So far in this chapter we have learned that molecular markers will be influenced by the manner in which they are inherited. We will now take a more detailed look at the properties of some of the most common markers that are used to generate data from one or more genomes. An important point to remember is that molecular markers are simply tools that can be used for generating data; like anything else, the job can be done properly only if the correct tools are chosen. Since we cannot make an informed choice until we understand how the tools operate, we need to learn about some of the key characteristics of different markers. The other point to bear in mind while learning about molecular markers is that we are using them to answer ecological questions. In molecular ecology, genetic data are often combined with ecological data that have been obtained either in the wild or in controlled laboratory experiments, following, for example, observations of mating behaviour, census counts, capture--mark-recapture studies, comparisons of growth patterns under different environmental conditions, and descriptions of morphological characters. In this chapter we will limit ourselves to a general understanding of what markers are, and how they can be used in molecular ecology; methods for analysing data from different markers and more detailed discussions of how genetic data can be applied to ecological questions can be found in later chapters.
Several factors need to be taken into account when choosing a marker. First, it is important to consider the expected level of variability. Some genetic regions are expected to evolve more rapidly than others, and the desired variability will depend on the question that is being asked. Generally speaking, markers that allow us to differentiate between closely related organisms will need to be highly variable, whereas the relationships among more distantly related taxa may be resolved by less variable markers. This ties back to an earlier part of this chapter and also to Chapter 1, when we noted that mutation rates vary both within and between genomes. As we shall see, many types of markers can be applied to either nuclear or organelle genomes; however, different mutation rates combined with alternative modes of inheritance means that the decision about which DNA region or genome to target should not be taken lightly.
There are also practical concerns surrounding the choice of marker. Time, money and expertise are all relevant, and there is often a trade-off between precision and convenience. This brings us to the two main categories of markers that will be described in this chapter: co-dominant and dominant. Co-dominant markers allow us to identify all of the alleles that are present at a particular locus, whereas dominant markers will reveal only a single dominant allele. As a result, co-dominant data are generally more precise than dominant data, although dominant markers usually require less development time and may therefore be a more convenient way to obtain data. In the rest of this section we will highlight some of the main features of markers in each of the two categories. Note that laboratory practice is, for the most part, beyond the scope of this text; readers looking for specific protocols are referred to the Further Reading section at the end of the chapter.
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