iScience
Volume 26, Issue 1, 20 January 2023, 105815
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Article
Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead

https://doi.org/10.1016/j.isci.2022.105815Get rights and content
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Highlights

  • Chromosome-level genome assemblies for two endangered species of shark

  • Great hammerhead had low heterozygosity with high inbreeding coefficients

  • Shortfin mako exhibited higher levels of heterozygosity suggesting adaptive potential

  • Both species showed precipitous declines in historical effective population size

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% 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.

Subject areas

Biological sciences
Genetics
Evolutionary biology
Genomics

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.

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Lead contact