Selecting ribosomal protein genes for invertebrate phylogenetic inferences: how many genes to resolve the Mollusca?

Abstract

1. Multi-gene analyses are currently the gold standard in phylogenetics, despite limited taxon sampling. To facilitate broad taxon representation on an economically tolerable level, we optimize the gene selection for future PCR-based sampling strategies. 2. Highly expressed ribosomal proteins (RP) were sampled chiefly for molluscs, the second largest metazoan phylum with largely unknown internal relationships. Thirty-two new sequences for Lepidochitona cinerea (Polyplacophora) were integrated into a data-matrix of 79 RP genes, comprising 16 mollusc species (five classes). The resulting maximum likelihood tree was used to evaluate each single-gene tree according to its topological fit. Genes were sorted in ascending order, successively concatenated and then evaluated. 3. The most efficient sub-alignment consists of 18 selected genes. All analyses reveal the Mollusca as monophyletic. The phylogenetic utility of the selected and concatenated 18 ribosomal genes is comparable to results from phylogenomic analyses. 4. This optimized data set can be assembled using PCR methods and will allow expanding the taxon coverage in deep molluscan phylogeny far beyond the current sampling.

A molecular palaeobiological hypothesis for the origin of aplacophoran molluscs and their derivation from chiton-like ancestors

“…Aplacophorans resolved as a monophyletic clade under the WAG þ G 4 model (PP ¼ 0.81) and as a paraphyletic clade under the CAT þ GTR þ G 4 model, albeit with very low support for Chaetoderma as a sister group to polyplacophorans (PP ¼ 0.63). The cephalopods were recovered as a sister group to aculiferans with high support under both (b) Sensitivity tests It could be posited that the relationship between aculiferans and cephalopods is owing to LBA [32,48]: previous analyses found a sister-group relationship between aplacophorans and cephalopods [29,30,32], which are both long-branched. However, the observed topology was robust to both phylogenetic signal dissection and the sequential exclusion of long-branched taxa, unstable taxa and compositionally heterogeneous taxa.…”

“…In most morphological scenarios of molluscan evolution, the aplacophorans and chitons are considered a sister group to all other molluscs (the Conchifera) [6]. However, several independent molecular studies [30 - 32,62], as well as this one, have recovered the Aculifera and cephalopods as a clade relative to gastropods and bivalves. This implies a paraphyletic Conchifera leading to the Aculifera, and suggests that the conchiferan condition is ancestral to the phylum.…”

“…Most early studies provided support for neither the Testaria nor Aculifera hypothesis, but instead found aplacophorans and chitons to be unrelated and nested within different conchiferan sub-groups [27 -29]. Later studies, however, found a relationship between aplacophorans, chitons and cephalopods, but until recently this has been largely unresolved [30][31][32]. ( f ) Neomeniomorph postlarva with seven naked dorsal regions and sclerites arranged in transverse rows and in lateral zones [4].…”

Phylogenomics reveals deep molluscan relationships

“…Traditionally, a sister relationship between gastropods and bivalves, which relates the two most speciose lineages of molluscs, has received little consideration. However, this relationship has been recovered in molecular studies with relatively limited taxon sampling across Mollusca 5,17 . Similarities between the veliger larvae of gastropods and lamellibranch bivalves have been long recognized.…”

“…In contrast, analysis of only ribosomal protein genes recovered all major lineages monophyletic with strong support in BI but moderate support for most deep nodes in ML (see also ref. 17). Although ribosomal protein and non-ribosomal protein genes seem to be contributing different amounts of phylogenetic signal, support for most nodes was greater when all gene classes were included, in accordance with previous phylogenomic studies 5,11 .…”