supplementary data · supplementary data sterner, beckett* and scott lidgard. (under revision)...

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

coding Publication

phenetic hyphomycetes fungi; morphology

phenetic Kendrick & Proctor 1964

phenetic helminthosporium fungi; morphology, pathogenicity, physiology, biochemistry

phenetic Ibrahim & Threlfall 1966

phenetic Listeria, Streptococci, related bacteria; morphology, biochemistry, sediment

phenetic Davis et al. 1969

phenetic Agrobacterium; morphology, biochemistry

phenetic Kesters et al. 1973

phenetic fossil nummulitid foraminifera; morphology

phenetic Barnett 1974

phenetic anaerobic bacteria; morphology, biochemistry

phenetic Holmberg & Nord 1975

phenetic actinomycete bacteria; morphology, biochemistry

phenetic Goodfellow et al. 1979

phenetic freshwater sediment bacteria; morphology, biochemistry

phenetic Mallory & Sayler 1984

phenetic nemerteans; morphology, ecology, development

phenetic Sundberg 1985

phenetic rhodococci bacteria; morphology, biochemistry

phenetic Goodfellow et al. 1990

phenetic actinomycete bacteria; morphology, biochemistry

phenetic O'Donnell et al. 1993

phenetic Bacillus bacteria; biochemistry, DNA base composition

phenetic Nielsen et al. 1995

phenetic fossil crinoids; skeletal morphology

phenetic Deline & Ausich 2011

phenetic fossil crinoids; skeletal morphology

phenetic Deline et al. 2012

phenetic & cladistic pygopodid lizards; morphology

cladistic Kluge 1976

phenetic & cladistic silverside fishes; morphology, alleles

cladistic Mickevich & Johnson 1976

phenetic & cladistic multiple taxonomic groups; morphology, amino acid sequences, cytochrome, globin

phenetic & cladistic

Mickevich 1978

phenetic & cladistic tenebrionid beetles; morphology


Doyen & Tschinkel 1982

phenetic & cladistic pomatiopsid gastropods; morphology

cladistic Davis et al. 1984

phenetic & cladistic decapod crustaceans; morphology, development


Abele & Felgenhauer 1986

phenetic & cladistic amphipod crustaceans; morphology

cladistic (with gap coding)

Conlan 1988

phenetic & cladistic agglutinating foraminifera; morphology


Hohenegger 1990

phenetic & cladistic multiple taxonomic groups; morphology


Sokal et al. 1992

phenetic & cladistic beans, rust fungi parasitism; infection traits, gene sequences

cladistic Eckenwalder & Heath 2001

cladistic (primarily) myrtacean angiosperms; morphology

cladistic Landrum 1981

cladistic prarie dogs; antigens cladistic McCullough et al. 1987

cladistic chironomid midges; morphology

cladistic Cranston & Humphries 1988

cladistic signiphorid wasps; morphology

cladistic James 1988

cladistic plectonemetid nemerteans; morphology

cladistic Sundberg 1989

cladistic Chorizema angiosperms; morphology

cladistic Taylor & Crisp 1992

cladistic velloziacean angiosperms; morphology

cladistic Menenes et al. 1993

cladistic hemerobiid lacewings; morphology

cladistic Oswald 1993

cladistic salmonid fishes; morphology

cladistic Stearley & Smith 1993

cladistic hymenopteran insects; morphology

cladistic Heraty et al. 1994

cladistic fossil & living seed plants; morphology, gene sequences

cladistic Nixon et al. 1994

cladistic geometrid moths; morphology

cladistic Scoble 1994

cladistic myrmicinid ants; morphology

cladistic Schultz & Meier 1995

cladistic surgeonfishes; morphology

cladistic Guiasu & Winterbottom 1998

cladistic platyninid beetles; morphology

cladistic Liebherr & Zimmerman 1998

cladistic Anolis lizards; morphology, allozymes, chromosomes, gene sequences

cladistic Poe 1998

cladistic echeneoid fishes; morphology

cladistic O'Toole 2002

cladistic fossil sauropod dinosaurs; skeletal morphology

cladistic Wilson 2002

cladistic butterflyfishes; morphology

cladistic Smith et al. 2003

cladistic flower weevils & palm angiosperm coevolution: morphology

cladistic Franz 2004

cladistic fossil & recent bats: morphology

cladistic Gunnell & Simmons 2005

cladistic flower weevils: morphology


cladistic (and Bayesian)

Lotus angiosperms; morphology & gene sequences

cladistic Degtjareva et al. 2006

cladistic dictyopteran insects; morphology, life history traits

cladistic Klass & Meier 2006

cladistic cypress angiosperms; morphology, biochemistry, reproductive traits, gene sequences

cladistic Little 2006

cladistic Polistes wasps; morphology, gene sequences

cladistic Pickett et al. 2006

cladistic unionid bivalves; allozymes

cladistic Zanatta et al. 2007

cladistic harvestmen arachnids; morphology

cladistic De Bivort et al. 2010

cladistic Anulocaulis angiosperms; morphology

cladistic Hernández-Ledesma et al. 2010

cladistic entiminid weevils; morphology, gene sequences

cladistic Rosas et al. 2011

cladistic (also Bayesian and maximum likelihood)

embiopteran insects; morphology

cladistic Miller et al. 2012

Table S2 Examples of non-additive coding procedures used in conjuction with both phenetic and cladistic methodologies. Methods Taxa & Characters Use of non-

additive coding Publication

phenetic helminthosporium fungi; morphology, pathogenicity, physiology, biochemistry

phenetic Ibrahim & Threlfall 1966

phenetic fossil nummulitid foraminifera; morphology

phenetic Barnett 1974

phenetic Opheodrys snakes; morphology

phenetic Cundall 1981

phenetic freshwater sediment bacteria; morphology, biochemistry

phenetic Mallory & Sayler 1984

phenetic nemerteans; morphology, ecology, development

phenetic Sundberg 1985

phenetic & cladistic pomatiopsid gastropods; morphology

cladistic Davis et al. 1984

cladistic auchenipterid catfishes; morphology

cladistic Curran 1989

cladistic fossil Amalda gastropods; morphology

cladistic Michaux 1989

cladistic Chorizema angiosperms; morphology

cladistic Taylor & Crisp 1992

cladistic velloziacean angiosperms; morphology

cladistic Menenzes et al. 1993

cladistic hemerobiid lacewings; morphology

cladistic Oswald 1993

cladistic hymenopteran insects; morphology

cladistic Heraty et al. 1994

cladistic geometrid moths; morphology

cladistic Scoble 1994

cladistic tetragnathid spiders; morphology, web construction behavior

cladistic Hormiga et al. 1995

cladistic myrmicinid ants; morphology

cladistic Schultz & Meier 1995

cladistic cockroaches; morphology

cladistic Grandcolas 1996

cladistic fossil proetoid trilobites; skeletal morphology

cladistic Edgecombe et al. 1997

cladistic cockroaches; morphology, social behaviors


cladistic euphorbacean angiosperms; morphology

cladistic Simmons & Hayden 1997

cladistic orb-web spiders; morphology, web architectures, behaviors


cladistic fossil envrinurid trilobites; morphology


cladistic surgeonfishes; morphology

cladistic Guiasu & Winterbottom 1998

cladistic platyninid beetles; morphology

cladistic Liebherr & Zimmerman 1998


cladistic Poe 1998

cladistic butterflyfishes; morphology

cladistic Smith et al. 2003

cladistic flower weevils & palm angiosperm coevolution: morphology


cladistic flower weevils: morphology



Lotus angiosperms; morphology & gene sequences

cladistic Degtjareva et al. 2006

cladistic cypress angiosperms; morphology, biochemistry, reproductive traits, gene sequences

cladistic Little 2006

cladistic unionid bivalves; allozymes

cladistic Zanatta et al. 2007

cladistic asilid flies; morphology, gene sequences

cladistic Dikow 2009

cladistic Anulocaulis angiosperms; morphology

cladistic Hernández-Ledesma et al. 2010

cladistic entiminid weevils; morphology, gene sequences

cladistic Rosas et al. 2011


embiopteran insects; morphology

cladistic Miller et al. 2012

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

angiosperms; mophology

phenetic Ladiges et al. 1984

phenetic & cladistic silverside fishes; morphology, alleles

phenetic & cladistic Mickevich & Johnson 1976

phenetic & cladistic ants; morphology, allozymes

phenetic & cladistic Ward 1985

phenetic & cladistic eucalyptus angiosperms; mophology

phenetic & cladistic Ladiges & Humphries 1986

phenetic & cladistic geckos; morphology, biochemistry

phenetic & cladistic Thorpe 1986

phenetic & cladistic barley angiosperms; morphology

cladistic (generalized gap coding)

Baum & Bailey 1988

phenetic & cladistic amphipod crustaceans; morphology

cladistic Conlan 1988

phenetic & cladistic chironomid midges; morphology & life history traits


Cranston & Humphries 1988

phenetic & cladistic chipmunks; morphology, allozymes

cladistic (modified generalized gap coding)

Sullivan & Petersen 1988

phenetic & cladistic (ordination, not trees)

Eucalyptus angiosperms; morphology

cladistic Ladiges et al. 1989

phenetic & cladistic caper angiosperms; pollen morphology

cladistic Vezey & Skvarla 1990

phenetic & cladistic cyprinid fishes; morphology

cladistic Mayden et al. 1991

phenetic & cladistic lophiiform fishes; morphology


Leslie & Grant 1994

phenetic & cladistic Daviesia angiosperms; morphology


Chandler & Crisp 1998

phenetic & cladistic gobiid fishes; morphology, karyotypes

cladistic Simonovic 1999

phenetic & cladistic cichlid fishes; morphology, gene sequences

cladistic (modified & step matrix gap weighting)

Říčan & Kullander 2006

phenetic & cladistic hominoids; skeletal morphology

cladistic Bjarnason et al. 2011

phenetic & cladistic fossil bryozoans; skeletal morphology

cladistic Pachut & Anstey 2013

cladistic grass snakes; morphology

cladistic Thorpe 1984

cladistic multiple taxonomic groups; morphology

cladistic (also generalized gap coding)

Archie 1985

cladistic Angophora angiosperms; morphology


Thiele & Ladiges 1988

cladistic eucalyptus angiosperms; morphology


Chappill 1989

cladistic fusilier fishes; morphology

cladistic (modified generalized gap coding)

Carpenter 1990

cladistic plethodontid salamanders; morphology

cladistic Collins-Rainboth & Buth 1990

cladistic rodent-nematode coevolution; morphology, karyotypes, allozymes


Gardner 1991

cladistic Anomochilus snakes; morphology

cladistic Cundall et al. 1993

cladistic humans; dental morphology

cladistic (gap weighting)

Stringer et al. 1997



Poe 1998

cladistic cephalobinid nematodes: morphology

cladistic Stock et al. 2001

cladistic acanthus angiosperms; morphology

cladistic Carine & Scotland 2002

cladistic Macromeria angiosperms; morphology


Boyd 2003

cladistic gastropods; embryonic cell lineage traits

cladistic Lindberg & Guralnick 2003

cladistic Asteracea angiosperms;

cladistic Pelser et al. 2004

morphology, gene sequences

cladistic bats; skeletal morphology

cladistic Bogdanowicz et al. 2005

cladistic fossil trilobites; skeletal morphology

cladistic Sundberg 2008

cladistic harvestmen arachnids; morphology

cladistic De Bivort et al. 2010

cladistic strabomantid frogs; mating call acoustics, gene sequences

cladistic Goicoechea et al. 2010


Phytoseiulus mites; morphology, gene sequences

cladistic Kanouh et al. 2010

cladistic Pacifigorgia octocorals; morphology


Vargas et al. 2010

cladistic mugilid fishes; skeletal morphology

cladistic Antović 2013

cladistic (and maximum likelihood)

Araceae angiosperms; gene sequences, morphology, pollinators, interaction types

cladistic Chartier et al. 2014

cladistic fossil synapsid vertebrates; skeletal morphology


Romano & Nicosa 2015

Table S4 Examples of Adams consensus tree procedures used in conjuction with both phenetic and cladistic methodologies. Methods Taxa & Characters Use of Adams

consensus tree(s) Publication

phenetic Crataegus angiosperms; morphology

phenetic Smith & Phipps 1984

phenetic & cladistic hemipteran insects; morphology

cladistic Schuh & Polhemus 1980


cladistic Colless 1981


phenetic & cladistic Sokal & Rohlf 1981

phenetic & cladistic tenebrionid beetles; morphology

phenetic & cladistic Doyen & Tschinkel 1982

phenetic & cladistic Solanum angiosperms; morphology, allozymes

phenetic & cladistic Whalen & Caruso 1983

phenetic & cladistic eupomphinid beetles; morphology, behavioral traits

phenetic Pinto 1984

phenetic & cladistic Rhytidoponera ants; morphology

phenetic & cladistic Ward 1985

phenetic & cladistic hamamelid angiosperms; pollen morphology

cladistic Zavada & Dilcher 1986

phenetic & cladistic Lagascea angiosperms; morphology

phenetic & cladistic Steussy 1987

phenetic & cladistic chironomid midges; morphology & life history traits

cladistic Cranston & Humphries 1988

phenetic & cladistic (ordination, not trees)

Eucalyptus angiosperms; morphology

cladistic Ladiges et al. 1989

phenetic & cladistic living & fossil priapulids; morphology

cladistic Wills 1998

cladistic catostomid fishes; morphology, revelopmental traits

cladistic Fulman 1985

cladistic Microloma angiosperms; morphology

cladistic Funk 1985

cladistic vespinid wasps; morphology

cladistic Carpenter 1987

cladistic florideophycidean rhodophytes;

cladistic Gabrielson & Garbary 1987

morphology, biochemistry

cladistic Maidenaria angiosperms; morphology

cladistic Chapill 1989

cladistic living & fossil actinopterygian fishes; skeletal morphology

cladistic Gardiner & Schaeffer 1989

cladistic fossil tabulate corals; skeletal morphology

cladistic Pandolfi 1989

cladistic platanaceaen & hamamelidaen angiosperms; morphology, biochemistry

cladistic Schwarzwalder & Dilcher 1991

cladistic Linstowia cestodes; morphology

cladistic Gardner & Campbell 1992

cladistic coreopsidean angiosperms; morphology

cladistic Ryding & Bremer 1992

cladistic Albinaria gastropods; morphology

cladistic Douris et al. 1995

cladistic Gambusia fishes; morphology, gene sequences

cladistic Lydeard et al. 1995

cladistic Metazoa; morphology cladistic Nielsen et al. 1996 cladistic Andira angiosperms;

morphology, gene sequences

cladistic Pennington 1996

cladistic Pinus conifers; morphology

cladistic Adams & Jackson 1997

cladistic living & fossil crocodylids; skeletal morphology

cladistic Brochu 1997

cladistic living & fossil crocodylids; morphology

cladistic Brochu 1997

cladistic Oreolalax frogs; morphology

cladistic Fu & Murphy 1997

cladistic Haumaniastrum angiosperms; morphology

cladistic Paton 1997

cladistic euphorbacean angiosperms; morphology

cladistic Simmons & Hayden 1997

cladistic fossil encrinurid trilobites; morphology


cladistic fossil & living perissodactyl, artiodactyl, & cetacean mammals; morphology, gene sequences

cladistic O'Leary 1999

cladistic fossil prosauropod dinosaurs; skeletal morphology

cladistic Benton et al. 2000

cladistic gesneriacean angiosperms; morphology, gene sequences

cladistic Smith 2000

cladistic eutherian mammals; morphology, gene sequences

cladistic (combined matrix construction of supertrees)

Liu et al. 2001

cladistic (& maximum likelihood)

Phrynosoma lizards; morphology, gene sequences; life history traits

cladistic Reeder et al. 2001

cladistic Procellariiform seabirds; morphology, gene sequence, isozyme, DNA-DNA hybridization, behavioral & life history traits

cladistic (combined matrix construction of supertrees)

Kennedy & Page 2002

cladistic tanaidacean crustaceans; morphology

cladistic Larson & Wilson 2002

cladistic fossil cynodonts & mammals; morphology

cladistic Luo et al. 2003

cladistic Chaetocerotacean diatoms; morphology

cladistic Rines & Theroit 2003


macrobiotid tardigrades; morphology, gene sequences

cladistic Guidetti et al. 2005

cladistic fossil & living primates; morphology

cladistic Seiffert et al. 2005

cladistic poltyinid spiders; morphology

cladistic Smith 2005

cladistic living & fossil crocodylids; morphology

cladistic Turner & Calvo 2005

cladistic fossil sauropod dinosaurs; skeletal morphology

cladistic Harris 2006

cladistic fossil theropod dinosaurs; skeletal morphology

cladistic Turner et al. 2007

cladistic fossil & living squamate reptiles; morphology, gene sequences

cladistic Conrad et al. 2008

cladistic fossil & living squamate reptiles; morphology

cladistic Norell et al. 2008

cladistic fossil & living turtles; morphology

cladistic Anquetin et al. 2009

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