Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead
Michael J. Stanhope,
Kristina M. Ceres,
Qi Sun,
Minghui Wang,
Jordan D. Zehr,
Nicholas J. Marra,
Aryn P. Wilder,
Cheng Zou,
Andrea M. Bernard,
Paulina Pavinski-Bitar,
Mitchell G. Lokey,
Mahmood S. Shivji
Affiliations
Michael J. Stanhope
Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USA; Corresponding author
Kristina M. Ceres
Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USA
Qi Sun
Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
Minghui Wang
Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
Jordan D. Zehr
Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
Nicholas J. Marra
Division of Science, Mathematics and Technology, Governors State University, University Park, IL 60484, USA
Aryn P. Wilder
Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92101, USA
Cheng Zou
Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
Andrea M. Bernard
Save Our Seas Foundation Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL 33004, USA
Paulina Pavinski-Bitar
Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USA
Mitchell G. Lokey
Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Mahmood S. Shivji
Save Our Seas Foundation Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL 33004, USA; Corresponding author
Summary: Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and 1 Mbp. Both these sharks experienced precipitous declines in effective population size (Ne) over the last 250 thousand years. While shortfin mako exhibited a large historical Ne that may have enabled the retention of higher genetic variation, the genomic data suggest a possibly more concerning picture for the great hammerhead, and a need for evaluation with additional individuals.
