Supplementary Data Sterner, Beckett* and Scott Lidgard. (Under revision) “Moving Past the Systematics Wars.” Journal of the History of Biology. *Corresponding author E-mail: [email protected] Table S1 Examples of additive coding procedures used in conjuction with both phenetic & cladistic methodologies. Methods Taxa & Characters Use of additive Publication coding phenetic hyphomycetes fungi; phenetic Kendrick & Proctor morphology 1964 phenetic helminthosporium phenetic Ibrahim & Threlfall fungi; morphology, 1966 pathogenicity, physiology, biochemistry phenetic Listeria, Streptococci, phenetic Davis et al. 1969 related bacteria; morphology, biochemistry, sediment phenetic Agrobacterium; phenetic Kesters et al. 1973 morphology, biochemistry phenetic fossil nummulitid phenetic Barnett 1974 foraminifera; morphology phenetic anaerobic bacteria; phenetic Holmberg & Nord morphology, 1975 biochemistry phenetic actinomycete bacteria; phenetic Goodfellow et al. morphology, 1979 biochemistry phenetic freshwater sediment phenetic Mallory & Sayler bacteria; morphology, 1984 biochemistry phenetic nemerteans; phenetic Sundberg 1985 morphology, ecology, development phenetic rhodococci bacteria; phenetic Goodfellow et al. morphology, 1990 biochemistry phenetic actinomycete bacteria; phenetic O'Donnell et al. 1993 morphology, biochemistry phenetic Bacillus bacteria; phenetic Nielsen et al. 1995 biochemistry, DNA base composition phenetic fossil crinoids; skeletal phenetic Deline & Ausich 2011 morphology phenetic fossil crinoids; skeletal phenetic Deline et al. 2012 morphology phenetic & cladistic pygopodid lizards; cladistic Kluge 1976 morphology phenetic & cladistic silverside fishes; cladistic Mickevich & Johnson morphology, alleles 1976 phenetic & cladistic multiple taxonomic phenetic & Mickevich 1978 groups; morphology, cladistic amino acid sequences, cytochrome, globin phenetic & cladistic tenebrionid beetles; phenetic & Doyen & Tschinkel morphology cladistic 1982 phenetic & cladistic pomatiopsid gastropods; cladistic Davis et al. 1984 morphology phenetic & cladistic decapod crustaceans; phenetic & Abele & Felgenhauer morphology, cladistic 1986 development phenetic & cladistic amphipod crustaceans; cladistic (with gap Conlan 1988 morphology coding) phenetic & cladistic agglutinating phenetic & Hohenegger 1990 foraminifera; cladistic morphology phenetic & cladistic multiple taxonomic phenetic & Sokal et al. 1992 groups; morphology cladistic phenetic & cladistic beans, rust fungi cladistic Eckenwalder & Heath parasitism; infection 2001 traits, gene sequences cladistic (primarily) myrtacean angiosperms; cladistic Landrum 1981 morphology cladistic prarie dogs; antigens cladistic McCullough et al. 1987 cladistic chironomid midges; cladistic Cranston & morphology Humphries 1988 cladistic signiphorid wasps; cladistic James 1988 morphology cladistic plectonemetid cladistic Sundberg 1989 nemerteans; morphology cladistic Chorizema cladistic Taylor & Crisp 1992 angiosperms; morphology cladistic velloziacean cladistic Menenes et al. 1993 angiosperms; morphology cladistic hemerobiid lacewings; cladistic Oswald 1993 morphology cladistic salmonid fishes; cladistic Stearley & Smith morphology 1993 cladistic hymenopteran insects; cladistic Heraty et al. 1994 morphology cladistic fossil & living seed cladistic Nixon et al. 1994 plants; morphology, gene sequences cladistic geometrid moths; cladistic Scoble 1994 morphology cladistic myrmicinid ants; cladistic Schultz & Meier 1995 morphology cladistic surgeonfishes; cladistic Guiasu & morphology Winterbottom 1998 cladistic platyninid beetles; cladistic Liebherr & morphology Zimmerman 1998 cladistic Anolis lizards; cladistic Poe 1998 morphology, allozymes, chromosomes, gene sequences cladistic echeneoid fishes; cladistic O'Toole 2002 morphology cladistic fossil sauropod cladistic Wilson 2002 dinosaurs; skeletal morphology cladistic butterflyfishes; cladistic Smith et al. 2003 morphology cladistic flower weevils & palm cladistic Franz 2004 angiosperm coevolution: morphology cladistic fossil & recent bats: cladistic Gunnell & Simmons morphology 2005 cladistic flower weevils: cladistic Franz 2006 morphology cladistic (and Lotus angiosperms; cladistic Degtjareva et al. 2006 Bayesian) morphology & gene sequences cladistic dictyopteran insects; cladistic Klass & Meier 2006 morphology, life history traits cladistic cypress angiosperms; cladistic Little 2006 morphology, biochemistry, reproductive traits, gene sequences cladistic Polistes wasps; cladistic Pickett et al. 2006 morphology, gene sequences cladistic unionid bivalves; cladistic Zanatta et al. 2007 allozymes cladistic harvestmen arachnids; cladistic De Bivort et al. 2010 morphology cladistic Anulocaulis cladistic Hernández-Ledesma angiosperms; et al. 2010 morphology cladistic entiminid weevils; cladistic Rosas et al. 2011 morphology, gene sequences cladistic (also embiopteran insects; cladistic Miller et al. 2012 Bayesian and morphology maximum likelihood) Table S2 Examples of non-additive coding procedures used in conjuction with both phenetic and cladistic methodologies. Methods Taxa & Characters Use of non- Publication additive coding phenetic helminthosporium phenetic Ibrahim & Threlfall fungi; morphology, 1966 pathogenicity, physiology, biochemistry phenetic fossil nummulitid phenetic Barnett 1974 foraminifera; morphology phenetic Opheodrys snakes; phenetic Cundall 1981 morphology phenetic freshwater sediment phenetic Mallory & Sayler bacteria; morphology, 1984 biochemistry phenetic nemerteans; phenetic Sundberg 1985 morphology, ecology, development phenetic & cladistic pomatiopsid gastropods; cladistic Davis et al. 1984 morphology cladistic auchenipterid catfishes; cladistic Curran 1989 morphology cladistic fossil Amalda cladistic Michaux 1989 gastropods; morphology cladistic Chorizema cladistic Taylor & Crisp 1992 angiosperms; morphology cladistic velloziacean cladistic Menenzes et al. 1993 angiosperms; morphology cladistic hemerobiid lacewings; cladistic Oswald 1993 morphology cladistic hymenopteran insects; cladistic Heraty et al. 1994 morphology cladistic geometrid moths; cladistic Scoble 1994 morphology cladistic tetragnathid spiders; cladistic Hormiga et al. 1995 morphology, web construction behavior cladistic myrmicinid ants; cladistic Schultz & Meier 1995 morphology cladistic cockroaches; cladistic Grandcolas 1996 morphology cladistic fossil proetoid trilobites; cladistic Edgecombe et al. skeletal morphology 1997 cladistic cockroaches; cladistic Grandcolas 1997 morphology, social behaviors cladistic euphorbacean cladistic Simmons & Hayden angiosperms; 1997 morphology cladistic orb-web spiders; cladistic Grandcolas 1998 morphology, web architectures, behaviors cladistic fossil envrinurid cladistic Edgecombe et al. trilobites; morphology 1998 cladistic surgeonfishes; cladistic Guiasu & morphology Winterbottom 1998 cladistic platyninid beetles; cladistic Liebherr & morphology Zimmerman 1998 cladistic Anolis lizards; cladistic Poe 1998 morphology, allozymes, chromosomes, gene sequences cladistic butterflyfishes; cladistic Smith et al. 2003 morphology cladistic flower weevils & palm cladistic Franz 2004 angiosperm coevolution: morphology cladistic flower weevils: cladistic Franz 2006 morphology cladistic (and Lotus angiosperms; cladistic Degtjareva et al. 2006 Bayesian) morphology & gene sequences cladistic cypress angiosperms; cladistic Little 2006 morphology, biochemistry, reproductive traits, gene sequences cladistic unionid bivalves; cladistic Zanatta et al. 2007 allozymes cladistic asilid flies; cladistic Dikow 2009 morphology, gene sequences cladistic Anulocaulis cladistic Hernández-Ledesma angiosperms; et al. 2010 morphology cladistic entiminid weevils; cladistic Rosas et al. 2011 morphology, gene sequences cladistic (also embiopteran insects; cladistic Miller et al. 2012 Bayesian and morphology maximum likelihood) Table S3 Examples of gap coding procedures used in conjuction with both phenetic & cladistic methodologies. Once data clusters have been separated by gaps, they are typically transformed to binary state characters by additive coding. Methods Taxa & Characters Use of gap coding Publication phenetic eucalyptus phenetic Ladiges et al. 1984 angiosperms; mophology phenetic & cladistic silverside fishes; phenetic & cladistic Mickevich & Johnson morphology, alleles 1976 phenetic & cladistic ants; morphology, phenetic & cladistic Ward 1985 allozymes phenetic & cladistic eucalyptus phenetic & cladistic Ladiges & Humphries angiosperms; 1986 mophology phenetic & cladistic geckos; morphology, phenetic & cladistic Thorpe 1986 biochemistry phenetic & cladistic barley angiosperms; cladistic (generalized Baum & Bailey 1988 morphology gap coding) phenetic & cladistic amphipod crustaceans; cladistic Conlan 1988 morphology phenetic & cladistic chironomid midges; cladistic (generalized Cranston & morphology & life gap coding) Humphries 1988 history traits phenetic & cladistic chipmunks; cladistic (modified Sullivan & Petersen morphology, generalized gap 1988 allozymes coding) phenetic & cladistic Eucalyptus cladistic Ladiges et al. 1989 (ordination, not angiosperms; trees) morphology phenetic & cladistic caper angiosperms; cladistic Vezey & Skvarla pollen morphology 1990 phenetic & cladistic cyprinid fishes; cladistic Mayden et al. 1991 morphology phenetic & cladistic lophiiform fishes; cladistic (generalized Leslie & Grant 1994 morphology gap coding) phenetic & cladistic Daviesia angiosperms; cladistic (generalized Chandler & Crisp morphology