Genomic Tools in Biological Invasions: Current State and Future Frontiers

Abstract

Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community.

Keywords: biological invasion; invasion genomics; invasive species; management; pest.

Fig. 1.

Conceptual diagram capturing various evolutionary factors and processes involved in biological invasions. The strength of some factors/processes is likely to vary depending on the invasion stage (i.e. preintroduction, transport, introduction, establishment, and spread). Lines represent overlap among different processes, which should be considered in unison when examining genetic patterns within invasive species.

Fig. 2.

Summary of genomic data types and their applications in invasion genomics. High-throughput sequencing data have begun to replace traditional genetic markers (e.g. organelle sequences or microsatellite markers) in the study of invasive species, with the figure demonstrating increasing genomic coverage across a range of genetic/genomic data types. Among high-throughput methods are environmental DNA (eDNA) and Pool-seq, single nucleotide polymorphism (SNP)-chip/reduced-representation sequencing, and whole genome resequencing (WGR) approaches for both short- and long-read data (SR and LR, respectively). While some types of genomic data are useful across a broad range of applications in invasion genomics, others have a more narrow application, as indicated by the colored lines. For example, eDNA and Pool-seq data, while useful for species identification and population genetics analysis, lack the individual sample level resolution needed for some other analysis types; and many data types may be used in niche modeling (or species distribution modeling), though microsatelites typically lack the resolution necessary for this type of analysis and others. Dashed lines indicate situationally useful/necessary data; for example WGR (LR) is ideal for population genetic studies looking at complex variants but may not be needed otherwise, and organelle DNA can be assessed for putative patterns of adaptation but lacks the genome-wide variant view afforded by sequencing technologies with higher genomic coverage.

Fig. 3.

The historical context of invasions. Historical samples can clarify mechanisms of invasion (e.g. preinvasion and postinvasion adaptive dynamics and connectivity across time and space) by aiding A) adaptation studies, as allele state information (ancestral, native, and introduced) is crucial for inferring changes in allele frequency and novel mutations in the native and introduced range (size of alleles A and B indicates relative frequency within each population); B) diversity studies, as it can help contextualize shifts in genetic diversity within both native and introduced ranges; and C) range modeling and landscape genomics studies to contextualize present day invasive species distributions and/or allele frequency correlates with environmental gradients.

Fig. 4.

Genome-informed invasive species control tools.