Invasive species are one of the main threats to global biodiversity and, within marine ecosystems, tunicates feature some prominent examples. Styela plicata is an ascidian species inhabiting harbors in all temperate oceans and seas, thus being considered a thriving invasive species. However, this species’ adaptive mechanisms, introduction history, and population structure have never been completely elucidated. Here, by genotyping 87 S. plicata individuals from 18 localities worldwide with 2b-RADseq, we confirm the presence of four chromosome inversions, demonstrate population structuring on this species, detect local adaptation signals, and infer historical demographic events. The locality of North Carolina constitutes an utterly unrelated population, Atlanto-Mediterranean and Pacific localities constitute their own genetic clusters, and the South Carolina locality presents an intermediate genetic position between North Carolina and the other two groups. For each biogeographic population we highlight substructuring, being the most evident the split between North Atlantic+Mediterranean and the South Atlantic localities. We identify genomic drivers for adaptation, with functions involved with cell processes, metabolism, development, and ion transport, among others. We model ancient effective population sizes, providing evidence on three main bottlenecks that could correspond to different introduction events. Finally, hybridization tests point to South Carolina having a hybrid origin, likely resulting from a secondary contact between North Carolina and other ancient populations. Overall, this study highlights the complex historical processes of S. plicata, which have led this species to its current distribution, population structure, and local adaptation footprint in oceans worldwide.

Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge disparity of genomic features. However, existing genome architecture studies are taxon biased, and thus a wider picture should be obtained by expanding the taxonomic scope. Moreover, the extent to which genomic architecture determines the typology of loci recovered in reduced representation sequencing techniques with digestion enzymes is largely unexplored. Here, we observed that whereas plants mostly increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. We found positive correlations between the percentage of loci obtained with in-silico digestion using 2b-enzymes mapping in introns, exons and intergenic categories and the percentage of these regions in the genome. However, exonic regions showed a significant enrichment regardless of the enzyme used. Moreover, the percentage of loci retained after secondary reductions varied with selective-adaptors and genome GC content. In summary, we show that genome architecture has an impact on the markers obtained in reduced representation sequencing that should be considered in conservation genomics for correct wildlife management.

Population genomic studies are increasing in the last decade, showing great potential to understand the evolutionary patterns in a great variety of organisms, mostly relying on RAD sequencing techniques to obtain reduced representations of the genomes. Among them, 2b-RAD can provide further secondary reduction to adjust study costs by using base-selective adaptors, although its impact on genotyping is unknown. Here we provide empirical comparisons on genotyping and genetic differentiation when using fully degenerate and base-selective adaptors and assess the impact of missing data. We built libraries with the two types of adaptors for the same individuals and generated independent and combined datasets with different missingness filters according to their presence (100%, 75% and 50%). Exploring locus-by-locus, we found 92% of identical genotypes between both libraries of the same individual when using loci present in 100% of the samples, which decreased to 35% when working with loci present in at least 50% of them. We show that missing data is a major source of individual genetic differentiation. The loci discordant by genotyping were in low frequency (7.67%) in all filtered files. Only 0.96% were directly attributable to base-selective adaptors, and 6.44% underestimated heterozygosity in NN libraries, of which ca. 70% had <10 reads per locus indicating that sufficient read depth should be ensured for a correct genotyping. Our work confirms that 2b-RAD libraries using base-selective adaptors are a robust tool to use in population genomics of species with large genome sizes.