How to Compare Homology Concepts: Class Reasoning About Evolution and Morphology in Phylogenetics and Developmental Biology

Abouheif E (1997) Developmental genetics and homology: a hierarchical approach. Trends Ecol Evol 12:405–408

Abouheif E (1999) Establishing homology criteria for regulatory gene networks: prospects and challenges. In: Hall BK (ed) Homology. Novartis Foundation Symposium 222. Wiley, Chichester, pp 207–225

Arendt J, Reznick D (2007) Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends Ecol Evol 23:26–32

Assis LCS, Brigandt I (2009) Homology: homeostatic property cluster kinds in systematics and evolution. Evol Biol 36:248–255

Bechly G (2005) Glossary of phylogenetic systematics. http://www.bernstein.naturkundemuseum-bw.de/odonata/glossary.htm . Accessed 25 July 2005

Bock W (1963) Evolution and phylogeny in morphologically uniform groups. Am Nat 97:265–285

Bolker JA, Raff RA (1996) Developmental genetics and traditional homology. BioEssays 18:489–494

Boyd R (1999) Kinds, complexity and multiple realization. Philos Stud 95:67–98

Brigandt I (2003) Homology in comparative, molecular, and evolutionary developmental biology. J Exp Zool 299:9–17

Brigandt I (2007) Typology now: homology and developmental constraints explain evolvability. Biol Philos 22:709–725

Butler AB, Saidel WM (2000) Defining sameness: historical, biological, and generative homology. BioEssays 22:846–853

Cartmill M (1994) A critique of homology as a morphological concept. Am J Phys Anthropol 94:115–123

Cracraft J (2005) Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development. Zoology 108:345–356

De Beer G (1971) Homology, an unsolved problem. Oxford University Press, London

De Pinna MCC (1991) Concepts and tests of homology in the cladistic paradigm. Cladistics 7:367–394

Donoghue MJ (1992) Homology. In: Keller EF, Lloyd EA (eds) Keywords in evolutionary biology. Harvard University Press, Cambridge, pp 170–179

Farris J (1979) The information content of the phylogenetic system. Syst Biol 28:483–519

Fitzhugh K (2006) The “requirement of total evidence” and its role in phylogenetic systematics. Biol Philos 21:309–351

Fitzhugh K (2008) Abductive inference: implications for “Linnean” and “phylogenetic” approaches for representing biological systematization. Evol Biol 35:52–82

Franz NM (2005) Outline of an explanatory account of cladistic practice. Biol Philos 20:489–515

Goodman N (1983) Fact, fiction and forecast. Harvard University Press, Boston

Griffiths PE (2007) The phenomena of homology. Biol Philos 22:643–658

Hall BK (1994) Introduction. In: Hall BK (ed) Homology. Academic Press, San Diego, pp 2–17

Hall BK (1999) Introduction. In: Hall BK (ed) Homology. Novartis Foundation Symposium 222. Wiley, Chichester, pp 1–4

Hall BK (2007) Homoplasy and homology: dichotomy or continuum. J Hum Evol 52:473–479

Haszprunar G (1992) The types of homology and their significance for evolutionary biology and phylogenetics. J Evol Biol 5:13–25

Janies D, DeSalle R (1999) Development, evolution and corroboration. Anat Rec 257:6–14

Kluge A (2003) The repugnant and mature in phylogenetic inference: atemporal similarity and historical identity. Cladistics 19:356–368

Laubichler MD (2000) Homology in development and the development of the homology concept. Am Zool 40:777–788

Lauder GV (1994) Homology, form and function. In: Hall BK (ed) Homology. Academic Press, San Diego, pp 152–197

Mayr E (1969) Principles of systematic zoology. McGraw-Hill, New York

Meyer A (1999) Homology and homoplasy: the retention of genetic programmes. In: Hall BK (ed) Homology. Novartis Foundation Symposium 222. Wiley, Chichester, pp 141–157

Mickevich MF (1978) Taxonomic congruence. Syst Zool 27:143–158

Minelli A (1996) Some thoughts on homology 150 years after Owen’s definition. Mem Soc Ital Sci Nat Mus Civ Stor Nat Milano 27:71–79

Minelli A (1999) Comparative issue: homology, homoplasy and evolution in functional adaptation. In: Savazzi E (ed) Functional morphology of the invertebrate skeleton. Wiley, New York, pp 15–24

Minelli A (2009) Phylo-evo-devo: combining phylogenetics with evolutionary developmental biology. BMC Biol 7:36–38

Müller GB (2003) Homology: the evolution of morphological organization. In: Müller GB, Newman SA (eds) Origination of organismal form: beyond the gene in developmental and evolutionary biology. MIT Press, Cambridge, pp 51–69

Müller GB, Wagner GP (1996) Homology, hox genes, and developmental integration. Am Zool 36:4–13

Nelson G (1994) Homology and systematics. In: Hall BK (ed) Homology. Academic Press, San Diego, pp 102–151

Nelson G, Platnick N (1981) Systematics and biogeography: cladistics and vicariance. Columbia University Press, New York

Newman SA, Müller GB (2010) Morphological evolution: epigenetic mechanisms. In: Encyclopedia of the life sciences (ELS), www.els.net . Wiley, Chichester

Owen R (1843) Lectures on comparative anatomy and physiology of the invertebrate animals. Royal College of Surgeons. Longman, Brown, Green and Longman, London

Patterson C (1982) Morphological characters and homology. In: Joysey KA, Friday AE (eds) Problems of phylogenetic reconstruction. Academic Press, London, pp 21–74

Peters DS (1973) Homologie—ein Wort und viele Begriffe. Aufsätze und Reden der Senckenbergischen Naturforschenden Gesellschaft 24:173–175

Rieppel O (1992) Homology and logical fallacy. J Evol Biol 5:701–715

Rieppel O (1994) Homology, topology, and typology: the history of modern debates. In: Hall BK (ed) Homology. Academic Press, San Diego, pp 64–101

Rieppel O (2006) Modules, kinds, and homology. J Exp Zool 304B:18–27

Rieppel O, Kearney M (2002) Similarity. Biol J Linn Soc 75:59–82

Rieppel O, Kearney M (2007) The poverty of taxonomic characters. Biol Philos 22:95–113

Roth LV (1984) On homology. Biol J Linn Soc 22:13–29

Roth LV (1988) The biological basis of homology. In: Humphries CJ (ed) Ontogeny and systematics. Columbia University Press, New York, pp 1–26

Roth LV (1991) Homology and hierarchies: problems solved and unresolved. J Evol Biol 4:167–194

Roth LV (1994) Within and between organisms: replicators, lineages, and homologues. In: Hall BK (ed) Homology. Academic Press, San Diego, pp 302–338

Sluys R (1996) The notion of homology in current comparative biology. J Zool Syst Evol Res 34:145–152

Spemann H (1915) Zur Geschichte und Kritik des Begriffs der Homologie. In: Chun C, Johanssen W (eds) Allgemeine Biologie. Teubner, Leipzig, pp 63–68

Striedter GF (1998) Stepping into the same river twice: homologues as recurring attractors in epigenetic landscapes. Brain Behav Evol 52:218–231

Striedter GF (1999) Homology in the nervous system: of characters, embryology and levels of analysis. In: Hall BK (ed) Homology. Novartis Foundation Symposium 222. Wiley, Chichester, pp 158–172

Striedter GF, Northcutt RG (1991) Biological hierarchies and the concept of homology. Brain Behav Evol 38:177–189

Tautz D (1998) Debatable homologies. Nature 395:17–18

Van Valen L (1982) Homology and causes. J Morphol 173:305–312

Wagner GP (1989a) The biological homology concept. Annu Rev Ecol Evol Syst 21:15–69

Wagner GP (1989b) The origin of morphological characters and the biological basis of homology. Evolution 43:1157–1171

Wagner GP (1994) Homology and mechanisms of development. In: Hall BK (ed) Homology. Academic Press, San Diego, pp 274–301

Wagner GP (1999) A research programme for testing the biological homology concept. In: Hall BK (ed) Homology. Novartis Foundation Symposium 222. Wiley, Chichester, pp 125–140

Wagner GP, Misof BY (1993) How can a character be developmentally constrained despite variation in developmental pathways? J Evol Biol 6:449–455

Wake D (1994) Comparative terminology. Science 265:268–269

West-Eberhard MJ (2003) Developmental plasticity and evolution. Oxford University Press, Oxford

Wiley EO (1975) Karl Popper, systematics and classification: a reply to Walter Bock and other evolutionary taxonomists. Syst Zool 24:233–243

Young B (1993) On the necessity of an archetypal concept in morphology, with special reference to the concepts of “structure” and “homology.” Biol Philos 8:225–248