Evolutionary biologists believe that speciation, the formation of a new species, often begins when some kind of physical barrier arises and divides a population of a single species into separate subpopulations. Physical separation between subpopulations promotes the formation of new species because once the members of one subpopulation can no longer mate with members of another subpopulation, they cannot exchange variant genes that arise in one of the subpopulations. In the absence of gene flow between the subpopulations, genetic differences between the groups begin to accumulate. Eventually the subpopulations become so genetically distinct that they cannot interbreed even if the physical barriers between them were removed. At this point the subpopulations have evolved into distinct species. This route to speciation is known as allopatry (“allo-” means “different”, and “patria” means “homeland”).

Allopatric speciation may be the main speciation route. This should not be surprising, since allopatry is pretty common. In general, the subpopulations of most species are separated from each other by some measurable distance. So even under normal situations the gene flow among the subpopulations is more of an intermittent trickle than a steady stream. In addition, barriers can rapidly arise and shut off the trickle. For example, in the 1800s a monstrous earthquake changed the course of the Mississippi River, a large river flowing in the central part of the United States of America. The change separated populations of insects now living along opposite shores, completely cutting off gene flow between them.

Geographic isolation can also proceed slowly, over great spans of time. We find evidence of such extended events in the fossil record, which affords glimpse into the breakup of formerly continuous environments. For example, during past ice ages, glaciers advanced down through North America and Europe and gradually cut off parts of populations from one another. When the glaciers retreated, the separated populations of plants and animals came into contact again. Some groups that had descended from the same parent population were no longer reproductively compatible – they had evolved into separate species. In other groups, however, genetic divergences had not proceeded so far, and the descendants could still interbreed – for them, reproductive isolation was not completed, and so speciation had not occurred.

Allopatric speciation can also be brought by the imperceptibly slow but colossal movements of the tectonic plates that make up Earth’s surface. About 5 million years ago such geologic movements created the land bridge between North America and South America that we call the Isthmus of Panama . While previously the gap between the continents had allowed a free flow of water, now the isthmus presented a barrier that divided the Atlantic Ocean from the Pacific Ocean. This division set the stage for allopatric speciation among populations of fishes and other marine species.

In the 1980s, John Graves studied two populations of closely related fishes, one population from the Atlantic side of isthmus, the other from the Pacific side. He compared four enzymes found in the muscles of each population. Graves found that all four Pacific enzymes function better at lower temperatures than the four Atlantic versions of the same enzymes. This is significant because Pacific seawater is typically 2 to 3 degrees cooler than seawater on the Atlantic side of isthmus. Analysis by gel electrophoresis revealed slight differences in amino acid sequence of the enzymes of two of the four pairs. This is significant because the amino acid sequence of an enzyme is determined by genes.

Graves drew two conclusions from these observations. First, at least some of the observed differences between the enzymes of the Atlantic and Pacific fish populations were not random but were the result of evolutionary adaptation. Second, it appears that closely related populations of fishes on both sides of the isthmus are starting to genetically diverge from each other. Because Graves’ study of geographically isolated populations of isthmus fishes offers a glimpse of the beginning of a process of gradual accumulation of mutations that are neutral or adaptive, divergences here might be evidence of allopatric speciation in process.