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

25 Scopus citations

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

Bibliographical note

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
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

Bibliographical note

Funding

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Keywords

Disciplines

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