Next-generation hybridization and introgression

Abstract

Hybridization has a major role in evolution-from the introgression of important phenotypic traits between species, to the creation of new species through hybrid speciation. Molecular studies of hybridization aim to understand the class of hybrids and the frequency of introgression, detect the signature of ancient hybridization, and understand the behaviour of introgressed loci in their new genomic background. This often involves a large investment in the design and application of molecular markers, leading to a compromise between the depth and breadth of genomic data. New techniques designed to assay a large sub-section of the genome, in association with next-generation sequencing (NGS) technologies, will allow genome-wide hybridization and introgression studies in organisms with no prior sequence data. These detailed genotypic data will unite the breadth of sampling of loci characteristic of population genetics with the depth of sequence information associated with molecular phylogenetics. In this review, we assess the theoretical and methodological constraints that limit our understanding of natural hybridization, and promote the use of NGS for detecting hybridization and introgression between non-model organisms. We also make recommendations for the ways in which emerging techniques, such as pooled barcoded amplicon sequencing and restriction site-associated DNA tags, should be used to overcome current limitations, and enhance our understanding of this evolutionary significant process.

Figure 1

Hybridization and incomplete lineage sorting revealed by molecular phylogenetics. The phylogenetic relationship of alleles (coloured lines) are shown in the context of the species tree (grey bars, and the tree in panel c). The pattern of alleles when species hybridize (a) or when incomplete lineage sorting occurs (b) are the same, even though they are due to different processes (d and e, respectively). However, lineage sorting always results in coalescence with the other species prior to the speciation event (t₂). Coalescence of alleles is not expected where hybridization events are significantly later than the speciation event (t₁). Adapted from Pollard et al. (2006). A full colour version of this figure is available at the Heredity journal online.

Figure 2

Workflow for using NGS in molecular phylogenomics and population genomics. Different genomic resources can be produced (a) and used in phylogenomic (b) and population genomic studies (d), where informative genetic differentiation is identified and markers designed to assay natural populations. These separate stages, including production of genomic resources, are not required for integrated studies (c) where marker detection and application are performed simultaneously, as shown here with RAD tags. Instead, in the integrated approach, DNA is cut with restriction enzymes (red arrows), an individual/population-specific adaptor (coloured box) is ligated and the product amplified on an NGS platform (not shown). The genomic data generated from these studies can then be analysed by using standard phylogenetic and population genetic programmes (e). A full colour version of this figure is available at the Heredity journal online.