Inside the ancestral genome of Aves: Were dinosaurs originally birds?

Well, not exactly. Ancient birds are theorized to have evolved from dinosaurs over 150 million years ago. But exactly how similar were they? While analyzing chromosomal-level differences, researchers revealed the genomic characteristics of an ancient common ancestor.

Long before humans existed, there was once a time when dinosaurs ruled the Earth. They first appeared over 240 million years ago and faced extinction about 175 million years later. A large asteroid hit Earth causing a mass extinction event and marking the end of the Cretaceous period. This extinction annihilated most plant and animal lifeforms, including dinosaurs. However, not all dinosaurs disappeared; some were able to survive. These are the theropods which included species like the famous Tyrannosaurus rex.

During this time, theropods eventually evolved creating the origin of modern birds. However, earlier species of birds appeared long before modern birds. The significant decrease in body size and the formation of wings were demonstrated to have appeared about 150 million years ago in Archaeopteryx, one of the earliest avians known to date.

Some recent studies have theorized that dinosaurs may have had similar characteristics to birds, such as feather-like hair, long before their evolutionary divergence. This came to the proposition that modern birds may be the closest existing animals to dinosaurs. So, what? If dinosaurs are said to have features that are similar to birds, then when did these features first appear? This creates a discussion on how close the typical features of an avian-like genome and the diapsid common ancestor genome are.

Phylogenetic tree adapted from O’Connor et al. (2018). Images modified from Wikipedia.

Simplified phylogenetic tree of the evolutionary divergence of turtles and birds from the diapsid common ancestor (DCA). The yellow box represents the DCA. Blue boxes represent the evolutionary divergence of the modern bird. Orange boxes represent the divergence of turtles and crocodilians. Green boxes represent the divergence of snakes and lizards.

Diapsids are a diverse group of amniotes (reptiles, birds and mammals) that have a distinct physical feature of two openings on the sides of their skull. It is observed in the above image that diapsids include snakes, lizards, turtles, crocodilians, and birds. While reconstructing the genome of a diapsid common ancestor, a study conducted by O’Connor et al. (2018) revealed that most characteristics associated with a typical avian-like karyotype were already present before the Archelosauria divergence, i.e., before turtles separated from Archosauria in the figure above.

The authors assessed chromosome-level assemblies of three bird species, including the modern chicken, and a reptile, the Carolina anole while comparing it to a mammalian outgroup. These genomes were aligned using a genome browser to identify homologous synteny blocks and evolutionary breakpoint regions (EBRs). Syntenic blocks are sections of genes located closely together on the same chromosome that are usually inherited together, whereas evolutionary breakpoints are gaps between these syntenic blocks. These are used to compare the orthologous regions within the genomes that are associated with these species, i.e., regions that share a common ancestor to which they are still relatively similar.

The authors tested the hypothesis that very few interchromosomal rearrangements have occurred since the Archelosauria divergence. Interchromosomal and intrachromosomal rearrangements are gene shufflings between chromosomes and within a chromosome, respectively. The figure below demonstrates that the karyotypes of the archelosaur ancestor and of the modern chicken look very similar to the typical avian-like karyotype. This suggests that most elements from the typical avian-like karyotype were already present before the divergence of turtles and birds. Furthermore, intrachromosomal rearrangements were the most common form of change between the diapsid common ancestor and chicken karyotypes. A total of 10 interchromosomal rearrangements and 49 intrachromosomal rearrangements were identified.

Modified from O’Connor et al. (2018).

Estimated individual chromosomal changes that occurred between the diapsid common ancestor (DCA) and the archelosaur ancestor, while comparing it to the modern chicken. The colours of the chromosomes were randomly assigned. One interchromosomal translocation was identified to have likely occurred between chromosomes 5 and 20 of the chicken (outlined in green). Some intrachromosomal rearrangements most likely occurred between the two ancestors, such as chromosome 1 and 17 through fusion, fission and/or translocations (outlined in purple).

However, conducting this study and analyzing the findings did not come so easy. Dr. Michael Romanov, an author of this study says, “The most difficult challenge we had to overcome when conducting this study was to properly identify EBRs [evolutionary breakpoint regions]. Our first guess delivered 378 EBRs that were enriched with genes affecting body size. However, that was an erroneous assignment because these EBRs were actually not specific for the Saurian ancestor. When we double checked the number of those, we ended up with 234 EBRs and the body size thing disappeared.” Identifying EBRs is essential in distinguishing evolutionary events, as specific EBRs are associated with the occurrence of certain events. Since these EBRs are so specific, one needs to replicate the data to ensure rational conclusions can be made. As observed above, it was thought that the identified EBRs can explain the evolution of reduced body size when, in reality, this was not the case.

The findings were not limited to the ones presented here. The authors were also able to infer the most probable sequence of events that took place between the diapsid common ancestor to archosaur ancestor, and between non-avian theropods to modern birds. Furthermore, enrichments in genes for chromatin modification, chromosome organisation, and proteasome structure were identified using the EBRs from the archelosaur ancestor. This allows for possible explanations of the evolutionary drive of avians. This study demonstrates the evolutionary importance of understanding the biological reasoning of how and why species are the way they are. In the study, it was determined that long before the evolution of dinosaurs, its ancient ancestors already had typical avian-like features. Altogether, this data allowed for the reconstruction of the inferred karyotype of the diapsid common ancestor.

Learn more about the evolution of modern birds

About the author

Brentha Rajakumaran is an undergraduate student that is still trying to figure out what she wants her future to be like after she graduates (such as what kind of job she wants or if she wants to continue with education). However, she is very interested in research, especially in biomedical engineering, and pharmacology and toxicology. So, she may pick a future path that includes these subjects. In her spare time, she loves watching dramas and movies with her sister which they’ve been doing quite often during the pandemic. Once things get better, she wants to do many ordinary things that she’s missed out on due to the pandemic, like seeing her extended family and friends, and going on trips.

Featured image: Lisa Yount on Unsplash (license).

2 thoughts on “Inside the ancestral genome of Aves: Were dinosaurs originally birds?

  1. Great post Brentha! It really highlights the utility of genetics/genomics in understanding evolution! As well as your ability to understand associated concepts and deliver them! The videos you gave at the end complemented your post very well! Good luck with your future endeavours!

    Liked by 2 people

  2. Congratulations, Brentha! You did a great job! As one of the key co-authors of this study, I would love to have you on board of our research team. 🙂

    Liked by 3 people

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