An enormous an asteroid hit the Earth around 65 million years ago. While land dinosaurs like the famous Tyrannosaurus rex were killed, many bird animals really started to prosper. There are over 10,000 species of birds on Earth, prosper may even be an understatement. Keeping birds organized in a neat family tree is a bit of a Herculean task, since there are so many species and their evolution has been a little unclear. However, some advances in genomic sequencing and analysis are beginning to create a more clear picture of how the planet’s living dinosaurs evolved.
In two studies published April 1 in the journals Proceedings of the National Academy of Sciences (PNAS) and Nature, scientists reveal that a genetic event around 65 million years ago has misled them about the true history of bird evolution. A section of one chromosome hasn’t mixed together with nearby DNA as it should have. This section is only tiny fraction of the bird genome, but was enough to make it difficult for scientists to build a more detailed bird family tree.
A sticky chunk of DNA
In 2014, advancements in computer technology used to study genomes helped scientists put together a family tree for the Neoaves. This group includes the majority of bird species. Using the genomes of 48 species, they divided the Neoaves into two major categories. Doves and flamingos were in one group and all the other bird species belonged to the other group.
When a similar genetic analysis was repeated using 363 bird species for this new study, the team saw a different family tree emerge. This one points to four main groups and reveals that flamingos and doves are more distantly related and it all came back to a specific spot in the chromosomes.
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Within these two family trees, the team looked for explanations that could tell them which one was correct. They found one spot on the genome, where the genes were not as mixed together as they should have been over millions of years of sexual reproduction.
“When we looked at the individual genes and what tree they supported, all of a sudden it popped out that all the genes that support the older tree, they’re all in one spot,” a co-author of the study published in PNAS and University of Florida biologist Edward Braun said in a statement. “That’s what started the whole thing.”
Birds combine genes from a father and a mother into the next generation, but they first mix the genes they inherited from their parents when creating sperm and eggs. This process is called recombination and it is also something that occurs in humans. Recombination maximizes a species’ genetic diversity by ensuring that no two siblings are exactly the same.
One section of one chromosome did not mix with DNA nearby like it should have and has basically spent millions of years frozen in time. This chromosomal section makes up only 2% of the bird genome, but was enough to convince scientists that most birds could be grouped into two major categories–Passerera and Columbea. This new and more accurate family tree takes into account that misleading section of the bird genome and identifies four main groups of birds.
The team also found evidence that this spot on the bird chromosome has prevented the recombination process since around the time the dinosaurs disappeared. It's not clear whether the Cretaceous-tertiary Extinction that wiped out the dinosaurs and these genomic anomalies are related.
This genetic suppression has caused flamingos and doves to appear similar in one section of DNA, but they are actually more distantly related when examining their entire genomes. Flamingos and doves are now considered more distantly related genetically. According to the team, similar genetic anomalies could be present in the genomes of other organisms.
Creating a more accurate bird family tree
The study published in Nature details a detailed chart illustrating 93 million years of evolutionary relationships between 363 bird species, or approximately 92 percent of all bird families. This updated family tree has revealed patterns in the evolutionary history of birds after the Cretaceous-tertiary Extinction.
[Related: Dinosaurs may have evolved into birds, but early flights were not very successful.]
The researchers observed significant increases in effective population size, substitution rates, and relative brain size in early birds. These evolutionary changes provide new insights into the adaptive mechanisms that drove the diversification of bird species after this significant extinction event.
To do this, they used a set of computer algorithms called ASTRAL. This program helps quickly and accurately infer evolutionary relationships and allows the team to integrate genomic data from over 60,000 regions in bird genomes. They then examined the evolutionary history of individual segments across the genome and combined several gene trees to construct a larger species tree.
“We found that our method of adding tens of thousands of genes to our analysis was actually necessary to determine the evolutionary relationships between bird species,” study co-author and University of California, San Diego computer engineer Siavash Mirarab said in a statement. “You really need all that genomic data to understand what happened in this specific period 65-67 million years ago with high confidence.”
These computational methods also helped the team shed light on that same specific section of one chromosome in the bird genome that has remained unchanged over millions of years and made it difficult for scientists to study these changes.
“What’s surprising is that this period of suppressed recombination could mislead the analysis,” said Braun. “And because it could mislead the analysis, it was actually detectable more than 60 million years in the future. That’s the cool part.”
In the future, similar computer models may assist in re-creating ancestral relationships among species for various animals. The team aims to continue working on creating a more comprehensive understanding of bird evolution. Biologists are also sequencing the genetic codes of other bird species to further expand their family tree.
The project is part of the international Bird 10,000 Genomes (B10K) Project, which involves multiple institutions collaborating to produce working drafts of genome sequences for approximately 10,500 living bird species.
