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 if 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.

进化论生物学家认为物种的形成，即形成一个新的物种，通常由某一障碍将一个族群分割成亚族群开始的。亚族群间的物理隔离可以促进物种形成是因为隔离之后一个亚族群里的个体无法与其他亚族群个体交配，因此该族群里突变的基因将无法与其他亚族群交流。之后亚族群间的基因差异将逐渐累积。最终即便物理隔离不复存在，亚族群间的基因差异过大而无法杂交。此时亚族群就进化为不同的物种。这种物种形成的轨迹称为异域分布。 异域分布可能是主要的物种形成路线。这不足奇怪，因为异域分布很常见。一般，绝大部分的物种的亚族群都由一定程度的距离隔离。所以就算在正常情况下，亚族群间基因交流更多可能像是间歇的细流而不是稳定的流动。另外，障碍可以迅速形成并切断这种细流。例如，十九世纪一场巨大的地震改变了密西西比河，美国中部的一条大河，的河道。这一改变将两岸的昆虫隔离开来，完全隔断了他们之间的基因交流。 地理隔离也可能进程缓慢，跨越很长时间。在化石记录中发现过这类事件。原本连续的环境突然终止。例如在以往的冰河时期，冰河从北美和欧洲向下扩张，逐渐切断了族群间的联系。冰河消退后分隔的动植物种群又重新接触。一些来自同一物种的后代就不能再相互交配----它们已形成新的物种。然而其它亚族群间基因差异没有如此之大，其后代仍可相互交配----对他们而言，繁殖隔离并未完成，因而新物种没有形成。 异域分布导致的物种形成也可能源自察觉不到但巨大的板块运动，他们造就了地球表面。约500万年前，这种地质运动产生了连接北美洲和南美洲的陆地通道，我们称为巴拿马地峡。地峡的形成对全球洋流的形式产生重大影响。之前两大陆之间的间隙可使洋流畅通流动，现在地峡将大西洋和太平洋隔开。这种分割为海洋生物和鱼类提供了异域分布导致物种形成的舞台。 在二十世纪80年代，John Graves研究了两种极相关的鱼群，一个族群来自地峡的大西洋一侧，另一个来自地峡太平洋一侧。他对比了族群个体肌肉中的四种酶。这很重要因为太平洋的海水一般比大西洋的低2-3度。胶体电泳分析表明四对酶的氨基酸系列有微小差别。其重要性在于酶的氨基酸系列是由基因决定的。 Graves得出两条结论。首先至少太平洋族群和大西洋族群酶的一些差别不是随机的，而是进化适应的结果。第二，地峡两侧关系紧密的鱼群的基因正在开始变异。Graves的关于地峡分割的鱼群的研究得以让我们窥见那些适应性变化的积累过程的开始。这里的变异可能是异地分布物种形成过程的证据。