The Idiot's Guide to Effective Population Size

This is a reference manual for the elegant, yet hideously complex concept of effective population size (Ne), inspired by a classic, self-published manual of automotive repair "for the compleat idiot." Two early encounters with Ne are described, which (1) considered what it means to find statistically significant genetic drift, and (2) explored consequences of expanding the original discrete-generation Ne concept to species with different life histories. The next section—Whither are we drifting with genomics and Ne?—considers both possibilities and challenges presented by the genomics revolution. The ready availability of vast numbers of genetic markers increases precision, but not as much as some might think. As annotated genomes become more common for non-model species, opportunities are opened to address qualitatively different questions, including reconstructing historical changes in Ne through time. The bulk of the paper brings together in a single location factual information about effective population size, with a focus on information of practical relevance to scientists and managers studying real populations. The Guide covers definition, computation, and estimation of effective size, both demographically and genetically. As appropriate, the reader is directed to other primary sources for more details. Finally, an Appendix provides useful tools and practical suggestions for interested users, and closes with a section "Don't Do These Things" that lists a number of ill-advised approaches to dealing with Ne.