Fallacies of false attribution: the defense of BPA by Brooks, Dowling, van Veller, and Hoberg

Siddall, Mark E.

doi:10.1111/j.1096-0031.2004.00028.x

Cited by 7 publications

(10 citation statements)

References 15 publications

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“…2002; Brooks et al . 2004; Siddall 2004; Stevens 2004; Siddall 2005). We selected three of the most commonly used software packages, treemap 1.0 (Page 1995), treemap 2.02β (Charleston & Page 2002), and parafit (Legendre et al .…”

Section: Methodsmentioning

confidence: 99%

“…Several statistical methods have been developed over the past decade to test for evidence of cospeciation using phylogenies and DNA sequence data (Page 1994;Paterson & Banks 2001;Legendre et al 2002;Brooks et al 2004;Siddall 2004;Stevens 2004;Siddall 2005). We selected three of the most commonly used software packages, treemap 1.0 (Page 1995), treemap 2.02β (Charleston & Page 2002), and parafit (Legendre et al 2002), to test for congruence between phylogenies of the different fig wasp genera (and species-groups for Idarnes, Heterandrium, and Aepocerus).…”

Section: Cophylogenetic Analysesmentioning

confidence: 99%

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Host‐specificity and coevolution among pollinating and nonpollinating New World fig wasps

2007

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Figs {Ficus spp., Moraceae) and their pollinating wasps (Hymenoptera, Agaonidae, Chalcidoidea) constitute a classic example of an obligate plant-pollinator mutualism, and have become an ideal system for addressing questions on coevolution, speciation, and the maintenance of mutualisms. In addition to pollinating wasps, figs host several types of nonpollinating, parasitic wasps from a diverse array of Chalcid subfamilies with varied natural histories and ecological strategies (e.g. competitors, gallers, and parasitoids). Our findings further challenge the classical notion of strict-sense coevolution between figs and their associated wasps, and mirror conclusions from detailed molecular studies of other mutualisms that have revealed common patterns of diffuse coevolution and asymmetric specialization among the participants.

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Section: Methodsmentioning

confidence: 99%

Section: Cophylogenetic Analysesmentioning

confidence: 99%

Host‐specificity and coevolution among pollinating and nonpollinating New World fig wasps

2007

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“…This is evident, for instance, in some applications of Parsimony Analysis of Endemicity (PAE), Brooks Parsimony Analysis (BPA), and phylogeography. The problems begin with the conceptual framework: these methods quite often conduce to naïve and limited interpretations of the phenomena under study, in opposition to a truly Croizatian approach (for comments and criticisms on these subjects, see Brooks and van Veller 2003;Siddall and Perkins 2003;Siddall 2004Siddall , 2005Santos 2005Santos , 2007Santos and Amorim 2007;Garzón-Orduña et al 2008). Here we claim for biogeographical studies that seek robust hypotheses with ongoing higher support.…”

Section: Reciprocal Illuminationmentioning

confidence: 99%

On Reciprocal Illumination and Consilience in Biogeography

Santos

Capellari

2009

Evol Biol

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Biogeography deals with the combined analysis of the spatial and temporal components of the evolutionary process. To this purpose, biogeographical analysis should consider two extra steps: a reciprocal illumination step, and a consilience step. Even if the traditional challenges of biogeography were successfully handled, the obtained hypothesis is not necessarily meaningful in biogeographical terms--it needs continuous test in the light of external hypotheses. For this reason, a concept analogous to Hennig's reciprocal illumination is valuable, as well as a sort of biogeographical consilience in Whewell's sense. Firstly, through the search for different classes of evidence, information useful to improve the hypothesis can be accessed via reciprocal illumination. Following, a more general hypothesis would arise through a consilience process, when the hypothesis explains phenomena not contemplated during its construction, as the distribution of other taxa or the existence (or absence) of fossils. This procedure aims to evaluate the robustness of biogeographical hypotheses as scientific theories. Such theories are reliable descriptions of how life changes its form both in space and time, putting historical biogeography close to Croizat's statement of evolution as a three dimensional phenomenon.

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“…Secondary BPA was not employed by Dowling (2002) and so neither SBPA nor Treemap 2.0 were evaluated by Siddall and Perkins' (2003) critique of Dowling (2002). Accompanying this obfuscation, and in spite of Kluge's insistence on ''honesty and accuracy'' (Brooks et al, 2004, p. 45), Brooks et al (2004) fabricated additional disagreements (see Siddall, 2004) rather than bring any clarity to the debate. In the end though, Siddall and Perkins (2003) seem to have wrought an admission from Brooks et al (2004, p. 41) that in fact ''the original formulation of BPA was a valiant failure''.…”

mentioning

confidence: 99%

Bracing for another decade of deception: the promise of Secondary Brooks Parsimony Analysis

Siddall

2005

Cladistics

Self Cite

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Brooks Parsimony Analysis (BPA) and secondary Brooks Parsimony Analysis (SBPA) are found to be lacking an optimality criterion and, more generally, to be lacking the coherence of a research program. Published descriptions of the methodology are selfcontradictory regarding whether they can be used on a priori specified host trees and whether they can be used in host-parasite cospeciation at all. The application of missing data introduces unacknowledged additional problems. Rules for the a posteriori duplication of entities in secondary BPA and the concatenation of associate codes never are specified. Duplication and concatenation are found to be applied both capriciously and unparsimoniously. Claims that SBPA removes inclusive or-ing from the method are found to be false. The simplest application of the method is found to be superficially unanalytical; others introduce temporal difficulties or defy logical interpretation altogether.

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Fallacies of false attribution: the defense of BPA by Brooks, Dowling, van Veller, and Hoberg

Cited by 7 publications

References 15 publications

Host‐specificity and coevolution among pollinating and nonpollinating New World fig wasps

Host‐specificity and coevolution among pollinating and nonpollinating New World fig wasps

On Reciprocal Illumination and Consilience in Biogeography

Bracing for another decade of deception: the promise of Secondary Brooks Parsimony Analysis

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