DELModern Evolutionary Systematics: Basic Literature
Richard H. Zander
Res Botanica, a Missouri Botanical Garden Web Site
http://www.mobot.org/plantscience/ResBot/index.htm

August 12, 2009

 

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Modern Evolutionary Systematics: Basic Literature

 

These recent papers support the insistence of modern evolutionary systematics that macroevolution, as ancestor-descendant relationships commonly involving paraphyly on molecular trees, should be represented in classification. [Some papers have been communicated to this Web site by others, for which many thanks!]

 

Barraclough, T. G. 2010. Evolving entities: towards a unified framework for understanding diversity at the species and higher levels. Phil. Trans. Roy. Soc. B 365: 1801-1813.

 

Bock, W. J. 2002. Classifications and other ordering systems. J. Zool. Syst. Evol. Research 40: 169-194.

 

Bock, W. J. 2004. Explanations in systematics. Milestones in Systematics, D. M. Williams & P. L. Forey, eds. Systematics Assoc. Special Volume 67. CRC Press, Boca Raton, Florida.

 

Bridgham, J. T., E. A. Ortlund & J. W. Thornton. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461: 515-519.

 

Brothers, D. J. 1985. Species concepts, speciation, and higher taxa. In: E. S. Vrba, ed. Species and Speciation. Transvaal Mus. Monogr. 4: 35–42. Pretoria. [Contributed by Denis J. Brothers.]

 

Brummitt, R. K. 2006. Am I a bony fish? Taxon 55: 268--269.

 

Cavalier-Smith, T. 2010. Deep phylogeny, ancestral groups and the four ages of life. Phil. Trans. Roy. Soc. B 365: 111--132.

 

Crawford, D. J. 2010. Progenitor-derivative species pairs and plant speciation. Taxon 59: 1413–1423.

 

Dayrat, B. 2005. Ancestor-descendant relationships and the reconstruction of the Tree of Life. Paleobiology 31: 347--353.

 

de Carvalho, M. R., F. A. Bockmann, D. S. Amorim & C. R. F. Brandão. 2008. Systematics must embrace comparative biology and evolution, not speed and automation.  Evol. Biol. (preprint)

 

Funk, D. J. & K. E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Syst. 34: 397--423.

 

Gould, S. J. & N. Eldredge. 1993. Punctuated equilibrium comes of age. Nature 366: 223--227.

 

Grant, V. 2003. Incongruence between cladistic and taxonomic systems. Am. J. Bot. 90: 1263--1270.

 

Hörandl, E. 2006. Paraphyletic versus monophyletic taxa---evolutionary versus cladistic classifications. Taxon 55: 564--570.

 

Hörandl, E. 2007. Neglecting evolution is bad taxonomy. Taxon 56: 1--5.

 

Hörandl, E. 2010. Beyond cladistics: extending evolutionary classifications into deeper time levels. Taxon 59: 345--350.

 

Hutchinson, J. M. C. & G. Gigerenzer. 2005. Simple heuristics and rules of thumb: Where psychologists and behavioural biologists might meet. Behavioural Processes 69: 97–124.

 

Fitzhugh, K. 2007. Fact, theory, test and evolution. Zoologica Scripta preprint

 

Knox, E. B. 1998. The use of hierarchies as organizational models in systematics. Biol. J. Linn. Soc. 63: 1--49. or http://tinyurl.com/nuo3x3

 

Koonin, E. V. 2009. Darwinian evolution in the light of genomics. Nucleic Acids Research 37: 1011--1034. or http://tinyurl.com/kwrqes

 

Lecointre, G. & P. Deleporte. 2004. Total evidence requires exclusion of phylogenetically misleading data. Zoologica Scripta 34: 101--117.

 

Mayr, E. & W. J. Bock. 2002. Classifications and other ordering systems. J. Zool. Evol. Research 40: 169--194.

 

Mercier, H. & D. Sperber. 2010. Why do humans reason? Arguments for an argumentative theory.  Behavioral and Brain Sciences (in press).

 

Quine, W. V. 1966. On simple theories of a complex world. The Ways of Paradox. Random House, New York. [Note by RHZ: Quine’s cautions about simplicity also may apply to certain aspects of statistical phylogenetics, even when probabilities are high, given certain assumptions about the model, like independence of data.]

Also at: http://tinyurl.com/debto8

 

Paul, C. R. C. 1992. The recognition of ancestors. Historical Biology 6: 239--250. Harwood Academic Publishers.

 

Rachootin, S. P. & K. S. Thomson. 1981. Epigenetics, paleontology, and evolution. Pp. 181-193, in G. G. E. Scudder & J. L. Reveal (eds.), Evolution Today, Proceedings of the Second International Congress of Systematic and Evolutionary Biology. Hunt Institute for Botanical Documentation, Carneigie-Melon University, Pittsburgh, Pennsylvania.

or http://tinyurl.com/cp4ogd

 

Rieppel, O. 2010. The series, the network, and the tree: changing metaphors of order in nature. Biol. Philos. 25: 475--496.

 

Rieseberg, L. H. & L. Brouillet. 1994. Are many plant species paraphyletic? Taxon 43: 21–32. [Contributed by Carlos Aedo Pérez.]

 

Sneath, P. H. A. 1995. Thirty years of numerical taxonomy. Syst. Biol. 44: 281--298. [“Do we indeed wish to classify crocodiles with birds and away from lizards and snakes on phylogenetic grounds (Mayr, 1969)? Is it useful to ecologists, conservationists, teachers, and others to separate the ostrich and the rhea so extremely widely as the DNA evidence (Sibley et al., 1988) indicates? These issues again raise the question of the purpose of our classifications. Evolutionary systematics may have a revival if it addresses these questions.”]

 

Stuessy,  T. F. & C. König. 2008. Patrocladistic classification. Taxon 57: 594--601.

 

Wilkinson, L., R. Rosenthal, R. Abelson,  J. Cohen, L. Aiken, M. Appelbaum, G. Boodoo, D. A. Kenny, H. Kraemer, D. Rubin, B. Thompson, & H. Wainer. 1999. Statistical methods in psychology journals: guidelines and explanations. American Psychologist 54: 594–604.

 

Zander, R. H. 2006. The Pottiaceae s.str. as an evolutionary Lazarus taxon. J. Hattori Bot. Lab. 100: 581--602. Note: [This file is 990 kb, and is an image-based reprint, but is searchable within Adobe Acrobat Reader. A text version is at click here.]

 

Zander, R. H. 2007. When biodiversity study and systematics diverge. Biodiversity 8: 43-48.

OR

http://tinyurl.com/27fq62.

 

Zander, R. H. 2007. Nine easy steps for constructing reliable trees from published phylogenetic analyses. Ann. Missouri Bot. Gard. 94: 691-709. See also: Supplement.

 

Zander, R. H. 2007. Neutralist evolution and strict monophyly adversely affect biodiversity study. Anales del Jardin Botánica de Madrid. 64: 107-108.

 

Zander, R. H. 2007. Paraphyly and the species concept, a reply to Ebach & al. Taxon 56: 642-644.

 

Zander, R. H. 2007 [2008]. Future FNA volumes with APG influence. FNA Newsletter 21 (1--2): 3--4.

 

Zander, R. H. 2008. Evolutionary inferences from non-monophyly on molecular trees. Taxon 57: 1182--1188. or http://tinyurl.com/6frd9l

 

Zander, R. H. 2008. Statistical evaluation of the clade “Rhabdoweisiaceae.” Bryologist 111: 292--301.

 

Zander, R. H. 2009. Short Essays on Macroevolution in Classification. Res Botanica (a Missouri Botanical Garden Web Site), St. Louis. November 3, 2009. Pg. 1–29. http://www.mobot.org/plantscience/resbot/21EvSy.htm

 

Zander, R. H. 2009. Evolutionary analysis of five bryophyte families using virtual fossils. Anales del Jardín Botánico de Madrid 66: 119--134.  or http://tinyurl.com/yfa9xjs

 

Zander, R. H. 2010. Taxon mapping exemplifies punctuated equilibrium and atavistic saltation. Plant Syst. Evol. 286: 69--90. or http://tinyurl.com/32cw5ms

 

Zander, R. H. 2010 (2011).  Structuralism in phylogenetic systematics. Biological Theory 5: 383–394.