DNA Analysis of Juvenile Scalloped Hammerhead Sharks Sphyrna lewini (Griffith, 1834) Reveals Multiple Breeding Populations and Signs of Adaptive Divergence in the South Pacific

Abstract

Shark species have undergone drastic population declines in recent decades due to overfishing and habitat destruction; thus, establishing connectivity among the populations of various shark species is important to determine the appropriate units and spatial scale for conservation and management, particularly as this group is longlived with late age of maturation. Consequently, we used DNA variation at 1,317 putatively neutral and 25 potentially adaptive single nucleotide polymorphisms (SNPs) to analyze population genetic structure among 174 unrelated individuals of scalloped hammerhead sharks (Sphyrna lewini) from the Rewa Delta and the Ba Estuary, where documented aggregations of neonates and young-of-the-year occur in the island of Viti Levu, Republic of Fiji. Results of the pairwise F ST analysis for the neutral loci revealed a small but significant genetic differentiation (F ST : 0.004; P-value = 0.0009). Furthermore, the 25 potentially adaptive loci (i.e., under putative selection) revealed a magnitude of differentiation four times bigger than the estimate obtained using neutral genetic diversity (F ST : 0.017; P-value = 0.0009). Interestingly, population assignment tests, using the neutral SNP data set and two different software packages, Admixture and assignPOP, provided evidence for the existence of up to four genetically differentiated populations among our samples. Assignment probabilities ranged from 0.98 ± 0.01 to 0.81 ± 0.03. Admixture and assignPOP assigned the same individuals to the same putative populations for all sampled neonates. Thus, our results provide unequivocal evidence that adult females from multiple genetically differentiated breeding populations contribute to these juvenile aggregation sites.

Phylogeography of the iconic Australian pink cockatoo,Lophochroa leadbeateri

“…see Forshaw, 2011), and the need to disentangle patterns of geographical, sexual and age-related variation. Genomic analyses have the potential to help to characterize conservation units, investigate connectivity among core breeding populations, and resolve lingering taxonomic uncertainties about subspecies boundaries (Baumsteiger et al, 2017;Marie et al, 2019;Tonzo et al, 2019;Ewart et al, 2020). Furthermore, genetic data could facilitate the development of wildlife forensic tools, such as geographical provenance and progeny testing, to increase the capacity for detection and prosecute trafficking crimes involving this species (Walker et al, 1999;Huffman & Wallace, 2011).…”

Local adaptation with gene flow in a highly dispersive shark

“…With the increased availability of genome‐wide SNP data for non‐model species, fine‐scale population genomics assessments have been conducted in a number of shark species, including the application of genome scans to identify patterns of local adaptation (Bernard et al., 2021 ; Boussarie et al., 2022 ; Marie et al., 2019 ; Momigliano et al., 2017 ; Pazmiño et al., 2018 ; Portnoy et al., 2015 ). Here, we provide the first seascape genomics assessment of a shark species along the highly heterogeneous coastline of southern Africa.…”

Genomic population structure of great hammerhead sharks (Sphyrna mokarran) across the Indo-Pacific

“…occurring in the blue shark, Prionace glauca; Veríssimo et al 2017), if movement is solely male (e.g. S. lewini; Marie et al 2019) or female mediated, or driven by natal philopatry like in other species (e.g. lemon sharks, Negaprion brevirostris; Feldheim et al 2001).…”