Genomic analysis, key to understanding bird evolution

December 11, 2014

66 million years ago, the dinosaurs, as we think about them, became extinct, but certain reptiles and birds survived this mass extinction. The birds that survived experienced rapid evolution and diversification. Until now, explaining the family tree of modern birds has been a difficult and controversial subject amongst scientists. Thanks to the research of an international consortium involving researchers from the Centre for Genomic Regulation in Barcelona, we now have new clues about this evolution and further information on other aspects of birds.

The international consortium studying bird genomics, led by Guoije Zhang, from the National Genebank BGI in China and the University of Copenhagen; Enrich D. Jarvis, at Duke University and the Howard Hughes Medical Institute in the United States; and M. Thomas P. Gilbert, from the Natural History Museum of Denmark; has spent four years working on the massive sequencing of 48 genomes from birds as well other animals such as crocodiles. More than 200 scientists from 80 institutes spread over 20 countries have taken part in this project. In Spain, researcher Toni Gabaldón, head of the Comparative Genomics group at the Centre for Genomic Regulation (CRG) in Barcelona and an ICREA research professor, has participated in the genome analysis and the proposal of the new bird family tree, as well as analysing the crocodile genomes and their relationship to birds.

The species studied include crows, ducks, falcons, budgerigars, cranes, ibis, woodpeckers and eagles, as representatives of the main families of modern fowl. The first results of this study are being published simultaneously in 8 articles in the journal Science and in a further 15 articles in other scientific publications including Genome Biology and GigaScience. All the articles are available at

The genome, key to establishing new family trees and explaining evolution

The phylogenetic studies on the evolution of modern birds available until now had been carried out together with specific genes related to anatomical characteristics or bird behaviour. Now, the results presented by the Avian Phylogenomics Consortium compare the entire genome of all of the species, something that has allowed them to reconstruct the phylogenetic tree of birds in much greater detail including information on kinship relationships between groups and the timings of the separations.

The scientists have discovered that to be accurate and include all the evolutionary trends of the species it is necessary to take into account even the DNA regions that do not code for protein manufacture.

Additionally, the fact of comparing entire genomes has enabled them to draw an evolutionary map of the bird genome. The researchers have observed that birds have few DNA repetitions and that since their first appearance they began to lose hundreds of genes that ancestrally they shared with humans. Specifically, the genes that the birds have lost are key for humans and are involved in important functions like reproduction, the formation of the skeleton and the lungs. Obviously, birds have dealt with these aspects from a different angle, explaining why they have a lighter skeleton, such a unique respiratory system, a wide variety of specialist diets and many other characteristic traits distinct to those of mammals.

Birds, beasts and relatives

In this study, apart from sequencing the genomes of 48 bird species, the genomes of the closest living reptiles to birds, the crocodiles, have also been sequenced and studied. The scientists were hoping to find common points between them to contribute data on the diversification of the archosaurs (a group that includes crocodiles, dinosaurs and birds).

"The sequencing of three different crocodile species puts the genomic study of birds in context. The data we have looked at demonstrated that crocodiles have evolved relatively little and that, therefore, they are a fairly reliable reflection of their ancestors", explains Toni Gabaldón, ICREA research professor at the CRG and one of the coauthors of the paper published in Science on the crocodile genomes. "At the same time, being able to compare this with bird genomes has enabled us to partially reconstruct what the genome of the common ancestor of the archosaurs would be, and it is therefore, a very valuable tool for studying of the origin of crocodiles, birds and dinosaurs", adds Dr Gabaldón. "The rapid diversification of birds into many visibly different groups contrasts with the stability and immobility of the crocodiles, which have remained practically the same even after a long period of evolution. This shows us how evolutionary speed is relative in different groups and how the opportunity for diversification and occupying new ecological niches very quickly generates morphological diversity and speciation", concludes the researcher.

Sing, talk, think

The main articles from this study indicate that vocal learning, i.e., the capacity of the birds to emit sound, modifying the tone and reproducing sounds by imitation, evolved independently of form on at least two occasions. In general, it has been discovered that the cerebral circuits for musical and vocal learning in birds and humans are similar but have been arrived at via different evolutionary paths.

Some of the papers published as part of this project highlight the fact that the majority of the genes related to vocal learning, are involved in the formation of neural connections.

And when did they lose their teeth?

In one of the articles published in Science the scientists compare modern birds with other vertebrate species and have ascertained that birds displayed mutations in groups of genes that code for enamel and dentine. Five of these genes related to teeth formation were switched off more than 100 million years ago, in an ancestor of today's birds.

Behind the scenes

This work has been challenging on various levels. Samples of frozen tissue collected over the last 30 years, from museums and other institutes, were analysed. The DNA was separated in Duke University and the University of Copenhagen. The majority of the genome sequencing and the first analysis was carried out at the BGI in China and the phylogenetic study of the data was shared between more than 80 institutes around the world.

The data generated will be available for the scientific community so that in the future other scientists will be able to study the genetic basis of bird characteristics.

Center for Genomic Regulation

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