My three PhD-chapters on avian hybrids have found their way into scientific journals. The trilogy is complete!
If you have read my PhD thesis (which you probably didn’t, but luckily you can find it here), you would notice that it was divided into two parts, each consisting of three chapters. Two trilogies, if you will. The first trilogy, focusing on hybridization in geese, was completed some months ago when I published the final part in BMC Evolutionary Biology. You can read more about the goose trilogy here. The second trilogy, which concerns avian hybridization in general, was finished this week with a publication in the ornithological journal Avian Research. Let’s have a closer look at these three papers.
Part 1: How many bird species hybridize?
Scientists familiar with the literature on avian hybridization would immediately respond to this question with “roughly 10%”. In 1992, Peter and Rosemary Grant (yes, those from the Darwin’s Finches) estimated that about 1 in 10 bird species has hybridized with at least one other species. But a lot of new data has accumulated since the beginning of the 1990’s. So, I decided to redo the analyses (using data from the Bird Hybrids Database). It turns out that the percentage has risen to 16% (and even as high as 22% if you include captive hybrids). And this estimate is probably too low given our ignorance of tropical birds.
In addition to this analysis I introduced the Avian Hybrids Project (the website you are currently reading). During the first months of my PhD, I read a lot on hybridization in birds (and other organisms). While I was plowing my way through this literature and writing small summaries per bird group, I thought “why not share this information with the world?” So, I started the Avian Hybrids Project and announced it with a publication in the journal Ibis: “The Avian Hybrids Project: gathering the scientific literature on avian hybridization.”
An overview of hybridization in birds. Green = no hybrids, Blue = wild hybrids, Red = captive hybrids. The size of the circles if proportional to the number of species in the bird order.
Part 2: From trees to bushes
The second part of the trilogy revolves around the implications of hybridization for phylogenetic research. Phylogenetics is the study of the evolutionary history and relationships between species. Traditionally, these relationships are depicted in bifurcating trees. But with the increasing amount of genome-wide data, it turned out that different genes often result in different phylogenetic trees. This phenomenon is known as gene tree discordance or phylogenetic incongruence. For example, an phylogenetic analysis of humans, chimps and gorillas showed that 30% of the genomic positions resulted in a different gene tree compared to the classical species tree (in which humans are most closely related to chimps).
There are many computational and biological processes that can explain these patterns. And hybridization is one possibility. When species interbreed, they might exchange genetic material, as process known as introgression. Analyses of these exchanged genetic regions often result in gene trees that conflict with the general species tree. It becomes difficult to capture these patterns in the traditional bifurcating phylogenetic tree. Therefore, I advocated for the use of phylogenetic networks. From trees to bushes!
You can read more about this in the paper “Birds in a Bush: Towards an Avian Phylogenetic Network“, which was published in The Auk.
A network of geese (from Ottenburghs et al. 2017 BMC Evol Biol)
Part 3: Genomics
And that brings us to part three, which was published this week in Avian Research. In this review paper, entitled “Avian Introgression in the Genomic Era“, I discuss the use of genomic data to study introgression in birds. In short, I introduce the following topics:
- Detecting hybrids
- Phylogenetic discordance (see also Part 2 of the trilogy)
- Hybrid Zones
- The Genomic Landscape
And here is the 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.
Different aspects of studying introgression with genomic data. I propose to use the outcomes from these methods to better inform modelling exercises.
I guess you know what to read this weekend…
Ottenburghs, J., Ydenberg, R.C., van Hooft, P., Van Wieren, S.E., & Prins, H.H.T. (2015). The Avian Hybrids Project: gathering the scientific literature on avian hybridization. Ibis, 157 (4), 892-894 DOI: 10.1111/ibi.12285
Ottenburghs, J., van Hooft, P., van Wieren, S.E., Ydenberg, R.C. & Prins, H.H.T. (2016). Birds in a Bush: Towards an Avian Phylogenetic Network. The Auk. 133:577-582 doi: http://dx.doi.org/10.1642/AUK-16-53.1
Ottenburghs, J., Kraus, R.H.S, van Hooft, P., van Wieren, S.E., Ydenberg, R.C. & Prins, H.H.T. (2017). Avian Introgression in the Genomic Era. Avian Research. 8:30 https://doi.org/10.1186/s40657-017-0088-z