Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure

Abstract

Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo‐Pacific lionfish, Pterois volitans, into waters off the US East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 single nucleotide polymorphism loci sequenced by restriction enzyme‐associated DNA sequencing for nine P. volitans sampling areas in the invaded range, including Florida and other sites throughout the Caribbean, as well as mitochondrial control region D‐loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from initial reports of between‐basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant in sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an FST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.

Genetic connectivity of lionfish (Pterois volitans) in marine protected areas of the Gulf of Mexico and Caribbean Sea

“…Although it is known that populations that present a recent bottleneck show apparent excess of heterozygotes (Cornuet & Luikart, ; Sakai et al, ), our analyses found heterozygosis in all loci; therefore, it is likely to be a reflection of the founder effect noted in other studies (Freshwater et al, ). Even so, this information differs with the studies of Pérez‐Portela et al () and Bors et al (). However, the differences may be inherent to the different molecular markers used.…”

From Pavement to Population Genomics: Characterizing a Long-Established Non-native Ant in North America Through Citizen Science and ddRADseq

“…Population genomic approaches, in particular, restriction siteassociated DNA sequencing (RADseq) (Miller et al, 2007;Baird et al, 2008;Peterson et al, 2012), offer a cost-effective solution for surveying genome-wide single nucleotide polymorphism (SNPs) in species without a sequenced genome. These techniques have proven useful to understanding species' invasion histories (Dupuis et al, 2018;Leydet et al, 2018;Bors et al, 2019;Cohen and Privman, 2019) and as a non-destructive method for identification and monitoring (reviewed in Taylor and Gemmell, 2016). More generally, emergence of RAD-based techniques have led to wide adoption of these methods in ecological and evolutionary studies of insects (Bagley et al, 2017;Storer et al, 2017;Lower et al, 2018;Zhang et al, 2018;De Jesús-Bonilla et al, 2019), including ants (Moreau and Wray, 2017;Boyle et al, 2018;Avril et al, 2019;Smith et al, 2019), which rank among the most damaging and difficult to control invasive species (Rabitsch, 2011).…”

Factors influencing taxonomic unevenness in scientific research: a mixed-methods case study of non-human primate genomic sequence data generation

“…Specifically, we focused on the use of massively parallel genomic sequencing methods. The development and continued technological innovation of these tools have helped scientists answer expanding sets of questions in species biology, evolutionary history, behavioural ecology and population dynamics [8][9][10][11]. The genetics and genomics community as a whole has been a leader in the data sharing movement, with standardly used online repositories including the National Center for Biotechnology Information's Sequence Read Archive (SRA), the Gene Expression Omnibus and GenBank [12].…”