Homology and Phylogenetic Reconstruction

Homology and Phylogenetic Reconstruction
Darwin recognized the major source of evidence for common descent in the concept of homology. Darwin’s contemporary, Richard Owen (1804 to 1892), used this term to denote “the same organ in different organisms under every variety of form and function.” A classic example of homology is the limb skeleton of vertebrates. Bones of vertebrate limbs maintain characteristic structures and patterns of connection despite diverse modifications for different functions (Figure 6- 13). According to Darwin’s theory of common descent, the structures that we call homologies represent characteristics inherited with some modification from a corresponding feature in a common ancestor.

Darwin devoted an entire book, The Descent of Man and Selection in Relation to Sex, largely to the idea that humans share common descent with apes and other animals. This idea was repugnant to the Victorian world, which responded with predictable outrage (Figure 6-14). Darwin built his case mostly on anatomical comparisons revealing homology between humans and apes. To Darwin, the close resemblances between apes and humans could be explained only by common descent.

Throughout the history of all forms of life, evolutionary processes generate new characteristics that are then inherited by subsequent generations. Every time a new feature arises on an evolving lineage, we see the origin of a new homology. That homology gets transmitted to all descendant lineages unless it is subsequently lost. The pattern formed by the sharing of homologies among species provides evidence for common descent and allows us to reconstruct the branching evolutionary history of life. We can illustrate such evidence using a phylogenetic tree for a group of large, ground-dwelling birds (Figure 6-15). A new skeletal homology arises on each of the lineages shown (descriptions of specific homologies are not included because they are highly technical). The different groups of species located at the tips of the branches contain different combinations of these homologies, which reflect ancestry. For example, ostriches show homologies 1 through 5 and 8, whereas kiwis show homologies 1, 2, 13, and 15. Branches of the tree combine these species into a nested hierarchy of groups within groups (see Classification and Phylogeny of Animals). Smaller groups (species grouped near terminal branches) are contained within larger ones (species grouped by basal branches, including the trunk of the tree). If we erase the tree structure but retain patterns of homology observed in the living species, we are able to reconstruct the branching structure of the entire tree. Evolutionists test the theory of common descent by observing the patterns of homology present within all groups of organisms. The pattern formed by all homologies taken together should specify a single branching tree that represents the evolutionary genealogy of all living organisms.

The nested hierarchical structure of homology is so pervasive in the living world that it forms the basis for our systematic classification of all forms of life (genera grouped into families, families grouped into orders, and other categories). Hierarchical classification even preceded Darwin’s theory because this pattern is so evident, but it was not explained adequately before Darwin. Once the idea of common descent was accepted, biologists began investigating the structural, molecular, and chromosomal homologies of animal groups. Taken together, the nested hierarchical patterns uncovered by these studies have permitted us to reconstruct evolutionary trees of many groups and to continue investigating others. Use of Darwin’s theory of common descent to reconstruct the evolutionary history of life and to classify animals is the subject of Classification and Phylogeny of Animals.

Note that the earlier evolutionary hypothesis that life arose many times, forming unbranched lineages, predicts linear sequences of evolutionary change with no nested hierarchy of homologies among species. Because we do observe nested hierarchies of homologies, that hypothesis is rejected. Note also that because the creationist argument is not a scientific hypothesis, it can make no testable predictions about any pattern of homology.