Homology in Character Evolution


Homology forms the basis of organisation for comparative biology. Richard Owen's simple definition of homology as the ‘same organ in different animals under every variety of form and function’ takes on new meaning in light of Darwin's concept of descent with modification. The modern study of comparative biology and phylogenetics is grounded in the notion that organisms share a greater proportion of homologous (i.e. ‘derived’) characteristics the more recently they share a common ancestor. Instead of solely being the purview of anatomical study, homology of these characteristics can be applied at the level of molecular evolution, genomic organisation and modern evolutionary developmental biology (‘evo/devo’). Aspects of homology help us formulate hypotheses about the meaning of changes in homologous structures in the inference of evolution of organisms at all levels of biological organisation.

Key Concepts:

  • Homology was originally a measure of correspondence between anatomical structures.

  • Descent with modification explains homology as a result of shared ancestry that reflects modifications in characteristics within related lineages.

  • Comparative methods use changes in homologous characteristics to infer evolution within groups (phylogenetics).

  • Recent advances in molecular biology allow for the comparison of homologous characteristics at more diverse levels, including DNA sequences, genomic arrangements and developmental pathways.

  • Recent work highlights homologous characteristics at a fundamental or ancient level, termed ‘deep homology’.

Keywords: archetype; evolution; correspondence; gene; morphology; genome; phylogeny; development; deep homology

Figure 1.

Concepts of homology. (a) Owen's homology was a concept of corresponding structures between organisms as similar or homologous based on their relationship to the archetype. (b) After Darwin, the similarity in structure is understood to arise from ancestor/descendant relationships.

Figure 2.

Phylogenetic analysis of characteristics. (a) Hypothetical list of taxa and traits analysed (b and c). ‘0’ and ‘1’ designate alternative forms for a feature, for example a forelimb might be a leg or a wing. Trait 12 is an autapomorphy and trait 1 is a symplesiomorphy. (b) A nesting of taxa showing their relatedness based on the traits in A (a Venn diagram). (c) A phylogenetic tree of the relationships shown in (b). Synapomorphies (from (a)) can be clearly mapped onto the branches since they are congruent with one another. All taxa above a marked branch share the same derived features. Homoplasies (shadowed in (a)) are in conflict with phylogenetic patterns of the tree presented.

Figure 3.

Homology in phylogenetic reconstruction. (a) An alignment of the first 30 bases of DNA for eight hypothetical taxa implies a hypothesis of positional homology among bases. Distribution of sequence change across taxa allows us to infer homology of a change at that position. Bases in blue boxes are inferred to be a homologous change for that base position, whereas bases in green boxes are inferred to be changes in conflict, or a result of homoplasy. (b) The distribution of these homologous changes are presented on a phylogenetic tree (* denotes homoplasy within a base/locus). (c) A gene tree of α and β genes for globins is presented (after Goodman et al., ). The duplication event for α and β globins precedes the diversification of vertebrates. This is supported by the independent phylogenies for each being congruent for each of the paralogous sequences. (d) Evidence of a homologous gene rearrangement in the mitochondrial DNA of eukaryotes (Boore, ). Hexapods and crustaceans share a similar arrangement of the leucine transfer ribonucleic acid (tRNA) (anticodon UUR) gene (L) occurring between the first and second subunits of cytochrome c oxidase. Chelicerates and other invertebrates do not share this arrangement. This supports the unity of mandibulate arthropods suggested earlier by some morphologists.

Figure 4.

Inverted expression of homologous gene products in transverse and longitudinal sections of fly and frog embryos (after De Robertis and Sasai, ). The fly embryo ventralising factor short gastrulation (sog) and the frog embryo dorsalising factor chordin (chd) are homologous genes. De Robertis and Sasai argued that the inverse position of their expression in these two distantly related organisms resurrects Geoffroy Saint‐Hilaire's notions of dorsal and ventral homology between vertebrates and arthropods.



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Further Reading

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Staton, Joseph L(Dec 2011) Homology in Character Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001776.pub2]