Avian introgression in the genomic era

Abstract

Introgression, the incorporation of genetic material from one (sub)species into the gene pool of another by means of hybridization and backcrossing, is a common phenomenon in birds and can provide important insights into the speciation process. In the last decade, the toolkit for studying introgression has expanded together with the development of molecular markers. In this review, we explore how genomic data, the most recent step in this methodological progress, impacts different aspects in the study of avian introgression. First, the detection of hybrids and backcrosses has improved dramatically. The most widely used software package is STRUCTURE. Phylogenetic discordance (i.e. different loci resulting in discordant gene trees) is another means for the detection of introgression, although it should be regarded as a starting point for further analyses, not as a definitive proof of introgression. Specifically, disentangling introgression from other biological processes, such as incomplete lineage sorting, remains a challenging endeavour, although new techniques, such as the D-statistic, are being developed. In addition, phylogenetics might require a shift from trees to networks. Second, the study of hybrid zones by means of geographical or genomic cline analysis has led to important insights into the complex interplay between hybridization and speciation. However, because each hybrid zone study is just a single snapshot of a complex and continuously changing interaction, hybrid zones should be studied across different temporal and/or spatial scales. A third powerful tool is the genome scan. The debate on which evolutionary processes underlie the genomic landscape is still ongoing, as is the question whether loci involved in reproductive isolation cluster together in 'islands of speciation' or whether they are scattered throughout the genome. Exploring genomic landscapes across the avian tree of life will be an exciting field for further research. Finally, the findings from these different methods should be incorporated into specific speciation scenarios, which can consequently be tested using a modelling approach. All in all, this genomic perspective on avian hybridization and speciation will further our understanding in evolution in general.

Digest: A single genetic origin and a role for bone development pathways in repeated losses of flight in steamer ducks*

“…This scenario is supported by the observation of hybrid individuals between T. patachonicus and T. brachypterus (Fulton et al 2012). Hybridization is relatively common in birds, often resulting in the exchange of genetic material (Ottenburghs et al 2017) ( Figure 1B). The possible acquisition of "flighted alleles" through hybridization provides a plausible mechanism for regaining flight.…”

“…Hybridization is relatively common in birds, often resulting in the exchange of genetic material (Ottenburghs et al. ) (Figure B). The possible acquisition of “flighted alleles” through hybridization provides a plausible mechanism for regaining flight.…”

Exploring the hybrid speciation continuum in birds

“…However, the authors were unable to differentiate between more complex speciation models with gene flow (Barrera‐Guzman et al, ). Phylogenetic network analyses or modeling approaches, such as Approximate Bayesian Computation (ABC), promise to be a fruitful avenue to tackle these issues (Ottenburghs, Kraus, et al, ).…”

Digest: White‐eye birds provide possible answer to the paradox of the great speciator*

“…Hence, when closely related bird species come into secondary contact, one can expect high levels of gene flow (Ottenburghs et al. ).…”

“…The combination of frequent hybridization and slow evolution of intrinsic reproductive isolation increases the potential for interspecific gene flow. Hence, when closely related bird species come into secondary contact, one can expect high levels of gene flow (Ottenburghs et al 2017).…”