Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

Department of Earth- and Environmental Sciences, Palaeontology and Geobiology & GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany.
Molecular Biology and Evolution (Impact Factor: 9.11). 04/2010; 27(9):1983-7. DOI: 10.1093/molbev/msq089
Source: PubMed


Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.

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    • "However, the position of the cluster indicates that they may have diverged and evolved asymmetrically and non-uniformly with respect to the other vertebrate orthologs, following hypothesized evolutionary impact for gene gains, losses and duplications (Canestro et al., 2013Canestro et al., , 2009 Panchin et al., 2010). Nevertheless, we have to take into account that an extended taxon sampling may evidence the existence of long-branch attraction artefacts (Pick et al., 2010). Finally, we can support the hypothesis that Ambra1 gene was not affected by the two rounds of whole-genome duplication occurred in early vertebrate evolution or, most parsimoniously, the paralogues have been lost early in vertebrate evolution, and the extant one did duplicate in teleosts. "
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