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, 27 (9), 1983-7

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

K S Pick et al. Mol Biol Evol.


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.


F<sc>IG</sc>. 1.
FIG. 1.
Phylogenetic tree based on refinements to the Dunn et al. (2008) 64-taxon set reconstructed with PhyloBayes (Lartillot et al. 2009) under the CAT + Γ4 model. Choanoflagellates were set as outgroup and an additional 18 nonbilaterian taxa included. Posterior probabilities >0.7 are indicated followed by bootstrap support values >70. A large black dot indicates maximum support in posterior probabilities and Bayesian bootstraps (=1/100).
F<sc>IG</sc>. 2.
FIG. 2.
Saturation plot of character sets. See Supplementary Material for method details. Gray line and filled dots: Dunn et al. (2008). Black line and open dots: Philippe et al. (2009).

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