Sacoglossa is a rather small taxon of marine slugs with about 300 described species, yet it is quite fascinating scientists for decades. This is mainly because of the ability of certain species to incorporate photosynthetically active plastids of their algae prey, a phenomenon known as functional kleptoplasty. With the stolen plastids, these slugs endure weeks (short-term retention) or months (long-term retention) of starvation, though contribution of the plastids to the survival and factors enhancing plastid longevity are unknown. Likewise, contrasting hypotheses on evolution of functional kleptoplasty exist and the phylogenetic relationship of Sacoglossa taxa is still under debate. We analyzed the phylogenetic relationship of 105 sacoglossan species to address the question of the origin of functional kleptoplasty. Based on our phylogenetic analysis and the ancestral character state reconstruction, we conclude that functional short-term retention most likely originated two times and long-term retention at least five times. Previous suggestions that functional longterm kleptoplasty is established with specific plastids are supported by our food analyses in Elysia clarki that finally harbors only plastids of certain algae species over a prolonged starvation period.

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Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

Background: Cladobranch sea slugs represent roughly half of the biodiversity of soft-bodied, marine gastropod molluscs (Nudibranchia) on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as bioindicators and providers of medical drug leads), the evolutionary history of cladobranch sea slugs is not yet fully understood. Here, we amplify the current knowledge on the phylogenetic relationships by extending the cladobranch and outgroup taxon sampling using transcriptome data. Results: We generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa. We complemented our taxon sampling with previously published transcriptome data, resulting in a final supermatrix covering 56 species from all but one accepted cladobranch superfamilies. Transcriptome assembly using six different assemblers, selection of those assemblies providing the largest amount of potentially phylogenetically informative sites, and quality-driven compilation of data sets resulted in three different supermatrices: one with a full coverage of genes per species (446 single-copy protein-coding genes) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1,767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximum statistical support for all major splits and phylogenetic relationships on family level. The only discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions: Our data matrices and the inferred trees inferred can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The correct placement of E. pulchra, however, proves challenging, even with large data sets. Moreover, quartet mapping shows that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.