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Tunicates and not cephalochordates are the closest living relatives of vertebrates
TLDR
It is shown that phylogenetic analyses of the genome sequencing of the appendicularian Oikopleura dioica provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Expand
Phylogenomics and the reconstruction of the tree of life
TLDR
This work has demonstrated the power of the phylogenomics approach, which has the potential to provide answers to several fundamental evolutionary questions, but challenges for the future have also been revealed. Expand
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
TLDR
Three recent large-scale phylogenomics studies, which deal with the early diversification of animals, produced highly incongruent findings despite the use of considerable sequence data, suggesting that merely adding more sequences is not enough to resolve the inconsistencies. Expand
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia.
TLDR
This study demonstrates that the incongruences observed between rRNA and multigene analyses were indeed due to long-branch attraction artifacts, illustrating the enormous impact of systematic biases on phylogenomic studies and suggests that urochordates are more closely related to vertebrates than are cephalochordates. Expand
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
TLDR
The CAT model appears to be more robust than WAG against LBA artefacts, essentially because it correctly anticipates the high probability of convergences and reversions implied by the small effective size of the amino-acid alphabet at each site of the alignment. Expand
Acoelomorph flatworms are deuterostomes related to Xenoturbella
TLDR
This phylogeny makes sense of the shared characteristics of Xenoturbellida and Acoelomorpha, and implies the loss of various deuterostome characters in the Xenobiology including coelomic cavities, through gut and gill slits. Expand
Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes
TLDR
These analyses provide the first strong support for a single endosymbiotic event that gave rise to primary photosynthetic eukaryotes, the Plantae, which are present in green plants, red algae, and glaucophytes. Expand
Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish
TLDR
Individual gene trees for these three genes and a concatenated dataset support the hypothesis that the fish-specific genome duplication event took place after the split of the Acipenseriformes and the Semionotiformes from the lineage leading to teleost fish but before the divergence of Osteoglossiformes. Expand
Phylogenomics: the beginning of incongruence?
TLDR
It is proposed that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence. Expand
The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a largeExpand
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