Total Evidence, Consensus, and Bat Phylogeny: A Distance-Based Approach

Lapointe, François‐Joseph; Kirsch, John A. W.; Hutcheon, James M.

doi:10.1006/mpev.1998.0561

Cited by 31 publications

(39 citation statements)

References 40 publications

(43 reference statements)

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“…However, it is worth repeating once more that any other data can be treated as distances and thus be combined in a coherent fashion. In previous papers, we have shown that matrices of character-state data converted to distances can be combined with each other, or with other distance matrices (Lapointe et al 1999). When this is done, the results of total-evidence and consensus analyses seldom differ much, as we found here.…”

Section: Methodological Considerationssupporting

confidence: 65%

“…In our application of the distance-based approach, DNA-hybridisation matrices were validated and combined (see also Kirsch et al 1997;Lapointe 1998a;Lapointe et al 1999). These pairwise comparisons (like serological data) are readily available in the form of distance matrices and can be directly treated as such.…”

Section: Methodological Considerationsmentioning

confidence: 99%

“…2. Flowchart illustrating the various steps of the combination procedure for distance and pathlength matrices (Lapointe et al 1999). Given a series of input distance matrices, SUTALL is used to combine them.…”

Section: Data and Total-evidence Analysismentioning

confidence: 99%

“…Would it be better to treat these different data sets independently before combining the resulting trees or should all data be combined prior to phylogenetic reconstruction? Proponents of either side of the socalled total-evidence versus consensus debate have raised a series of philosophical and empirical arguments to demonstrate the superiority of their approach (Kluge 1989;Barrett et al 1991;de Queiroz 1993;Eernisse and Kluge 1993;Kluge and Wolf 1993;Chippindale and Wiens 1994;Huelsenbeck et al 1994;Wiens and Chippindale 1994;de Queiroz et al 1995;Miyamoto and Fitch 1995;Huelsenbeck et al 1996;Nixon and Carpenter 1996;Page 1996a;Lapointe et al 1999). A third position has emerged recently which claims that data should sometimes be combined, and sometimes not, depending on the outcome of tests for compatibility (Bull et al 1993;Rodrigo et al 1993;Farris et al 1995;Huelsenbeck and Bull 1996).…”

mentioning

confidence: 99%

“…A third position has emerged recently which claims that data should sometimes be combined, and sometimes not, depending on the outcome of tests for compatibility (Bull et al 1993;Rodrigo et al 1993;Farris et al 1995;Huelsenbeck and Bull 1996). Interestingly, Lapointe et al (1999) have shown that data and trees (bearing identical, inclusive, or overlapping sets of taxa) can be combined in a coherent fashion, when treated as distances. Thus, the debate on whether one should combine or not combine data becomes one about how to combine the ever-increasing amount of data and their corresponding phylogenies.…”

mentioning

confidence: 99%

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Construction And Verification Of A Large Phylogeny Of Marsupials

Lapointe¹,

Kirsch²

2001

Aust. Mammalogy

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Much of the controversy over marsupial phylogeny at higher-categorical levels stems from the piecemeal nature of the contributing studies or the paucity of taxonomic representation in many of them. Yet the problems of constructing large phylogenies are manyfold, involving the initial generation of the data as well as their efficient analysis. Often unaddressed, also, is the need to validate extremely large data sets and trees. Many of these problems can be ameliorated by treating the data as distances (or generating distances directly). We show that, contrary to the assertions of many protagonists in the total-evidence versus consensus debate, the validated data and pathlength (tree) matrices usually give very similar results, although a few additional unstable nodes may be found when the results of internal and external validations are themselves combined in a global-congruence test. Here we illustrate our protocols with a 109-taxon data set, representing combination of marsupial DNA-hybridisation data with similar information on a series of outgroups. Phylogenetically, the results affirm the marsupial groupings we have previously found, and suggest but do not unambiguously support a nearer relationship of monotremes than placentals to marsupials. This paper represents the first attempt to validate the tree of 101 marsupials presented earlier.

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Section: Methodological Considerationssupporting

confidence: 65%

Section: Methodological Considerationsmentioning

confidence: 99%

Section: Data and Total-evidence Analysismentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Construction And Verification Of A Large Phylogeny Of Marsupials

Lapointe¹,

Kirsch²

2001

Aust. Mammalogy

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A comprehensive phylogeny of extant horses, rhinos and tapirs (Perissodactyla) through data combination

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Bininda‐Emonds

2009

Zool. Reihe

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We present the first phylogenies to include all extant species of Perissodactyla (odd‐toed hoofed mammals) and the recently extinct quagga (Equus quagga). Two independent data sets were examined; one based on multiple genes and analyzed using both supertree and supermatrix approaches, and a second being a supertree constructed from trees collected from the scientific literature. All methods broadly confirmed the traditional view of perissodactyl interfamily relationships, with Equidae (= Hippomorpha) forming the sister‐group to the clade Rhinocerotidae + Tapiridae (= Ceratomorpha). The contentious affinity of the Sumatran rhino (Dicerorhinus sumatrensis) is resolved in favour of it forming a clade with the two Asian rhinos (genus Rhinoceros). However, no data set or tree‐building method managed to satisfactorily resolve the historically contentious relationships among extant equids; little agreement appears among the different trees for this group. In general, both the supertree and supermatrix approaches performed equally well, but both were hindered by the current paucity of data (e.g. no single gene has been sequenced to date for all 17 species) and its patchy distribution within Equidae. More data, both molecular and morphological, are required for all species to resolve the poorly supported nodes. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

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Everything You always wanted to Know about the Average Consensus, and More

Lapointe¹,

Levasseur²

2004

Computational Biology

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Total Evidence, Consensus, and Bat Phylogeny: A Distance-Based Approach

Cited by 31 publications

References 40 publications

Construction And Verification Of A Large Phylogeny Of Marsupials

Construction And Verification Of A Large Phylogeny Of Marsupials

A comprehensive phylogeny of extant horses, rhinos and tapirs (Perissodactyla) through data combination

Everything You always wanted to Know about the Average Consensus, and More

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