README: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus

Abstract
The oceanic whitetip shark, Carcharhinus longimanus, is a Critically Endangered, circumtropical, and highly migratory, pelagic shark. Yet,
little information exists on its population genetic dynamics to guide conservation management practice. We present a first worldwide,
mitochondrial and nuclear DNA assessment of the population genetic status of this imperiled species based on sequences of the complete
mitochondrial control region (n = 173) and partial ND4 gene (n = 172), and genotypes from 12 nuclear microsatellites (n = 164). Statistically
significant mitochondrial and nuclear DNA population genetic differentiation was detected across all marker datasets between Western Atlantic
and Indo-Pacific oceanic whitetip sharks. Additionally, our data, combined with previously published, partial (701-base pairs) mitochondrial
control region sequences from additional locations in the Atlantic and Indian Oceans, confirmed significant matrilineal population structure
between the Western and Eastern Atlantic. The combined data also provisionally (i.e., with FST but not ΦST) indicated differentiation between
Western North and Central-South Atlantic sharks, pointing to the need for further assessment in this region. Matrilineal differentiation was also
detected between Indian and Pacific Ocean sharks via pairwise analyses, albeit with the ND4 gene sequence only (ΦST = 0.051; FST = 0.092).
Limited sampling in the Pacific leaves open questions about the connectivity dynamics in this large region. Despite the presence of geographic
population genetic structure, the mitochondrial data showed no evidence of across ocean basin phylogeographic lineages. A provisional
assessment of mitochondrial and nuclear genetic diversity indicated the oceanic whitetip shark’s status falls in the middle to upper ranges
compared to other shark species, potentially lending some optimism for the present adaptability and resiliency of this species if strong
conservation measures are effectively implemented.

Description of the Data and file structure

Oceanic whitetip shark samples were genotyped at 14 microsatellite loci including three loci from Carcharhinus longimanus (OCS_08, OCS_13, OCS_19) previously described by Mendes et al. (2015) and 11 loci isolated in other shark species that also cross-amplified in C. longimanus [Cl13, Cl15, Cl17 from Carcharhinus leucas (Pirog et al. 2015); Cli107 from Keeney and Heist (2003); Cpe141, Cpe334, Cpe352 from Carcharhinus perezi (Bernard et al. 2017); Pgla-02 from Prionace glauca (Fitzpatrick et al. 2011); Ct06 from Carcharhinus tilstoni (Ovenden et al. 2006); and A2ASY, CY92Z from Prionace glauca (Taguchi et al. 2013)]
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.).

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This dataset consists of one file:

Ruck et al. 2024_oceanic whitetip microsatellite genotypes.csv: contains microsatellite genotypes of young-of-year scalloped hammerhead sharks collected from the Eastern Tropical Pacific.

Description of data:
column 1 contains unique sample identifier (OC-Number);
column 2 contains sample location information (Location);
columns 3 to 30 contain microsatellite genotypes; one locus = two columns.