Introduction

More than 30% of the over 500 extant shark species are currently classified globally as Vulnerable, Endangered, or Critically Endangered (Dulvy et al. 2021; Fricke et al. 2023). Moreover, shark conservation often suffers from inaccurate assessments, mostly coming from non-systematic observations such as sightings per unit effort, among others (e.g. Pacoureau et al. 2021). Detailed molecular assessments can contribute to shark conservation by assessing population-level characteristics such as population structuring, population sizes, local genetic, and adaptive potential to environmental change (reviewed in Hohenlohe et al. 2021). However, in the case of molecular studies relevant to shark conservation, research for many species still relies on small parts of the mitochondrial genome, and/or nuclear microsatellite DNA (e.g. Hoelzel 2001; Hoelzel et al. 2006; Veríssimo et al. 2010; Thorburn et al. 2018; González et al. 2020; Lieber et al. 2020). Both types of marker have limitations, both biological and technical (see e.g. Teske et al. 2018; Choquet et al. 2023).
Such limitations can be overcome by use of genome-wide markers such as Single Nucleotide Polymorphisms (SNPs, e.g. Cairns et al. 2023; Choquet et al. 2023). Genome wide SNPs can be derived in various ways, such as from whole genome resequencing (e.g. Foote et al. 2016; Lamichhaney et al. 2017), providing the widest range of genomic information possible, or from reduced representation methods (e.g. Baird et al. 2008). The latter is ideally suited in cases where a high-quality genome is not available, the genome of interest is too large for cost effective re-sequencing at sufficient depth for the required number of individuals, or when computational resources are limited. Only thirteen nuclear shark genomes have been published to date (Read et al. 2017; Hara et al. 2018; Marra et al. 2019; Weber et al. 2020; Zhang et al. 2020; Rhie et al. 2021; Nishimura et al. 2022; Sayers et al. 2022; Stanhope et al. 2023; Wagner et al. 2023) and are in general large, with assembly sizes from 2.8 to 5.0 Gb; hence the relevance of reduced representation methods.
Reduced-representation sequencing approaches popular in conservation studies include, but are not limited to, restriction site associated DNA (RAD) sequencing (Miller et al. 2007) and target gene capture (TGC, Gnirke et al. 2009). Methods like RAD sequencing have been applied to several shark species (e.g. Devloo-Delva et al. 2019; Domingues et al. 2022; Nikolic et al. 2023). However, while the TGC approach requires a closely related reference genome, it has the advantages of higher quality data, potentially larger number of SNPs, and enriched sequencing data for known genomic regions, which can be used to address additional questions related to selection and adaptation (Bartoš et al. 2023). TGC approaches are particulary suited for species with large/complex genomes for which RAD-seq are often not cost efficient (e.g. Choquet et al. 2019; Domingues et al. 2022). Furthermore, TGC approaches show potential when used on museum specimens (e.g.Kollias et al. 2015; Agne et al. 2022).
To improve the availability of molecular resources for multiple shark species, we present a new genomic TGC marker set, derived from nuclear coding regions of the white shark genome (Carcharodon carcharias , Marra et al. 2019; Rhie et al. 2021), and show its utility in six additional species (bull shark, Carcharhinus leucas , tope,Galeorhinus galeus , basking shark, Cetorhinus maximus , porbeagle, Lamna nasus , shortfin mako, Isurus oxyrinchus , and spurdog, Squalus acanthias ). These species represent three different shark orders (Carcharhiniformes, Lamniformes and Squaliformes), and are all considered threatened (Rigby et al. 2019a, b, 2021a, b, 2022; Finucci et al. 2020; Walker et al. 2020).