Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class

Jarvis, Erich D.

doi:10.1146/annurev-animal-021815-111216

Cited by 52 publications

(52 citation statements)

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“…In this review, we focus on the final step in this methodological progress: genomic data, which has become standard practise in ornithology (Kraus and Wink 2015;Jarvis 2016;Oyler-McCance et al 2016;Toews et al 2016). Following Toews et al (2016), we consider the following next generation sequencing techniques as genomic tools: genome sequencing and resequencing, reduced representation techniques (genotype-bysequencing [GBS] and restriction-site-associated DNA sequencing [RADseq]), sequence capture and RNA sequencing.…”

Section: Open Accessmentioning

confidence: 99%

Avian introgression in the genomic era

et al. 2017

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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: Open Accessmentioning

confidence: 99%

Avian introgression in the genomic era

et al. 2017

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“…Future research into avian hybrid zones and introgression is expected to rely on genomic data (Toews et al, 2016, Kraus and Wink, 2015, Jarvis, 2016. Whole-genome sequences will provide detailed information about patterns of divergence between hybridizing and diverging taxa and about patterns of variation across hybrid zones (Harrison and Larson, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…Genomics has become a standard practise, also in ornithology (Toews et al, 2016, Kraus andWink, 2015), opening avenues to answer longstanding questions in speciation and hybridization (Jarvis, 2016, Seehausen et al, 2014. Studies in speciation and hybridization genomics revealed that levels of genetic differentiation between species can be highly variable across the genome: genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape (Nosil et al, 2009, Nosil and Feder, 2012b, Harrison and Larson, 2016.…”

Section: Reinforcement Speciation Reversal Hybrid Speciation Stable Hmentioning

confidence: 99%

“…For example, a high frequency of hybrids and backcrosses might suggest high levels of recent gene flow, whereas the occurrence of sterile hybrids might be a remnant of an old syngameon, suggesting ancient gene flow. The recent developments in avian genomics offer opportunities to quantify levels of recent and ancient gene flow (Kraus and Wink, 2015, Jarvis, 2016, Toews et al, 2016 and to reconstruct the evolutionary history of a syngameon. For example, many studies have quantified the amount of recent gene flow between certain species pairs in the genus Anas (McCracken and Wilson, 2011, Guay et al, 2015, and see studies on Mallard hybridization listed above) and several studies suggested high levels of ancient gene flow in this genus (Kraus et al, 2012, Lavretsky et al, 2014, Peters et al, 2014b.…”

Section: Step 1: Detecting Putative Syngameons By Hybrid Networkmentioning

confidence: 99%

“…A genomic approach will be adopted to answer this question. Genomics has become a standard practise in ornithology (Toews et al, 2016, Kraus andWink, 2015), opening avenues to answer longstanding questions (Jarvis, 2016).…”

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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Exploring the hybrid speciation continuum in birds

Ottenburghs

2018

Ecology and Evolution

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Hybridization is increasingly recognized as a creative evolutionary force contributing to adaptation and speciation. Homoploid hybrid speciation—the process in which hybridization results in a stable, fertile, and reproductively isolated hybrid lineage where there is no change in ploidy—has been documented in several taxa. Hybridization can directly contribute to reproductive isolation or reinforce it at a later stage. Alternatively, hybridization might not be related to the evolution of reproductive isolation. To account for these different scenarios, I propose to discriminate between two types of hybrid speciation: type I where reproductive isolation is a direct consequence of hybridization and type II where it is the by‐product of other processes. I illustrate the applicability of this classification scheme with avian examples. To my knowledge, seven hybrid bird species have been proposed: Italian sparrow, Audubon's warbler, Genovesa mockingbird, Hawaiian duck, red‐breasted goose, golden‐crowned manakin, and a recent lineage of Darwin's finches on the island of Daphne Major (“Big Bird”). All studies provide convincing evidence for hybridization, but do not always confidently discriminate between scenarios of hybrid speciation and recurrent introgressive hybridization. The build‐up of reproductive isolation between the hybrid species and their parental taxa is mainly driven by premating isolation mechanisms and comparable to classical speciation events. One hybrid species can be classified as type I (“Big Bird”) while three species constitute type II hybrid species (Italian sparrow, Audubon's warbler, and golden‐crowned manakin). The diversity in hybrid bird species across a range of divergence times also provides an excellent opportunity to study the evolution of hybrid genomes in terms of genome stabilization and adaptation.

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Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class

Cited by 52 publications

References 79 publications

Avian introgression in the genomic era

Avian introgression in the genomic era

Crossing species boundaries : the hybrid histories of the true geese

Exploring the hybrid speciation continuum in birds

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