Non-coding DNA drives the evolution of avian beak morphology

“Living things do not inherit skulls, backbones, or cell layers from their ancestors—they inherit the processes to build them.”

– Neil Shubin (Some Assembly Required)

A few days ago, I finished the book “Some Assembly Required” by Neil Shubin. It is a great read about the big changes during evolution. Combining insights from paleontology, genomics and development biology, Shubin explains how major evolutionary transitions took place. One key idea that I took away from this book is illustrated by the quote above: if we want to reconstruct the evolution of complex traits, we need to understand how they are build. In other words, we have to unravel the genetic and developmental underpinnings of these traits.

One of the most important traits in avian evolution is the shape of the bill. Variations in bill morphology – from the sharp beaks of predators to the long bills of avocets – have allowed birds to exploit a myriad of ecological niches and diversify into the many species we see today. Surprisingly, little is known about the genetic and developmental processes underlying this variation. A recent study in the journal Genome Research took a macroevolutionary perspective on the avian beak.

The diversity of bird beaks – Adapted from L. Shyamal | Wikimedia Commons

 

Candidate Genes

To be honest, we do know quite a bit about the genetics of beak morphology. Studies on particular species have uncovered several candidate genes. For example, the beak shapes of Darwin’s finches are determined by, among others, the genes BMP4 (depth and width) and CALM1 (beak length). Recent genomic work suggested additional roles for ALX1 (craniofacial development) and HGMA2 (beak size). Interestingly, in great tits (Parus major) another gene – COL4A5 – was linked to variation in beak morphology. These examples indicate that beak shape is probably influenced by many genes and that different genes are under selection in different bird groups.

Leeban Yusuf and his colleagues compared the genomes of 72 bird species to see whether there is a common genetic mechanism underlying the evolution of beak morphology. They divided the species into separate bins based on the rates of beak shape evolution. Next, they estimated the rate at which different protein-coding genes evolved (using the dN/dS approach). If certain protein-coding genes are involved in the evolution of beak morphology, you expect a positive correlation between the bird-bins and the rate of molecular evolution. This analysis uncovered 1434 candidate genes of which several are part of developmental pathways that are involved in beak morphology (namely the Wnt signalling pathway and the ESC pluripotency pathways). There was, however, no positive correlation between the rates of beak shape change and molecular evolution. This result shows that the evolution of beak morphology is more complicated than a few mutations in protein-coding genes.

An example of how rates of beak morphology change are divided into different bins (six in this case) from slowest to fastest. From: Yusuf et al. (2020) Genome Research.

 

Non-coding DNA

Next, the researchers turned to non-coding genomic regions, which make up the majority of the genome. Neil Shubin formulated it nicely in his book: “Gene sequences that code for proteins compose less than 2 percent of the human genome. That leaves some 98 percent with no genes at all in it. Genes are but islands in a sea of DNA.” These non-coding regions were initially seen as “junk DNA” without a function, but we now know that some of these regions play crucial roles in regulating gene expression. The search for significant non-coding regions involved in beak morphology evolution resulted in no less than 39,806 of these genetic elements. But which genes were they regulating?

These regulatory regions come in two main types: cis-regulatory elements that are linked to nearby genes and trans-regulatory elements that affect distant genes (millions of DNA-letters apart). Analyses focused on cis-regulatory elements pointed to 884 genes of which most are involved in early craniofacial development, as shown in mice (including the the ESC pluripotency pathways that were also found for the protein-coding genes). Similarly, detailed analyses of trans-regulatory elements identified genes associated with the development of beak morphology.

The difference between cis- and trans-regulatory elements. Cis-regulatory elements affect nearby genes, while trans-regulatory elements code for proteins (e.g., transcription factors) that influence distant genes. Adapted from: Signor & Nuzhdin (2018) Trends in Ecology & Evolution.

 

Endless Forms

These findings highlight that fundamental developmental pathways underlie the evolutionary changes in beak morphology. Mutations in the non-coding elements that regulate these pathways can result in novel beak phenotypes, providing the raw material for natural selection. In addition, changes in protein-coding genes – which seem to be specific to particular bird lineages – add more variation to this pool of possibilities. Together, coding and non-coding genomic regions drive the spectacular diversification of avian beaks. To end with a famous quote from Charles Darwin, who would have been delighted by these findings: “From so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”

 

References

Yusuf, L., Heatley, M. C., Palmer, J. P., Barton, H. J., Cooney, C. R., & Gossmann, T. I. (2020). Noncoding regions underpin avian bill shape diversification at macroevolutionary scales. Genome research30(4), 553-565.

 

Figuring out the origin of two Fire-eye Antbird species in the Atlantic Forest

Genetic study uncovers a complicated series of events.

A common mistake in discussions is the “False Dilemma”, which states that if X is wrong than Y must be true. Creationists often apply this style of reasoning when attacking evolutionary theory. They claim that if evolution is wrong, then creationism must be true (which explains why they put so much effort in discrediting evolution). This statement is obviously not true: an inconsistency in the current evolutionary theory does not automatically support creationism.

But let’s not get caught up in this useless and silly debate, because there is a much more interesting discussion about the origin of bird species in the Atlantic Forest of South America. Two main hypotheses have been put forward to explain how new species arise in this region. The refuge hypothesis states that during the Pleistocene vast stretches humid forests were replaced with dry vegetation, creating isolated forest patches in which species diversified. The river-barrier hypothesis, however, focuses on the role of rivers as isolating barriers between populations. It seems that there are only two possibilities: refuges versus rivers. But a recent study in the journal Molecular Phylogenetics and Evolution revealed that this is a false dilemma. There is another option to consider.

A White-shouldered Fire-eye in Brazil © Dario Sanches | Wikimedia Commons

 

Refuges and Rivers

Using genetic data, Manuelita Sotelo-Muñoz and her colleagues reconstructed the evolutionary history of two Atlantic Forest species: the white-shouldered fire-eye (Pyriglena leucoptera) and the fringe-backed fire-eye (P. atra). The analyses revealed that these species diverged about 260,000 years ago, probably driven by habitat fragmentation. The species recently established secondary contact, resulting in the exchange of genetic material. Clearly, these fire-eyes were not isolated long enough for reproductive isolation to evolve. All in all, this scenario seems to support the refuge hypothesis. But wait, there is more…

Within the white-shouldered fire-eye, the researchers uncovered more fine-grained population structure. This species can be divided into three genetically distinct populations: a northern, central and southern lineage. Some of these populations come into contact around the major rivers in the Atlantic Forest. The northern and central population meet at the interfluvium of the de Contas and Pardo rivers, while the southern and the central population mix at the Doce and Grande rivers. These results support the river hypothesis, right? Well, not quite…

The distribution and genetic structure of the white-shouldered and the fringe-backed fire-eye in the Atlantic Forest. Notice the hybrid zones between the different populations (locations 25-27 and 37-44). From Sotelo-Muñoz et al. (2020) Molecular Phylogenetics and Evolution

 

Extinction and Dispersal

A detailed look at the genetic patterns points to a complicated scenario. After divergence from the fringe-backed fire-eye, individuals from the white-shouldered fire-eye spread southwards and diversified into several populations. At some point, the population north of the Pardo river went extinct. This gap was later filled when birds from the central population dispersed northwards. Similarly, the southern populations originated when birds from the central population dispersed southwards. Later on, these populations re-established contact at the rivers. These rivers probably limited dispersal, accentuating the genetic differences between the populations.

Based on this information, the authors argue that “our results support neither the river-barrier nor the refuge hypothesis as originally conceived. Here, dispersal as opposed to vicariance, seems to be the main cause of intraspecific differentiation.” As I mentioned in the beginning of this blog post, there is more to evolution in the Atlantic Forest than refuges and rivers. Don’t ignore dispersal.

 

References

Sotelo-Muñoz, M., Maldonado-Coelho, M., Svensson-Coelho, M., dos Santos, S. S., & Miyaki, C. Y. (2020). Vicariance, dispersal, extinction and hybridization underlie the evolutionary history of Atlantic forest fire-eye antbirds (Aves: Thamnophilidae). Molecular Phylogenetics and Evolution, 106820.

 

This paper has been added to the Thamnophilidae page.

The speciation cycle of Taiga and Tundra Bean Goose

Are these bean geese merging into one species or not?

“I’ve been following your progress into the world of bird speciation and I wondered whether you’d be interested in a proposal.” This was the first sentence of an e-mail from Joe Tobias that I received in December 2019. He had been invited to write a review on bird diversification for the journal Annual Reviews in Ecology, Evolution, and Systematics and was looking for co-authors to write some sections. The only catch: the deadline was approaching fast (19th of January 2020). I did not have to think long about my decision, this was a great opportunity to work with one of the leading scientists in avian research and publish in one of my favorite journals. Moreover, I enjoy writing and I am always up for a challenge. A few days later, Alex Pigot joined the writing team and together we produced an extensive review that recently appeared online: “Avian Diversity: Speciation, Macroevolution, and Ecological Function“.

 

Road Trip along the Speciation Cycle

The resulting review paper centered around the concept of the speciation cycle (see figure below) which involves a series of evolutionary and ecological events. First, populations become geographically isolated and diverge in allopatry. When these populations establish secondary contact, several scenarios are possible. They might be reproductively isolated and transition into sympatry (and the cycle can start again). Or they might still be able to hybridize and establish a hybrid zone. The dynamics in these hybrid zones consequently determine the next phase in the speciation cycle. If hybrids are unfit – for instance, sterile or unable to find a mate – selection against hybrids can lead to character displacement, leading to further differentiation between the hybridizing species that eventually transition to sympatry. Alternatively, hybridization levels are so high that the populations collapse into one species. Regardless of the outcome (sympatry or collapse), the cycle can start again.

The different phases of the speciation cycles. The colored circles surrounding the diagram indicate different fields of research that are relevant to specific phases. From: Tobias et al. (2020) Annual Review in Ecology, Evolution, and Systematics.

 

Crossroads

The review paper elaborates on numerous interesting aspects of the speciation cycle. In this blog post, however, I want to focus on one particular point in this cycle: the crossroads at the hybrid zone phase. Will the populations transition into sympatry or will they merge into one species? One of my recent papers, published in the journal Heredity, provides a nice case study of this situation. During my postdoc at Uppsala University (Sweden), I studied the evolutionary history of the taiga bean goose (Anser fabalis fabalis) and the tundra bean goose (Anser fabalis serrirostris). Using whole genome resequencing data, I reconstructed their evolution history and tried to understand the genetic make-up of these birds.

It turned out that these geese diverged about 2.5 million years ago in allopatry and came into secondary contact ca. 60,000 years ago. Their genomes are largely undifferentiated but a few genomic regions – so-called ‘islands of differentiation’ – stand out. These islands might contain genes that contribute to reproductive isolation. For example, we found the gene KCNU1 which is involved in spermatogenesis. However, other evolutionary forces, such as background selection, can also give rise to these islands of differentiation. These results raise an important question: Are taiga and tundra bean goose now merging into one species?

A strolling taiga bean goose © Marton Berntsen | Wikimedia Commons

 

Merging or Diverging?

Which path of the speciation cycle the bean geese will follow, is difficult to predict. I suspect that these two populations have been stuck in a cycle of merging and diverging for thousands of years. With the genomic analyses, we managed to capture the latest merging event about 60,000 years ago. More powerful techniques might be able to find evidence for older hybridization events. In the future, taiga and tundra bean goose might start diverging again, possibly driven by the differences in the genetic islands of differentiation that we uncovered. However, if levels of hybridization increase, they might collapse into one species. Clearly, they are at an important crossroads in their evolution and future studies will reveal which turn they eventually took.

The current situation complicates the taxonomy of the bean geese. Should they be considered separate species or are they better classified as subspecies? Personally, I find this discussion nonsensical and uninteresting. Taiga and tundra bean goose are obviously in the grey zone of the speciation continuum where subjective taste determines their taxonomic status. Although I was a bit reluctant to enter this discussion, my co-authors and the reviewers advised me to discuss the taxonomy of the bean geese in the paper. So, based on low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argued that taiga and tundra bean goose should be treated as subspecies.

A tundra bean goose flying over Sweden. © Stefan Berndtsson | Wikimedia Commons

 

Trivial Taxonomy

This conclusion struck a chord with some birdwatchers, who reacted furiously to the taxonomic recommendations (even though they were only a minor part of the study) on Twitter. One random birder – who would not recognize a DNA-sequence if it hit him in the face – even had the audacity to question how the paper made it through peer review. Just because you disagree with a certain conclusion, doesn’t mean that you should trash the entire study. To use a common saying: Don’t throw the baby out with the bathwater! Instead of reacting in the same manner as the birdwatchers, I did not lower myself to their level and politely explained the reasoning behind my conclusions (which you can also find in the paper).

Unfortunately, the unnuanced and emotional responses of these birdwatchers reflect the current level of discourse in our society, especially on social media. When someone doesn’t agree with the statement of a particular person, they immediately vilify everything about that person. I hope this style of discussion does not find its way into science and we can continue to carefully consider each others arguments, culminating in a strong consensus or at least politely agree to disagree.

But to end on a positive note: there was also a nice discussion on the website Dutch Birding about the taxonomy of the Bean Geese. In contrast to the blunt messages on Twitter, several birders provided constructive feedback. It is possible!

An online posting guide that the birdwatchers should have followed…

 

References

Ottenburghs, J., Honka, J., Muskens, G. & Ellegren, H. (2020) Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity. 125: 73–84.

Tobias, J.A., Ottenburghs, J. & Pigot, A. (2020) Avian Diversity: Speciation, Macroevolution, and Ecological Function. Annual Review of Ecology, Evolution and Systematics. Early View.

Are we missing something? Exploring the diversity of white-eye species on the African mainland

Most white-eye species have been found on islands, but what about the diversity on the mainland?

When I say white-eyes, you say islands (if you are an ornithologist). About 90 percent of described white-eye species – the bird family Zosteropidae – occurs on islands. This bias is also apparent on the Avian Hybrids blog: all the papers about white-eyes that I covered took place on islands, such as the interactions between Solomons white-eye (Zosterops kulambangrae) and Kolombangara white-eye (Z. murphyi) on Kolombangara Island (see here) and the evolution of the Reunion grey white-eye (Z. borbonicus) on the small island of Reunion (see here). Could this focus on islands distort our perspective on these small passerines? What about the species diversity on the mainland? A recent study in the journal Molecular Phylogenetics and Evolution explored the diversity of white-eye species on the African mainland.

Cape white-eye (Zosterops virens) © Alandmanson | Wikimedia Commons

 

A Single Colonization Event

Frederico Martins and his colleagues collected genetic material from the 14 white-eye species and 18 subspecies that are currently recognized on the African mainland. Comparing these specimens with species from Asia revealed that the African mainland was colonized about 1.3 million years ago. After this single colonization event, the white-eyes spread to different African oceanic islands (for example, in the Gulf of Guinea) and several ecological sky-islands in the mountains. There, they diversified into a range of new species and subspecies. This begs the question: how many species are there on the African mainland?

The distribution of white-eyes on the African continent. The colors indicate the main species groups. From: Martins et al. (2020) Molecular Phylogenetics and Evolution

 

Species Boundaries

A species delimitation analysis based on mitochondrial DNA indicated that several taxa should be elevated to species level, resulting in 27 African white-eye species (remember, we started with 14). However, the researchers realize that this analysis relies on just one molecular marker. Clearly, there is more to a species than mitochondrial DNA (see this blog post on species concepts), indicating that more detailed studies are needed to describe all the white-eye species on the African continent. Nonetheless, this study shows that we are probably underestimating the diversity of white-eye species on the mainland.

 

References

Martins, F. C., Cox, S. C., Irestedt, M., Prŷs-Jones, R. P., & Day, J. J. (2020). A comprehensive molecular phylogeny of Afrotropical white-eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history. Molecular Phylogenetics and Evolution149, 106843.