Homology is a biological concept describing similarities between species resulting from shared ancestry. It is a central idea in the study of evolution because it reflects the branching of the phylogenetic tree. Generally speaking, if two species share many properties and genes, they are likely to have diverged from each other — i.e., speciated — relatively recently in evolutionary time.
All organisms are related to other organisms through evolution from a small number of common ancestors. Consequently, homologies abound in the biological world. Oxidative phosphorylation, the process of using oxidation to produce adenosine triphosphate, is a nearly universal biological homology. The process was used by the earliest organisms, and subsequent developments in evolution have modified but not replaced it.
Brains, by contrast, do not appear in every organism. They are a feature belonging only to animals. Not all animals have brains, but most do. Whether or not a species possesses a brain provides a clear indication of its position in the evolutionary tree. Some organisms, which have undergone less change since this point in time, have brains that are similar to the earliest ones. It is important to remember, however, that these organisms have survived and changed over the course of just as much evolutionary time as more complicated ones.
Homology is often discussed in contrast to analogy. Not every similarity between two organisms is the result of common evolutionary ancestry. If two species find themselves in an environment conducive to some particular adaptation, this adaptation may emerge independently in both species. For example, opossums evolved opposable thumbs independently from primates. This outcome isn't too surprising, since opposable thumbs are useful. Since evolution is unpredictable and chaotic, however, analogy is much less common than homology.
The study of genetics has refined the concept of homology with direct comparison between sequences of DNA. Before it was possible to read genetic information directly, scientists had to guess about homology — and taxonomy generally — on the basis of physiological observations. Now, the relative similarity of alleles found in different organisms can provide strong evidence concerning their evolutionary relatedness. Uncertainty about whether a shared property is homologous or analogous can be completely resolved upon examination of the DNA; statistically, a certain level of similarity between sequences could not have occurred on its own.
Genetics has also created the need for subclassifications within the concept of homology. Orthology refers to gene similarities that result from speciation. Paralogy describes homologies between genes that resulted from duplication within a single organism's genome. Xenolgy is the existence of homology resulting from lateral gene transfer: genetic material transmitted through a virus or by scientists, for example. The existence of xenologous homologies complicates the idea of a perfectly unidirectional branching of the evolutionary tree.