Genotyping and Sequencing Technologies in Population Genetics and Genomics

Genotypes are the central data to any population genetic and genomic study, and genotyping methods have steadily evolved since the first direct glimpses of genetic variation were enabled through enzyme protein electrophoresis. Following the development of the polymerase chain reaction, allozymes were supplanted by methods that directly measured allelic variation in nuclear and organellar DNA, most notably through the use of restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs), and microsatellites. At the turn of the millennium, genome-scale polymorphism detection and scoring still was hampered by the low-throughput nature of Sanger sequencing. This limitation changed with the advent of genotyping microarrays that at first yielded hundreds of data points per sample – a revolution at the time – and that subsequently improved to the point where hundreds of thousands of genetic variants could be scored simultaneously. These methods suffered a major flaw, however, in that their cost put them out of reach for studies of most ecologically important but economically unimportant species. The democratization of population genomics arrived with the advent of high-throughput, short-read sequencers and subsequent development of DNA library techniques to subsample the genome in a large number of individuals. Today, such methods – genotyping-by-sequencing, restriction site-associated DNA sequencing, RNA sequencing, and sequence capture – have become mainstays of the population geneticist’s toolkit. Refinements to existing library and sequencing methods continue to emerge at a rapid pace, and novel sequencing platforms may soon put the gold standard of long-read, genome-wide coverage within a broader reach. In this chapter, we comprehensively review genotyping methods used in population genetics, beginning with allozymes and progressing through AFLPs, microsatellites, and SNP arrays. We subsequently turn to a detailed discussion of methods that leverage next-generation technologies to enable truly genome-scale genotyping. Finally, we discuss recent developments and emerging technologies that constitute the “third wave” of sequencing and genotyping methods. Throughout, our aim is to provide methodological details that will be of use to population geneticists.