Incorporating Molecular Evolution into Phylogenetic Analysis, and a New Compilation of Conserved Polymerase Chain Reaction Primers for Animal Mitochondrial DNA Chris Simon, 1,2 Thomas R. Buckley, 3 Francesco Frati, 4 James B. Stewart, 5,6 and Andrew T. Beckenbach 5 1 Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269; email: chris.simon@uconn.edu 2 School of Biological Sciences, Victoria University of Wellington, Wellington 6014, New Zealand 3 Landcare Research, Auckland 1142, New Zealand; email: BuckleyT@landcareresearch.co.nz 4 Department of Evolutionary Biology, University of Siena, 53100 Siena, Italy; email: frati@unisi.it 5 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; email: jbs@alumni.sfu.ca, beckenba@sfu.ca 6 Department of Laboratory Medicine, Division of Metabolic Diseases, Karolinska Institutet, Norvum 141 86, Stockholm, Sweden Annu. Rev. Ecol. Evol. Syst. 2006. 37:545–79 First published online as a Review in Advance on August 16, 2006 The Annual Review of Ecology, Evolution, and Systematics is online at http://ecolsys.annualreviews.org This article’s doi: 10.1146/annurev.ecolsys.37.091305.110018 Copyright c  2006 by Annual Reviews. All rights reserved 1543-592X/06/1201-0545$20.00 Key Words among-site rate variation, covarion-like evolution, molecular clocks, mtDNA genomes, nodal support, PCR primers Abstract DNA data has been widely used in animal phylogenetic studies over the past 15 years. Here we review how these studies have used ad- vances in knowledge of molecular evolutionary processes to create more realistic models of evolution, evaluate the information content of data, test phylogenetic hypotheses, attach time to phylogenies, and understand the relative usefulness of mitochondrial and nuclear genes. We also provide a new compilation of conserved polymerase chain reaction (PCR) primers for mitochondrial genes that comple- ments our earlier compilation. 545 Annu. Rev. Ecol. Evol. Syst. 2006.37:545-579. Downloaded from arjournals.annualreviews.org by Prof Chris Simon on 11/10/06. For personal use only.