CHAPTER 2: Genetic Markers for Population Genetics

Summary of key concepts included in this chapter: Genetic markers are used to assess variation, from which inferences about evolutionary processes can be made. Ideal markers are selectively neutral, polymorphic within populations, lacking in homoplasy, locus-specific, codominant, reproducible, and affordable. Few phenotypes, such as races, vegetative compatibility groups (VCGs), and mating types, were available as markers before techniques of molecular biology were developed. PCR and sequencing technologies made the widespread application of genetic markers possible in nonmodel organisms. Microsatellites and single-nucleotide polymorphisms (SNPs) are the markers of choice for most applications in population genetics. With recent advances in sequencing technology, it is possible to mine genomic databases for microsatellites and discover large numbers of SNPs. Care must be taken when screening for polymorphisms and choosing markers to avoid ascertainment bias. We are in the population genomics era; next-generation sequencing makes it possible to resequence entire genomes or to generate huge amounts of SNP data. Large numbers of SNPs are ideal for genome-wide association studies that look for locus-specific effects on complex phenotypes.