Homology and Homoplasy 431deep within animal phylogeny (exemplified by the paired appendages of insects
and vertebrates.^6
3 HIERARCHY AND EMBRYONIC DEVELOPMENTWhen considered from the perspective of embryonic development, phenotypic fea-
ture may share developmental pathways, share portions of pathways, or develop
using divergent developmental pathways. Furthermore, developmental pathways
may be shared (and so by implication, conserved) even when a feature is not fully
formed but exists as a rudiment or vestige, or when a structure appears only in
some individuals as an atavism (a feature not expressed in the previous genera-
tion). These apparent discontinuities or disjunctions occur — and a hierarchical
approach to homology is required — because the evolution of processes and pat-
terns (final form) need not be congruent.
Homology, therefore, must be approachedhierarchically. Homology at one level
— a feature such as a limb — need not correspond to homology at other levels —
the developmental processes that produce the limb, or the genetic cascades under-
lying those processes. Hall [1995a] discussed mechanisms of gastrulation, the origin
of germ cells, and the mode of induction of the lens of the eye and of Meckel’s
cartilage as examples of homologous features arising from non-homologous de-
velopmental process. Stone and Hall [2004] discussed the transition of fish fins to
tetrapod limbs, anterior walking appendages to feeding appendages in crustaceans,
the origin of insect wings and the evolution(s) of the mesoderm as examples that
highlight the need for a hierarchical approach to any consideration of homology.^7
4 RECONCEPTUALIZING HOMOLOGY AND HOMOPLASYHomoplastic features (independent evolution) can share an affiliation (shared de-
velopmental processes) with homologous features. Can we find a common thread
uniting developmental and phylogenetic approaches that might reveal a fundamen-
tal relationship between homology and homoplasy? Would that common thread
constitute adeep homologyof shared genetic, biochemical, cellular and develop-
mental mechanisms? The sharing of regulatory genes, gene cascades, or gene
networks is an important aspect of deep homology: homologues usually retain
these shared bases, but need not; the processes underlying homoplastic features
can diverge.^8
(^6) See Clack [2002] and Hall [2005a] for fins fish and tetrapod limbs, Cole and Hall [2004a,b]
for cartilages in the Metazoa, and Shubinet al.[1997] and Carrollet al.[2005] for insect and
vertebrate appendages.
(^7) See de Beer [1938; 1971], Bolker [1992], Hall [1995a; 1998; 1999a] Minsuck and Keller [1996]
and Stone and Hall [2004] for further examples, and see Freeman and Martindale [2002] and
Martindaleet al.[2004] for the origination of mesoderm.
(^8) See McShea [1996], Shubinet al. [1997], Gerhart [2000], Hall [2002a,b; 2003a; 2007a] and
Valentine [2004] for deep homology, and see Weiss [1994/1995], Abouheif [1997; 1999], Duboule