Birds in a bush: Toward an avian phylogenetic network

Ottenburghs, Jente; Hooft, Pim van; Wieren, S.E. van; Ydenberg, Ronald C.; Prins, Herbert H. T.

doi:10.1642/auk-16-53.1

Cited by 20 publications

(20 citation statements)

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“…Specifically, disentangling introgression from incomplete lineage sorting remains a challenging endeavour, although new techniques, such as the D-statistic, are being developed. Furthermore, with the advent of genomic data, phylogenetics might require a shift from trees to networks (Edwards et al 2016;Ottenburghs et al 2016).…”

Section: Discussionmentioning

confidence: 99%

“…Another way to deal with introgression and incomplete lineage sorting is to switch from phylogenetic trees to phylogenetic networks (Huson and Bryant 2006;Ottenburghs et al 2016Ottenburghs et al , 2017. Some methods for constructing phylogenetic networks allow for hybridization while ignoring incomplete lineage sorting (Beiko and Hamilton 2006), whereas other methods take into account incomplete lineage sorting while ignoring hybridization (Maddison and Knowles 2006; Than and Nakhleh 2009).…”

Section: Phylogenetic Discordancementioning

confidence: 99%

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Avian introgression in the genomic era

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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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Section: Discussionmentioning

confidence: 99%

Section: Phylogenetic Discordancementioning

confidence: 99%

Avian introgression in the genomic era

et al. 2017

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“…This set the stage for the production of numerous plant hybrids. This period, ranging from 1700 until 1760, is described in detail by Conway Zirkle (1935) in his book The Beginnings of Plant Hybridization.…”

Section: Dialogue From Jurassic World (2015)mentioning

confidence: 99%

“…For example, in Historiae Animalium Conrad Gesner (1560) reported several peculiar hybrids, such as the Jumar (an alleged cross between a donkey and a cow). Most of the hybrids described by Gesner (1560) turned out to be fictional, but the interest in hybridization did not diminish (Zirkle, 1935). However, opinions about the importance of hybridization in evolution differed: some regarded hybridization as a creative evolutionary force (Lotsy, 1916, Anderson, 1949, Anderson and Stebbins, 1954, Lewontin and Birch, 1966, while others considered it a byproduct of the speciation process (Mayr, 1942, Mayr, 1963, Dobzhansky, 1937, Templeton, 1989.…”

Section: General Introductionmentioning

confidence: 99%

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Crossing species boundaries : the hybrid histories of the true geese

Ottenburghs¹

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. Crossing Species Boundaries: The Hybrid Histories of the True Geese. PhD thesis, Wageningen University, the Netherlands. Hybridization, the interbreeding of different species, is a common phenomenon in birds: about 16% of bird species is known to have hybridized with at least one other species. Numerous avian hybrid zones have been studied from a morphological or genetic perspective, often documenting the interspecific exchange of genetic material by hybridization and backcrossing (i.e. introgression). The incidence of hybridization varies among bird orders with the Anseriformes (waterfowl: ducks, geese and swans) showing the highest propensity to hybridize. In this thesis, I provide a genomic perspective on the role of hybridization in the evolutionary history of one particular anseriform tribe, the Anserini or "True Geese", which comprises 17 species divided over two genera: Anser and Branta . The diversification of this bird group took place in the late Pliocene and the early Pleistocene (between four and two million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of temperate grasslands. Most species show a steady population increase during this period, followed by population subdivision during the Last Glacial Maximum about 110,000 to 12,000 years ago. The combination of large effective population sizes and occasional range shifts facilitated contact between the diverging goose species, resulting in high levels of interspecific gene flow. Introgressive hybridization might have enabled these goose populations to quickly adapt to changing environments by transferring of advantageous alleles across species boundaries, increasing standing genetic variation or expanding phenotypic variation of certain traits (e.g., beak morphology). Hybridization seems to be a common and integral component in the evolution and diversification of geese. The pervasiveness of rapid speciation and hybridization in geese complicates the attempt to capture their evolutionary history in a phylogenetic tree, therefore I advocate a phylogenetic network approach. Indeed, trying to capture the complex diversification of the True Geese in a branching tree can be regarded as a wild goose chase. Abstract TABLE OF CONTENTS

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Ghost Introgression: Spooky Gene Flow in the Distant Past

Ottenburghs

2020

BioEssays

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Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present-day genomes, so-called ghost introgression. The increasing availability of high-quality genome assemblies for non-model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly reveal more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed.

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Birds in a bush: Toward an avian phylogenetic network

Cited by 20 publications

References 58 publications

Avian introgression in the genomic era

Avian introgression in the genomic era

Crossing species boundaries : the hybrid histories of the true geese

Ghost Introgression: Spooky Gene Flow in the Distant Past

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