DOI: 10.5061/dryad.ht76hdrp9
title: Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus

description: 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: Oceanic whitetip shark samples were genotyped at 14
 microsatellite loci including three loci from <em>Carcharhinus
 longimanus</em> (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 <em>C. longimanus</em> [Cl13, Cl15, Cl17
 from <em>Carcharhinus leucas </em>(Pirog et al. 2015); Cli107
 from Keeney and Heist (2003); Cpe141, Cpe334, Cpe352 from
 <em>Carcharhinus perezi</em> (Bernard et al. 2017); Pgla-02
 from <em>Prionace glauca</em> (Fitzpatrick et al. 2011); Ct06
 from <em>Carcharhinus tilstoni</em> (Ovenden et al. 2006); and
 A2ASY, CY92Z from <em>Prionace glauca</em> (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.). 
 Bernard AM, Horn RL, Chapman DD, Feldheim KA, Garla RC, Brooks
 EJ, Gore MA, Shivji MS (2017) Genetic connectivity of a coral reef
 ecosystem predator: the population genetic structure and evolutionary
 history of the Caribbean reef shark (<em>Carcharhinus
 perezi</em>). J Biogeogr 44:2488-2500. https://doi.org/10.1111/jbi.13062 Fitzpatrick S, Shivji MS, Chapman DD, Prodöhl PA (2011) Development and characterization of 10 polymorphic microsatellite loci for the blue shark, <em>Prionace glauca</em>, and their cross shark-species amplification. Conserv Genet Resour 3:523-527. https://doi.org/10.1007/s12686-011-9395-6 Keeney DB, Heist EJ (2003) Characterization of microsatellite loci isolated from the blacktip shark and their utility in requiem and hammerhead sharks. Mol Ecol Notes 3:501-504. https://doi.org/10.1046/j.1471-8286.2003.00492.x Mendes NJ, Cruz VP, Mendonça FF, Pardo BG, Coelho R, Ashikaga FY, Camargo SM, Martínez P, Oliveira C, Santos MN, Foresti F (2015) Microsatellite loci in the oceanic whitetip shark and cross-species amplification using pyrosequencing technology. Conserv Genet Resour 7:585-589. https://doi.org/10.1007/s12686-015-0435-5 Ovenden JR, Street R, Broderick D (2006) New microsatellite loci for Carcharhinid sharks (<em>Carcharhinus tilstoni </em>and <em>C. sorrah</em>) and their cross-amplification in other shark species. Mol Ecol Notes 6:415-418. https://doi.org/10.1111/j.1471-8286.2005.01254.x Pirog A, Blaison A, Jaquemet S, Soria M, Magalon H (2015) Isolation and characterization of 20 microsatellite markers from <em>Carcharhinus leucas</em> (bull shark) and cross-amplification in <em>Galeocerdo cuvier</em> (tiger shark), <em>Carcharhinus obscurus</em> (dusky shark), and <em>Carcharhinus plumbeus</em> (sandbar shark). Conserv Genet Resour 7:121-124. https://doi.org/10.1007/s12686-014-0308-3 Taguchi M, Shigenobu Y, Ohkubo M, Yanagimoto T, Sugaya T, Nakamura Y, Saitoh K, Yokawa K (2013) Characterization of 12 polymorphic microsatellite DNA loci in the blue shark, <em>Prionace glauca</em>, isolated by next generation sequencing approach. Conserv Genet Resour 5:117-119. https://doi.org/10.1007/s12686-012-9746-y
description: # 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.). Bernard AM, Horn RL, Chapman DD, Feldheim
 KA, Garla RC, Brooks EJ, Gore MA, Shivji MS (2017) Genetic connectivity of
 a coral reef ecosystem predator: the population genetic structure and
 evolutionary history of the Caribbean reef shark (*Carcharhinus perezi*).
 J Biogeogr 44:2488-2500. 
 Fitzpatrick S, Shivji MS, Chapman DD, Prodöhl PA (2011) Development and
 characterization of 10 polymorphic microsatellite loci for the blue shark,
 *Prionace glauca*, and their cross shark-species amplification. Conserv
 Genet Resour 3:523-527. 
 Keeney DB, Heist EJ (2003) Characterization of microsatellite loci
 isolated from the blacktip shark and their utility in requiem and
 hammerhead sharks. Mol Ecol Notes 3:501-504.
 Mendes NJ, Cruz
 VP, Mendonça FF, Pardo BG, Coelho R, Ashikaga FY, Camargo SM, Martínez P,
 Oliveira C, Santos MN, Foresti F (2015) Microsatellite loci in the oceanic
 whitetip shark and cross-species amplification using pyrosequencing
 technology. Conserv Genet Resour 7:585-589.
 Ovenden JR, Street R,
 Broderick D (2006) New microsatellite loci for Carcharhinid sharks
 (*Carcharhinus tilstoni* and *C. sorrah*) and their cross-amplification in
 other shark species. Mol Ecol Notes 6:415-418.
 Pirog A, Blaison
 A, Jaquemet S, Soria M, Magalon H (2015) Isolation and characterization of
 20 microsatellite markers from *Carcharhinus leucas* (bull shark) and
 cross-amplification in *Galeocerdo cuvier* (tiger shark), *Carcharhinus
 obscurus* (dusky shark), and *Carcharhinus plumbeus* (sandbar shark).
 Conserv Genet Resour 7:121-124.
 Taguchi M, Shigenobu Y,
 Ohkubo M, Yanagimoto T, Sugaya T, Nakamura Y, Saitoh K, Yokawa K (2013)
 Characterization of 12 polymorphic microsatellite DNA loci in the blue
 shark, *Prionace glauca*, isolated by next generation sequencing approach.
 Conserv Genet Resour 5:117-119.
 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.