Testing the accuracy of TreeMap and Brooks parsimony analyses of coevolutionary patterns using artificial associations

Dowling, Ashley P. G.

doi:10.1016/s0748-3007(02)00007-5

Cited by 28 publications

(86 citation statements)

References 28 publications

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“…Phylogenetic information for hosts and parasites is the foundation for the discovery of the extent of coevolutionary processes, e.g., cospeciation, coadaptation, colonization, and extinction, involved in diversification and as determinants of the history and structure of faunal assemblages (Brooks, 1979(Brooks, , 1981; for pertinent reviews on methods see Brooks and McLennan, 1991Page, 2002;Dowling et al, 2003;Siddall and Perkins, 2003;Brooks et al, 2004). This integrative approach fosters a broader comprehension of biodiversity and is also strongly bolstered by inclusion of data regarding regional history and historical biogeography for recognized hosts of an assemblage (Hoberg, 1997a;Brooks and Hoberg, 2000).…”

Section: Parasite-host Coevolution and Historical Biogeographymentioning

confidence: 99%

Phylogeny for Species of Haemonchus (Nematoda: Trichostrongyloidea): Considerations of Their Evolutionary History and Global Biogeography Among Camelidae and Pecora (Artiodactyla)

Hoberg¹,

Lichtenfels²,

Gibbons³

2004

Journal of Parasitology

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Section: Parasite-host Coevolution and Historical Biogeographymentioning

confidence: 99%

Phylogeny for Species of Haemonchus (Nematoda: Trichostrongyloidea): Considerations of Their Evolutionary History and Global Biogeography Among Camelidae and Pecora (Artiodactyla)

Hoberg¹,

Lichtenfels²,

Gibbons³

2004

Journal of Parasitology

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“…The method is based on the ideas of Brooks (1981) to study coevolution between hosts and parasites. It is one of the most commonly used method in historical biogeography nowadays, including several applications in freshwater fishes (e.g., Matamoros et al, 2015), despite criticism in the literature (Cracraft, 1988;Platnick, 1988;Page, 1990aPage, , 1994aPage, , 1994bRonquist, Nylin, 1990;Nelson, Ladiges, 1991;Carpenter, 1992;van Welzen, 1992;Enghoff, 2000;Ebach, Edgecombe, 2001;Warren, Crother, 2001;Dowling, 2002;Ebach, Humphries, 2002;Siddall, 2004;Siddall, 2005;Siddall, Perkins, 2003;Parenti, 2007;Santos, 2007). In our analyses, the method was applied in two distinct forms, herein called BPA, its original version and BPA 0 , its transformed version.…”

Section: Introductionmentioning

confidence: 99%

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

2017

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Biogeography of Amazonian fishes (2,500 species in vastly disjunct lineages) is complex and has so far been approached only partially. Here, we tackle the problem on the basis of the largest database yet on geographical distribution and phylogenetic relationships of Amazonian fishes, including all information available. Distributions of 4,095 species (both Amazonian and outgroups) and 84 phylogenetic hypotheses (comprising 549 phylogenetically-informative nodes) were compiled, qualified and plotted onto 46 areas (29 Amazonian and 17 non-Amazonian). The database was analyzed with PAE, CADE, BPA and BPA 0 , yielding largely congruent results and indicating that biogeographic signal is detectable on multiple dimensions of fish distribution, from single species ranges to cladistic congruence. Agreement is especially pronounced in deeper components, such as Trans-Andean, Cis-Andean, Western Amazon and Orinoco basins. Results show that all major Amazonian tributaries, as well as the Amazon basin itself, are non-monophyletic and constitute hybrid sets of heterogeneous biotic partitions. Amazonian drainages should not be assumed a priori as historically cohesive areas, contrary to widespread practice. Our hypothesis allows reevaluation of broader issues in historical biogeography, such as the predictive power of biogeographic hypotheses, the vicariant/ dispersal duality, the significance of widely distributed taxa, and the need for temporal dimension in biogeographic patterns. A biogeografia dos peixes amazônicos (2.500 espécies de diferentes linhagens) é complexa e até agora foi abordada apenas parcialmente. Aqui abordamos o problema com base no maior banco de dados já feito sobre a distribuição geográfica e as relações filogenéticas dos peixes amazônicos, incluindo todas as informações disponíveis. A distribuição de 4.095 espécies (tanto amazônicas como de grupos-externos) e 84 hipóteses filogenéticas (que incluíam 549 nós filogeneticamente informativos) foram compiladas e qualificadas em 46 áreas (29 amazônicas e 17 não-amazônicas). O banco de dados foi analisado a partir das metodologias PAE, CADE, BPA e BPA0, resultando em topologias amplamente congruentes e indicando que o sinal biogeográfico é detectável em múltiplas dimensões, desde a simples distribuição de peixes até em congruência cladística. A concordância topológica é especialmente pronunciada em componentes mais profundos, como as bacias Trans-Andina, Cis-Andina, Amazonas Ocidental e Orinoco. Os resultados demonstram que todos os principais afluentes amazônicos, bem como a própria bacia amazônica, não são monofiléticos e constituem conjuntos híbridos formados a partir de parcelas bióticas heterogêneas. As drenagens amazônicas não devem ser consideradas a priori como áreas historicamente coesas, contrariamente à prática generalizada. Nossa hipótese permite a reavaliação de questões mais amplas na biogeografia histórica, como o poder preditivo de hipóteses biogeográficas, a dualidade vicariante/dispersão, significância de táxons amplamente distribuídos e a n...

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“…Presently there are several working methodologies (Brooks, 1981;Charleston, 1998;Page, 1994b;Ronquist, 1998) and with the exception of Brooks Parsimony Analysis (BPA) (Brooks, 1981) each has an associated software package for implementation (Charleston and Page, 2002;Page, 1995;Ronquist, 2000). Recently, Dowling (2002) confined his performance evaluation of cospeciation to the reconciled tree approach implemented in TreeMap 1.0 (Page, 1995) and BPA implemented with MacClade (Maddison and Maddison, 1992).…”

Section: Introductionmentioning

confidence: 99%

Brooks Parsimony Analysis: a valiant failure

Siddall

Perkins

2003

Cladistics

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A recent comparison of two methods for examining correlated host and parasite phylogenies, namely TreeMap 1.0 and Brooks Parsimony Analysis concluded that the latter method performed better and is to be preferred. Reevaluation of the examples contrived for that study demonstrates that the two methods were only compared on one kind of problem (widespread parasite) for which there is an easy fix for TreeMap 1.0. Other kinds of problems like host-switching among sister taxa or host-switching over great distances across a host tree befuddle BPA even as they are readily resolved parsimoniously by TreeMap 1.0. These difficulties, compounded with inaccurate counting of ad hoc hypotheses required by its solutions render BPA unsuitable for comparison of host and parasite phylogenies.

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Testing the accuracy of TreeMap and Brooks parsimony analyses of coevolutionary patterns using artificial associations

Cited by 28 publications

References 28 publications

Phylogeny for Species of Haemonchus (Nematoda: Trichostrongyloidea): Considerations of Their Evolutionary History and Global Biogeography Among Camelidae and Pecora (Artiodactyla)

Phylogeny for Species of Haemonchus (Nematoda: Trichostrongyloidea): Considerations of Their Evolutionary History and Global Biogeography Among Camelidae and Pecora (Artiodactyla)

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

Brooks Parsimony Analysis: a valiant failure

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