Assessing the root of bilaterian animals with scalable phylogenomic methods

Abstract

A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.

Figure 1.

Genes are ranked by decreasing taxon sampling. (a) The number of taxa sampled for each gene is shown along the left vertical axis and indicated by blue data points, while the cumulative matrix completeness is shown on the right vertical axis indicated by a green continuous line. Vertical lines indicate the gene cutoffs for the four matrices that were analysed. (b) ‘Bird's eye’ view of the matrix. A white cell indicates a sampled gene. Taxa are sorted from the best sampled at the top to the least sampled at bottom (gene ordering is the same as in (a)).

Figure 2.

Phylogram of the most likely tree found in ML searches of the 1487-gene matrix (37 searches, log likelihood = −6 124 157.6). The area of the yellow circle at each tip is proportional to the number of genes present in the 1487-gene matrix for the indicated species (see table S2 in the electronic supplementary material for values). Bootstrap support from analyses of the 844-gene (black values above nodes, 201 bootstrap replicates) and 330-gene (red values below nodes, 210 bootstrap replicates) subsamples of the 1487-gene matrix are also shown at each node. Asterisk indicates 100 per cent bootstrap support. Species for which new EST data are produced are highlighted with green species names.

Figure 3.

Cladogram showing bootstrap support for relationships between taxa from figure 2 with a leaf stability of 87 per cent or higher. This criterion was met by 87 taxa, though only bilaterian taxa are shown (other relationships were not impacted by the removed taxa). The 844-gene (black values above nodes) and 330-gene (red values below nodes) subsamples are also shown at each node. Asterisk indicates 100 per cent bootstrap support.

Figure 4.

Cladogram showing bootstrap support for relationships between taxa from figure 2 with a leaf stability of 90 per cent or higher. This criterion was met by 84 taxa, though only bilaterian taxa are shown (other relationships were not impacted by the removed taxa). The 844-gene (black values above nodes) and 330-gene (red values below nodes) subsamples are also shown at each node. Asterisk indicates 100 per cent bootstrap support. The taxa included in figure 3, but not here, are Xenoturbella bocki, Spinochordodes tellinii and Priapulus caudatus.