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 D. Pavinski Bitar; Mitchell G. Lokey; Mahmood 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

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 D. Pavinski Bitar, Mitchell G. Lokey, Mahmood Shivji

Research output: Contribution to journal › Article › peer-review

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.

Original language	American English
Article number	105815
Journal	iScience
Volume	26
Issue number	1
DOIs	https://doi.org/10.1016/j.isci.2022.105815
State	Published - Jan 20 2023

Funding

We thank Peter Schweitzer and the Cornell Genomics facility for the Illumina sequencing that was performed on both hammerhead and mako; Dovetail Genomics for scaffolding of both species; Brewster Kingham and the University of Delaware Sequencing and Genotyping Center for PacBio genome sequencing of both species and isoseq transcriptome sequencing from mako tissue; the Cornell Bioinformatics Facility for various technical and analytical assistance; and Megan Supple for helpful discussions. 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 .

Funders	Funder number
Shark Foundation/Hai-Stiftung
Guy Harvey Ocean Foundation
Save our Seas Foundation

ASJC Scopus Subject Areas

General

Keywords

Evolutionary biology
Genomics
Genetics
Biological sciences

Disciplines

Biology
Genetics and Genomics
Life Sciences

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10.1016/j.isci.2022.105815

Genomes of endangered great hammerhead and shortfin mako sharks rFinal published version, 7.07 MBLicense: CC BY

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Stanhope, M. J., Ceres, K. M., Sun, Q., Wang, M., Zehr, J. D., Marra, N. J., Wilder, A. P., Zou, C., Bernard, A. M., Pavinski Bitar, P. D., Lokey, M. G., & Shivji, M. (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), Article 105815. https://doi.org/10.1016/j.isci.2022.105815

Stanhope, MJ, Ceres, KM, Sun, Q, Wang, M, Zehr, JD, Marra, NJ, Wilder, AP, Zou, C, Bernard, AM, Pavinski Bitar, PD, Lokey, MG & Shivji, M 2023, 'Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead', iScience, vol. 26, no. 1, 105815. https://doi.org/10.1016/j.isci.2022.105815

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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.",

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

Abstract

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