The Logical Basis of Phylogenetic Analysis

By J. Farris. 2004

528 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/03a43b127806cfcabf961da3c49f57c1e19b3761

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Citations in the corpus

TNT version 1.5, including a full implementation of phylogenetic morphometrics (2016, background): “In other types of characters, evaluating a tree requires identifying the optimal ancestral conditions, those conditions that minimize the amount of difference across all branches of the tree (e.g. Farris, 1983, 2008).”
Classification of basal Cucujoidea (Coleoptera : Polyphaga): cladistic analysis, keys and review of new families (2005, methodology): “To date there is no completely satisfactory statistical method to determine confidence intervals for branches on a cladogram (see Sanderson 1995), though for parsimony analyses the co-occurrence of minimised character state changes on branches are acceptable as adequate and testable hypotheses for d”
Phylogenetics of Sigmodontinae (Rodentia, Muroidea, Cricetidae), with special reference to the akodont group, and with additional comments on historical biogeography (2003, methodology): “Since species diversifications are necessarily unique events that have already occurred (Kluge, 2002), no probabilistic approach was used to reconstruct them; aligned sequences were subjected to maximum parsimony analysis (MP; Farris, 1982; Kluge and Farris, 1969).”
Morphological phylogeny of cobweb spiders and their relatives (Araneae, Araneoidea, Theridiidae) (2004, unknown): “Farris JS. 1983.”
Parsimony, likelihood, and simplicity (2003, background): “Farris (1983) did connect homoplasies with the (philosophical) principle of parsimony in a very specific sense: they both concern disregarding nonconforming observations for the sole purpose of protecting a theory from rejection.”
Weighting against homoplasy improves phylogenetic analysis of morphological data sets (2008, background): “But if the support for arguments against weighting is supposed to come from Farris (1983), then there is no support at all: Farris (1983, p. 1011) had been (as noted by Goloboff, 1993, 1995) explicit that parsimony is not equivalent to equal weights, and that step counts must be weighted step…”
Applying the Bootstrap in Phylogeny Reconstruction (2003, methodology): “…the support for cladistic hypotheses is evidenced by the degree of corroboration (cf. Hennig, 1966; Wiley, 1975; Platnick and Gaffney, 1977, 1978; Farris, 1983; Kluge, 1997, 1999) and that the application of a statistical method requires the specification of an underlying probability…”
Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae) (2009, methodology): “…Magnolia Press · 33LASIOGLOSSUM (DIALICTUS) TEGULARE SPECIES GROUP i) The use of a neighbour-joining algorithm to provide specimen identification ignores several decades of study that demonstrate the superiority of phylogenetic over phenetic philosophical criteria (Farris 1977, 1983; Hull 1988).”
Stochastic mapping of morphological characters. (2003, background): “Changes in excess of the parsimonious reconstructions should not be considered ad hoc as has been argued by Farris (1983); as shown here, such changes are quite probable under simple yet reasonable models of evolution.”