On Consensus, Collapsibility, and Clade Concordance

Abstract

-Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter-cladogram character conflict for all characters among a set of cladograms.

Sistemática, filogenia e distribuição geográfica das espécies sul-americanas de Centris (Paracentris) Cameron, 1903 e de Centris (Penthemisia) Moure, 1950, incluindo uma análise filogenética do "grupo Centris" sensu Ayala, 1998 (Hymenoptera, Apoidea, Centridini)

“…A diferença no número de cladogramas, em relação ao obtido com o NONA, deve-se ao fato de que o PAUP (versão 3.1) retém alguns cladogramas com resoluções de politomias não suportadas pelos caracteres, o que não ocorre no NONA (NIXON & CARPENTER 1996). Mas, isso não afeta os consensos estritos, que são idênticos nas duas análises (Fig.…”

Phylogeny, Biogeography, and Processes of Molecular Differentiation in Quercus Subgenus Quercus (Fagaceae)

“…Using PAUP 3.1.1, unweighted parsimony analysis of these 80 phylogenetically informative sites recovered 15 minimum-length trees of 102 steps. In contrast, PAUP*, when set to ''amb-,'' and NONA recovered only 1 unambiguously supported tree (see Nixon and Carpenter, 1996a). This tree identified seven cpDNA lineages within subgenus Quercus (Fig.…”

A Phylogenetic Analysis of Ant Morphology (Hymenoptera: Formicidae) with Special Reference to the Poneromorph Subfamilies

“…In order to explore further potential islands of parsimonious trees (Maddison, 1991) and achieve total collapsibility of the most parsimonious trees (Nixon and Carpenter, 1996a), the final pool of trees resulting from the ratchet runs was resubmitted to NONA using the commands ''hold 50000''; ''amb 5''; ''poly -''; and ''max*'' (i.e., consider trees as dichotomous and keep trees with ambiguous support; perform a round of TBR swapping hold up to 50,000 trees in memory), followed by ''amb-'' ''poly 5''; and ''best'' (i.e., treat trees as polytomous and discard trees with ambiguous support, keep trees that are topologically different and of highest fit).…”