The molecular methods presented in this chapter have question-related advantages and disadvantages (see Table 1). Before choosing a marker, it is essential to evaluate (1) which ecological question ought to be answered, (2) the spatial and temporal scales which ought to be explored, and (3) how exhaustive populations can be sampled (sample design; for detailed sample strategies, see Lowe et al. (2004), and (4) the available financial resources. Furthermore, the popularity of a specific marker might be important for the acceptance in a high ranking peer-reviewed journal, even though many markers could be suitable to answer the same question (Assmann et al. 2007).
In conclusion, we can say that microsatellites are currently one of the most popular genetic markers in ecological studies (see Fig. 1). Especially, the elevated rate of polymorphism is ideal to study small geographical scales of extant species (e.g., Finger et al. 2009). The use of allozyme markers is decreasing since several years (Fig. 1), although the low costs allow a high throughput for studying large geographical scales of extant species (Schmitt 2007). Similarly, AFLPs, RAPDs, and RFLPs can be used to study small to large geographical scales. These markers have their own drawbacks (AFLPs: no detection of alleles, RAPDs: low reproduc-
Fig. 2 Different time and geographical scales applicable using mtDNA, Allozymes, Microsatellites, RFLPs, RAPDs, and AFLPs
Fig. 2 Different time and geographical scales applicable using mtDNA, Allozymes, Microsatellites, RFLPs, RAPDs, and AFLPs ibility, RFLPs: high amount of DNA required, see Table 1). Finally, mtDNA is the best choice to study species history and phylogeography on broad geographical scales or deeper timescales (see Fig. 2).
Acknowledgements We would like to thank the professorship of Ecosystem Management, ETH (Jaboury Ghazoul) for funding. Furthermore, we are grateful for comments and corrections from Christopher Kaiser, Chris Kettle, Axel Hochkirch, and Andrea Pluess.
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