Hybridization and Gene Flow

With human-induced destruction of habitats and climate-change issues pervading the news, researchers have renewed interest in natural processes that generate and preserve biodiversity on this planet. Understanding these natural processes requires looking at the interface between species—those instances in which the rules of differentiation are broken, and species exchange genes with one another in nature.

In the mid-nineteenth century, Darwin explored the nature of species by interbreeding them and demonstrating that mating between groups can be difficult (Darwin, 1859). Surprisingly, however, hybridization between species in nature is not as uncommon as this early result would imply (Mallet, 2005). After Darwin, botanists and zoologists took different paths to understanding hybridization. For example, botanist G. Ledyard Stebbins focused on hybridization as an important generator of genetic diversity (Stebbins, 1950). In contrast, zoologists such as Theodosius Dobzhansky and Ernst Mayr considered animal hybrids to be "rare" or "exceptional," and they instead discussed hybridization as a negative selective agent that favored the strengthening of discrimination to maintain species (Dobzhansky, 1937; Mayr, 1942).

Since then, scientists have been able to uncover many examples of hybridization across several branches of life. This evidence initially came from fossil or extant species morphology, but more recently, molecular tools have enhanced hybridization research in a wealth of biological systems (Mallet, 2005). Over the last 50 years, the study of hybridization has yielded valuable insights, not only refining scientists' systematic understanding of the taxa involved, but also helping researchers understand those forces that limit hybridization, as well as how gene flow and recombination can act to generate novel haplotypes to facilitate adaptation (Arnold, 1997).

Just as sexual reproduction can bring different sets of alleles together in a common genetic background to facilitate adaptation, hybridization between species can allow alleles from one genetic background to integrate into another if favored by selection. This special case in which genomes from different species fuse to generate a new hybrid species lineage, a process called reticulation, has been most intensively studied in plants. For instance, reticulation drove diversification within the sunflower genus Helianthus, in which researchers have uncovered three species of hybrid origin. Each of these three hybrid species inhabits extreme environments relative to the parental species, suggesting that hybridization has generated novel adaptive traits (Figure 1). Loren Rieseberg's research team has tested this hypothesis directly by generating artificial hybrids with the same genetic origins as the ancient hybrid species found in nature (Rieseberg et al., 2003). These artificial hybrids resemble natural hybrids in adaptive allelic combinations, demonstrating that hybridization may be a unique way for species to invade novel habitats with the generation of novel allelic combinations at many genes in a single generation.

When different genomes come into contact, gene exchange is not necessarily homogeneous, because alleles of some genes disperse across species boundaries more easily than others. This observation has been reported across many different organisms, and it is associated with both single genes and large genomic regions, such as whole chromosomes or chromosomal regions. One well-studied example involves reduced gene flow associated with inversion events on whole chromosomes in the North American Drosophila species D. pseudoobscura and D. persimilis. These co-occurring species are less than 1 million years diverged and differ by three chromosomal inversions (reversals in a segment of the DNA sequence). Despite their limited nucleotide divergence and genomic rearrangements, these species hybridize at a low level in nature. Moreover, when examined genetically, allelic exchange (also known as introgression) between the species appears highest away from inverted regions and lowest within inverted regions (Noor et al., 2007), suggesting that the inversions themselves cannot readily cross the species boundary. Although there is still much to learn, this system suggests a role for inversions in the persistence of hybridizing species.

In addition to fruit flies, house mice have also been studied extensively for variance in gene exchange across the genome. A large house mouse hybrid zone is found in central Europe, and the Nachman lab at the University of Arizona has analyzed the spread of traits and alleles across this hybrid zone to understand the evolutionary forces at work (Payseur et al., 2004). Researchers hypothesize that differential gene flow across species boundaries is a pattern resulting from selection, in which the absence of selection on some traits or alleles between species results in gradual transitions of these traits across a hybrid zone. In contrast, ongoing selection to maintain species at other traits prevents the dispersal of alleles across species boundaries and is expected to produce a pattern of steep transitions of traits across a hybrid zone. In house mice, researchers found that alleles near the center of the X chromosome exhibit steep transitions across the hybrid zone, and these alleles are in a region previously shown to be associated with hybrid sterility. This work demonstrates the utility of hybrid zones to test for the effect of selection on interspecies gene flow in particular regions of the genome.

By continuing to study hybridizing species and hybrid zones, researchers can further understand which sets of genes have permissible gene flow and which are more restricted. Then, by studying genes in the latter category, scientists can learn which genes or gene sets may be important in maintaining species integrity in the face of gene flow.

Although research in some systems has brought insights into the nature of hybridization, detecting and quantifying interspecies gene flow is surprisingly difficult. Until recent advances in sequencing technologies, scientists relied on phenotypic characters to study hybridization, which sometimes yielded results incongruent with molecular data. Furthermore, identification of hybrids is also difficult using phenotype alone because of the paucity of early generation hybrids in the wild and because introgression is not always apparent in phenotypes.

These limitations are now becoming obsolete as scientists have the ability to assess hybridization using neutral molecular markers. As with phenotypic characters, closely related species may share some molecular variation that persists after their initial split, making it difficult to distinguish this shared variation from gene flow after speciation, as explained by coalescent theory (Hey, 2006). Additionally, phylogenetic estimates of species relationships often contrast with one another because forces such as drift, selection, and recombination affect different parts of the genome differently. One way to tackle this difficulty is to examine sequences of many genes or whole genomes to assess gene flow, and to then apply statistical or simulation tests to evaluate whether an evolutionary model without gene flow can be rejected (Hey & Nielsen, 2004; Machado et al., 2002). Acquiring the DNA sequences and executing the statistics for such tests can be expensive and computationally challenging (Excoffier & Heckel, 2006; Felsenstein, 2006). Thus, it is not surprising that with the advent of new high-throughput sequencing technologies and more powerful processors in the last decade, the number of studies focusing on testing hybridization between species has increased by orders of magnitude.

Apart from the technological difficulties of studying hybridization are the philosophical problems associated with interpreting interspecies gene exchange. One's perception of species is important if one is to describe processes across species boundaries. Thus, some biologists work their definitions of hybridization around species concepts (Arnold, 1997), while some species concepts allow for gene flow (Mallet, 1995).

Nonetheless, it is by overcoming these difficulties that scientists have been able to advance the study of hybridization in the last half century. With this advancement comes the ability to apply the knowledge from systems such as Drosophila and mice to nonmodel systems, such as sunflowers, irises, and red wolves (Arnold, 2000; Fredrickson & Hedrick, 2006), with equally complex histories of hybridization. As scientists continue to explore the interface of species through hybrid zones and analysis of introgression, they also continue to discover the facets of genetic diversity that contribute to generating and maintaining the biodiversity of our living planet.