Conservation studies rely increasingly on molecular methods to evaluate species "status quo," historical distributions (biogeographical traits), and to develop management strategies for the restoration of populations. Since the invention of the polymerase chain reaction in the late 1980s (Mullis et al. 1996), further possibilities have opened up to apply genetic tools for diverse biological methods (see Fig. 1). Zhang and Hewitt (2003) revealed that, among the 1,758 primary papers and primer notes published between 1994 and 2003 in the journal of Molecular Ecology, 29.8 and 42.5% were indexed with mitochondrial and microsatellite DNA markers, respectively. Nevertheless, many more genetic methods exist to answer different ecological and genetic questions. Scientists, unfamiliar with the most commonly used genetic methods in the "conservation genetics field," tend to get lost in the different molecular techniques as each has its own advantages and disadvantages,

ETH Zürich, ITES-Ecosystem Management, Universitätstrasse 16, CH-8G92

Zürich, Switzerland e-mail: [email protected]

J.C. Habel and T. Assmann (eds.), Relict Species: Phylogeography and Conservation Biology, 309 DOI 10.1007/978-3-540-92160-8_18, © Springer-Verlag Berlin Heidelberg 2010

and can be applied in diverse forms. However, all these molecular techniques aim to detect genetic variation and differences within species, populations, or even individuals. This is generally achieved by comparing special DNA sections "marked" by the individual genetic method.

This chapter aims to present an overview of the most commonly used molecular methods during the last two decades (microsatellites, AFLPs, RFLPs, RAPDs, mtDNA, and allozymes) and the variety of ecological questions which can be answered with each method.

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