Brooks Parsimony Analysis: a valiant failure

Siddall, Mark E.; Perkins, Susan L.

doi:10.1111/j.1096-0031.2003.tb00388.x

Cited by 22 publications

(30 citation statements)

References 59 publications

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“…In addition, because one cannot specify the number and types of area duplications that will be needed a priori , some have been led to believe that the duplication convention in BPA is idiosyncratic rather than algorithmic (e.g. Ronquist, 2002; Siddall & Perkins, 2003).…”

Section: Introductionmentioning

confidence: 99%

PACT: an efficient and powerful algorithm for generating area cladograms

Wojcicki

Brooks

2005

Journal of Biogeography

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Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y− = Y(Y−’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies.

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Section: Introductionmentioning

confidence: 99%

PACT: an efficient and powerful algorithm for generating area cladograms

Wojcicki

Brooks

2005

Journal of Biogeography

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“…Although BPA has been criticized by some authors because it uses dispersal and vicariance explanations to fit taxa and areas to the same tree (e.g. Siddall & Perkins, 2003), other authors (e.g. Brooks et al.…”

Section: Introductionmentioning

confidence: 99%

Do the Oaxacan Highlands represent a natural biotic unit? A cladistic biogeographical test based on vertebrate taxa

Paniagua¹,

Morrone²

2009

Journal of Biogeography

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Aim We analysed the distributional patterns of six terrestrial vertebrate taxa from the Oaxacan Highlands (Sierra Mazateca, Nudo de Zempoaltépetl and Sierra de Juárez) through a cladistic biogeographical approach, in order to test their naturalness as a biotic unit. Location The Oaxacan Highlands, Mexico. Methods The cladistic biogeographical analysis was based on the area cladograms of the Pseudoeurycea bellii species group (Amphibia: Plethodontidae), the genus Chlorospingus (Aves: Thraupidae), the genera Microtus, Reithrodontomys and Habromys, and the Peromyscus aztecus species group (Mammalia: Rodentia). We obtained paralogy‐free subtrees, from which the components were coded in a data matrix for parsimony analysis. The data matrix was analysed with Nona through WinClada. Results The parsimony analysis resulted in a single general area cladogram in which areas were fragmented following the sequence Sierra Madre Occidental, Trans‐Mexican Volcanic Belt, Chiapas, Sierra Madre Oriental + Sierra Mazateca, Sierra Madre del Sur, Nudo de Zempoaltépetl and Sierra de Juárez. Main conclusions The general area cladogram shows that the Oaxacan Highlands do not constitute a natural unit. The Sierra Mazateca is the sister area to the Sierra Madre Oriental, whereas the Nudo de Zempoaltépetl and the Sierra de Juárez are closely related to the Sierra Madre del Sur. The events that might have caused these patterns include cycles of expansion and contraction of mountain pinyon, juniper and oak woodlands during the Pleistocene.

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“…Brooks parsimony analysis (BPA) received some criticism from Siddall and Perkins (2003) in the context of Dowling's (2002) admittedly flawed (Dowling, 2003) examination of BPA's utility. In addition to conflating BPA with its derivative (secondary or SBPA), which was not evaluated either by Dowling (2002) or by Siddall and Perkins (2003), Brooks et al. (2004, p. 43) level the quite serious charge that Siddall and Perkins (2003) “reinvented” aspects of coevolutionary methodology “without attribution”.…”

mentioning

confidence: 99%

“…In addition to conflating BPA with its derivative (secondary or SBPA), which was not evaluated either by Dowling (2002) or by Siddall and Perkins (2003), Brooks et al. (2004, p. 43) level the quite serious charge that Siddall and Perkins (2003) “reinvented” aspects of coevolutionary methodology “without attribution”. Herein I revisit some false accusations made by Brooks et al.…”

mentioning

confidence: 99%

“…Refutation: In fact, Siddall and Perkins (2003, p. 555) did attribute the duplications in secondary BPA to Brooks (1990) indicating that the “methodological and theoretical update had a slant toward biogeographic questions (Brooks, 1990) and introduced a duplication to accommodate homoplasy (secondary BPA) only for Type I BPA; it was not clear that this ‘fix’ could be applied to Type II BPA for comparison of two known topologies.”…”

mentioning

confidence: 99%

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