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Invasive ascidians can be a menace to both ecosystems and marine aquaculture in the coastal United States. One of the very recent introductions of an ascidian species in Puget Sound, a large inland waterway in the Northwest of the United States, appears to be the same species, Didemnum vexillum (Kott, 2002) that has caused significant economic and environmental harm in New England, California, British Columbia, northern Europe, and New Zealand. In light of such grave threats, identifying the vectors and sources of introduced organisms in order to prevent and possibly combat invasions is crucial. Distinguishing between primary introduction (source population from native range) and secondary introduction (source population from a previously colonized site) is fundamental to identifying pathways of introduction. We have developed three molecular markers that can be used to address these "source" questions as well as other basic questions of molecular evolution in D. vexillum. Two of these markers (Dnr1 and DL2.1A1) are polymorphic sequence regions which we found to each have four alleles. A third marker is a microsatellite locus, D6, which we observed has ten alleles. Including all samples characterized with these three markers, the proportion of heterozygotes for each marker was 0.682, 0.721, and 0.773 for Dnr1, DL2.1A1, and D6 respectively. Using these markers, we show significant genetic differentiation between population samples from New Hampshire and Puget Sound (FST= 0.226, p<0.05). These markers will thus be helpful in genetically characterizing worldwide populations of D. vexillum and providing a means to reconstruct pathways of introduction by determining the genetic relationships of these populations. In addition, we report the discovery of multiple genotypes at microsatellite locus D6 found in DNA samples derived from larvae within single colonies of D. vexillum. This marker may prove useful in gaining insight into multiple paternity in D. vexillum, which is a topic rarely studied in ascidians.

New molecular markers to genetically differentiate populations of Didemnum vexillum (Kott, 2002) - an invasive ascidian species