* Darwin predicted, based on homologies with African apes, that human ancestors arose in Africa. That prediction has been supported by fossil and genetic evidence (Ingman et al. 2000).
* Theory predicted that organisms in heterogeneous and rapidly changing environments should have higher mutation rates. This has been found in the case of bacteria infecting the lungs of chronic cystic fibrosis patients (Oliver et al. 2000).
* Predator-prey dynamics are altered in predictable ways by evolution of the prey (Yoshida et al. 2003).
* Ernst Mayr predicted in 1954 that speciation should be accompanied with faster genetic evolution. A phylogenetic analysis has supported this prediction (Webster et al. 2003).
* Several authors predicted characteristics of the ancestor of craniates. On the basis of a detailed study, they found the fossil Haikouella "fit these predictions closely" (Mallatt and Chen 2003).
* Evolution predicts that different sets of character data should still give the same phylogenetic trees. This has been confirmed informally myriad times and quantitatively, with different protein sequences, by Penny et al. (1982).
* Insect wings evolved from gills, with an intermediate stage of skimming on the water surface. Since the primitive surface-skimming condition is widespread among stoneflies, J. H. Marden predicted that stoneflies would likely retain other primitive traits, too. This prediction led to the discovery in stoneflies of functional hemocyanin, used for oxygen transport in other arthropods but never before found in insects (Hagner-Holler et al. 2004; Marden 2005).
# Bioinformatics, a multi-billion-dollar industry, consists largely of the comparison of genetic sequences. Descent with modification is one of its most basic assumptions.
# Diseases and pests evolve resistance to the drugs and pesticides we use against them. Evolutionary theory is used in the field of resistance management in both medicine and agriculture (Bull and Wichman 2001).
# Evolutionary theory is used to manage fisheries for greater yields (Conover and Munch 2002).
# Artificial selection has been used since prehistory, but it has become much more efficient with the addition of quantitative trait locus mapping.
# Knowledge of the evolution of parasite virulence in human populations can help guide public health policy (Galvani 2003).
# Sex allocation theory, based on evolution theory, was used to predict conditions under which the highly endangered kakapo bird would produce more female offspring, which retrieved it from the brink of extinction (Sutherland 2002).
# Tracing genes of known function and comparing how they are related to unknown genes helps one to predict unknown gene function, which is foundational for drug discovery (Branca 2002; Eisen and Wu 2002; Searls 2003).
# Phylogenetic analysis is a standard part of epidemiology, since it allows the identification of disease reservoirs and sometimes the tracking of step-by-step transmission of disease. For example, phylogenetic analysis confirmed that a Florida dentist was infecting his patients with HIV, that HIV-1 and HIV-2 were transmitted to humans from chimpanzees and mangabey monkeys in the twentieth century, and, when polio was being eradicated from the Americas, that new cases were not coming from hidden reservoirs (Bull and Wichman 2001). It was used in 2002 to help convict a man of intentionally infecting someone with HIV (Vogel 1998). The same principle can be used to trace the source of bioweapons (Cummings and Relman 2002).
# Phylogenetic analysis to track the diversity of a pathogen can be used to select an appropriate vaccine for a particular region (Gaschen et al. 2002).
# Ribotyping is a technique for identifying an organism or at least finding its closest known relative by mapping its ribosomal RNA onto the tree of life. It can be used even when the organisms cannot be cultured or recognized by other methods. Ribotyping and other genotyping methods have been used to find previously unknown infectious agents of human disease (Bull and Wichman 2001; Relman 1999).
# Phylogenetic analysis helps in determining protein folds, since proteins diverging from a common ancestor tend to conserve their folds (Benner 2001).
These are taken from http://www.talkorigins.org/indexcc/CA/CA215.html