Genomics-informed models reveal extensive stretches of coastline under threat by an ecologically dominant invasive species

Abstract

Explaining why some species are widespread, while others are not, is fundamental to biogeography, ecology, and evolutionary biology. A unique way to study evolutionary and ecological mechanisms that either limit species' spread or facilitate range expansions is to conduct research on species that have restricted distributions. Nonindigenous species, particularly those that are highly invasive but have not yet spread beyond the introduced site, represent ideal systems to study range size changes. Here, we used species distribution modeling and genomic data to study the restricted range of a highly invasive Australian marine species, the ascidian Pyura praeputialis This species is an aggressive space occupier in its introduced range (Chile), where it has fundamentally altered the coastal community. We found high genomic diversity in Chile, indicating high adaptive potential. In addition, genomic data clearly showed that a single region from Australia was the only donor of genotypes to the introduced range. We identified over 3,500 km of suitable habitat adjacent to its current introduced range that has so far not been occupied, and importantly species distribution models were only accurate when genomic data were considered. Our results suggest that a slight change in currents, or a change in shipping routes, may lead to an expansion of the species' introduced range that will encompass a vast portion of the South American coast. Our study shows how the use of population genomics and species distribution modeling in combination can unravel mechanisms shaping range sizes and forecast future range shifts of invasive species.

Keywords: climate change; intertidal; invasion biology; population genomics; range expansion.

Fig. 1.

Sampling sites of Pyura praeputialis along the coast of (A) Australia and (B) within Antofagasta Bay on the Chilean coastline. The bar plots in A and B represent the results of the ADMIXTURE clustering analysis inferred with neutral loci at K = 2 (see full details in SI Appendix). (C) The most likely scenario, as revealed using approximate Bayesian computation (see full details in SI Appendix), depicts the most likely evolutionay scenario and invasion route that P. praeputialis followed from Australia to Antofagasta Bay.

Fig. 2.

Habitat suitability for Pyura praeputialis across (A) its native range, (B) the coastline adjacent to Antofagasta Bay (Inset; Antofagasta Bay indicated with an arrow), and the western coastline of South America. The scale bar represents Maxent’s logistic output, with “yellow” indicating high habitat suitability. Note that the Maxent’s logistic output only considers the genomics-informed relevant sites (i.e., sites from Chile and the eastern coastline of Australia; see details in main text and SI Appendix). This model includes distance to shore as a variable, explaining the observed narrow regions of suitable habitat. For a full list of variables used in model creation, see SI Appendix, Table S3.

Fig. 3.

Maps illustrating habitat suitability for Pyura praeputialis when the introduced range is not considered in model construction. The figures show the output of Maxent modeling using occurrence data from: both native lineages (A–C), only the southeastern Australian lineage (D–F), and only the eastern Australian lineage (G–I). Maps depict native range (A, D, and G), adjacent coastlines of Antofagasta Bay (bay represented by arrow) (B, E, and H), and extensive coastlines along the western coast of South America continent (C, F, and I). The scale bar represents Maxent’s logistic output on habitat suitability (see details in SI Appendix).