Title

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

Authors

Michael J. Stanhope, Cornell University
Kristina M. Ceres, Cornell University
Qi Sun, Cornell University
Minghui Wang, Cornell University
Jordan D. Zehr, Temple University
Nicholas J. Marra, Governors State University
Aryn P. Wilder, San Diego Zoo Wildlife Alliance
Cheng Zou, Cornell University
Andrea M. Bernard, Nova Southeastern UniversityFollow
Paulina D. Pavinski Bitar, Cornell University
Mitchell G. Lokey, Cornell University
Mahmood Shivji, Nova Southeastern UniversityFollow

Document Type

Article

Publication Date

1-20-2023

Publication Title

iScience

ISSN

2589-0042

Volume

26

Issue/No.

1

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 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.

Comments

Data and code availability

• Genome assembly data for the great hammerhead and shortfin mako have been deposited at GenBank and are publicly available as of the date of publication. The genome sequencing reads and transcriptome sequence data are deposited in the NCBI Sequence Read Archive. Accession numbers are listed in the key resources table.

• Preliminary genome annotations for both the great hammerhead and shortfin mako have been deposited at Dryad and are publicly available as of the date of publication. DOIs are listed in the key resources table.

• Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Additional Comments

Major funding for this study was provided by grants from the Save Our Seas Foundation, the Guy Harvey Ocean Foundation, and the Shark Foundation/Hai Stiftung.

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International License.

NSUWorks Citation

Stanhope, Michael J.; Kristina M. Ceres; Qi Sun; Minghui Wang; Jordan D. Zehr; Nicholas J. Marra; Aryn P. Wilder; Cheng Zou; Andrea M. Bernard; Paulina D. Pavinski Bitar; Mitchell G. Lokey; and Mahmood Shivji. 2023. "Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead." iScience 26, (1). doi:10.1016/j.isci.2022.105815.

ResearcherID

G-4080-2013

DOI

10.1016/j.isci.2022.105815