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NMSU researchers collaborate on massive bird genome study

A New Mexico State University professor and a graduate student are part of an international collaboration among more than 200 researchers in sequencing the DNA of all major groups of birds. It is the first study of its kind, resulting in the release of dozens of publications in special issues of several premier scientific journals.

NMSU biology professor Peter Houde holds up a specimen related to the birds that he and a graduate student studied as part of an international collaboration sequencing the DNA of all major groups of birds. (NMSU Photo by Darren Phillips)
Bird perched on a branch
The red-throated bee-eater is among the 48 groups of birds whose genome was sequenced and studied. It is representative of a group of many diverse but closely related land birds including songbirds, parrots, and all the birds of prey. NMSU biology professor Peter Houde took this photograph in July 2013 on the Nile River in Murchison Falls National Park, Uganda. (Photo courtesy Peter Houde)
Photo of a man from waist up
Nitish Narula, an NMSU master’s student in biology who graduated in May 2014, worked with NMSU Professor Peter Houde on sequencing the genome of the South American hoatzin, as part of a massive DNA study of all major bird groups, published Dec. 12 in the journal “Science.” (Courtesy Photo)

“Broadly speaking, the project discovered much about what genes make birds different from everything else, what genes make birds different from one another, and how and when various birds evolved from a single dinosaur ancestor,” said Peter Houde, biology professor in the College of Arts and Sciences.

Houde and Nitish Narula, an NMSU master’s student in biology who graduated in May 2014, sequenced the DNA of the South American hoatzin, a bird with clawed wings. Houde and Narula are among 104 co-authors of “Whole Genome Analyses Resolve the Early Branches to the Tree of Life of Modern Birds,” published Friday, Dec. 12 in the journal “Science.”

The avian phylogenomics project led by scientists from the Beijing Genome Institute, University of Copenhagen and Duke University enlisted specialists worldwide to use what amounts to a combined 400 years of computer time on eight supercomputers to gather extensive information on bird DNA. Houde is also a co-author on four other papers as part of this project.

A second paper Houde co-authored titled, “Comparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation,” also is published in the Dec. 12 edition of “Science.”

NMSU’s involvement in the study came out of Houde’s role as principal investigator of NMSU’s core genome sequencing lab and a Manassee Award, which supported his project to sequence the hoatzin genome.

In 2004, Houde made a breakthrough when he discovered genetic evidence that roughly a third of all major groups of birds were incorrectly classified based on convergent adaptations.

“Our new genomic data and analyses show that we were right about which birds are unrelated, but we were only half right a decade ago about their correct relationships,” Houde said. “We had relatively very little data on which to base our conclusions then.”

“Textbooks and field guides on birds will have to be re-written. This will set new standards for future genomic studies of all organisms.”

Some ornithologists suspected the reason why the relationships among birds were particularly difficult to determine might be that they appeared in great diversity very suddenly after the extinction of the dinosaurs from which they arose. If the many lineages of birds arose explosively then each would not have had time to evolve distinctive characteristics to leave a bread-trail of each shared relationship before the next branched off.

More recently researchers hypothesized that the lineages of birds evolved very gradually over a much longer period of time, and well before the catastrophic meteor impact that wiped out the dinosaurs.

One of Houde’s main contributions to the project was integrating the genetic data with the fossil record. His research shows the lineages of birds split apart very quickly after the extinction of the dinosaurs, but the distinctive characteristics, which we now recognize in particular birds, did not appear until much later.

“Flamingos, for example, share traits with other long-legged wading birds, not because they are closely related but because they evolved the adaptations independently,” Houde said.

While the study found that ostriches are the most primitive of all living birds, the chicken genome is probably the most like that of dinosaurs.

Houde and Narula also conducted an analysis of “indels,” mutations that represent the addition or deletion of bits of DNA.

“These mutations occur with sufficient frequency to objectively track evolution across the entire genome as never before possible,” Houde said. “The physical or reproductive isolation that results in the splitting of an ancestral species into daughter lineages can be thought of as an event, but the evolutionary processes from which daughter species ultimately emerge continue long afterward.”

Houde explained it takes millions of years before genes uniformly track the branching order of species. Until then, different genes have different evolutionary histories because the genes are older than the species by varying amounts.

“We see the same phenomenon in ourselves,” Houde said. “Some human genes are most closely related to those of chimpanzees, others to gorillas, and a few are even most closely related to monkeys. We are truly genetic ‘mosaics’ of both close and distant relatives.”

Houde co-authored a third paper about this study to be published in BMC Genomics and a fourth to be published in “GigaScience.” Another paper Houde co-authored connected with this project was published earlier this year.