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

doi:10.1016/j.isci.2022.105815

Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead

iScience. 2022 Dec 17;26(1):105815. doi: 10.1016/j.isci.2022.105815. eCollection 2023 Jan 20.

Authors

Affiliations

¹ Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USA.
² Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA.
³ Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
⁴ Division of Science, Mathematics and Technology, Governors State University, University Park, IL 60484, USA.
⁵ Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92101, USA.
⁶ Save Our Seas Foundation Shark Research Center and Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL 33004, USA.
⁷ Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

Abstract

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% in ROH > 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.

Keywords: Biological sciences; Evolutionary biology; Genetics; Genomics.

Associated data

Dryad/10.5061/dryad.mgqnk992h