Abstract
There is long-standing conflict between genealogical and developmental accounts of homology. This paper provides a general framework that shows that these accounts are compatible and clarifies precisely how they are related. According to this framework, understanding homology requires both (a) an abstract genealogical account that unifies the application of the term to all types of characters used in phylogenetic systematics and (b) locally enriched accounts that apply only to specific types of characters. The genealogical account serves this unifying role by relying on abstract notions of ‘descent’ and ‘character’. As a result, it takes for granted the existence of such characters. This requires theoretical justification that is provided by enriched accounts, which incorporate the details by which characters are inherited. These enriched accounts apply to limited domains (e.g. genes and proteins, or body parts), providing the needed theoretical justification for recognizing characters within that domain. Though connected to the genealogical account of homology in this way, enriched accounts include phenomena (e.g. serial homology, paralogy, and xenology) that fall outside the scope of the genealogical account. They therefore overlap, but are not nested within, the genealogical account. Developmental accounts of homology are to be understood as enriched accounts of body part homology. Once they are seen in this light, the conflict with the genealogical account vanishes. It is only by understanding the fine conceptual structure undergirding the many uses of the term ‘homology’ that we can understand how these uses hang together.
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Notes
I do not here consider phylogenetic networks (Huson et al. 2010) that take into account tokogenetic relationships (produced by e.g. hybridization and lateral gene transfer). This issue is discussed briefly below (“The enriched account of gene homology” section).
This distinction is controversial (Minelli 2016). The issue is treated below (“Wagner’s enriched account of body part homology” section).
Unlike paralogy, xenology is not a problem to be avoided in systematics, but a phenomenon to included. Where xenology is prevalent, systematists cannot simply assume that relationships between taxa can be captured by a strict tree, and must instead infer from the data to a phylogenetic network (Huson et al. 2010). However, whether one infers a tree or a network, one must still undertake a sequence alignment step that furnishes the relevant transformation series, and this is presupposed, but not tested, by the data-to-tree/network inference.
The discussion of development in this section primarily applies to animal development, and it focuses exclusively on the role of gene regulation in development, ignoring the role of non-genetic resources that shape development. I exclude such considerations because they do not feature in Wagner’s account of body part homology.
In this discussion, I have simplified things for ease of exposition. In fact, the appropriate bearer of character states is not the entire organism (or part) over the entire course of its life, but a suitably thick time-slice of the organism (part), called a semaphoront. In an excellent paper, Havstad et al. (2015) show that ontogenetic identity (identity of a part across the different semaphoronts of a single individual) and phylogenetic identity (identity of a part across evolutionary transformations) can come apart. For example, in Drosophila melanogaster, female genitalia develop from the embryonic segment A8. In males, however, A8 develops into a tergite-like structure (Keisman et al. 2001). A8 in females is phylogenetically identical to A8 in males, and it is ontogenetically identical to the adult female genitalia. Likewise, A8 in males is ontogenetically identical to the tergite-like structure. Yet the female genitalia and the male tergite-like structure are not homologous. Over the course of development, a homologous precursor develops into non-homologous structures. One task of an enriched account is to explain why this is so. Wagner’s account would analyze such cases as involving initially homologous precursors that come to express non-homologous ChINs.
For reasons of space, I do not discuss serial homology and paralogy, but similar considerations apply.
For additional critique of this assumption, see Currie (2014).
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Acknowledgements
The author thanks Günter Wagner, James Lennox, Sandra Mitchell, Mark Wilson, Mark Rebeiz, James Woodward, Nora Boyd, David Colaço, Adrian Currie, Karen Kovaka, Liam Kofi Bright, Catherine Kendig, Maureen O’Malley, and two anonymous reviewers for helpful comments and discussion.
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Novick, A. The fine structure of ‘homology’. Biol Philos 33, 6 (2018). https://doi.org/10.1007/s10539-018-9617-3
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DOI: https://doi.org/10.1007/s10539-018-9617-3