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NMSU researcher collaborates on phase two of massive bird genome study

New Mexico State University biology Professor Peter Houde is among more than 200 researchers involved in phase two of a massive effort at mapping the genomes of each of the world’s 10,500 bird species. In the project known as B10K, researchers from University of Copenhagen and partner institutions have sequenced 363 genomes from 92.4 percent of all bird families on Earth.


Man holding a bird
New Mexico State University biology Professor Peter Houde holds up a specimen related to the birds that he and three graduate students studied as part of an international collaboration sequencing the DNA of all major groups of birds. (NMSU Photo by Darren Phillips)
Painting of Passeriformes
Passeriformes, perching birds or songbirds, are the most diverse bird lineage with more than 6,500 described species. To better represent this diversity, the B10K sequenced 149 new genomes across Passeriformes. (Courtesy: Paintings: Jon Fjeldå, Design: Josefin Stiller)

Completion of the first phase of the study in 2014 resulted in the release of dozens of publications in special issues of several premier scientific journals. Initial phase two results were published in the Nov. 12 issue of the journal “Nature.” Each of the four phases work incrementally higher up the family tree of birds to the species level, analyzing how their genomes have evolved from dinosaurs over the last 150 million years.

The new study required segmented data analysis of the huge data set by various scientists around the world. Houde, who also played a significant role in phase one of the B10K project, was among them.

“Our data set is so much larger than anything else that has ever been produced previously that specialists in our consortium had to develop new methods to tackle it,” Houde said. “The role of people like me was to work with manageably small subsets of the data to see if and how well the computational tools were working from a biological perspective. It is not a trivial proposition.”

In the current study, researchers investigated the genomic differences and similarities in the birds, and can confirm that their genetic material is remarkably similar.

“We are surprised by the similarities among avian DNA. Also, birds have lost numerous genes in their common ancestor since their evolution from dinosaurs during the last more than 150 million years. This is a result of their adaptation towards being able to fly,” explained Professor Guojie Zhang, of the University of Copenhagen’s Department of Biology and one of B10K’s lead researchers.

According to Leopold Eckhart who is a professor at the Medical University of Vienna and a researcher on the B10K, songbirds have lost a gene known as cornulin, which controls mechanical resilience and elasticity of the esophagus and affects their ability to sing.

“Most birds communicate through sounds but songbirds are outstanding. Surprisingly, it was not the evolution of new genes but the loss of an old gene that helped songbirds to become the best singers,” Eckhart said.

Houde has had three graduate students who coauthored B10K phase one and/or two genome publications to date. Although phase three has already been initiated, B10K phase two analyses are now only beginning to get underway.

“I am anxious to enlist new students to exploit the untold wealth of unpublished data,” he said.

His involvement in both phases will include continued phylogenomic analysis of avian interrelationships, dating the origins of avian lineages based on fossils, demographic inference and interpretation of ecological and adaptive trends.