Random genetic drift
In populations of finite size, the genetic structure of a new generation is not necessarily that of the previous one. The explanation lies in a sampling effect, based on the fact that a subsample from any large set is not always representative of the larger set. The gametes that form any generation can be thought of as a sample of the alleles from the parental one. By chance the sample might not be random; it could be skewed in either direction. For example, if p = 0.600 and q = 0.400, sampling “error” might result in the gametes having a p value of 0.601 and a q of 0.399. If by chance this skewed sampling occurs in the same direction from generation to generation, the allele frequency can change radically. This process is known as random genetic drift. As might be expected, the smaller the population, the greater chance of sampling error and hence significant levels of drift in any one generation. In extreme cases, drift over the generations can result in the complete loss of one allele; in these occurrences the other is said to be fixed.
Other cases of sampling error occur when new colonies of plants or animals are founded by small numbers of migrants (founder effect) and when there is radical reduction in population size because of a natural catastrophe (population bottleneck). One inevitable effect of these processes is a reduction in the amount of variation in the population after the size reduction. Two species that have gone through drastic bottlenecks with the associated reduction of genetic variation are cheetahs (Africa) and northern elephant seals (North America).
Microevolution
There is ample evidence that the processes described above are at work in natural populations. Together, these changes are called microevolution—in other words, small-scale evolution. Even within the relatively short period of time since Darwin, it has been possible to document such processes. Allelic variation has been found to be common in nature. It is detected as polymorphism, the presence of two or more distinct hereditary forms associated with a gene. Polymorphism can be morphological, such as blue and brown forms of a species of marine mussel, or molecular, detectable only at the DNA or protein level. Although much of this polymorphism is not understood, there are enough examples of selection of polymorphic forms to indicate that it is potentially adaptive. Selection has been observed favouring melanic (dark) forms of peppered moths in industrial areas and favouring resistance to toxic agents such as the insecticide DDT, the rat poison warfarin, and the virus that causes the disease myxomatosis in rabbits.
More-complex genetic changes have been documented, leading to special locally adapted “ecotypes.” Anoles (a type of lizard) on certain Caribbean islands show convincing examples of adaptations to specific habitats, such as tree trunks, tree branches, or grass. Introductions of lizards onto uncolonized islands result in demonstrable microevolutionary adaptations to the various vacant niches. On the Galapagos Islands, studies over several decades have documented adaptive changes in the beaks of finches. In some studies, documented changes have led to incipient new species. An example is the apple maggot, the larva of a fly in North America that has evolved from a similar fly living on hawthorns—all in the period since the introduction of apples. The formation of new species was a key component of Darwin’s original theory. Now it appears that the accumulation of enough small-scale genetic changes can lead to the inability to mate with members of an ancestral population; such reproductive isolation is the key step in species formation.
It is reasonable to assume that the continuation of microevolutionary genetic changes over very long periods of time can give rise to new major taxonomic groups, the process of macroevolution. There are few data that bear directly on the processes of macroevolution, but gene analysis does provide a way for charting macroevolutionary relationships indirectly.
DNA phylogeny
The ability to isolate and sequence specific genes and genomes has been of great significance in deducing trees of evolutionary relatedness. An important discovery that enables this sort of analysis is the considerable evolutionary conservation between organisms at the genetic level. This means that different organisms have a large proportion of their genes in common, particularly those that code for proteins at the central core of the chemical machinery of the cell. For example, most organisms have a gene coding for the energy-producing protein cytochrome C, and furthermore, this gene has a very similar nucleotide sequence in all organisms (that is, the sequence is conserved). However, the sequences of cytochrome C in different organisms do show differences, and the key to phylogeny is that the differences are proportionately fewer between organisms that are closely related. The interpretation of this observation is that organisms that share a common ancestor also share common DNA sequences derived from that ancestor. When one ancestral species splits into two, differences accumulate as a result of mutations, a process called divergence. The greater the amount of divergence, the longer must have been the time since the split occurred. To carry out this sort of analysis, the DNA sequence data are fed into a computer. The computer positions similar species together on short adjacent branches showing a relatively recent split and dissimilar species on long branches from an ancient split. In this way a molecular phylogenetic tree of any number of organisms can be drawn.
DNA difference in some cases can be correlated with absolute dates of divergence as deduced from the fossil record. Then it is possible to calculate divergence as a rate. It has been found that divergence is relatively constant in rate, giving rise to the idea that there is a type of “molecular clock” ticking in the course of evolution. Some ticks of this clock (in the form of mutations) are significant in terms of adaptive changes to the gene, but many are undoubtedly neutral, with no significant effect on fitness.
One of the interesting discoveries to emerge from molecular phylogeny is that gene duplication has been common during evolution. If an extra copy of a gene can be made, initially by some cellular accident, then the “spare” copy is free to mutate and evolve into a separate function.
Molecular phylogeny of some genes has also pointed to unexpected cases of, say, a plant gene nested within a tree of animal genes of that type or a bacterial gene nested within a plant phylogenetic tree. The explanation for such anomalies is that there has been horizontal transmission from one group to another. In other words, on rare occasions a gene can hop laterally from one species to another. Although the mechanisms for horizontal transmission are presently not known, one possibility is that bacteria or viruses act as natural vectors for transferring genes.
Synteny
Genomic sequencing and mapping have enabled comparison of the general structures of genomes of many different species. The general finding is that organisms of relatively recent divergence show similar blocks of genes in the same relative positions in the genome. This situation is called synteny, translated roughly as possessing common chromosome sequences. For example, many of the genes of humans are syntenic with those of other mammals—not only apes but also cows, mice, and so on. Study of synteny can show how the genome is cut and pasted in the course of evolution.
Polyploidy
Genomic analysis also has shown that one of the important mechanisms of evolution is multiplication of chromosome sets, resulting in polyploidy (“many genomes”). In plants and animals, spontaneous doubling of chromosomes can occur. In some plants, the chromosomes of two related species unite via cross-pollination to form a fusion product. This product is sterile because each chromosome needs a pairing partner in order for the plant to be fertile. However, the chromosomes of the fusion product can accidentally double, resulting in a new, fertile species. Wheat is an example of a plant that evolved by this means through a union between wild grasses, but a large proportion of plants went through similar ancestral polyploidization.