Background: Whether position Xenacoelomorpha as an early branch of Bilateria (Protostomes + Deuterostomes) has been intensely debated during last several decades. Considering Darwin’s “tree of life”, with the “Phylogenetic Species Concept”, we choose mitochondrial genome as the subject to predict phylogenetic position of Xenacoelomorpha, by genes genealogy.
Results: Herein, we sequence Heterochaerus australis’s mitochondrial genome and infer intrinsic relationships of Metazoan with Xenacoelomorpha. The optimal tree under the popular maximum likelihood (ML) and Bayesian phylogenetic reconstructions are consensus with each other being strongly supported. The relationship between Chordates, Ambulacrarians and Xenoturbella/Acoelomorph is resolved. To avoid previous query about alignment process, the datasets are alignmented and trimmed automatically. Reducing taxon or cutting outgroups can not affect the relationship between Xenacoelomorpha and other Metazoan. Meanwhile, analysis using CAT model and Dayhoff groups also supporting the prediction made by mtZOA, relaxing the restriction of alignment criteria ( MAFFT, strategy G–ins–1, BLOSUM 62, 45, 30 ) introducing potential misleading signals can not challenge the tree topology indicating our auto-alignmented mitochondrial dataset is not artificially restricted one.
Conclusions: Finally, a repeatable prediction of the genes genealogy with reliable statistical support places Xenacoelomorpha as a basal Deuterostome. Let's enjoy the elegent metapher about Tree of LIfe—— "As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation we believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications". (Darwin 1964 [1859], p. 130).