Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments

Abstract

Resolving the relationships between Metazoa and other eukaryotic groups as well as between metazoan phyla is central to the understanding of the origin and evolution of animals. The current view is based on limited data sets, either a single gene with many species (e.g., ribosomal RNA) or many genes but with only a few species. Because a reliable phylogenetic inference simultaneously requires numerous genes and numerous species, we assembled a very large data set containing 129 orthologous proteins ( approximately 30,000 aligned amino acid positions) for 36 eukaryotic species. Included in the alignments are data from the choanoflagellate Monosiga ovata, obtained through the sequencing of about 1,000 cDNAs. We provide conclusive support for choanoflagellates as the closest relative of animals and for fungi as the second closest. The monophyly of Plantae and chromalveolates was recovered but without strong statistical support. Within animals, in contrast to the monophyly of Coelomata observed in several recent large-scale analyses, we recovered a paraphyletic Coelamata, with nematodes and platyhelminths nested within. To include a diverse sample of organisms, data from EST projects were used for several species, resulting in a large amount of missing data in our alignment (about 25%). By using different approaches, we verify that the inferred phylogeny is not sensitive to these missing data. Therefore, this large data set provides a reliable phylogenetic framework for studying eukaryotic and animal evolution and will be easily extendable when large amounts of sequence information become available from a broader taxonomic range.

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

“…These results are supported by simulation studies, which suggest that the mere presence of missing data may not itself be misleading, beyond the reduced amount of data included (e.g. Wiens, 2003;Philippe et al, 2004;Wiens and Morrill, 2011).…”

On the origin and functions of RNA-mediated silencing: from protists to man

“…This conclusion is reinforced when the phylogenetic tree for the family in question conforms to the topology of the eukaryotic tree. However, none of the best phylogenetic trees for Ago-Piwi, Dicer-like, or RdRP polypeptides strictly coincided with the consensus tree of Eukaryota (Medina 2005) nor could reconstruct the monophyly of some higher-order eukaryotic groups, as previously reported for individual gene/protein trees (Arisue et al 2004;Philippe et al 2004). Besides the usual problems of weakness of phylogenetic signal, lateral gene transfers, hidden paralogy, and tree reconstruction artefacts (Philippe et al 2004), incorrectly predicted protein models (since some sequences were extracted from draft genomes) may have contributed to greater than usual divergences making the relationship among deep branches difficult to resolve.…”

Additional molecular support for the new chordate phylogeny

“…We built upon previous phylogenomic datasets assembled in the Philippe lab Jimenez-Guri et al, 2007;Lartillot and Philippe, 2008;Philippe et al, 2004Philippe et al, , 2005b to select a set of 179 orthologous markers showing sufficient conservation across metazoans to be useful for inferring the phylogeny of metazoans. Alignments were built and updated with available sequences downloaded from the Trace Archive (http://www.ncbi.nlm.nih.gov/Traces/) and the EST Database (http://www.ncbi.nlm.nih.gov/dbEST/) of GenBank at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) using the program ED from the MUST package (Philippe, 1993).…”

“…The complete alignment consists of 179 genes and 51 taxa for 53,799 unambiguously aligned amino-acid sites with 32% missing data. To study the potential impact of missing data on phylogenetic inference (Hartmann and Vision, 2008;Philippe et al, 2004;Wiens, 2006), a concatenation of the 106 genes with sequences available for at least 41 of the 51 OTUs was also constructed with SCAFOS. This reduced alignment consists of 106 genes and 51 taxa for 25,321 amino-acid sites and contains only 20% of missing data.…”

“…Empirical protocols have been designed to detect and reduce the impact of systematic error in genome-scale studies (Rodríguez-Ezpeleta et al, 2007) but the ultimate solution lies in the development of improved models of sequence evolution (Felsenstein, 2004;Philippe et al, 2005a;Steel, 2005). The reliance of current phylogenomic studies on a relatively limited number of highly expressed genes (Philippe and and the potential impact of missing data on phylogenomic inference (Hartmann and Vision, 2008;Philippe et al, 2004) are also regularly cited as limitations of the phylogenomic approach.…”