What molecules can tell us about populations: choosing and using a molecular marker

Ecology, March, 1998 by Patricia G. Parker, Allison A. Snow, Malcolm D. Schug, Gregory C. Booton, Paul A. Fuerst

INTRODUCTION

Population biologists seek to understand how variations in survivorship, fertility, and gene flow contribute to changes in allele frequencies within and among populations. Events such as mate acquisition, reproduction, immigration, and hybridization are of particular interest in efforts to understand the process of adaptation to particular ecological circumstances. To determine ecological correlates of fitness within populations and to determine the extent of divergence among populations, one often needs access to independently segregating genetic markers that do not influence the organism's phenotype. Empirical studies that employ allozyme polymorphisms as genetic markers have contributed a great deal to our understanding of population processes. However, due to a lack of sufficient allozyme variation, many enticing research directions have been impractical to date, especially those requiring information about genetic relatedness of individuals within populations.

In the last decade, a diverse array of new molecular genetic tools has become available for high-resolution genetic studies of population-level processes. The hope of obtaining highly informative genetic markers for tracking individuals and/or their genes under field conditions has led many population biologists to consider switching to DNA-based techniques. At present, though, the rate at which new molecular techniques are being developed far outstrips their efficient and reasoned incorporation into studies of population ecology. In many cases, statistical methods for analyzing novel genetic data have yet to be formulated. This has led to confusion among population biologists about various new techniques, often causing people to prematurely abandon standard techniques (such as electrophoresis of allozymes) that provide readily interpretable data. The allure of exploring newly accessible variation in DNA sequences needs to be tempered by a thorough consideration of the trade-offs associated with different techniques and the types of data obtained from them.

Our aim is to provide this perspective. First we define the basic categories of genetic techniques available for use in population ecological studies, including explanations of fundamental procedures common to all techniques as well as features unique to particular classes of techniques. We present the basic categories of techniques in order of increasing resolution of resulting information, and we evaluate how these techniques can be applied to a standard range of questions in population ecology. Features such as cost, technical difficulty, appropriateness of resulting data, and sophistication of existing statistical methods are all considered. Technological innovations are proceeding so quickly that "new" molecular techniques may soon be viewed as outdated, while seemingly impossible approaches become more feasible. In this climate of technical change, this review is meant to serve as a foundation for those now in need of high-resolution genetic markers.

Another goal of this paper is to make molecular techniques more accessible to a general audience. With the recent proliferation of ecological and evolutionary studies that employ molecular markers, population biologists must have some understanding of these techniques in order to comprehend and evaluate current literature. This review is intended to provide more information than recent essays on minisatellite, microsatellite, and RAPD [random amplified polymorphic DNA] markers (Burke 1989, Queller et al. 1993, and Hadrys et al. 1992, respectively), and less detail than texts by Hoelzel and Dover (1991), Hoelzel (1992), Avise (1994), and Hillis et al. (1996).

BASIC TECHNIQUES

In this section, we begin with a brief review of allozyme variation, followed by a more detailed explanation of genetic markers obtained from DNA itself (e.g., RFLPs [restriction fragment length polymorphisms], RAPDs, mini- and microsatellite DNA). All of these techniques involve careful extraction of molecules, either proteins or DNA, and electrophoretic separation of the molecules on a gel so that polymorphisms can be detected. The type of genetic variation that is sampled by these methods includes allelic variation in gene products (allozymes) and length variation in specific DNA fragments. For the greatest possible resolution, divergence in nucleotide base sequences can also be examined using DNA sequencing techniques.

Allozymes

Background and technical considerations. - Prior to the development of electrophoretic techniques in the 1950s (Smithies 1955, Hunter and Markert 1957), few single-locus genetic markers were available to population biologists. Early markers included genes for Mendelian traits such as flower or fruit color and serological incompatibility reactions. Protein electrophoresis provided a new source of marker genes, and allowed individuals to be identified as homozygotes or heterozygotes at a given locus. The term "allozyme" refers to different allelic forms of nuclear-encoded enzymes, whereas "isozyme" is a more general term referring to different biochemical forms of an enzyme identified by electrophoresis.