Molecular Systematic sand Evolution : Theoryand Practice

R. DeSalle G. Giribet W. Wheeler

List of contributors VII

General introduction IX

Part 1. Evolutionary analysis at different levels

Introduction to part 1 3

Andrew V.Z. BrowerCladistics, populations and species in geographical space : the cas eof Heliconius butterflies 5

Patrick M. O'GradySpecies to genera: phylogenetic inference in the HawaiianDrosophilidae 1 7

Scott E. Stanley and Joel L. CracraftHigher-level systematic analysis of birds : current problems andpossible solutions 3 1

John GatesyRelative quality of different systematic datasets for cetartiodactylmammals : assessments within a combined analysis framework 45

Michael F WhitingPhylogeny of the holometabolous insect orders based on 18 Sribosomal DNA: when bad things happen to good data 6 9

Gonzalo GiribetRelationships among metazoan phyla as inferred from 18S rRN Asequence data: a methodological approach 8 5

Part 2. Current problems in molecular systematic s

Introduction to part 2 10 5

Gonzalo Giribet, Ward C. Wheeler and Jyrki MuonaDNA multiple sequence alignments 107

Daniel A . Janies and Ward C. WheelerTheory and practice of parallel direct optimization 11 5

Mike Stee lSome statistical aspects of the maximum parsimony method 125

Gonzalo Giribet, Rob DeSalle and Ward C. Wheeler`Pluralism' and the aims of phylogenetic research 14 1

Paul Z. Goldstein and Andrew V.Z. Browe rMolecular systematics and the origin of species : new syntheses ormethodological introgressions? 14 7

Richard H. Baker and John GatesyIs morphology still relevant? 16 3

Ranhy Bang, Ted R . Schultz and Rob DeSalleDevelopment, homology and systematics 17 5

Part 3 . New approaches to molecular evolution

Introduction to part 3 18 9

Joe Thornto nGene family phylogenetics : tracing protein evolution on trees 19 1

Cheryl Y. Hayash iEvolution of spider silk proteins : insight from phylogenetic analyses . . 209

Alfried P. Vogler and Andy PurvisComparative methods and evolution 225

Michele K. Nishiguch iThe use of physiological data to corroborate cospeciation event sin symbiosis 237

Paul J. Plane tReexamining microbial evolution through the lens of horizonta ltransfer 247

References 27 1

Subject index 305