An international team of scientists comprised of more than 200 researchers from 80 institutions from 20 countries has sequenced and analyzed the genomes of 48 species of birds and 3 species of crocodilians to better understand the fundamental evolutionary events that led to feathers, flight, and song. The Avian Phylogenomics Consortium is simultaneously publishing 28 papers today — eight papers in a special December 12 issue of Science and 20 more in Genome Biology, GigaScience and other journals. The University of Georgia’s Associate Professor of Environmental Health Science (EHS) Travis Glenn co-authors two of the papers in Science , Assistant Professor Liang Liu of the Institute of Bioinformatics (IOB) and Department of Statistics, and Toxicology PhD student John Finger Jr. each coauthor one paper in Science. UGA alumni authors of the papers in Science include: Brant Faircloth (PhD, Forestry & Natural Resources), Richard E. Green (B.S., Genetics), Daniel Peterson (PhD, Plant Biology), and Beth Shapiro (B.S., Genetics).
One of the flagship papers in Science reports the relationships of major groups of birds. This is one of the most challenging problems in evolutionary biology because these groups diverged in a very short period of time, quite a long time ago – about 66 million years ago, shortly after dinosaurs became extinct. The Avian Phylogenomics Consortium used the new genome sequences and developed new laboratory and computational methods developed by Liu and Glenn to tackle this problem.
Liu has developed computational methods to analyze DNA sequences to understand relationships among species. These methods provide more robust results than traditional approaches. These methods are to key to solving the puzzle about relationships among birds because they are designed to overcome the problems associated with short bursts of speciation, even when they happened long ago. Liu and Glenn have collaborated previously to make these methods available to public health workers and evolutionary biologists (http://bioinformatics.publichealth.uga.edu/).
A new genomic tool that Glenn and colleagues developed for this research uses ultraconserved elements (UCEs), which consist of short DNA sequences that are nearly identical in birds, reptiles, and humans. Glenn says, “Brant Faircloth and I developed UCEs to address a variety of questions. In the avian phylogenome paper, we have used UCEs to understand how different birds are related to each other, making it easier to make apples to apples comparisons of DNA sequences among all birds as well as their distant relatives.”
In the crocodilian genome paper published in Science, Glenn and colleagues also used UCEs to compare the rate of molecular evolution of all major groups of tetrapods (vertebrates with 4 limbs) – ranging from the coelacanth to amphibians, birds, reptiles and mammals, including humans. By directly comparing DNA fragments that started with identical DNA sequences hundreds of millions of years ago, and yet still contain short stretches that are nearly identical today, the team discovered that crocodilians have remarkably slow rates of molecular evolution compared to other tetrapods. Turtles were the only other group with similarly slow rates of evolution. They also use UCEs and other parts of the genome to show the impact of glacial cycles on the population size of alligators, as well as reconstructing the genome of the ancestor of birds, crocodiles, and dinosaurs.
“The crocodilian genome paper is the culmination of more than 20 years of work developing genetic and genomic tools for alligators and crocodiles. UGA has supported this research through training of students, who are now among the lead authors and co-authors on these papers, hosting sponsored research on alligators and crocodiles, as well as providing international travel support and faculty research enhancement support for alligator genome resources when I was a research scientist at the Savannah River Ecology Laboratory (SREL)”, said Glenn.
John Finger, Jr., a PhD student in the Interdisciplinary Toxicology Program (ITP) and EHS worked with Glenn and colleagues at SREL and Australia to obtain alligator and saltwater crocodile samples used in the project. “Being a co-author on a publication in Science is a great graduation gift”, said Finger, who will graduate next week. “I want to thank the ITP as well as my mentors in EHS, SREL, and Veterinary Medicine, for giving me the opportunity to conduct research on alligators in the USA and saltwater crocodiles in Australia.” Finger is returning to Australia following graduation to continue research on crocodiles.
“This research provides the foundation for further work to understand how diseases, such as avian flu, and the effects of environmental toxicants, such as heavy metals, can be shared between humans, birds, reptiles, and other animals”, said Glenn. “Many additional faculty and students at UGA, especially those at SREL, EHS, IOB and the ITP, have contributed to this body of work. I wish there were space to recognize and thank them all for their support, but that would be an extremely long list. I look forward to working with even more colleagues at UGA to use these new resources and new genomic tools to continue research that improves human and environmental health“ added Glenn.