Single zooids, multiple loci: independent colonisations revealed by population genomics of a global invader

Abstract

Assessing genomic diversity and population structure of non-indigenous species is crucial to develop adequate management strategies. However, in species with scarce material for DNA extraction, applying genomic techniques can be a difficult task. Here we set a protocol for small DNA samples combining whole genome amplification (WGA) and genotyping-by-sequencing (GBS). This protocol was applied to the worldwide invasive colonial ascidian Didemnum vexillum using a single zooid per colony. WGA-GBS performance was tested using half zooids, providing empirical demonstration for genotyping reliability. We analysed 296 individuals from 12 localities worldwide including native and the main invaded areas. Polymorphic loci datasets generated by locality, area and globally, identified genetic differentiation at all levels. The two groups found in Japan, the native area, matched Cytochrome Oxidase I clades and were strongly differentiated at the genomic level suggesting reproductive isolation. Our genomic analyses confirmed that only one clade spread worldwide. We also detected some clones, always within the same locality. Genetic diversity was high in both the introduced and in the native area.Three independent colonisation events determined the global distribution of the species, although population pairwise comparisons within each introduced genetic cluster were significant. Human-mediated transportation seems to drive the distribution pattern of this species worldwide and regionally, as there is a lack of isolation by distance within introduced areas. Diverse and well differentiated populations point to a high expansion potential of this worrisome worldwide invader.

The Microbiome of the Worldwide Invasive Ascidian Didemnum vexillum

“…A total of 65 colonies of D. vexillum from 12 locations spanning the native (NW Pacific) and the known introduced distribution of the species were sampled during 2015 and 2016 in marinas and artificial substrates (Table 1 and Figure 1). Sequences of the specimens showed that five colonies were D. vexillum clade B from Sugashima (Japan), whereas the remaining 60 colonies were D. vexillum clade A from different temperate regions of the world (Casso et al, 2019b). Thus, only in one of the two populations (Sugashima and Aomori) corresponding to the native range of the species did we find the two described mitochondrial clades in sympatry.…”

“…All 70 colonies were collected in marinas and other artificial substrates, at least 2 m apart from each other to avoid pseudoreplication (Smith et al, 2012), and preserved at −20 • C in 96% ethanol. Samples were coded by geographic region as defined in previous studies (Stefaniak et al, 2012;Casso et al, 2019b). Clade A introduced samples were assigned to the previously defined genetic groups (Casso et al, 2019b): Europe (EUR), West North America (WNA), and New Zealand plus East North America (NZ-ENA).…”

“…Samples were coded by geographic region as defined in previous studies (Stefaniak et al, 2012;Casso et al, 2019b). Clade A introduced samples were assigned to the previously defined genetic groups (Casso et al, 2019b): Europe (EUR), West North America (WNA), and New Zealand plus East North America (NZ-ENA).…”

“…Kott (2002) is an invasive colonial ascidian, native from the NW Pacific, with two main mitochondrial clades, named clade A and clade B, of which only clade A has spread in temperate seas worldwide (New Zealand, East and West coasts of North America, Atlantic and Mediterranean coasts of Europe, and South East of Russia: Lambert, 2009;Stefaniak et al, 2012;Ordóñez et al, 2015;Zvyagintsev et al, 2016). This clade shows a strong population structure, with three main invasive genetic groups and a high genetic differentiation between populations (Casso et al, 2019b). Environmental conditions are different between the main regions of distribution of the species and even between localities in the same region (e.g., Mediterranean and Atlantic localities in Europe).…”

“…In the present study, we (i) describe and compare the microbiome of D. vexillum at different levels (species, mitochondrial clades, localities, and invasive genetic groups); (ii) identify the core microbiome of the invasive clade; and (iii) evaluate the relationship between microbiome composition and several environmental and genetic variables. We had the unique opportunity to assess individually the relationship between host genetics and microbiome as the same colonies analyzed in the present study were previously genotyped at a panel of genome-wide loci (Casso et al, 2019b).…”