The Avian Hybrids Project: gathering the scientific literature on avian hybridization

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

doi:10.1111/ibi.12285

Cited by 90 publications

(87 citation statements)

References 21 publications

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“…The relative importance of hybridization in the evolution ary history of the True Geese remains to be investigated. The wide spread occurrence of hybridization in birds (Ottenburghs et al, 2015), and specifically waterfowl (Kraus et al, 2012;Randler, 2008;Ottenburghs et al, 2016), suggests that hybridization can act as an important component in avian speciation (Rheindt and Edwards, 2011). By integrating over the full exon set of genes we made a first step to quantitatively describe both species and gene histories.…”

Section: Resultsmentioning

confidence: 99%

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

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a b s t r a c tPhylogenetic incongruence can be caused by analytical shortcomings or can be the result of biological processes, such as hybridization, incomplete lineage sorting and gene duplication. Differentiation between these causes of incongruence is essential to unravel complex speciation and diversification events. The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, until now, con tentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing seventeen spe cies of which three subspecies of the Brent Goose, Branta bernicla) and used an exon based phylogenomic approach (41,736 exons, representing 5887 genes) to unravel the evolutionary history of this bird group. We thereby provide general guidance on the combination of whole genome evolutionary analyses and analytical tools for such cases where previous attempts to resolve the phylogenetic history of several taxa could not be unravelled. Identical topologies were obtained using either a concatenation (based upon an alignment of 6,630,626 base pairs) or a coalescent based consensus method. Two major lineages, corre sponding to the genera Anser and Branta, were strongly supported. Within the Branta lineage, the White cheeked Geese form a well supported sub lineage that is sister to the Red breasted Goose (Branta ruficol lis). In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese. The results from the consensus method suggest that the diversification of the genus Anser is heavily influ enced by rapid speciation and by hybridization, which may explain the failure of previous studies to resolve the phylogenetic relationships within this genus. The majority of speciation events took place in the late Pliocene and early Pleistocene (between 4 and 2 million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of tem perate grasslands. Our approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

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Section: Resultsmentioning

confidence: 99%

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs

Megens

Kraus

et al. 2016

Molecular Phylogenetics and Evolution

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“…Most studies focused on members of the Passeriformes, Galliformes, Anseriformes and Charadriiformes, bird orders that display high levels of hybridization (Ottenburghs et al 2015). Furthermore, several hybridizing species pairs have become model systems in the study of avian hybridization and introgression: among others, Collared Flycatcher (Ficedula albicollis) and Pied Flycatcher (F. hypoleuca), White-collared Manakin (Manacus candei) and Golden-collared Manakin (M. vitellinus), and Red-legged Partridge (Alectoris rufa) and Chukar Partridge (A. chukar).…”

Section: Open Accessmentioning

confidence: 99%

“…For several reasons, it is a common phenomenon in birds: the widespread occurrence of avian hybridization (Ottenburghs et al 2015) and the slow evolution of intrinsic postzygotic isolation (i.e. hybrids between distantly related species are still fertile), which enables backcrossing, increase the potential for introgression (Fitzpatrick 2004).…”

Section: Introductionmentioning

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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“…Although waterfowl are the most readily hybridizing family of birds (Grant and Grant 1992;Ottenburghs et al 2015), hybridization is unlikely to fully account for the observed widespread sharing of AvBD alleles. First, the occurrence of hybrid duck species decreases with phylogenetic distance (Tubaro and Lijtmaer 2002;Kraus et al 2012), yet shared alleles were found among species, genera, and families separated by millions of years of evolution (Gonzalez et al 2009) (fig.…”

Section: Inter-specific Variation: Allele Sharing Across Species Dividesmentioning

confidence: 99%

The Evolution of Innate Immune Genes: Purifying and Balancing Selection on β-Defensins in Waterfowl

et al. 2016

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In disease dynamics, high immune gene diversity can confer a selective advantage to hosts in the face of a rapidly evolving and diverse pathogen fauna. This is supported empirically for genes involved in pathogen recognition and signalling. In contrast, effector genes involved in pathogen clearance may be more constrained. b-Defensins are innate immune effector genes; their main mode of action is via disruption of microbial membranes. Here, five b-defensin genes were characterized in mallards (Anas platyrhynchos) and other waterfowl; key reservoir species for many zoonotic diseases. All five genes showed remarkably low diversity at the individual-, population-, and species-level. Furthermore, there was widespread sharing of identical alleles across species divides. Thus, specific b-defensin alleles were maintained not only spatially but also over long temporal scales, with many amino acid residues being fixed across all species investigated. Purifying selection to maintain individual, highly efficacious alleles was the primary evolutionary driver of these genes in waterfowl. However, we also found evidence for balancing selection acting on the most recently duplicated b-defensin gene (AvBD3b). For this gene, we found that amino acid replacements were more likely to be radical changes, suggesting that duplication of b-defensin genes allows exploration of wider functional space. Structural conservation to maintain function appears to be crucial for avian b-defensin effector molecules, resulting in low tolerance for new allelic variants. This contrasts with other types of innate immune genes, such as receptor and signalling molecules, where balancing selection to maintain allelic diversity has been shown to be a strong evolutionary force.

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The Avian Hybrids Project: gathering the scientific literature on avian hybridization

Cited by 90 publications

References 21 publications

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Avian introgression in the genomic era

The Evolution of Innate Immune Genes: Purifying and Balancing Selection on β-Defensins in Waterfowl

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