Structural variants: a new tool in the conservation genomics toolbox

Over the past 10 years, the field of conservation genomics has largely focused on transitioning from a handful of microsatellite markers to thousands of genome-wide single nucleotide polymorphisms (SNPs) (Allendorf, Hohenlohe, & Luikart, 2010; Mable, 2019). Whether characterized using reduced-representation data or whole-genome sequence (WGS) methods, SNP-based estimates of genome-wide variation are being used to better inform conservation by delineating species, including cryptic species (e.g., Binks, Steane, & Byrne, 2021; Quattrini et al., 2019; but see Stanton et al., 2019), detecting hybridization and introgression (Dufresnes & Dubey, 2020; Peters et al., 2016; but see Forsdick et al., 2021; Hauser, Athrey, & Leberg, 2021 preprint), identifying conservation units (Liddell et al., 2020), informing conservation translocations (Dresser, Ogle, & Fitzpatrick, 2017; Glassock, Grueber, Belov, & Hogg, 2021), guiding conservation breeding programs (e.g., Galla et al., 2020; Wright et al., 2020) and identifying the genomic basis of adaptive traits (Duntsch et al., 2020). However, SNPs constitute only one component of genome-wide variation (Ho, Urban, & Mills, 2020). Structural variants (SVs) are genomic rearrangements such as insertions, deletions, duplications, inversions and translocations, and are generally defined as ≥50 bp in length (Figure 1). Variation in chromosome structure was one of the earliest types of genetic variation studied (e.g., McClung, 1905; Sturtevant, 1921), and a recent focus on the impacts of these genomic rearrangements on sequence variation has found that SVs affect more overall genome content and intersect with genes more often than SNPs (Catanach et al., 2019; Chakraborty, Emerson, Macdonald, & Long, 2019; Chiang et al., 2017; Frayling, 2014; Pang et al., 2010).
Structural variants can have significant evolutionary impacts on species. These impacts include genomic incompatibilities between ancestral and novel variants that may influence hybridization and introgression (Weissensteiner et al., 2020) and may even lead to speciation (Davey et al., 2016; Todesco et al., 2020). In addition, emerging evidence indicates that SVs can underlay fine-scale population structure, and may facilitate local adaptation (Cayuela et al., 2021; Dorant et al., 2020; Tigano et al., 2021). These findings–which are generally the result of integrating SNPs and SVs–highlight the opportunity for both variant types to inform conservation. Nevertheless, the broad application of SVs in conservation remains challenging in part due to the uncertainty in how best to detect and genotype all SV types at the population scale (Mérot, Oomen, Tigano, & Wellenreuther, 2020). Further, although SVs are more likely to impact fitness traits than SNPs (Pang et al., 2010), the overall impacts of SVs on population persistence is relatively unexplored (Oomen et al., 2020).