Construction And Verification Of A Large Phylogeny Of Marsupials

Abstract

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.

A morphological analysis of marsupial mammal higher‐level phylogenetic relationships

“…Colgan (1999) analyzed phosphoglycerate kinase DNA sequences and found Dromiciops together with other taxa either at the base of an unresolved Australasian radiation (neighbor joining) or at the base of a poorly resolved marsupial tree (maximum parsimony). A variety of studies, including DNA-DNA hybridization (Kirsch et al, 1991Lapointe and Kirsch, 2001), most analyses of mitochondrial DNA sequences (12S rRNA, valine tRNA, 16S rRNA, and cytochrome b; Burk et al, 1999), and an analysis of nuclear DNA sequences from exon 1 of IRBP (Jansa and Voss, 2000) favor a close relationship of Dromiciops with Diprotodontia, a group consisting of kangaroos, wallabies, koalas, wombats, the various groups of possums, cuscuses, and brushtails. A recent analysis of several nuclear genes (apolipoprotein V gene, breast and ovarian cancer susceptibility gene 1, recombination activating gene 1, IRBP gene, and vWF gene) employing different methods including maximum parsimony yielded a tree where Dromiciops was the sister group of the Australasian radiation (Amrine-Madsen et al, in press).…”

Some Desiderata for Liberal Supertrees

“…Several workers have explored a range of weighting regimes to explore the robustness of real supertrees (e.g. Bininda-Emonds et al 1999;Lapointe and Kirsch, 2001;Liu et al, 2001;Purvis, 1995b). Alternative weighting schemes that reverse known or suspected biases might be particularly useful when methods that are known to be biased are used.…”