Matrix Representation with Parsimony, Taxonomic Congruence, and Total Evidence

—Many biogeographic problems are tested on phylogenetic trees. Typically, the uncertainty in the phylogeny is not accommodated when investigating the biogeography of the organisms. Here we present a method that accommodates uncertainty in the phylogenetic trees. Moreover, we describe a simple method for examining the support for competing biogeographic scenarios. We illustrate the method using mitochondrial DNA sequences sampled from modern humans. The geographic origin of modern human mtDNA is inferred to be in Africa, although support for this hypothesis was ambiguous for data from an early paper. Debate on the origin of anatomically modern humans has concentrated on two competing hypotheses. The “out-of-Africa hypothesis” argues that modern humans originated in Africa and then migrated to other parts of the world, replacing other species of Homo as they spread (Stringer and McKie, 1996). The “regional continuity hypothesis,” on the other hand, argues LAPOINTE, F. J., AND G. CUCUMEL. 1997. The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst. Biol. 46:306–312. LIU, R. F., M. M. MIYAMOTO, N. P. FREIRE, P. Q. ONG , M. R. TENNANT, T. S. YOUNG, AND K. F. GUGEL. 2001. Molecular and morphological supertrees for eutherian (placental) mammals. Science 291:1786–1789. PURVIS, A. 1995a. A composite estimate of primate phylogeny. Philos. Trans. R. Soc. London B 348:405–421. PURVIS, A. 1995b. A modiŽcation to Baum and Ragan’s method for combining phylogenetic trees. Syst. Biol. 44:251–255. RAGAN, M. A. 1992. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1:53–58. SEMPLE, C., AND M. STEEL. 2000. A supertree method for rooted trees. Discrete Appl. Math. 105:147–158. STRIMMER, K., AND A. VON HAESELER. 1996. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964– 969. WILKINSON, M., J. L. THORLEY, D. T. J. LITTLEWOOD, AND R. A. BRAY. 2001. Towards a phylogenetic supertree for the Platyhelminthes? Pages 292–301 in Interrelationships of the Platyhelminthes (D. T. J. Littlewood and R. A. Bray, eds.). Chapman-Hall, London. Received 24 April 2001; accepted 2 September 2001 Associate Editor: M. Sanderson for a single species of Homo widely spread throughout the Old World, with populations connected through gene ow (Wolpoff and Caspari, 1997). Anatomically modern humans are then thought to have originated over a wide geographic area and after any migration event from Africa. The usual approach taken in a molecular test of these competing hypotheses is to collect DNA D ow naded rom http/academ ic.p.com /sysbio/articlact/51/1/151/1631316 by gest on 01 Feruary 2019