Data from: Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

Background: Understanding the phylogenetic relationships among major
lineages of multicellular animals (the Metazoa) is a prerequisite for
studying the evolution of complex traits such as nervous systems, muscle
tissue, or sensory organs. Transcriptome-based phylogenies have
dramatically improved our understanding of metazoan relationships in
recent years, although several important questions remain. The branching
order near the base of the tree, in particular the placement of the
poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum
Ctenophora) lineages is one outstanding issue. Recent analyses have
suggested that the comb jellies are sister to all remaining metazoan phyla
including sponges. This finding is surprising because it suggests that
neurons and other complex traits, present in ctenophores and eumetazoans
but absent in sponges or placozoans, either evolved twice in Metazoa or
were independently, secondarily lost in the lineages leading to sponges
and placozoans. Results: To address the question of basal metazoan
relationships we assembled a novel dataset comprised of 1080 orthologous
loci derived from 36 publicly available genomes representing major
lineages of animals. From this large dataset we procured an optimized set
of partitions with high phylogenetic signal for resolving metazoan
relationships. This optimized data set is amenable to the most appropriate
and computationally intensive analyses using site-heterogeneous models of
sequence evolution. We also employed several strategies to examine the
potential for long-branch attraction to bias our inferences. Our analyses
strongly support the Ctenophora as the sister lineage to other Metazoa. We
find no support for the traditional view uniting the ctenophores and
Cnidaria. Our findings are supported by Bayesian comparisons of
topological hypotheses and we find no evidence that they are biased by
long-branch attraction. Conclusions: Our study further clarifies
relationships among early branching metazoan lineages. Our phylogeny
supports the still-controversial position of ctenophores as sister group
to all other metazoans. This study also provides a workflow and
computational tools for minimizing systematic bias in genome-based
phylogenetic analyses. Future studies of metazoan phylogeny will benefit
from ongoing efforts to sequence the genomes of additional invertebrate
taxa that will continue to inform our view of the relationships among the
major lineages of animals.