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).