University of Sydney scientists study croc evolution

16 January 2015

Crocodilians, including the Australian saltwater crocodile, mutate at about a quarter of the rate of birds, new research has revealed.
The discovery is the result of genome sequencing three crocodilian species—the Australian saltwater crocodile, the American alligator and the Indian gharial—by an international collaboration of scientists, including six from the Sydney Faculty of Veterinary Science. The research is reported in a special edition of Science published in December dedicated to all aspects of bird evolution and its closest living biological grouping, crocodilians. The ambitious publication is the first time a single study has deliberately targeted the full diversity of any major vertebrate group.

University of Sydney Veterinary Science
Sydney study shows crocs are slow to evolve

“The research shows that compared to bird genomes, crocodilians evolved approximately four times more slowly than birds,” said Associate Professor Jaime Gongora from the Sydney Faculty of Veterinary Science and a team leader on the project.
“It challenges us to solve the mystery of how the crocodilians have maintained their genetic diversity and survived for hundreds of millions of years—given this slow mutation rate. Comparing these crocodilian genomes to related groups, including birds and turtles, allowed us to unveil characteristics of the common ancestors between these lineages. For instance, many genes have remained stably ordered and oriented mapping back to that common ancestor,” said project leader Associate Professor David Ray from Texas Tech University.
The findings are crucial to providing a comprehensive understanding of the genomic underpinnings of the diversity, natural history, immunity and biology of crocodilians and will certainly open new frontiers in crocodile research.
“We can use these genome resources to investigate the diversity of captive and wild saltwater crocodile populations to better understand their disease resistance, and their susceptibility and specific adaptations to their environments,” Professor Gongora said.
Related findings by Associate Professor Gongora and his team are being published simultaneously in companion papers in the journals Retrovirology and PLOS ONE.
The research in PLOS ONE and Retrovirology identifies new lineages of viruses within the crocodilian genomes, some of which have captured crocodilian genes. It reveals that genes of adaptive immunity have diversified in crocodilians and shown a different organisational pattern from that in birds and other reptiles, which may provide some advantage to fight microbes.
Dr Sally Isberg from the Centre for Crocodile Research and Honorary Associate in at the Sydney Veterinary School, coauthored these papers and was the main crocodile industry driver behind the project: “While bridging the gap in evolutionary studies, this knowledge will also help crocodile producers by enhancing the genetic regulation of the immune and endocrine systems, maximizing growth and ensuring skin quality. Crocodile farming is a conservation success story but understanding the underlying genomic differences will enhance our ability to farm crocodiles ethically, efficiently and effectively.”
“The work does not end here. We are now in the process of identifying an enormous number of sites in the DNA that show variation so that crocodile producers can select breeding crocodiles in the same way they select dairy cattle,” Emeritus Professor Christopher Moran said.
Associate Professor Gongora, Dr Isberg, Dr Amanda Chong, Dr Weerachai Jaratlerdsiri, Dr Lee Miles and Emeritus Professor Moran are the Sydney Faculty of Veterinary Science authors on the Science paper.
Associate Professor Gongora, Dr Jaratlerdsiri (first author), Dr Chong, Dr Isberg and Dr Damien Higgins are the Faculty’s authors on the PLOS ONE paper.
Associate Professor Gongora, Dr Chong (first author), and Dr Isberg and Dr Chong are the Faculty’s authors on the Retrovirology paper.
Professor Eddie Holmes and Associate Professor Simon Ho, both from the Sydney School of Biological Sciences have also contributed to the international project that sequenced, assembled and compared the full genomes of 48 bird species and are authors on papers in Science and accompanying journals.
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