鈥淏roadly 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,鈥� said Peter Houde, biology professor in the College of Arts and Sciences.
Houde and Nitish Narula, an NMSU master鈥檚 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 鈥淲hole Genome Analyses Resolve the Early Branches to the Tree of Life of Modern Birds,鈥� published Friday, Dec. 12 in the journal 鈥淪cience.鈥�
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, 鈥淐omparative Genomics Reveals Insights into Avian Genome Evolution and Adaptation,鈥� also is published in the Dec. 12 edition of 鈥淪cience.鈥�
NMSU鈥檚 involvement in the study came out of Houde鈥檚 role as principal investigator of NMSU鈥檚 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.
鈥淥ur 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,鈥� Houde said. 鈥淲e had relatively very little data on which to base our conclusions then.鈥�
鈥淭extbooks and field guides on birds will have to be re-written. This will set new standards for future genomic studies of all organisms.鈥�
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鈥檚 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.
鈥淔lamingos, for example, share traits with other long-legged wading birds, not because they are closely related but because they evolved the adaptations independently,鈥� 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 鈥渋ndels,鈥� mutations that represent the addition or deletion of bits of DNA.
鈥淭hese mutations occur with sufficient frequency to objectively track evolution across the entire genome as never before possible,鈥� Houde said. 鈥淭he 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.鈥�
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.
鈥淲e see the same phenomenon in ourselves,鈥� Houde said. 鈥淪ome 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 鈥榤osaics鈥� of both close and distant relatives.鈥�
Houde co-authored a third paper about this study to be published in BMC Genomics and a fourth to be published in 鈥淕igaScience.鈥� Another paper Houde co-authored connected with this project was published earlier this year.
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