polymorphisms
would not be surprised if the surviving populations experienced serious bottlenecks. The subsequent diversification of the surviving organisms, such as the Dinosauria which includes the extinct dinosaurs and modern birds and the Cynodontia, which includes the ancestors of modern mammals, including us, could be due in part to these bottleneck-associated effects, for example, through the removal of competing species or predators. An astreroid impact, known as the Cretaceous-Tertiary event, occurred ~65 million years ago; it contributed to the extinction of the dinosaurs and led to the diversification of mammals which had first appeared in the fossil record ~160 million years ago . While surviving an asteroid impact or other dramatic changes in climate may be random, in other cases who survives a bottleneck is not. Consider the effects of a severe drought or highly virulent bacterial or viral infection; the organisms that survive may have specific phenotypes and associated genotypes that significantly influence their chance of survival. In such a case, the effect of the bottleneck event would produce non-random changes in the distribution of genotypes and alleles in the post-bottleneck population these selective effects could continue to influence the population in various ways. For example, a trait associated with pathogen resistance may also have negative phenotypic effects. After the pathogen-driven bottleneck, mutations that mitigate the resistance trait's negative effects and may have their own effects can be selected. The end result is that traits that would not be selected in the absence of the pathogen, are selected. In addition, the very occurrence of a rapid and extreme reduction in population size has its own effects. For example, it would be expected to increase the effects of genetic drift see below and could make finding a mate more difficult. We can identify extreme population reduction events, such as founder effects and bottlenecks, by looking at the variation in genotypes that is, the sequence of DNA molecules , particularly in genotypic changes not expected to influence phenotypes, mating preference, or reproductive success. These so-called neutral polymorphisms are expected to accumulate in the regions of the genome between genes intragenic regions at a constant rate over time can you suggest why? The rate of the accumulation of neutral polymorphisms serves as a type of population-based biological clock. Its rate can be estimated, at least roughly, by comparing the genotypes of individuals of different populations whose time of separation can be accurately estimated assuming of course that there has been no migrations between the populations . Such studies of genomic sequence data which we will return to later in much greater detail indicate that the human population arose in Africa ~500,000 years ago. 119 Before this, the population leading to humans is thought to have undergone a bottleneck around ~1.2 million years ago.120 Once established, groups of modern humans migrated within and out of African, undergoing a series of founder effect events between ~45,000 to 60,000 years ago first as they migrated from southern Africa into the regions of the Horn of Africa, then into the Arabian peninsula, and from there into Europe, Asia, Oceania, and finally the Americas. Comparing genotypes, that is, neutral polymorphisms, between 119.