Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
Department of Earth- and Environmental Sciences, Palaeontology and Geobiology & GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 München, Germany.Molecular Biology and Evolution (Impact Factor: 9.11). 04/2010; 27(9):1983-7. DOI: 10.1093/molbev/msq089
Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.
Get notified about updates to this publicationFollow publication
Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. The impact factor represents a rough estimation of the journal's impact factor and does not reflect the actual current impact factor. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.
[Show abstract] [Hide abstract]
- "However, the position of the cluster indicates that they may have diverged and evolved asymmetrically and non-uniformly with respect to the other vertebrate orthologs, following hypothesized evolutionary impact for gene gains, losses and duplications (Canestro et al., 2013Canestro et al., , 2009 Panchin et al., 2010). Nevertheless, we have to take into account that an extended taxon sampling may evidence the existence of long-branch attraction artefacts (Pick et al., 2010). Finally, we can support the hypothesis that Ambra1 gene was not affected by the two rounds of whole-genome duplication occurred in early vertebrate evolution or, most parsimoniously, the paralogues have been lost early in vertebrate evolution, and the extant one did duplicate in teleosts. "
ABSTRACT: Ambra1 is a positive regulator of autophagy, a lysosome-mediated degradative process involved both in physiological and pathological conditions. Nowadays, Ambra1 has been characterized only in mammals and zebrafish. Through bioinformatics searches and targeted cloning, we report the identification of the complete Ambra1 transcript in a non-vertebrate chordate, the tunicate Botryllus schlosseri. Tunicata is the sister group of Vertebrata and the only chordate group possessing species that reproduce also by blastogenesis (asexual reproduction). B. schlosseri Ambra1 deduced amino acid sequence is shorter than vertebrate homologues but still contains the typical WD40 domain. qPCR analyses revealed that the level of B. schlosseri Ambra1 transcription is temporally regulated along the colonial blastogenetic cycle. By means of similarity searches we identified Wdr5 and Katnb1 as proteins evolutionarily associated to Ambra1. Phylogenetic analyses on Bilateria indicate that: Wdr5 is the most related to Ambra1, so that they may derive from an ancestral gene, ii) Ambra1 forms a group of ancient genes evolved before the radiation of the taxon, iii) these orthologous Ambra1 share the two conserved WD40/YVTN repeat-like-containing domains, and iv) they are characterized by ancient duplications of WD40 repeats within the N-terminal domain.
[Show abstract] [Hide abstract]
- "Cnidarians ( jellyfish, corals, sea anemones) are the sister clade of the Bilateria (Hejnol et al., 2009; Pick et al., 2010), and they possess simple, nerve-net based nervous systems comprising three classes of neural cells – sensory neurons, ganglion neurons (analogous to interneurons) and nematocytes (mechano-/chemoreceptor cells). Due to their relative phylogenetic positions, identifying conserved features of cnidarian and bilaterian neurogenesis can inform reconstructions of the ancestral neurogenic characters of eumetazoans (herein referring to Bilateria+Cnidaria). Indeed, genomic comparisons have shown that cnidarians possess many orthologues to key bilaterian neural-related genes (Chapman et al., 2010; Galliot et al., 2009; Putnam et al., 2007; Watanabe et al., 2009), but a functional characterisation of the majority of these candidates is lacking. "
ABSTRACT: Notch signalling, SoxB and Group A bHLH 'proneural' genes are conserved regulators of the neurogenic program in many bilaterians. However, the ancestry of their functions and interactions is not well understood. We address this question in the sea anemone Nematostella vectensis, a representative of the Cnidaria, the sister clade to the Bilateria. It has previously been found that the SoxB orthologue NvSoxB(2) is expressed in neural progenitor cells (NPCs) in Nematostella and promotes the development of both neurons and nematocytes, whereas Notch signalling has been implicated in the negative regulation of neurons and the positive regulation of nematocytes. Here, we clarify the role of Notch by reporting that inhibition of Notch signalling increases the numbers of both neurons and nematocytes, as well as increasing the number of NvSoxB(2)-expressing cells. This suggests that Notch restricts neurogenesis by limiting the generation of NPCs. We then characterise NvAth-like (Atonal/Neurogenin family) as a positive regulator of neurogenesis that is co-expressed with NvSoxB(2) in a subset of dividing NPCs, while we find that NvAshA (Achaete-scute family) and NvSoxB(2) are co-expressed in non-dividing cells only. Reciprocal knockdown experiments reveal a mutual requirement for NvSoxB(2) and NvAth-like in neural differentiation; however, the primary expression of each gene is independent of the other. Together, these data demonstrate that Notch signalling and NvSoxB(2) regulate Nematostella neural progenitors via parallel yet interacting mechanisms; with different aspects of these interactions being shared with Drosophila and/or vertebrate neurogenesis.
[Show abstract] [Hide abstract]
- "While a consensus is emerging with respect to the relationships and composition of these major clades (Halanych 2004; Giribet 2008; Edgecombe et al. 2011; Dunn et al. 2014), a few aspects remain uncertain (see Fig. 1). These include mostly the internal relationships of Ecdysozoa, Spiralia, and Lophotrochozoa, and the base of the animal tree—specifically , the relative position of Porifera or Ctenophora as the sister group to all remaining Metazoa, a topic that remains contentious due to data and model dependence (e.g., Pick et al. 2010; Nosenko et al. 2013; Whelan et al. 2015). In this review, the progress and future challenges to reconstruct the animal tree of life are discussed. "
ABSTRACT: The science of phylogenetics, and specially the subfield of molecular systematics, has grown exponentially not only in the amount of publications and general interest, but also especially in the amount of genetic data available. Modern phylogenomic analyses use large genomic and transcriptomic resources, yet a comprehensive molecular phylogeny of animals, including the newest types of data for all phyla, remains elusive. Future challenges need to address important issues with taxon sampling—especially for rare and small animals—orthology assignment, algorithmic developments, and data storage and to figure out better ways to integrate information from genomes and morphology in order to place fossils more precisely in the animal tree of life. Such precise placement will also aid in providing more accurate dates to major evolutionary events during the evolution of our closest kingdom.