In biology we study life at all levels of organization—from genes, cells, organisms, populations, and species to the major divisions of life. In most cases, however, no individual gene or organism (or other unit of study) is exactly like any other gene or organism that we investigate.

Consider the individuals in your biology class. We recognize each person as an individual human, but we know that no two are exactly alike. If we knew everyone’s family tree in detail, the genetic similarity of any pair of students would be more predictable. We would find that more closely related students have many more traits in common (from the color of their hair to their susceptibility or resistance to diseases). Likewise, biologists use phylogenies to make comparisons and predictions about shared traits across genes, populations, and species.

The evolutionary relationships among species, as represented in the tree of life, form the basis for biological classification. Biologists estimate that there are tens of millions of species on Earth. So far, however, only about 1.8 million species have been classified—that is, formally described and named. New species are being discovered all the time and phylogenetic analyses are constantly reviewed and revised, so our knowledge of the tree of life is far from complete. Yet knowledge of evolutionary relationships is essential for making comparisons in biology, so biologists build phylogenies for groups of interest as the need arises. The tree of life’s evolutionary framework allows us to make many predictions about the behavior, ecology, physiology, genetics, and morphology of species that have not yet been studied in detail.

When biologists compare species, they observe traits that differ within the group of interest and try to understand when these traits evolved. In many cases, investigators are interested in how the evolution of a trait relates to environmental conditions or selective pressures. For instance, scientists have used phylogenetic analyses to discover changes in the genome of human immunodeficiency viruses (HIVs) that result in resistance to particular drug treatments. The association of a particular genetic change in HIV with a particular treatment provides a hypothesis about the evolution of resistance that can be tested experimentally.

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Any features shared by two or more species that have been inherited from a common ancestor are said to be homologous. Homologous features may be any heritable traits, including DNA sequences, protein structures, anatomical structures, and even some behavior patterns. For example, all living vertebrates have a vertebral column, as did the ancestral vertebrate. Therefore the vertebral column is judged to be homologous in all vertebrates.