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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.


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Avian introgression in the genomic era

Show Author's information Jente Ottenburghs1Robert H. S. Kraus2,3Pim van Hooft1Sipke E. van Wieren1Ronald C. Ydenberg1,4Herbert H. T. Prins1
Resource Ecology Group, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands
Department of Biology, University of Konstanz, 78457 Constance, Germany
Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg 1, 78315 Radolfzell, Germany
Centre of Wildlife Ecology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada

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.

Keywords: Hybridization, Admixture, Cline theory, D-statictic, Genomic landscape, Phylogenetic discordance

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Received: 20 July 2017
Accepted: 16 November 2017
Published: 30 November 2017
Issue date: January 2017

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We are grateful to Leo Joseph and Peter Grant for their useful comments on early versions of this manuscript. We also thank the anonymous reviewer whose suggestions greatly improved the manuscript.

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