DOI: 10.5061/dryad.7h44j103q
title: Single nucleotide polymorphism genotypes for the Australian blackspot shark and the milk shark in Northern Australian waters

description: Charles Darwin University and the Northern Territory (NT) Department of
 Industry, Tourism and Trade (DITT) Fisheries Division used genetic data to
 investigate the population structure of two small tropical shark species
 (Milk Shark [Rhizoprionodon acutus] and Australian Blackspot Shark
 [Carcharhinus coatesi]), which are caught as bycatch from commercial
 fisheries in the NT.   The aim of this study was to gain
 information on the genetic stock structure to inform the future management
 of these two species in the NT. This project was conducted in parallel
 with a PhD project investigating the biology and ecology of both species
 for applications to fisheries management. There is motivation by the NT
 Government to develop these two shark species into a commercial product.
 This project used genetic analysis to understand the patterns of
 connectivity of populations of these two shark species in NT waters and
 adjacent regions, including Northern Western Australia and Papua New
 Guinea.   Background   These two shark species that are
 captured as bycatch in the NT Demersal Trawl fishery have the potential to
 be developed into a byproduct to add value to that fishery. A sustainable
 commercial harvest of these two species could greatly reduce the waste
 from fisheries, where they are currently abundant and caught in relatively
 large numbers. We address current knowledge gaps in biological information
 about populations of R. acutus and C. coatesi to inform the potential
 development of a byproduct fishery for these two species in the NT.
   Aims   Our research aimed to:   · 
        identify the genetic population
 structure for R. acutus and C. coatesi in NT waters   · 
        develop capacity for genetic
 research and monitoring of shark species in the NT   · 
        provide baseline information on
 genetic structure to inform potential genetic monitoring of these species,
 including initial estimates of effective population size.  
 Methods   We used single-nucleotide polymorphism genetic analyses
 to measure genetic structure among R. acutus and C. coatesi samples
 obtained from commercial trawl fishing in NT waters between May 2018 and
 November 2019. Our aim was to determine whether the two species each occur
 as a single population in NT waters or as a set of discrete populations
 that may warrant separate monitoring and management. We also analysed
 samples of these species from Western Australia and Papua New Guinea to
 provide broader context for the degree of genetic differentiation among
 the samples from different regions in the NT.   Our secondary aim
 was to provide a baseline for deciding whether genetic estimates of
 effective population size could be used to monitor trends in abundance of
 these species, and whether samples from across the NT could be combined
 for the genetic estimation of effective population size for this purpose.
   Results   Genetic data from R. acutus and C. coatesi
 strongly suggest that each species exists as a single, highly connected
 population in the NT. Genetic differentiation among the sampling locations
 for each species was low, and genetic clustering analyses provided strong
 support for a single population of each species in the region. Sharks of
 both species captured within a single location (within 50 km of one
 another) were more genetically related than those further apart; however,
 this does not constitute evidence for multiple, spatially discrete
 populations of either species in NT waters. Preliminary applications of
 effective population size estimators were used, but further work is needed
 to determine if these can be used to indicate trends in abundance.
   Implications for relevant stakeholders   The immediate
 implications of our research are for fisheries scientists and managers
 from NT DITT. Our results indicate that these two shark species can be
 monitored and managed in the NT under the assumption that each species
 occurs as a single population in this region. Further information relevant
 to shorter-term movements of individuals may refine management strategies
 for the two species.   Our research has potential implications
 for commercial fishers, particularly from the Demersal Trawl Fishery and
 Australia Bay Seafoods company. Currently, those implications are
 indirect, as the information from our research will flow through to the
 industry by contributing to the information required to develop a
 byproduct fishery for the two species, mitigating bycatch and increasing
 economic return.   Recommendations   Future research
 could develop genetic methods, such as effective population size or
 close-kin mark-recapture, for population monitoring. Comparing the genetic
 data against other data that indicate individual movement patterns on
 shorter timescales would help develop a holistic understanding of shark
 movement and population connectivity to inform sustainable harvest
 strategies.
description: The two datasets presented here include single nucleotide
 polymorphism (SNP data for the milk shark (<em>Rhizoprionodon
 acutus</em>) and the Australian blackspot shark
 (<em>Carcarhinus coatesi</em>) generated by Diversity Arrays
 Pty Ltd using the DArTSeq method. DArTSeq (Kilian et al 2012) involves an
 initial step of ‘genome reduction’ to subset a small fraction of the
 genome of each individual for high-throughput sequencing, followed by
 bioinformatics analysis to identify DNA sequences containing single
 nucleotide positions that vary among individuals within and among
 populations. The DArTSeq protocols for <em>Carcharhinus
 </em>and <em>Rhizoprionodon</em><em>
 </em>are available for future projects via Diversity
 Arrays.  Using the DArTSeq protocol, 196 individual
 <em>R. acutus</em>  and 634 individual <em>C. coatesi
 sampled </em>were genotyped. The samples came from sharks that were
 collected in Northern Territory (Australia) waters between May 2018 and
 November 2019 and from three additional regions including Western
 Australia (Pilbara and Kimberley regions) and Papua New Guinea.
 Sampling locations of individuals and full unfilltered SNP
 genotypes are included in the dataset. Kilian, A.,
 Wenzl, P., Huttner, E., Carling, J., Xia, L., Blois, H., Caig, V.,
 Heller-Uszynska, K., Jaccoud, D., & Hopper, C. (2012). Diversity
 arrays technology: A generic genome profiling technology on open
 platforms. In <em>Data production and analysis in population
 genomics</em> (pp. 67–89). Springer.
description: # Single nucleotide polymorphism genotypes for the Australian blackspot
 shark and the milk shark in northern Australian waters
 [https://doi.org/10.5061/dryad.7h44j103q](https://doi.org/10.5061/dryad.7h44j103q) ## Description of the data and file structure ## Sample collection We took tissue samples from 196 individual *Rhizoprionodon acutus*  (Figure 1) and 634 individual *Carcharhinus coatesi *(Figure 2) that were collected in Northern Territory (Australia) waters between May 2018 and November 2019. These sharks were caught as bycatch from the commercial trawl fisheries from Australia’s Exclusive Economic Zone (EEZ) and retained for our research use. Australia’s EEZ around the NT encompasses the Timor Sea in the north-west, the Arafura Sea in the north and the Gulf of Carpentaria in the east (Figure 1, Figure 2). For initial analyses of patterns of population genetics, we grouped the NT samples into four regions. We included three additional regions (Pilbara, Kimberley and Papua New Guinea [PNG]) for *R. acutus* (Figure 1) and two additional regions (Kimberley and PNG) for *C. coatesi* (Figure 2). We included these additional samples from Western Australia (WA) and PNG to provide broader context to help understand the degree of genetic differentiation and connectivity among populations in NT waters relative to a broader sample across the regional distribution of these species. The Western Australian samples were provided by Alister Harry (WA Department of Primary Industries and Regional Development), and the PNG samples were provided by Will White (CSIRO). We extracted DNA for single-nucleotide polymorphism (SNP) genotyping using the DArTSeq protocol through Diversity Arrays P/L (Kilian et al., 2012). We sent tissue samples in 100% ethanol to Diversity Arrays for DNA extraction and genomic library preparation for sequencing. DArTSeq involves an initial step of ‘genome reduction’ to subset a small fraction of the genome of each individual for high-throughput sequencing, followed by bioinformatics analysis to identify DNA sequences containing single nucleotide positions that vary among individuals within and among populations. The DArTSeq protocols for *Carcharhinus *and *Rhizoprionodon *are available for future projects via Diversity Arrays. The data were used for genetic analyses to infer population structure as described in the published report for the Fisheries Research and Development Corporation associated with this dataset. Kilian, A., Wenzl, P., Huttner, E., Carling, J., Xia, L., Blois, H., Caig, V., Heller-Uszynska, K., Jaccoud, D., & Hopper, C. (2012). Diversity arrays technology: A generic genome profiling technology on open platforms. In *Data production and analysis in population genomics* (pp. 67–89). Springer. ### Files and variables **Description:** Unfiltered SNP datasets for Rhizoprionodon acutus and Carcharinus coatesi as well as CSV files with individual sample information including sampling location ('id' = individual sample identifier; 'pop' = stratum variable for calculation of genetic diversity metrics based on broad sampling region; 'lat' = latitude of sampling location (rounded); 'lon' = longitude of sampling location (rounded); and 'Full pop name' = full name of population strata for analysis. The files are in the default format required for filtering and analysis in the dartR package for the R statistical environment. The two metadata files describe the unfiltered SNP data provided by Diversity arrays P/L. Gruber, B., Unmack, P. J., Berry, O. F., & Georges, A. (2018). dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. *Molecular Ecology Resources, 18*(3), 691–699. [https://doi.org/10.1111/1755-0998.12745](https://doi.org/10.1111/1755-0998.12745) R Core Team. (2024). *R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria*. [https://www.R-project.org](https://www.R-project.org) ## Code/software Do, C., Waples, R. S., Peel, D., Macbeth, G. M., Tillett, B. J., & Ovenden, J. R. (2014). NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. *Molecular Ecology Resources, 14*(1), 209–214. [https://doi.org/10.1111/1755-0998.12157](https://doi.org/10.1111/1755-0998.12157) Gruber, B., Unmack, P. J., Berry, O. F., & Georges, A. (2018). dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. *Molecular Ecology Resources, 18*(3), 691–699. [https://doi.org/10.1111/1755-0998.12745](https://doi.org/10.1111/1755-0998.12745) Jombart, T., & Ahmed, I. (2011). adegenet 1.3-1: New tools for the analysis of genome-wide SNP data. *Bioinformatics, 27*(21), 3070–3071. [https://doi.org/10.1093/bioinformatics/btr521](https://doi.org/10.1093/bioinformatics/btr521) Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—an update. *Bioinformatics, 28*(19), 2537–2539. [https://doi.org/10.1093/bioinformatics/bts460](https://doi.org/10.1093/bioinformatics/bts460) Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. *Genetics,* *155*(2), 945–959. [https://doi.org/10.1093/genetics/155.2.945](https://doi.org/10.1093/genetics/155.2.945) R Core Team. (2024). *R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria*. [https://www.R-project.org](https://www.R-project.org)