Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers

Abstract

Recent improvements in genetic analysis and genotyping methods have resulted in a rapid expansion of the power of molecular markers to address ecological questions. Microsatellites have emerged as the most popular and versatile marker type for ecological applications. The rise of commercial services that can isolate microsatellites for new study species and genotype samples at reasonable prices presents ecologists with the unprecedented ability to employ genetic approaches without heavy investment in specialized equipment. Nevertheless, the lack of accessible, synthesized information on the practicalities and pitfalls of using genetic tools impedes ecologists' ability to make informed decisions on using molecular approaches and creates the risk that some will use microsatellites without understanding the steps needed to evaluate the quality of a genetic data set. The first goal of this synthesis is to provide an overview of the strengths and limitations of microsatellite markers and the risks, cost and time requirements of isolating and using microsatellites with the aid of commercial services. The second goal is to encourage the use and consistent reporting of thorough marker screening to ensure high quality data. To that end, we present a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike.

Evolution along the Great Rift Valley: phenotypic and genetic differentiation of East African white‐eyes (Aves, Zosteropidae)

“…Non‐hierarchical analyses of molecular variance were performed with arlequin using the microsatellite‐specific R ‐statistics (Slatkin 1995; Selkoe and Toonen 2006). Furthermore, we calculated pairwise D est values (Jost 2008) across all populations (excluding Eburu Forest, due to very small sampling size) with the program smogd v.1.2.5.…”

Genomic resources for the conservation and management of the harpy eagle (Harpia harpyja, Falconiformes, Accipitridae)

“…Of the various types of molecular markers used today, microsatellites have many positive attributes, including hypervariability, co-dominance, abundance and tolerance to variation in DNA quality and quantity (Selkoe and Toonen, 2006). Additionally, due to our reasonably good understanding of molecular evolution and the development of robust computational methods, microsatellites are wellsuited to answer questions related to effective population size, population structure, migration and colonization rates, and reproductive system, thus providing essential data for conservation.…”

“…Although mutations in the flanking regions of microsatellite loci may prevent amplification, many studies have shown that microsatellites isolated from one species can amplify homologous products in related species (e.g. Martínez-Cruz et al, 2002;Busch et al, 2005), a characteristic known as transferability or cross-species amplification (Selkoe and Toonen, 2006).…”

Isolation and characterization of microsatellite loci from blue-footed boobies (Sula nebouxii)

“…Mendelian inheritance, combined with high levels of polymorphism, makes microsatellite loci ideal for these purposes and for analyses of small and isolated populations, like blue-footed boobies (Hedrick 1999;Selkoe and Toonen 2006). In this manuscript, we describe the isolation and characterization of 11 microsatellite loci, which we tested using 31 S. nebouxii.…”