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Phylogenomics and the reconstruction of the tree of life
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.
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
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.
Tunicates and not cephalochordates are the closest living relatives of vertebrates
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.
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia.
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.
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
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.
Acoelomorph flatworms are deuterostomes related to Xenoturbella
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.
Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes
Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish
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.
Phylogenomics: the beginning of incongruence?
The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
- E. Bapteste, H. Brinkmann, H. Philippe
- BiologyProceedings of the National Academy of Sciences…
- 5 February 2002
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 large…