Big Bang for Birds

On the heels of one of the greatest findings in the field of ornithology, announced last month, bird researchers are now entering a new frontier in the study of what makes birds tick. A multinational project involving 200 scientists from 20 countries revealed that the bird species we know today in fact originated right after the dinosaurs became extinct. Science Magazine declared the news as one of the 10 biggest discoveries of 2014.

To reach their conclusion, the scientists, collectively known as the Avian Phlogenomics Consortium, mapped the genomes of 45 different species. Their database can now be used to learn all kinds of other interesting avian tidbits, including when birds lost their teeth.

Lead researcher Erich Jarvis, associate professor at the Duke Institute for Brain Sciences, gives a taste of what’s still to come.

How can this research aid bird conservation?

We are sequencing genomes of species that are nearly extinct and won’t be around much longer or that are recovering with the help of humans. We also sequenced some iconic species like the Bald Eagle or Darwin’s Finch just so that we can say we have. And then there are species that have been hard to place in the tree, like the Hoatzin.

Can you point to some other examples of why this is important for conservation?

From the 1950s to the 1970s people thought that there were no more Crested Ibises in the wild. Then in 1981 there was a surprise discovery of two pairs surviving in some high mountainous areas in China where they normally don’t live. Now there are over 2,000 individuals from those two “Adam and Eve” couples and these are some of the genomes they sequenced.

You can calculate the amount of diversity you would expect to see in a genome over a period of tens of thousands of years. If you see a low diversity back in time, that indicates there was some kind of decrease in the population. The bigger a population is, the more diversity that every individual in that population will have in their genome.

We found for the Crested Ibis that not only in the last hundred years has there been a big genetic bottleneck caused by humans, but also 10,000 years ago in the ice age.  The diversity in these individuals in the last 30 years has now been increasing at a more rapid rate than what you’re seeing in other birds—which is a good thing.

One of the things that was done for that study was developing a breeding software program based upon the genome of the Crested Ibis that they’re now actually using to do more effective breeding to enhance diversity of the species.

You work on vocal learning—the ability to learn and produce sounds that are heard. How does the database help your research?

Vocal learning is a pretty rare trait, found in only a few groups of mammals and birds. Amongst the birds, it’s hummingbirds, songbirds, and parrots. You find it also in dolphins and whales and elephants, but those animals are too big to study for this trait—and compared to them, the birds are even better at it. So I’ve been on a long-term search for genes that are responsible for setting up the brain pathways for vocal learning. And I always thought I could identify those genes by an evolutionary comparative approach: take species who have the ability and compare their genomes to the genomes of their closest relatives who don’t have it.

But a problem is that different trees are saying that different relatives are closest to these vocal learners, so we needed to get the tree right first. With those genomes, we were then able to do some experiments to identify genes that evolved in parallel between each of the vocal learning bird groups and our own brains.

Which species do you hope to map in the future?

We still want to spread out across the family tree. We also want to sequence targeted species that are either endangered or we know we could answer some interesting questions about vocal learning, loss of flight, and so on.

So for vocal learning, I want to sequence the genomes of species that are really good imitators like the African Grey Parrot and ones that have more difficulty imitating, like Lovebirds, and try to get at genes involved in behavioral complexity.

We have preliminary evidence from these genomes that shows that these species that imitate human vocalizations more readily than other species have differences in the size of their song nuclei in their brain. We’re interested in genes that make those differences.