (1) February 2009: 68–76 pdf
Phenetics

Telford, M.J. & Budd, G.E. 2003. The place of phylogeny and cladistics in Evo-Devo research Int. J. Dev. Biol. 47: 479-490 (2003)
Phylogenetic systematics, Polarity

Dale Tshudy and Ulf Sorhannus, 2003 Hoploparia, the best-known fossil clawed lobster (Family Nephropidae), is a "wastebasket" genus, Journal of Crustacean Biology 23(3):700-711. 2003 doi: http://dx.doi.org/10.1651/C-2353
matrix

Wagner, P. J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21: 153–178.

Wang, Xiaoming, Tedford, Richard H.; Taylor, Beryl E., 1999 Phylogenetic systematics of the Borophaginae (Carnivora, Canidae). Bulletin of the AMNH ; no. 243. online
"Evolutionary phylogeny" - Speciation - Dendrogram

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