https://www.cell.com/current-biology/pdf/S0960-9822(15)00795-2.pdf

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

Pentastomids are a small group of vermiform animals with unique morphology and parasitic lifestyle. They are generally recognized as being related to the Arthropoda, however the nature of this relationship is controversial. We have determined the complete sequence of the mitochondrial DNA (mtDNA) of the pentastomid Armillifer armillatus and complete, or nearly complete, mtDNA sequences from representatives of four previously unsampled groups of Crustacea: Remipedia (Speleonectes tulumensis), Cephalocarida (Hutchinsoniella macracantha), Cirripedia (Pollicipes polymerus), and Branchiura (Argulus americanus). Analyses of the mtDNA gene arrangements and sequences determined in this study indicate unambiguously that pentastomids are a group of modified crustaceans likely related to branchiurans. In addition, gene arrangement comparisons strongly support an unforeseen assemblage of pentastomids with maxillopod and cephalocarid crustaceans, to the exclusion of remipedes, branchiopods, malacostracans and insects.

/pdf/phylogenetic-position-of-the-pentastomida-and-pan-crustacean-1p0fyszf2m.pdf

Phylogenetic position of the pentastomida and [pan]crustacean relationships - eScholarship

Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to inve...

/pdf/revisiting-metazoan-phylogeny-with-genomic-sampling-of-all-5ctreka6u4.pdf

Revisiting metazoan phylogeny with genomic sampling of all phyla

Animal evolution is often presented as a march toward complexity, with different living animal groups each representing grades of organization that arose through the progressive acquisition of complex traits. There are now many reasons to reject this classical hypothesis. Not only is it incompatible with recent phylogenetic analyses, but it is also an artifact of ‘hidden biology', that is, blind spots to complex traits in non-model species. A new hypothesis of animal evolution, where many complex traits have been repeatedly gained and lost, is emerging. As we discuss here, key details of this new model hinge on a better understanding of the Porifera and Ctenophora, which have each been hypothesized to be sister to all other animals, but are poorly studied and often misrepresented.

The hidden biology of sponges and ctenophores

Based on molecular data three major clades have been recognized within Bilateria: Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized animals such as flatworms, gastrotrichs, and gnathostomulids have recently been grouped together as Platyzoa. However, the representation of putative platyzoans was low in the respective molecular phylogenetic studies, in terms of both, taxon number and sequence data. Furthermore, increased substitution rates in platyzoan taxa raised the possibility that monophyletic Platyzoa represents an artifact due to long-branch attraction. In order to overcome such problems, we employed a phylogenomic approach, thereby substantially increasing 1) the number of sampled species within Platyzoa and 2) species-specific sequence coverage in data sets of up to 82,162 amino acid positions. Using established and new measures (long-branch score), we disentangled phylogenetic signal from misleading effects such as long-branch attraction. In doing so, our phylogenomic analyses did not recover a monophyletic origin of platyzoan taxa that, instead, appeared paraphyletic with respect to the other spiralians. Platyhelminthes and Gastrotricha formed a monophylum, which we name Rouphozoa. To the exclusion of Gnathifera, Rouphozoa and all other spiralians represent a monophyletic group, which we name Platytrochozoa. Platyzoan paraphyly suggests that the last common ancestor of Spiralia was a simple-bodied organism lacking coelomic cavities, segmentation, and complex brain structures, and that more complex animals such as annelids evolved from such a simply organized ancestor. This conclusion contradicts alternative evolutionary scenarios proposing an annelid-like ancestor of Bilateria and Spiralia and several independent events of secondary reduction.

Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia

The growing success of molecular methods has challenged traditional views of animal evolution and a large number of alternative hypotheses are hotly debated today. For the deep metazoan phylogeny project, data sets of hitherto unmatched quality and quantity were compiled and analysed with innovative bioinformatics tools. The book begins at the base of the tree of life to discuss the origin of animals and early branches of the phylogenetic tree. The following section presents special data sets gained from mitochondrial genomes and from morphology, with a focus on nervous systems. The final section is dedicated to theoretical aspects of data analysis and new bioinformatics tools. The book closes with a unique general discussion of all hypotheses contained in previous chapters. This work provides the most comprehensive overview available of the state of the art in this exciting field of evolutionary research.

Johann Wolfgang Wägele

Papers

Deep metazoan phylogeny : the backbone of the tree of life : new insights from analyses of molecules, morphology, and theory of data analysis