Natural selection is the process in which organisms with certain traits survive and reproduce while organisms that are less able to adapt to their environment die off. As Darwin pointed out, natural selection does not necessarily produce evolutionary progress, much less perfection. The limits to the effectiveness of natural selection are most clearly revealed by the universality of extinction. More than 99.9 percent of all evolutionary lines that once existed on Earth have become extinct. Mass extinctions remind us forcefully that evolution is not a steady approach to an ever-higher perfection but an unpredictable process in which the best-adapted organisms may be suddenly exterminated by a catastrophe and their place taken by lineages that prior to the catastrophe seemed to be without distinction or prospects.

There are numerous constraints, or limits, on the power of natural selection to bring about change. First, the genetic variation needed to perfect a characteristic may not be forthcoming. Second, during evolution, the adoption of one among several possible solutions to a new environmental opportunity may greatly restrict the possibilities for subsequent evolution. For instance, when a selective advantage for a skeleton developed among the ancestors of the vertebrates and the arthropods, the ancestors of the arthropods had the prerequisites for developing an external skeleton, and those of the vertebrates had the prerequisites for acquiring an internal skeleton. The entire subsequent history of these two large groups of organisms was affected by the two different paths taken by their remote ancestors. The vertebrates were able to develop such huge creatures as dinosaurs, elephants, and whales. A large crab is the largest type that the arthropods were able to achieve.

Another constraint on natural selection is developmental interaction. The different components of an individual organism—its structures and organs—are not independent of one another, and none of them responds to selection without interacting with the others. The whole developmental machinery is a single interacting system. Organisms are compromises among competing demands. How far a particular structure or organ can respond to the forces of selection depends, to a considerable extent, on the resistance offered by other structures and organs, as well as components of the genotype (the totality of an individual’s genes).

The structure of the genotype itself imposes limits on the power of natural selection. The classical metaphor of the genotype was that of a beaded string on which the genes were lined up like pearls in a necklace. According to this view, each gene was more or less independent of the others. Not much is left of this previously accepted image. It is now known that there are different functional classes of genes, some charged to produce material, others to regulate it, and still others that are apparently not functioning at all. There are single coding genes, moderately repetitive DNA, highly repetitive DNA, and many other kinds of DNA. Discovering exactly how they all interact with one another is still a rather poorly understood area of genetics.

A further constraint on natural selection is the capacity for nongenetic modification. The more plastic the organism’s body characteristics are (owing to developmental flexibility), the more this reduces the force of adverse selection pressures. Plants, and particularly microorganisms, have a far greater capacity for individual modification than do animals. Natural selection is involved even in this phenomenon, since the capacity for nongenetic adaptation is under strict genetic control. When a population shifts to a new specialized environment, genes will be selected during the following generations that reinforce and may eventually largely replace the capacity for nongenetic adaptation.

Finally, which organisms survive and reproduce in a population is partly the result of chance, and this also limits the power of natural selection. Chance operates at every level of the process of reproduction, from the transmission of parental chromosomes to the survival of the newly formed individual. Furthermore, potentially favorable gene combinations are often destroyed by indiscriminate environmental forces such as storms, floods, earthquakes, or volcanic eruptions, without natural selection being given the opportunity to favor these genotypes. Yet over time, in the survival of those few individuals that become the ancestors of subsequent generations, relative fitness always plays a major role.

在自然选择的过程中，有着某些特质的有机体得以生存和繁殖，而不能适应周围环境的有机体则相继死亡。正如达尔文所指明的，自然选择未必会产生进化性的进步，其实是更不完美的。灭绝的普遍性很大程度上揭示了自然选择的有效性的限制。曾经在地球上存在的所有的进化方式中，超过99.9%的已经消失了。大规模的灭绝强烈地提醒着我们，进化不是追求更高完美的一种稳定方式，而是一种不可预知的过程，其间适应性最好的有机体可能会因为灾难而灭绝，它们就会被世系取代，而在灾难发生前，一切看起来都没有区别和预兆。 带来变化的自然选择的力量存在着极大的制约因素和限制。首先，基因需完善一种特征的改变可能不会马上出现。其次，进化期间，在多种可能的解决方法中采取一种可适应新环境的方法也许会极大地限制后续进化的可能性。例如，当脊椎动物和节肢动物祖先的骨骼发育有选择性优势时，节肢动物的祖先有发育外部骨骼的先决条件，而脊椎动物的祖先有获得外部骨骼的先决条件，从而，这两个大群有机体的整个后续历史被它们的远古祖先所选的不同进化方式影响着。像恐龙、大象和鲸鱼这样巨大的脊椎动物能够繁衍，而大型螃蟹是节肢动物能够达到的最大体型。 自然选择的另一个制约因素是发展的相互作用。有机体个体的不同成分，如它们的结构和器官，不是相互独立的，它们都是相互影响才能实现自然选择的。整个发展是单一的相互作用的系统，有机体在争夺需求的过程中妥协。在很大程度上，一种特定的结构或者器官能够对自然选择的力量做出怎样的反应取决于其他结构、器官以及基因型（个体基因的总体）所带来的阻力。 基因型自身的结构给自然选择的力量带来了限制。基因型的经典隐喻是基因像珍珠般排列的串珠串。据此观点，每个基因或多或少的都是独立于其他基因的。现在人们知道，基因有不同的功能类型，一些负责“生产材料”，其他的一部分负责“管理材料”，还有一些显然不起任何作用。除此之外，还有一些单一的编码基因、中度重复DNA序列、高度重复DNA序列以及其他种类的DNA。它们之间是如何相互作用的问题仍然是基因领域的一块贫瘠之地。 自然选择的进一步制约因素是非基因修复的能力。有机体的体特征越是可塑（取决于发育的灵活性），不利的自然选择的压力就会越少。植物，尤其是微生物，比动物拥有的个体修复力的能力要强得多。自然选择也存在在这种现象中，因为基因严格控制着非基因的适应能力。当一个群体转移到一个新的特色环境时，基因将会在之后的一代代中强化，最终，可能会大幅度地代替非基因的适应能力。 最后，有机体能在群体中生存和繁衍的部分因素是运气，这也限制了自然选择的力量。从亲代染色体的传输到新生个体的生存，每一次的繁衍都涉及到了机会因素。此外，潜在的有利基因组合经常会被任意的环境力量破坏，如风暴、洪水、地震或者火山喷发，然而，随着时间的推移，在成为祖先的后代的那些极少数个体的生存中，相对适合度总是起着重要作用。