A penalty of using anonymous dominant markers (AFLPs, ISSRs,推荐.pdfVIP

Molecular Phylogenetics and Evolution 42 (2007) 528–542 /locate/ympev A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference Mark P. Simmons a,¤, Li-Bing Zhang a,1, Colleen T. Webb a, Kai Müller b a Department of Biology, Colorado State University, Fort Collins, CO 80523, USA b Nees-Institut für Biodiversität der PX anzen, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 170, Bonn, D-53115, Germany Received 18 March 2006; revised 30 June 2006; accepted 13 August 2006 Available online 22 August 2006 Abstract AFLPs (and to a lesser extent ISSRs and RAPDs) are increasingly being used for phylogenetic inference among closely related species. Presence/absence characters for each AFLP allele treat all absences as homologous to one another. With three or more alleles, terminals are grouped by their shared absence of alleles in character-based phylogenetic-inference methods in a manner that is not redundant with their shared presence of an alternative allele. We conducted simulations to quantify how severe the negative eVect of using presence/ absence characters of individual bands is for phylogenetic inference relative to standard multistate characters. We examined alternative tree topologies, relative branch lengths, numbers of characters, rates of evolution, and numbers of alternative alleles, using both parsi- mony and Nei-and-Li distance analyses. Multistate parsimony generally outperformed presence/absence parsimony, which in turn out- performed Nei-and-Li distance. Increasing the character-state space (i.e., the numb