that reproductive proteins evolve more rapidly than most other types of proteins (Swanson and Vacquier, 2002). For example, in abalone (genus Haliotis) the gene lysin codes for a protein that dissolves a tunnel through the glycoprotein coat surrounding the egg, and the gene verl codes for the glycoprotein. From the sperm’s perspective, a lysin gene product that more rapidly dissolves a tunnel through the glycoprotein coat is favored because it helps the sperm win in sperm competition. But, from the egg’s perspective, slower penetration of the sperm through the glycoprotein coat is expected to be favored because it provides more time for a block to polyspermy (polyspermy is fatal to the egg) when many sperm compete to fertilize the same egg. This opposing selection on sperm penetration rate sets up a potential arms race between the verl and lysin genes (Frank, 2000; Rice, 1998; Rice and Holland, 1997; Swanson and Vacquier, 2002; Vacquier et al., 1997). In support of this arms race, studies of molecular evolution have demonstrated that both verl and lysin are evolving rapidly due to positive Darwinian selection (Swanson and Vacquier, 2002). As the arms race progresses independently among allopatric populations, the capacity for fertilization to occur between sperm and eggs derived from different populations would be expected to diminish due to coevolution between lysin and verl following different evolutionary trajectories in separated populations.
However, the pattern observed in the studies of molecular evolution has an alternative explanation. The verl gene may be antagonistically evolving due to an interspecific arms race with one or more pathogens that gain entry to the egg by transgressing the glycoprotein coat (Rice, 1998; Rice and Holland, 1997; Vacquier et al., 1997). In this case, the evolution at the lysin locus does not create a lag-load at the verl locus, but instead it evolves to track the evolution in verl that occurs in response to an interspecific arms race between host and pathogen. This alternative explanation for the same molecular data illustrates the problem with using descriptive studies of molecular evolution to test the hypothesis that inter-locus arms races are driving genetic divergence among populations. Because the data are correlative and do not directly measure selection, descriptive studies of molecular evolution can provide supporting evidence for inter-locus arms races but cannot provide definitive evidence.
Studies of experimental evolution in the laboratory are capable of measuring simultaneously standing genetic variance, selection on this variation, and response to the selection at a level of detail that cannot be achieved in natural populations. As a consequence, these studies can be used to provide a direct assessment of the potential for inter-locus antagonistic coevolution within and between the sexes. In the following section, we describe an experimental approach (hemiclonal analysis) to screen nearly the complete genome of Drosophila melanogaster for both genetic