The new animal phylogeny: Reliability and implications

“Studies based on rRNA have demonstrated that nematodes had previously been misplaced, and their true position is in a sister group of the arthropods (Adoutte et al., 2000; Aguinaldo et al., 1997).”

“An ongoing debate in protostome phylogeny concerns the affiliation of the arthropods either to the annelids in the traditional articulates, or with the nematodes in the clade Ecdysozoa (Adoutte et al., 2000).”

“The best supported tree grouped Hro-hh with hh from Drosophila and Patella, s parate from the deuterostome hh-class genes, in accord with the accepted metazoan phylogenetic tree based on rRNA sequence (Adoutte et al., 2000; Aguinaldo et al., 1997).”

“Some of these differentiated cells may have been arranged into localised functional units—i.e., simple tissues.”

“…studies were the first to reveal Lophotrochozoa and Ecdysozoa (Aguinaldo et al., 1997; Halanych et al., 1995), leading to the ‘‘new animal phylogeny’’ (Adoutte et al., 2000; Halanych, 2004). rRNA studies reinforced the now-accepted clade of Ambulacraria (Cameron et al., 2000; Castresana et al.,…”

“Echinoderms and hemichordates are grouped together into the clade Ambulacraria, which is treated as a sister group to the chordate lineage [1-4].”

“…and pseudocoelomate (e.g., nematodes, priapulids, rotifers, gastrotrichs, and gnathostomulids) phyla, formerly held at lower positions in morphologically based trees were found displaced at higher positions within the Ecdysozoa and the Lophotrochozoa superclades (Adoutte et al. 1999, 2000).”

“Despite the ancient evolutionary separation of arthropods from vertebrates (Adoutte et al., 2000), the genetic and molecular components are remarkably similar (Rubin et al.”

“352 V.S. Mashanov et al. / Tissue and Cell 40 (2008) 351–372 sue and t m t ( m a o b c t p 2 t s a t p h t H c t m W ( g b W u s t a r t 2 a r r s a e a e s t g a n e g f n b t o t T i b c 2 2 1 V w l n r w p c m s t s c i a n r c d i F B s e h p b V.S. Mashanov et al. / Tis The clade Deuterostomia includes, besides c…”

“Figure 1 shows a cladogram for metazoan evolution [10] with the premetazoan choanoflagellate M.”

“This observation is consistent with the evolutionary proximity of Annelids and Mollusks, grouped in the Lophotrochozoan taxon (Adoutte et al., 2000).”

“The WG topology followed the ‘‘Coelomata hypothesis,’’ whereas the alternate topology reflects the ‘‘Ecdysozoa hypothesis’’ and unites nematodes and arthropods in a monophyletic group [17].”

“Several other authors (Finnerty, ’98; Finnerty and Martindale, ’98; Martinez et al., ’98; Adoutte et al., ’99, 2000; de Rosa et al., ’99) suggest that the “animal zootype” is flawed on the basis of examination of the first occurrence of the “Hox cluster” in animal evolution.”

“Phylogenetic relationships between the species used in this study (as depicted in Figure 1) are based on [38-42].”

“Valentine 1997; Adoutte et al. 2000). Although based on embryologic characteristics chaetognaths have been regarded as deuterostomes, they are placed in the lophotrochozoa (Halanych 1996; Peterson et al. 2000). The present study reveals two developmental features of chaetognaths that are also found in the eutrochozoa:…”

“Although hypotheses abound, it is not known how these nervous systems relate to the axial nervous systems of other groups, particularly with respect to the chordates to which they are related (Garstang 1894; Lacalli 1994; Adoutte et al. 2000; Swalla et al. 2000; Morris and Byrne 2005).”

“Therefore, it could not be ruled out that the lophotrochozoa (Adoutte et al., 2000), including snails and flatworms, might indeed harbor metabotropic histamine receptors.”

“Schematic representations of protein domains of representative STIM molecules based on phylogeny of bilaterian animals [51].”

“For example the new molecule-based animal phylogeny proposes a view of the evolution of protostomes and deuterostomes clearly more consistent than the previous phylogenies (Adoutte et al., 2000).”

“Probably the best illustration of the importance and success of this approach is the establishment and elaboration of the new animal phylogeny [1-5].”

“…2005) but not others (Copley et al. 2004; Dopazo and Dopazo 2005; Philippe et al. 2005) and runs against the view of animal evolution that is currently prevailing in the evolutionary developmental biology (evo-devo) community (Aguinaldo et al. 1997; Adoutte et al. 2000; Telford and Copley 2005).”

“Molluscs belong to one of the three great branches of bilaterians, the lophotrochozoans (the two others are deuterostomes, that include chordates, and ecdysozoans, that include arthropods and nematodes; for review, Adoutte et al. 2000).”

“Specifically, it is now thought that the majority of flatworm classes belong within the protostome group and therefore have no special claim to be representative of the first bilaterians (Adoutte et al., 2000).”

“…of otd orthologs in onychophorans would prove particularly useful in helping to resolve questions regarding ancestral features of head patterning and brain development in the Ecdysozoa and may settle the debate regarding the positional origin and innervation patterns associated with the…”

“However, acceptance of the 18S-based ‘new animal phylogeny’ [38–40] and subsequent studies [29,41] showing that the flatworms were not simple, primitive animals, but rather were members of a much larger clade including the molluscs, annelids and other minor phyla christened the Lophotrochozoa, suggested that the absen…”

“As regards the phylogenetic relationships between organisms which are continuously rearranged after newmolecular studies,wewill follow the classifications of Adoutte et al. (2000) and Pechenik (2015).”

“Comparative analyses of Hox clusters from representatives of the three major triploblastic phyla suggested that the last common bilaterian ancestor (LCBA) contained at least seven Hox genes: two anterior genes, lab/Hox1 (Paralogy Group 1, PG1) and pb/Hox2 Edited by M. Akam D. Papillon ()) · Y. Le Parco Centre d’Oc ano…”

“Other phyla such as the chaetognaths and the lophophorates, once thought to have affinities with the deuterostomes, have now been placed within the Protostomia (Halanych et al. 1995; Halanych 1996; Mackey et al. 1996; Aguinaldo et al. 1997; Adoutte et al. 2000).”

“The use of protein and eventually gene sequences and other genetic markers in quantitative approaches (Zuckerkandl & Pauling, 1965) has permitted a systematic, although not necessarily complete or incontrovertible view of animal phylogeny (Adoutte et al., 2000; Halanych, 2004).”

“The resulting tree is consistent with the current phylogeny of bilaterians (Adoutte et al. 2000) and the class-level phylogenetic relationships among the cnidarians, grouping together the two hydrozoan species (Bridge et al. 1995).”

“However, contemporary zoologists have become deeply puzzled by the origination of the arthropods because molecular biologists have firmly separated the two groups into distinct superphyla Ecdysozoa and Lophotrochozoa, respectively (Aguinaldo et al. 1997; Halanych et al. 1997; Adoutte et al. 2000).”

“With widespread adoption of PCR, comparisons of the easily amplified SSU gene formed the basis for a series of studies of animal evolution, culminating, in the late 1990s, in what has become known as the new animal phylogeny (Adoutte et al., 2000).”

“…are shown as being monophyletic, and are subdivided into two large branches : the lophotrochozoans (who share a similar ciliated larva), and the ecdysozoans (characterized, in part, by moulting of an exoskeleton) (see Aguinaldo et al., 1997; Martindale & Kourakis, 1999; Adoutte et al., 2000).”

“…in a recently constructed planarian database (Reddien et al., 2005), because planarians, which serve as one of the best characterized animal models of regeneration, have recently been assigned to the same phylogenic group, the “Lophotrochozoa,” as the annelids and mollusks (Adoutte et al., 2000).”

“arthropods, all belonging to Ecdysozoans in Protostomia (Adoutte et al., 2000).”

“Interestingly, when we applied the Dollo parsimony method to remaining characters, we obtained the evolutionary tree consistent with the Coelomata hypothesis (Adoutte et al., 2000; Blair et al., 2002; Wolf et al., 2004).”

“It is of interest, therefore, to identify neuropeptides that act as muscle relaxants in animals that occupy an ‘intermediate’ position with respect to the vertebrates and protostomes in animal phylogeny – the deuterostomian invertebrates, which include two chordate subphyla that are closely related to vertebrates (Uro…”

“With the advent of molecular phylogenetics a decade ago, a major revision of the classical bilaterian phylogeny became necessary (Adoutte et al. 1999, 2000).”

“Despite the arthropod lineage being separated from the vertebrate lineage more than 600 million years ago (Adoutte et al, 2000; Peterson et al, 2004), many basic biological, physiological, and neurological properties are conserved between mammals and Drosophila (Edgar and Lehner, 1996; Rubin et al,…”

“…et al. 1997), as well as a re-analysis of morphological characters (Peterson and Eernisse 2001), have shown that bilaterians are subdivided into three major clades: one deuterostome clade and two protostome clades, the ecdysozoans and the lophotrochozoans (for a review see Adoutte et al. 2000).”

“They place hemichordates, not as sharing a direct ancestor, but as the sister group of echinoderms (Halanych, 1995; Adoutte et al., 2000; Cameron et al., 2000).”

“Looking at the evolution of BMP15 and GDF9 in deuterostomes, the topology of our maximum likelihood tree is in accordance with the phylogeny of Adoutte et al. [66] and Cameron et al. [67].”

“However, based onmolecular phylogeny, theywere subsequently grouped in the Lophothrocozoa (Adoutte et al., 2000), and their simple traits are now regarded by the majority of scientists as secondary losses (De Robertis, 2008).”

“Data for the schematic metazoan phylogeny were from numerous sources [157–163].”

“As discussed by Adoutte et al. (1999; 2000) the revised classifications are not without their problems because of phenomena such as mutational saturation, and different rates of evolution within lineages, resulting in long-branch attraction artefact1.”

“…most bilaterally symmetric animals fall into three superphyla, Deuterostomia, Ecdysozoa and Lophotrochozoa (Aguinaldo et al., 1997; Collins and Valentine, 2001; Ruiz-Trillo et al., 1999), which were already separated from one another at the time of the Cambrian radiation (Adoutte et al., 2000).”

“In contrast, information is less consistent in lophotrochozoans, the third clade of bilaterian animals (Adoutte et al., 2000).”

“The oyster Crassostrea (Lophotrochozoans) and fruit fly Drosophila (Ecdysozoans) represent two deeply divergent classes of protostomes, which are thought to have diverged from the deuterostomes long before the Cambrian [53].”

“The so-called "new animal phylogeny", however, does not support this close relationship between annelids and arthropods and rather places them in two different branches of protostome phylogeny termed Lophotrochozoa and Ecdysozoa, respectively [2].”

“(Adoutte et al., 2000: 4455, my emphasis) get a treelike top–down structure that tries to explain how genes encode for features.”

“Since it evolves at a slow rate, 18S rRNA is unable to resolve species-level differences between lineages and is considered well suited for evaluating deep-level relationships among organisms (Adoutte et al. 2000; Van de Peer et al. 2000; Fontaneto 2011).”

“The bilaterian lineage arose in the late Neoproterozoic and predates the Cambrian explosion, 540 million years ago (Adoutte et al., 2000; Balavoine and Adoutte, 1998).”

“However, the increase in molecular data has given rise to so-called “new animal phylogeny” (Adoutte et al., 2000; Halanych, 2004; Giribet et al., 2007) supporting the monophyly of Bilateria, which is again divided into two major lineages, Protostomia, and Deuterostomia.”

“Although the resolution of the phylogeny of animals is not complete [25], the available data indicate that maximum cell type numbers range between 16 and 22 for the early divergent poriferans and cniderians, and between 9 and 69 for the mollusks and arthropods.”

“…studies have become the standard for providing an independent test of existing morphology-based phylogenies (Halanych et al., 1995; Winnepenninckx et al., 1995; Giribet et al., 1996; Aguinaldo et al., 1997; Carranza et al., 1997; Balavoine, 1998; Adoutte et al., 2000 and references therein).”