Genetic Mutation

The diversity of beetle species.

Genetic mutation is the basis of species diversity among beetles, or any other organism.

© 2009 Courtesy of John C. Abbot, Abbott Nature Photography. All rights reserved.

Mutations are changes in the genetic sequence, and they are a main cause of diversity among organisms. These changes occur at many different levels, and they can have widely differing consequences. In biological systems that are capable of reproduction, we must first focus on whether they are heritable; specifically, some mutations affect only the individual that carries them, while others affect all of the carrier organism's offspring, and further descendants. For mutations to affect an organism's descendants, they must: 1) occur in cells that produce the next generation, and 2) affect the hereditary material. Ultimately, the interplay between inherited mutations and environmental pressures generates diversity among species.

Although various types of molecular changes exist, the word "mutation" typically refers to a change that affects the nucleic acids. In cellular organisms, these nucleic acids are the building blocks of DNA, and in viruses they are the building blocks of either DNA or RNA. One way to think of DNA and RNA is that they are substances that carry the long-term memory of the information required for an organism's reproduction. This article focuses on mutations in DNA, although we should keep in mind that RNA is subject to essentially the same mutation forces.

If mutations occur in non-germline cells, then these changes can be categorized as somatic mutations. The word somatic comes from the Greek word soma which means "body", and somatic mutations only affect the present organism's body. From an evolutionary perspective, somatic mutations are uninteresting, unless they occur systematically and change some fundamental property of an individual--such as the capacity for survival. For example, cancer is a potent somatic mutation that will affect a single organism's survival. As a different focus, evolutionary theory is mostly interested in DNA changes in the cells that produce the next generation.

The statement that mutations are random is both profoundly true and profoundly untrue at the same time. The true aspect of this statement stems from the fact that, to the best of our knowledge, the consequences of a mutation have no influence whatsoever on the probability that this mutation will or will not occur. In other words, mutations occur randomly with respect to whether their effects are useful. Thus, beneficial DNA changes do not happen more often simply because an organism could benefit from them. Moreover, even if an organism has acquired a beneficial mutation during its lifetime, the corresponding information will not flow back into the DNA in the organism's germline. This is a fundamental insight that Jean-Baptiste Lamarck got wrong and Charles Darwin got right.

However, the idea that mutations are random can be regarded as untrue if one considers the fact that not all types of mutations occur with equal probability. Rather, some occur more frequently than others because they are favored by low-level biochemical reactions. These reactions are also the main reason why mutations are an inescapable property of any system that is capable of reproduction in the real world. Mutation rates are usually very low, and biological systems go to extraordinary lengths to keep them as low as possible, mostly because many mutational effects are harmful. Nonetheless, mutation rates never reach zero, even despite both low-level protective mechanisms, like DNA repair or proofreading during DNA replication, and high-level mechanisms, like melanin deposition in skin cells to reduce radiation damage. Beyond a certain point, avoiding mutation simply becomes too costly to cells. Thus, mutation will always be present as a powerful force in evolution.

So, how do mutations occur? The answer to this question is closely linked to the molecular details of how both DNA and the entire genome are organized. The smallest mutations are point mutations, in which only a single base pair is changed into another base pair. Yet another type of mutation is the nonsynonymous mutation, in which an amino acid sequence is changed. Such mutations lead to either the production of a different protein or the premature termination of a protein.

As opposed to nonsynonymous mutations, synonymous mutations do not change an amino acid sequence, although they occur, by definition, only in sequences that code for amino acids. Synonymous mutations exist because many amino acids are encoded by multiple codons. Base pairs can also have diverse regulating properties if they are located in introns, intergenic regions, or even within the coding sequence of genes. For some historic reasons, all of these groups are often subsumed with synonymous mutations under the label "silent" mutations. Depending on their function, such silent mutations can be anything from truly silent to extraordinarily important, the latter implying that working sequences are kept constant by purifying selection. This is the most likely explanation for the existence of ultraconserved noncoding elements that have survived for more than 100 million years without substantial change, as found by comparing the genomes of several vertebrates (Sandelin et al., 2004).

Mutations may also take the form of insertions or deletions, which are together known as indels. Indels can have a wide variety of lengths. At the short end of the spectrum, indels of one or two base pairs within coding sequences have the greatest effect, because they will inevitably cause a frameshift (only the addition of one or more three-base-pair codons will keep a protein approximately intact). At the intermediate level, indels can affect parts of a gene or whole groups of genes. At the largest level, whole chromosomes or even whole copies of the genome can be affected by insertions or deletions, although such mutations are usually no longer subsumed under the label indel. At this high level, it is also possible to invert or translocate entire sections of a chromosome, and chromosomes can even fuse or break apart. If a large number of genes are lost as a result of one of these processes, then the consequences are usually very harmful. Of course, different genetic systems react differently to such events.

Finally, still other sources of mutations are the many different types of transposable elements, which are small entities of DNA that possess a mechanism that permits them to move around within the genome. Some of these elements copy and paste themselves into new locations, while others use a cut-and-paste method. Such movements can disrupt existing gene functions (by insertion in the middle of another gene), activate dormant gene functions (by perfect excision from a gene that was switched off by an earlier insertion), or occasionally lead to the production of new genes (by pasting material from different genes together).

Figure 1: The overwhelming majority of mutations have very small effects.

This example of a possible distribution of deleterious mutational effects was obtained from DNA sequence polymorphism data from natural populations of two Drosophila species. The spike at 10-10 includes all smaller effects, whereas effects are not shown if they induce a structural damage that is equivalent to selection coefficients that are 'super-lethal' (see Loewe and Charlesworth 2006 for more details).

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A single mutation can have a large effect, but in many cases, evolutionary change is based on the accumulation of many mutations with small effects. Mutational effects can be beneficial, harmful, or neutral, depending on their context or location. Most non-neutral mutations are deleterious. In general, the more base pairs that are affected by a mutation, the larger the effect of the mutation, and the larger the mutation's probability of being deleterious.

To better understand the impact of mutations, researchers have started to estimate distributions of mutational effects (DMEs) that quantify how many mutations occur with what effect on a given property of a biological system. In evolutionary studies, the property of interest is fitness, but in molecular systems biology, other emerging properties might also be of interest. It is extraordinarily difficult to obtain reliable information about DMEs, because the corresponding effects span many orders of magnitude, from lethal to neutral to advantageous; in addition, many confounding factors usually complicate these analyses. To make things even more difficult, many mutations also interact with each other to alter their effects; this phenomenon is referred to as epistasis. However, despite all these uncertainties, recent work has repeatedly indicated that the overwhelming majority of mutations have very small effects (Figure 1; Eyre-Walker & Keightley, 2007). Of course, much more work is needed in order to obtain more detailed information about DMEs, which are a fundamental property that governs the evolution of every biological system.

Many direct and indirect methods have been developed to help estimate rates of different types of mutations in various organisms. The main difficulty in estimating rates of mutation involves the fact that DNA changes are extremely rare events and can only be detected on a background of identical DNA. Because biological systems are usually influenced by many factors, direct estimates of mutation rates are desirable. Direct estimates typically involve use of a known pedigree in which all descendants inherited a well-defined DNA sequence. To measure mutation rates using this method, one first needs to sequence many base pairs within this region of DNA from many individuals in the pedigree, counting all the observed mutations. These observations are then combined with the number of generations that connect these individuals to compute the overall mutation rate (Haag-Liautard et al., 2007). Such direct estimates should not be confused with substitution rates estimated over phylogenetic time spans.

Mutation rates can vary within a genome and between genomes. Much more work is required before researchers can obtain more precise estimates of the frequencies of different mutations. The rise of high-throughput genomic sequencing methods nurtures the hope that we will be able to cultivate a more detailed and precise understanding of mutation rates. Because mutation is one of the fundamental forces of evolution, such work will continue to be of paramount importance.