Concluding remarks

Structural variants provide an exciting opportunity to complement SNP-based approaches and expand our understanding of genome-wide variation. However, there remains much to learn about the integration of SVs in the small population paradigm. In the meantime, mounting evidence indicates that SVs play an important role in determining fitness traits for both model and non-model species. Whereas SNPs impact single nucleotides, SVs can capture multiple genes and gene regions simultaneously and are therefore more likely to impact fitness. Emerging approaches for SV discovery and genotyping, and relating SVs to fitness traits, are now in reach for threatened species, and we are confident that discoveries related to the role of SVs in determining fitness traits of conservation interest are imminent. Moreover, the development of SV-specific tools for analyses of within and between population variation will further enhance the utility of SVs in species of conservation concern (e.g., SV-Pop; Ravenhall, Campino, & Clark, 2019).
However, developing strategies to manage fitness traits will be challenging, as selection for or against them can lead to the reduction of genome-wide diversity (Kardos et al., 2021 preprint; Kardos & Shafer, 2018). Despite this, current management practice can include such actions. For example, individuals that carry, or express, negative fitness traits can be assessed in conservation breeding programs, followed by appropriate actions or recommendations (e.g., Attwater's prairie chicken; Grueber, Hogg, Ivy, & Belov, 2015; Hammerly, Morrow, & Johnson, 2013). Alternatively, when inheritance of these traits are known, individuals may be screened prior to selective pairing (e.g., California Condor; Moran et al., 2021). Regardless, as we learn more about the mechanisms underlying fitness traits, especially traits associated with negative fitness, there is a pressing need to establish comprehensive evidence-based management strategies that mitigate the impact of these traits while minimizing the loss of genome-wide diversity. Where we see the most promise for this is the emerging practice of integrating WGS data into individual-based models, which will enable different management actions to be modelled and compared (Seaborn et al., 2021). Such models will allow researchers to forecast the consequences of selection-based management of fitness traits underpinned by adaptive or deleterious SVs on genome-wide diversity, thus better informing conservation management actions. To achieve this, strong collaboration between conservation practitioners, population ecologists (e.g., modelers), quantitative geneticists, and conservation genomicists will be required to establish the most effective models possible (Hohenlohe, Funk, & Rajora, 2020).

Glossary

Breakpoint: A double-stranded break in the DNA, occurring on either side of an inversion, or a translocation.
Chromatin Conformation Capture (3C): A suite of molecular biology techniques for capturing the spatial organization of chromatin within the nucleus of the cell. Common iterations include Hi-C, Pore-C and Omni-C.
Complex structural variants: An instance where multiple SV types occur in close proximity, such as an inversion with different deletions at breakpoints.
Deletion: A chromosomal rearrangement where a sequence of DNA is missing in an individual but present in the reference. The inverse of an insertion.
Duplication: A chromosomal rearrangement where there is more than one copy of a particular region of the genome. This can be anywhere from ≥50bp to whole chromosomes and even the whole genome (whole genome duplication).
Functional diversity: Genomic variation in regions underpinning phenotypic traits, may occur directly in genes or within regulatory elements. Variation in these regions can have consequences for individual fitness.
Genome-wide diversity: Genomic variation inclusive of functional and neutral diversity. The sum of all variation within the genome.
Genome graph: A representation of multiple possible sequences.
Insertion: A chromosomal rearrangement where a sequence of DNA is ‘inserted’ into the original sequence. May also be defined as a sequence of DNA present in an individual that is missing in the reference. The inverse of a deletion.
Inversion: A chromosomal rearrangement where a section of the DNA is reversed in order in an individual compared to a reference.
Pangenome: A reference genome approach where the genomes of multiple individuals are assembled and aligned to form genome graphs. A pangenome is divided into variable ‘accessory’ and invariable ‘core’ components, with the goal to characterize all the variation present within a group of interest. Currently the scale of pangenome projects range from populations/strains to subfamilies.
Regulatory element: Regions of non-coding DNA involved in the regulation of gene expression, the two primary regulatory elements are enhancers and promoters.
Structural Variant (SV): A genomic rearrangement ≥50bp in length. Common classes of structural variants include deletions, duplication, insertions, inversions and translocations.
Topologically Associated Domain (TAD): Region of the genome that physically interacts with itself more frequently than with regions outside of the TAD.
Translocation: A chromosomal rearrangement where a segment of one nonhomologous chromosome is transferred to another.

Acknowledgements

We wish to thank the Guest Editors of the ‘Whole-genome sequences in Molecular Ecology’ Special Issue for the invitation to contribute this Perspective. We are grateful to the Kākāpō125+ Consortium led by Genomics Aotearoa for providing the opportunity to explore structural variants in a conservation context. We extend our thanks to the University of Canterbury’s Conservation, Systematics and Evolution Research Team (ConSERT), including Roger Moraga at Tea Break Bioinformatics for robust dialogue–and Kylie Price and Joanna Roberts for their support and guidance–on this topic. We acknowledge the NSF Track 2 EPSCoR Program (award number OIA-1826801) for their support of SJG. We also thank three reviewers for their insightful comments on a previous version of the manuscript.