Early Metazoan Evolution Research Articles

Functional transition of Pak proto-oncogene during early evolution of metazoans

Proto-oncogenes encode signaling molecular switches regulating cellular homeostasis in metazoans, and can be converted to oncogenes by gain-of-function mutations. To address the molecular basis for development of the regulatory system of proto-oncogenes during evolution, we screened for ancestral proto-oncogenes from the unicellular choanoflagellate Monosiga ovata by monitoring their transforming activities, and isolated a Pak gene ortholog encoding a serine/threonine kinase as a 'primitive oncogene'. We also cloned Pak orthologs from fungi and the multicellular sponge Ephydatia fluviatilis, and compared their regulatory features with that of M. ovata Pak (MoPak). MoPak is constitutively active and induces cell transformation in mammalian fibroblasts, although the Pak orthologs from multicellular animals are strictly regulated. Analyses of Pak mutants revealed that structural alteration of the auto-inhibitory domain (AID) of MoPak confers higher constitutive kinase activity, as well as greater binding ability to Rho family GTPases than the multicellular Paks, and this structural alteration is responsible for cell transformation and disruption of multicellular tissue organization. These results show that maturation of AID function was required for the development of the strict regulatory system of the Pak proto-oncogene, and suggest a potential link between the establishment of the regulatory system of proto-oncogenes and metazoan evolution.

The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters

Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades.

Origins and evolution of ADAR‐mediated RNA editing

Adenosine deaminases acting on RNA (ADARs) convert adenosines to inosines in double-stranded RNA in animals. Identification of more ADAR targets and genome sequences of diverse eukaryotes present an opportunity to elucidate the origin and evolution of ADAR-mediated RNA editing. Comparative analysis of the adenosine deaminase family indicates that the first ADAR might have evolved from adenosine deaminases acting on tRNAs after the split of protozoa and metazoa. ADAR1 and ADAR2 arose by gene duplications in early metazoan evolution, approximately 700 million years ago, while ADAR3 and TENR might originate after Urochordata-Vertebrata divergence. More ADAR or ADAR-like genes emerged in some animals (e.g., fish). Considering the constrained structure, ADAR targets are proposed to have evolved from transposable elements and repeats, random selection, and fixation, and intermolecular pairs of sense and antisense RNA. In some degree, increased ADAR-mediated gene regulation should substantially contribute to the emergence and evolution of complex metazoans, particularly the nervous system.

Monociliated epidermal cells in Gastrotricha: Significance for concepts of early metazoan evolution

Monociliated epidermal cells in Gastrotricha: Significance for concepts of early metazoan evolution

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

For more than a century, the origin of metazoan animals has been debated. One aspect of this debate has been centered on what the hypothetical “urmetazoon” bauplan might have been. The morphologically most simply organized metazoan animal, the placozoan Trichoplax adhaerens, resembles an intriguing model for one of several “urmetazoon” hypotheses: the placula hypothesis. Clear support for a basal position of Placozoa would aid in resolving several key issues of metazoan-specific inventions (including, for example, head–foot axis, symmetry, and coelom) and would determine a root for unraveling their evolution. Unfortunately, the phylogenetic relationships at the base of Metazoa have been controversial because of conflicting phylogenetic scenarios generated while addressing the question. Here, we analyze the sum of morphological evidence, the secondary structure of mitochondrial ribosomal genes, and molecular sequence data from mitochondrial and nuclear genes that amass over 9,400 phylogenetically informative characters from 24 to 73 taxa. Together with mitochondrial DNA genome structure and sequence analyses and Hox-like gene expression patterns, these data (1) provide evidence that Placozoa are basal relative to all other diploblast phyla and (2) spark a modernized “urmetazoon” hypothesis.

FGF signalling controls formation of the apical sensory organ in the cnidarianNematostella vectensis

Fibroblast growth factor (FGF) signalling regulates essential developmental processes in vertebrates and invertebrates, but its role during early metazoan evolution remains obscure. Here, we analyse the function of FGF signalling in a non-bilaterian animal, the sea anemone Nematostella vectensis. We identified the complete set of FGF ligands and FGF receptors, of which two paralogous FGFs (NvFGFa1 and NvFGFa2) and one FGF receptor (NvFGFRa) are specifically coexpressed in the developing apical organ, a sensory structure located at the aboral pole of ciliated larvae from various phyla. Morpholino-mediated knockdown experiments reveal that NvFGFa1 and NvFGFRa are required for the formation of the apical organ, whereas NvFGFa2 counteracts NvFGFRa signalling to prevent precocious and ectopic apical organ development. Marker gene expression analysis shows that FGF signalling regulates local patterning in the aboral region. Furthermore, NvFGFa1 activates its own expression and that of the antagonistic NvFGFa2, thereby establishing positive- and negative-feedback loops. Finally, we show that loss of the apical organ upon NvFGFa1 knockdown blocks metamorphosis into polyps. We propose that the control of the development of sensory structures at the apical pole of ciliated larvae is an ancestral function of FGF signalling.

Genesis and Expansion of Metazoan Transcription Factor Gene Classes

We know little about the genomic events that led to the advent of a multicellular grade of organization in animals, one of the most dramatic transitions in evolution. Metazoan multicellularity is correlated with the evolution of embryogenesis, which presumably was underpinned by a gene regulatory network reliant on the differential activation of signaling pathways and transcription factors. Many transcription factor genes that play critical roles in bilaterian development largely appear to have evolved before the divergence of cnidarian and bilaterian lineages. In contrast, sponges seem to have a more limited suite of transcription factors, suggesting that the developmental regulatory gene repertoire changed markedly during early metazoan evolution. Using whole-genome information from the sponge Amphimedon queenslandica, a range of eumetazoans, and the choanoflagellate Monosiga brevicollis, we investigate the genesis and expansion of homeobox, Sox, T-box, and Fox transcription factor genes. Comparative analyses reveal that novel transcription factor domains (such as Paired, POU, and T-box) arose very early in metazoan evolution, prior to the separation of extant metazoan phyla but after the divergence of choanoflagellate and metazoan lineages. Phylogenetic analyses indicate that transcription factor classes then gradually expanded at the base of Metazoa before the bilaterian radiation, with each class following a different evolutionary trajectory. Based on the limited number of transcription factors in the Amphimedon genome, we infer that the genome of the metazoan last common ancestor included fewer gene members in each class than are present in extant eumetazoans. Transcription factor orthologues present in sponge, cnidarian, and bilaterian genomes may represent part of the core metazoan regulatory network underlying the origin of animal development and multicellularity.

Reduced reliance on the trace element selenium during evolution of mammals.

Evolution from fish to mammals was accompanied by decreased use of selenocysteine, raising questions about the need for selenium dietary supplements when pathology is not imminent.

The Hedgehog protein family

Hedgehog proteins, which are important in developmental signaling, have been joined by other newly discovered proteins from throughout the eukaryotes in the Hint-domain-containing group of proteins.

Phylogenetic position of sponges in early metazoan evolution and bionic applications of siliceous sponge spicules

Sponges are the oldest and the simplest but not primitive multicellular animals. They represent the earliest evolutionary metazoan phylum still extant. It was a long and painful scientific process to position the most enigmatic and mysterious metazoan, the Porifera, into their correct phylogenetic place among the eukaryotes in general and multicellular animals in particular. As living fossils, sponges provide the best evidence for the early evolution of Metazoa. More recently, interest has been focused on the bionic applications of sponges’ siliceous spicules, after the discovery of their unique structure and high fiber performance. In this review, the emergence of sponges, evolutionary novelties found in sponges, and the phylogenetic position of sponges in early metazoan evolution are highlighted. In addition, the present state of knowledge on silicatein-mediated “biosilica” formation in marine sponges, including the involvement of other molecules in silica metabolism and their potential application in nanobiotechnology and medicine, is given.

Early Cambrian crown-group crustacean analysis

Crown-group crustaceans (Eucrustacea) are common in the fossil record of the past 500 million years back to the early Ordovician period, and very rare representatives are also known from the late Middle and Late Cambrian. With phosphatized cuticle and three-dimensional completion of soft parts, ‘Orsten’-type fossils, which are typically tiny embryos and cuticle-bearing animals, provide detailed morphological and phylogenetic information on the early evolution of metazoans.

An epipodite-bearing crown-group crustacean from the Lower Cambrian

Crown-group crustaceans (Eucrustacea) are common in the fossil record of the past 500 million years back to the early Ordovician period, and very rare representatives are also known from the late Middle and Late Cambrian periods. Finds in Lower Cambrian rocks of the Phosphatocopina, the fossil sister group to eucrustaceans, imply that members of the eucrustacean stem lineage co-occurred, but it remained unclear whether crown-group members were also present at that time. 'Orsten'-type fossils are typically tiny embryos and cuticle-bearing animals, of which the cuticle is phosphatized and the material is three-dimensional and complete with soft parts. Such fossils are found predominantly in the Cambrian and Ordovician and provide detailed morphological and phylogenetic information on the early evolution of metazoans. Here we report an Orsten-type Konservat-Lagerstätte from the Lower Cambrian of China that contains at least three new arthropod species, of which we describe the most abundant form on the basis of exceptionally well preserved material of several growth stages. The limb morphology and other details of this new species are markedly similar to those of living cephalocarids, branchiopods and copepods and it is assigned to the Eucrustacea, thus representing the first undoubted crown-group crustacean from the early Cambrian. Its stratigraphical position provides substantial support to the proposition that the main cladogenic event that gave rise to the Arthropoda was before the Cambrian. Small leaf-shaped structures on the outer limb base of the new species provide evidence on the long-debated issue of the origin of epipodites: they occur in a set of three, derive from setae and are a ground-pattern feature of Eucrustacea.

Fossils and phylogenies: integrating multiple lines of evidence to investigate the origin of early major metazoan lineages

Understanding the nature and timing of metazoan origins is one of the most important, yet elusive, questions in evolutionary biology. Fossil data provide the most tangible evidence for the origin of early animal lineages, although additional evidence from molecular phylogenetics, molecular clock studies, and development has contributed to our current understanding. We review several lines of evidence to explore the nature and timing of early metazoan evolution and discuss how these data, when considered together, provide a more cohesive picture of the origin of animal diversity. We discuss how trace fossils and biomarkers provide compelling evidence for the origins of Bilateria and siliceous sponges. Using a molecular phylogenetic framework for metazoans, we discuss how fossils can be used to date the origin of clades. We use these fossil dates to perform a relaxed molecular clock analysis for estimating dates of nodes when no fossils are available. We also discuss current data from developmental biology that suggest that early metazoans possessed a sophisticated molecular toolkit for building complex body plans. We conclude that the best evidence for the origin of major metazoan lineages lies in the careful interpretation of the fossil record and that these data, when considered with phylogenetic and developmental evidence, support the notion that the Cambrian radiation is a real phenomenon that marks a critically important time in the history of life.

Early Cambrian record of failed durophagy and shell repair in an epibenthic mollusc

Predation is arguably one of the main driving forces of early metazoan evolution, yet the fossil record of predation during the Ediacaran-Early Cambrian transition is relatively poor. Here, we present direct evidence of failed durophagous (shell-breaking) predation and subsequent shell repair in the Early Cambrian (Botoman) epibenthic mollusc Marocella from the Mernmerna Formation and Oraparinna Shale in the Flinders Ranges, South Australia. This record pushes back the first appearance of durophagy on molluscs by approximately 40Myr.

An ancient chordin-like gene in organizer formation of Hydra

Signaling centers or organizers play a key role in axial patterning processes in animal embryogenesis. The function of most vertebrate organizers involves the activity of secreted antagonists of bone morphogenetic proteins (BMPs) such as Chordin or Noggin. Although BMP homologs have been isolated from many phyla, the evolutionary origin of the antagonistic BMP/Chordin system in organizer signaling is presently unknown. Here we describe a Chordin-like molecule (HyChdl) from Hydra that inhibits BMP activity in zebrafish embryos and acts in Hydra axis formation when new head organizers are formed during budding and regeneration. hychdl transcripts are also up-regulated in the head regeneration-deficient mutant strain reg-16. Accordingly, HyChdl has a function in organizer formation, but not in head differentiation. Our data indicate that the BMP/Chordin antagonism is a basic property of metazoan signaling centers that was invented in early metazoan evolution to set up axial polarity.

Phylochronology of early metazoans: combined evidence from molecular and fossil data

AbstractTiming the evolutionary appearances of early Metazoa on Earth may rely on the combined information of fossil occurrences, molecular divergences and the geological background. Recent advances in the studies of Neoproterozoic and earliest Cambrian strata in South China and elsewhere, together with numerous works on molecular dating, provide an opportunity to draw a more precise timescale for the early metazoan evolution. This study presents a synthesis of available molecular and fossil dating results, placed in the palaeoenvironmental background, which leads to the recognition of the following time events for early metazoan cladogenesis: (1) Animal multicellularity occurred most probably during early to middle Neoproterozoic times (between ∼1000 and ∼660 Ma) during the geological period of gradual increase in oxygen content; (2) Eumetazoans and sponges (or sponge‐like organisms) parted from each other during the Neoproterozoic glaciation interval (ca. 750–580 Ma), but both experienced adaptive radiation after the glaciations as evidenced by the Doushantuo Biota (ca. 635–551 Ma); (3) A great metazoan radiation event (MRE) occurred during the late Ediacaran and earliest Cambrian periods (ca. 550–530 Ma), interpreted here as a metazoan radiation at higher taxonomic levels, as compared with the early Cambrian radiation representing one at lower taxonomic levels (lower than subphylum or class). In order to better constrain the phylochronology of early metazoans, we present evidence for the divergences of arthropod subgroups on the basis of molecular dating results and the fossil record. It is shown that the arthropod stem group diverged from its sister taxon at between ∼700 and ∼565 Ma and major arthropod subgroups originated coevally with MRE. The MRE is probably correlatable with the δ13C negative anomaly in the late Ediacaran Period.Although the phylochronology of early Metazoa is gradually emerging, a great deal of research still will be needed in the following directions in order to reduce uncertainties in, and discrepancies among, dating results: (1) Evaluate different molecular dating techniques so as to establish a proper set of standard procedures for dating early metazoan events; (2) Set up a standard set of fossil calibration points suitable for dating early metazoan divergences; (3) Use both molecular and fossil constraints as far as possible; (4) Place the time sequence in the geological and palaeoecological background so that one can visualize a logical evolutionary scenario. We suggest that the fossil record plus the geological background should serve to construct a general timeframe for evolution, while molecular dating will supplement and probably increase the precision of the chronology. Copyright © 2007 John Wiley & Sons, Ltd.

Mitochondrial Genome of Savalia savaglia (Cnidaria, Hexacorallia) and Early Metazoan Phylogeny

Mitochondrial genomes have recently become widely used in animal phylogeny, mainly to infer the relationships between vertebrates and other bilaterians. However, only 11 of 723 complete mitochondrial genomes available in the public databases are of early metazoans, including cnidarians (Anthozoa, mainly Scleractinia) and sponges. Although some cnidarians (Medusozoa) are known to possess atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization is similar to that of other metazoans. Because the phylogenetic relationships among Anthozoa as well as their relation to other early metazoans still need to be clarified, we tested whether sequencing the complete mitochondrial genome of Savalia savaglia, an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such relationships. Compared to other anthozoans, S. savaglia's genome is unusually long (20,766 bp) due to the presence of several noncoding intergenic regions (3691 bp). The genome contains all 13 protein coding genes commonly found in metazoans, but like other Anthozoa it lacks most of the tRNAs. Phylogenetic analyses of S. savaglia mitochondrial sequences show Zoantharia branching closely to other Hexacorallia, either as a sister group to Actiniaria or as a sister group to Actiniaria and Scleractinia. The close relationships suggested between Zoantharia and Actiniaria are reinforced by strong similarities in their gene order and the presence of similar introns in the COI and ND5 genes. Our study suggests that mitochondrial genomes can be a source of potentially valuable information on the phylogeny of Hexacorallia and may provide new insights into the evolution of early metazoans.

Continuous Molecular Evolution of Protein-Domain Structures by Single Amino Acid Changes

Protein structures cluster into families of folds that can result from extremely different amino acid sequences [1]. Because the enormous amount of genetic information generates a limited number of protein folds [2], a particular domain structure often assumes numerous functions. How new protein structures and new functions evolve under these limitations remains elusive. Molecular evolution may be driven by the ability of biomacromolecules to adopt multiple conformations as a bridge between different folds [3-6]. This could allow proteins to explore new structures and new tasks while part of the structural ensemble retains the initial conformation and function as a safeguard [7]. Here we show that a global structural switch can arise from single amino acid changes in cysteine-rich domains (CRD) of cnidarian nematocyst proteins. The ability of these CRDs to form two structures with different disulfide patterns from an identical cysteine pattern is distinctive [8]. By applying a structure-based mutagenesis approach, we demonstrate that a cysteine-rich domain can interconvert between two natively occurring domain structures via a bridge state containing both structures. Comparing cnidarian CRD sequences leads us to believe that the mutations we introduced to stabilize each structure reflect the birth of new protein folds in evolution.

The problem of germ layers in sponges (Porifera) and some issues concerning early metazoan evolution

Nowadays the formation of germ layers (endoderm and mesoderm) is associated with gastrulation. The question of whether the cell movements during early embryonic development in sponges (Porifera) are gastrulation as in eumetazoans remains in dispute. Recent data on the histological organization, digestion and embryonic morphogenesis in sponges are analyzed here in an attempt to answer this question. Unique features of these basal Metazoa are the lack of intestinal epithelium, digestive parenchyma or any cell population specialized in digestion. Food particles are captured by cells of almost all types. These data show that sponges have no embryonic layers such as ectoderm or endoderm, characteristic to eumetazoans, and, consequently, no gastrulation. We make an assumption that the formation of germ layers cannot be considered as a recapitulation of events that took place in the common ancestor of Porifera and Eumetazoa. The unity of Metazoa is expressed not in the presence of gastrulation processes per se, but in the universal nature of cell movement mechanisms ensuring various types of morphogenesis, including those underlying gastrulation. It is concluded that metazoan mechanisms of morphogenetic movements must have emerged in the course of evolution prior to the separation of the germ layers like endoderm and ectoderm.

Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA

Calcareous sponges (Porifera, Calcarea) play an important role for our understanding of early metazoan evolution, since several molecular studies suggested their closer relationship to Eumetazoa than to the other two sponge ‘classes,’ Demospongiae and Hexactinellida. The division of Calcarea into the subtaxa Calcinea and Calcaronea is well established by now, but their internal relationships remain largely unresolved. Here, we estimate phylogenetic relationships within Calcarea in a Bayesian framework, using full-length 18S and partial 28S ribosomal DNA sequences. Both genes were analyzed separately and in combination and were further partitioned by stem and loop regions, the former being modelled to take non-independence of paired sites into account. By substantially increasing taxon sampling, we show that most of the traditionally recognized supraspecific taxa within Calcinea and Calcaronea are not monophyletic, challenging the existing classification system, while monophyly of Calcinea and Calcaronea is again highly supported.