Scientists have learned so much about birds from  sequencing the genomes of 48 different species of them. And there is plenty more they will learn as they continue to analyze the data. (Wikimedia Commons)
Scientists have learned so much about birds from sequencing the genomes of 48 different species of them. And there is plenty more they will learn as they continue to analyze the data. (Wikimedia Commons)

In a stunning feat of scientific prowess, a large group of scientists has completely sequenced the genomes of 48 different bird species. Well, actually getting all those A’s, G’s, C’s and T’s wasn’t the big deal. This part gets easier and easier.

No, the really hard part of the project was organizing and managing all of that data. The researchers needed to create new computational tools and use over 300 years of computing time to take the data and use it to create an evolutionary tree for these 48 birds. No wonder this part of the project took over three years!

This will be a common theme in the big genome projects to come. Sequencing will be easy, managing the data hard. Hopefully what these researchers learned can be used to help future researchers deal more easily with these mountains of data.

Even though it took a lot of work, this bird project was definitely worth it.  These scientists learned a whole lot about birds and their evolutionary history that couldn’t be learned any other way.

For example, they found that the patterns of genes that are turned on for birdsong are similar to the ones that are turned on for human speech. That blue jay is using some of the same genes to sing that Taylor Swift uses! This is just one of their many findings about how modern birds work.

There was a burst of bird evolution right after the dinosaurs disappeared. (Flickr)
There was a burst of bird evolution right after the dinosaurs disappeared. (Flickr)

Their biggest findings, though, were about the evolutionary history of birds. For example, the researchers could see in bird DNA an explosive burst of diversity that happened between 67 and 50 million years ago. Most likely birds first flocked to and then adapted to the new niches made available when most of the dinosaurs were wiped out.

Researchers could also see that vocal learning probably appeared independently in a variety of birds. In other words, there wasn’t a single ancestor back in time who developed this trait and who then passed that ability on to all birds alive today. This trait popped up multiple times.

They could also see that most land birds came from one really nasty carnivore. And they could see the effects of inbreeding on the DNA of the crested ibis. And the list goes on. What I have described so far is really just the tip of the iceberg of what they have learned and what they will continue to learn from this data in the future.  I can’t wait until this is applied to turtles or snakes or whatever else. We are going to learn so much about how plants and animals work and how they evolved. Stay tuned.

The Fall of Teeth

One fascinating bit of detective work to come out of this study was the evolutionary history of tooth loss in birds. The ancestors of birds used to have teeth and modern birds do not. Tooth loss might have been like vocal learning and popped up independently multiple times. Or it might have appeared in a common ancestor of all birds. It looks like the second possibility is the right one.

Unlike his cousins the birds, this crocodile's tooth development genes still work which is why he still has teeth. (Flickr)
Unlike his cousins the birds, this crocodile’s tooth development genes still work which is why he still has teeth. (Flickr)

The way to tell which possibility is correct is to look at the tooth development genes that still linger in bird genomes. If all birds have the same inactivating mutation, then they all probably came from the same common, toothless ancestor. This is because there are lots of ways to break a gene and the odds of it happening in the same way in two different populations is very unlikely.

But if different groups of birds have unique mutations that inactivated gene(s), then toothlessness probably appeared independently a number of times.

By comparing six of these genes in the 48 different bird species, the researchers concluded that most likely birds can be traced back to a common toothless ancestor from around 116 million or so years ago. Birds all shared the same inactivating mutations in six key tooth development genes.

Now after 116 million years, these genes are understandably a bit beat up since once a gene is inactivated, there is no natural selection to keep the gene from building up mutations. This is why the researchers needed to look at the genomes of 48 different bird species to figure out that tooth loss happened once in bird history. You need to be able to see many different genomes to be able to put the pieces back together again from the remnants of old genes.

Just because birds share the same common, toothless ancestor that does not necessarily mean that all animals that have lost their teeth do. When the researchers compared these bird genes to the same genes of other toothless animals like turtles and anteaters, they found these animals had different mutations. So all toothless reptiles, birds, and mammals did not come from some common ancestor. Teeth were lost at multiple times through multiple mutations over the course of the last hundreds of millions of years.

This will undoubtedly be the first of many future studies that may allow us to see how animals gained and lost traits. And who knows, maybe a similar study will one day help us learn why we gained traits like speech and lost traits like body hair over time. It is amazing what we are learning and what we will be able to learn sooner than you might think.

Bird Biology Knowledge Expands with the Sequencing of 48 Genomes 29 December,2014Dr. Barry Starr

Author

Dr. Barry Starr

Dr. Barry Starr (@geneticsboy) is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA and runs their Stanford at The Tech program. The program is part of an ongoing collaboration between the Stanford Department of Genetics and The Tech Museum of Innovation. Together these two partners created the Genetics: Technology with a Twist exhibition.

You can also see additional posts by Barry at KQED Science, and read his previous contributions to QUEST, a project dedicated to exploring the Science of Sustainability.

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