Plant Molecular Biology 42: 205–224, 2000. © 2000 Kluwer Academic Publishers. Printed in the Netherlands. 205 Hybridization, introgression, and linkage evolution Loren H. Rieseberg * , Stuart J. E. Baird and Keith A. Gardner Dept. of Biology, Indiana University, Bloomington, IN 47405-6801, USA ( * author for correspondence) Key words: genetic mapping, graphical genotypes, hybridization, introgression, junction theory Abstract Genetic mapping methods provide a unique opportunity to study the interactions of differentiated genes and genomes in a hybrid genetic background. After a brief discussion of theoretical and analytical concerns, we review the application of these methods to a wide range of evolutionary issues. Map-based studies of experimental hybrids indicate that most postzygotic reproductive barriers in plants are polygenic and that the expression of extreme or novel traits in segregating hybrids (transgressive segregation) results from the complementary action of divergent parental alleles. However, genetic studies of hybrid vigor do not concur in their interpretations of the relative roles of dominance, overdominance, and epistasis. Map-based studies of natural hybrids are much rarer, but the few existing studies confirm the polygenic basis of postzygotic barriers and demonstrate the utility of genetic linkage for detecting cryptic introgression. In addition, studies of experimental and natural hybrid lineages provide compelling evidence that homoploid hybrid speciation has occurred in nature, and that it represents a rapid and repeatable mode of speciation. Data further indicate that this mode is facilitated by strong fertility selection and high chromosomal mutation rates. We recommend that future studies of hybrid genomes focus on natural hybrids, not only because of the paucity of data in this area, but also because of the availability of highly recombinant hybrid genotypes in hybrid zones. Of particular value will be studies of long-lived or difficult-to-propagate organisms, which previously have not been amenable to genetic study. Introduction Hybridization can be viewed as a reunion between differentiated genetic material. Until recently, the re- sults of these reunions could only be studied in a fairly indirect manner. One method was to analyze the phenotype of hybrids, such as the symmetry of morphological characters or the viability of pollen or seed. Alternatively, meiosis in hybrids could be studied by light microscopy and the degree of dif- ferentiation between hybridizing taxa estimated by analyses of chromosome pairing behavior and mei- otic abnormalities. Although both of these approaches have been extremely valuable, they can only provide glimpses into the complex interactions of alien genes and genomes following genetic reunions. This decade has seen two technological advances that have revolutionized our ability to study hy- brid genomes: molecular-marker-based genetic link- age mapping [145, 146] and in situ hybridization (ISH) of genomic probes to cytological preparations [10, 61, 66, 74, 88, 111]. These approaches are advantageous relative to traditional methods because they allow the dynamics of parental species chromo- somal segments to be monitored in a hybrid genetic background. With the ISH approach, hybrid or introgressive karyotypes are ‘painted’ using genome-specific DNA probes [69]. Probes typically are generated by fluo- rescence labeling of entire genomes or repetitive se- quences [43, 124]. The extent of introgression across the entire genome can then be visualized in a sin- gle hybridization experiment. However, the method is limited by the requirement of substantial genomic divergence between the taxa studied and by the diffi- culty of detecting introgression of small chromosomal segments. In addition, the data generated are not con- ducive to analysis with quantitative genetic theory