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Genetic population dynamics of the critically endangered scalloped hammerhead shark (Sphyrna lewini) in the Eastern Tropical Pacific

Cite this dataset

Bernard, Andrea; Harned, Sydney; Shivji, Mahmood (2022). Genetic population dynamics of the critically endangered scalloped hammerhead shark (Sphyrna lewini) in the Eastern Tropical Pacific [Dataset]. Dryad.


The scalloped hammerhead shark, Sphyrna lewini, is a Critically Endangered, migratory species known for its tendency to form iconic and visually spectacular large aggregations. Herein, we investigated the population genetic dynamics of the scalloped hammerhead across much of its distribution in the Eastern Tropical Pacific (ETP), ranging from Costa Rica to Ecuador, focusing on young‐of‐the‐year animals from putative coastal nursery areas and adult females from seasonal aggregations that form in the northern Galápagos Islands. Nuclear microsatellites and partial mitochondrial control region sequences showed little evidence of population structure, suggesting that scalloped hammerheads in this ETP region comprise a single genetic stock. Galápagos aggregations of adults were not comprised of related individuals, suggesting that kinship does not play a role in the formation of the repeated, annual gatherings at these remote offshore locations. Despite high levels of fisheries exploitation of this species in the ETP, the adult scalloped hammerheads here showed greater genetic diversity compared with adult conspecifics from other parts of the species' global distribution. A phylogeographic analysis of available, globally sourced, mitochondrial control region sequence data (n = 1,818 sequences) revealed that scalloped hammerheads comprise three distinct matrilines corresponding to the three major world ocean basins, highlighting the need for conservation of these evolutionarily unique lineages. This study provides the first view of the genetic properties of a scalloped hammerhead aggregation, and the largest sample size‐based investigation of population structure and phylogeography of this species in the ETP to date.


Scalloped hammerhead shark samples were genotyped at 9 microsatellite loci including five loci from Sphyrna lewini (SLE027, SLE033, SLE045, SLE038, SLE089) previously described by Nance et al. (2009) and four loci isolated in other shark species that also cross‐amplified in S. lewini [Cli‐12 from Carcharhinus limbatus (Keeney & Heist, 2003) and SMO3, SMO7, and SMO8 from Sphyrna mokarran (Feldheim et al., 2020).

Electrophoresis of amplified microsatellite loci was performed on an Applied Biosystems 3130 Genetic Analyzer. Alleles were sized using GeneScan LIZ 600 size standard and scored using the software GeneMapper v.3.7 (Applied Biosystems Inc.).

  • FeldheimK. A.JabadoR. W.ChapmanD. D.CardeñosaD., & MaddoxJ. D. (2020). Microsatellite primer development in elasmobranchs using next generation sequencing of enriched librariesMolecular Biology Reports47(4), 26692675.
  • KeeneyD. B., & HeistE. J. (2003). Characterization of microsatellite loci isolated from the blacktip shark and their utility in requiem and hammerhead sharksMolecular Ecology Notes3(4), 501504.
  • NanceH. A.Daly‐EngelT. S., & MarkoP. B. (2009). New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewiniMolecular Ecology Resources9(3), 955957.

Usage notes

This dataset consists of two files:

1) Harned et al._msats_ETP.csv: contains microsatellite genotypes of young-of-year scalloped hammerhead sharks collected from the Eastern Tropical Pacific.

2) Harned et al_msats_GalFLSey.csv: contains microsatellite genotypes of all putative adult scalloped hammerhead sharks collected from the Galápagos, Florida east Coast USA, and the Seychelles. 


Save Our Seas Foundation

Guy Harvey Ocean Foundation

Swiss Shark Foundation/Hai‐Stiftung

National Geographic Pristine Seas

Gordon and Betty Moore Foundation

Nova Southeastern University

Mark and Rachel Rohr Foundation

Co‐Exist Projects

Mark Qi Wong