Abstract
BackgroundIn trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms.MethodologyBased on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony.ConclusionsSuperalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.
Highlights
The need for resolving the evolutionary relationships of all life on Earth has never been more important than in today’s times of high-throughput data
Contigs that were at least 400 nt in length were used for further analysis; these were combined with 2,900 M. cirriferum ESTcontigs that were derived from Sanger sequencing [4]
Superalignments, and gene tree reconciliation are not new methods, but they are currently being applied to increasingly large data sets that often focus on nonmodel organisms
Summary
The need for resolving the evolutionary relationships of all life on Earth has never been more important than in today’s times of high-throughput data. The current flood of sequence data from model and non-model organisms is a great starting point for resolving the tree of life These data present us with new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done carefully for single-gene analyses. In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, and reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms
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