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Dunn Lab completes evolutionary tree for mollusks

Montage of mollusks photographed in Belize. Credit: Casey Dunn/Brown University

October, 2011 (press release)

In a paper in Nature, researchers from the Casey Dunn Lab (Department of Ecology and Evolutionary Biology) and collaborating institutions have compiled the most comprehensive evolutionary tree for mollusks to date. Their analysis surprisingly places two enigmatic groups, cephalopods and monoplacophorans, as sister clades. The team has also shown that there was a single origin for shelled mollusks.

To accomplish this, the team sequenced thousands of genes and matched them up through intensive computational analyses using the Center for Computation and Visualization's flagship computing cluster Oscar. Stephen Smith, a postdoctoral researcher in the Dunn Lab, designed the computational analysis pipeline, which combines the teams collected data with publicly available data from the NCBI dbEST database using a modified version of the PartiGene tool. Next, the pipeline assembles the raw reads using Velvet/Oases (Illumina data) and Newbler/CAP3 (Roche 454 data). Assemblies are compared against a subset (Fungi/Metazoa) of the NCBI nr database with BLASTX, using the scalable mpiBLAST package available on Oscar, and the resulting hits are translated with prot4EST. Pairwise comparisons from an all-to-all BLASTP are used to cluster genes into homologues using the MCL algorithm. Finally, phylogenetic analyses using RAxML, MrBayes, and PhyloBayes divide the homologues into orthologues. Full details of the analysis are available as a supplement to the Nature paper.

Prior to sequencing, the team collected hard-to-find specimens through a global sampling effort, including a group of organisms thought until recently to be extinct for millions of years. In all, the team collected specimens for 15 species.