About the Authors

Weerachai Jaratlerdsiri

Affiliation Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia

Janine Deakin

Affiliations Evolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia

Ricardo M. Godinez

Affiliations Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, United States of America, Department of Genetics, Harvard Medical School, 77 Louis Pasteur Ave., Boston, Massachusetts 02115, United States of America

Xueyan Shan

Affiliation Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America

Daniel G. Peterson

Affiliation Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America

Sylvain Marthey

Affiliation Animal Genetics and Integrative Biology, INRA, UMR 1313 Jouy-en-Josas 78352, France

Eric Lyons

Affiliation School of Plant Science, University of Arizona, Tucson, Arizona 85721, United States of America

Fiona M. McCarthy

Affiliation School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States of America

Sally R. Isberg

Affiliations Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia, Center for Crocodile Research, P.O. Box 329, Noonamah, Northern Territory 0837, Australia

Damien P. Higgins

Affiliation Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia

Amanda Y. Chong

Affiliation Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia

John St John

Affiliation Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, United States of America

Travis C. Glenn

Affiliation Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602, United States of America

David A. Ray

Current address: Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, United States of America.

Affiliations Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America, Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America

Jaime Gongora

jaime.gongora@sydney.edu.au

Affiliation Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: WJ SRI JG. Performed the experiments: WJ JD TCG. Analyzed the data: WJ RGM SM EL FMM AYC JSJ JG. Contributed reagents/materials/analysis tools: WJ JD XS DGP EL FMM JSJ TCG DAR JG. Wrote the paper: WJ JD RGM XS DGP SM EL FMM SRI DPH AYC JSJ TCG DAR JG. Contributed to the experimental design, undertook primary experiments, performed data analyses and led the writing up of this paper: WJ. Initiated, directed and supervised this work, contributed with the interpretation of the data and preparation of the manuscript and provided extensive feedback: JG. Provided assistance in BAC library screening: JD. Contributed to data of the green anole MHC used in this paper: RGM. Provided saltwater crocodile BAC library, prepared BAC clones containing MHC genes in the USA, and shipped them to Australia: XS DGP. Provided invaluable assistance on data analyses and offered useful suggestions on the manuscript: SM EL FMM. Contributed to supervision of the project and discussions concerning the project plan and manuscript preparation: SRI DPH. Provided assistance in the lab, performed the second run of de novo BAC assemblies for cross-referencing purposes, and contributed useful comments on retroelements: AYC. Offered advice on techniques and analyses of BAC-based sequencing, and provided genome and transcriptome resources of the saltwater crocodile, American alligator and Indian gharial used in the data analyses: JSJ TCG DAR. Read, commented on and approved the drafts of the manuscript: WJ JD RGM XS DGP SM EL FMM SRI DPH AYC JSJ TCG DAR JG.