The Essential Role of "Minor" Phyla in Molecular Studies of Animal Evolution

SYNOPSIS. Molecular studies have revealed many new hypothesesof metazoan evolution in recent years. Previously, using morphologicalmethods, it was difficult to relate "minor" animal groups representingmicroscopic metazoans to larger, more well known groups suchas arthropods, molluscs, and annelids. Molecular studies suggestthat acanthocephalans evolved from rotifers, that priapulidsshare common ancestry with all other molting animals (Ecdysozoa),and that flatworms, gnathostomulids and rotifers form a sistergroup to the remaining non-molting protostomes (Lophotrochozoa),together forming Spiralia. The lophophorate phyla (phoronids,brachiopods and bryozoans) appear as protostomes, allied withannelids and molluscs rather than with deuterostomes. Thesefindings present a very different view of metazoan evolution,and clearly show that small and simple animals do not necessarilyrepresent ancestral or primitive taxa.     

The Position of Arthropods in the Animal Kingdom: A Search for a Reliable Outgroup for Internal Arthropod Phylogeny

Morphological evidence for the phylogeny of the animal kingdom has been discussed by numerous authors. DNA sequencing and phylogenetic methods for analyzing these data are alternative approaches to animal phylogeny, but the phenomenon of long branch attraction and poor taxonomic sampling have caused misinterpretations of metazoan relationships. Here we report a cladistic approach to metazoan evolution including 133 18S rDNA sequences of 31 animal phyla. Despite the difficulties associated with analyzing large data sets, our data suggest that the Bilateria and Protostomia are monophyletic. The internal phylogeny of the protostomes is divided into two main clades. One clade includes the classical protostome worms (annelids, sipunculans, echiurans, pogonophorans, and vestimentiferans), mollusks, nemerteans, “lophophorates,” platyhelminths, rotiferans, and acanthocephalans, although the internal resolution of the clade is very low. The second clade includes arthropods and other molting animals: tardigrades, onychophorans, nematodes, nematomorphans, kinorhynchs, and priapulans. The arthropods and related phyla lack a ciliated larvae, lack a multiciliate (locomotory) epithelium, and share many features, notably, a reduced coelomic cavity and the presence of a cuticle which molts. The use of these outgroups within the molting clade to root arthropod phylogenies is recommended instead of using annelids or other spiralians. The data are quite conclusive in those phyla with a good taxonomic sampling (i.e., platyhelminths and arthropods).     

Metazoan phylogeny and the Cambrian radiation

Sequence analysis of small-subunit ribosomal RNA (18S rRNA) has provided important new pieces for the great puzzle of metazoan phylogeny and has generated new perspectives on the Precambrian-Cambrian fossil record of the metazoan radiation. While the puzzle is far from resolved and the early results are plagued by difficulties in data analysis, intriguing insights have appeared. Early results suggest that molluscs and lophophorates are protostomes, and that deuterostomes may be derived from protostomes. More speculatively, annelids and molluscs may be derived from arthropods or an arthropod ancestor. The molecular evidence further strengthens paleontological arguments for an explosive metazoan radiation near the Vendian-Cambrian boundary, rather than a lengthy, but hidden, period of Precambrian diversification.     

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences

SUMMARY Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.     

The Articulata hypothesis – or what is a segment?

The long held view that annelids and arthropods are closely related (Articulata) has been challenged recently by phylogenetic analyses using molecular data. The outcome of these studies is a clade of moulting animals (Ecdysozoa) comprising arthropods and some taxa of the nemathelminth worms. Monophyly of the Ecdysozoa has not yet been shown convincingly on morphological evidence, but is strongly supported by molecular data. The implication of the Ecdysozoa hypothesis is that the type of segmentation found in annelids and arthropods must be either convergent or an ancestral feature of protostomes or even bilaterians. The present review discusses aspects of segmentation in annelids and arthropods at the genetic, cellular, morphogenetic and morphological levels. Based on numerous similarities not shared with other bilaterian taxa it is suggested that segmentation of annelids and arthropods is homologous and apomorphic for a monophyletic Articulata. However, the challenge provided by the molecular analyses should stimulate research programmes gaining more data such as on additional genes, cleavage patterns, molecular developmental biology, and the comparison of nervous systems at the level of single neurons.     

苔藓动物的起源与系统发生研究进展—形态学和分子生物学的证据

苔藓动物是后生动物中的一个重要类群。然而,和其它主要后生动物类群相比,长期以来对它的系统学研究却相对滞后。其起源,系统发生地位以及与其它后生物门类之间、其内部各高级分类群间的谱系发生关系一直存在争议。一般认为它是介于原口动物和后口动物之间的过渡类群。但是,近年来的分子系统学研究已经证实了它的原口归属。古生物学资料表明,虽然苔藓动物的大多数类群在奥陶纪已经分化出来,但它在寒武纪却缺乏任何化石记录。另外,苔藓动物起源的时间和方式、其内部各类群间的系统发生关系特别是现生类群和化石类群之间的关系等诸多问题的解决,还有待于大量的形态学和不同的分子数据的进一步积累,并结合其地层分布等各种相关资料进行综合研究。     

Molecular data indicate the protostome affinity of brachiopods

Although the phylogenetic position of brachiopods has always been subject to debate, many authors place them as a sister group to deuterostomes on the basis of morphological and developmental characters. However, molecular phylogeny consistently places them among protostomes. More precisely, brachiopods are predicted to branch inside the lophotrochozoan assemblage, together with annelids, molluscs, nemerteans, flatworms, and others. That result has been criticized on the basis of (1) prior knowledge of brachiopod morphology and (2) the known limitations of molecular phylogenies. Here I review recent data of molecular origin, particularly those displaying qualitative properties close to those of morphological characters. The complement of Hox genes present in all metazoa tested to date has proved to be a powerful tool for broad phylogenetic reconstruction. The mitochondrial genome also provides qualitative characters, showing discrete events of gene rearrangements. After discussing the data and the way they should be interpreted in the perspective of several hypotheses for metazoan phylogeny, I conclude that they argue strongly in favor of the protostome (and lophotrochozoan) affinity of the brachiopods. There is therefore a need for a reinterpretation of brachiopod morphological and developmental characters. I also identify some research axes on brachiopod morphology.     

Ecdysozoa: The Relationship between Cycloneuralia and Panarthropoda

The hypothesis that molting protostomes such as nematodes and arthropods form a monophyletic group known as Ecdysozoa is directly opposed to Articulata, in which some segmented protostomes such as annelids and arthropods form a monophyletic taxon. Ultrastructural and cladistic studies have led to the widely accepted hypothesis that nematodes belong among the protostomes. While early molecular studies suggested that nematodes were basal triploblasts, more recent molecular evidence suggests that this was an artifact of ‘long branch attraction’ and 18S rRNA gene, total evidence and hox gene studies all support the placement of nematodes within Ecdysozoa. The branching pattern within Ecdysozoa has been difficult to elucidate, but it now appears that priapulids and kinorhynchs form the earliest branching clade, followed by nematodes + nematomorphs, and finally the panarthropods. This suggests that Cycloneuralia is paraphyletic and that arthropods are the most derived of the ecdysozoans.     

A Brief Review of Metazoan Phylogeny and Future Prospects in Hox-Research

Underlying any analysis on the evolution of development is aphylogenetic framework, whether explicitly stated or implied.As such, differing views on phylogenetic relationships leadto variable interpretations of how developmental mechanismshave changed through time. Over the past decade, many long-standinghypotheses about animal evolution have been questioned causingsubstantial changes in the assumed phylogenetic framework underlyingcomparative developmental studies. Current hypotheses aboutearly metazoan history suggest that three, not two, major lineagesof bilateral animals originated in the Precambrian: the Deuterostomes(e.g., seastars, acorn worms, and vertebrates), the Ecdysozoans(e.g., nematodes and arthropods), and the Lophotrochozoans (e.g.,annelids, mollusks, and lophophorates). Although informationin Hox-genes bears directly on our understanding of early metazoanevolution and the formation of body plans, research effort hasbeen focused primarily on two taxa, insects and vertebrates.By sampling a greater diversity of metazoan taxa and takingadvantage of biotechnological advances in genomics, we willnot only learn more about metazoan phylogeny, but will alsogain valuable insight as to the key evolutionary forces thatestablished and maintained metazoan bauplans.     

The partial mitochondrial genome of the Cephalothrix rufifrons (Nemertea, Palaeonemertea): characterization and implications for the phylogenetic position of Nemertea

A continuous 10.1kb fragment of the Cephalothrix rufifrons (Nemertea, Palaeonemertea) mitochondrial genome was sequenced and characterized to further assess organization of protostome mitochondrial genomes and evaluate the phylogenetic potential of gene arrangement and amino acid characters. The genome is A-T rich (72%), and this biased base composition is partly reflected in codon usage. Inferred tRNA secondary structures are typical of those reported for other metazoan mitochondrial DNAs. The arrangement of the 26 genes contained in the fragment exhibits marked similarity to those of many protostome taxa, most notably molluscs with highly conserved arrangements and a phoronid. Separate and simultaneous phylogenetic analyses of inferred amino acid sequences and gene adjacencies place the nemertean within the protostomes among coelomate lophotrochozoan taxa, but do not find a well-supported sister taxon link.     

A lophotrochozoan twist gene is expressed in the ectomesoderm of the gastropod mollusk Patella vulgata

The twist gene is known to be involved in mesoderm formation in two of the three clades of bilaterally symmetrical animals: viz. deuterostomes (such as vertebrates) and ecdysozoans (such as arthropods and nematodes). There are currently no data on the spatiotemporal expression of this gene in the third clade, the lophotrochozoans (such as mollusks and annelids). To approach the question of mesoderm homology across bilaterians, we decided to analyze orthologs of this gene in the gastropod mollusk Patella vulgata that belongs to the lophotrochozoans. We present here the cloning, characterization, and phylogenetic analysis of a Patella twist ortholog, Pv-twi, and determine the early spatiotemporal expression pattern of this gene. Pv-twi expression was found in the trochophore larva in a subset of the ectomesoderm, one of the two sources of mesoderm in Patella. These data support the idea that twist genes were ancestrally involved in mesoderm differentiation. The absence of Pv-twi in the second mesodermal source, the endomesoderm, suggests that also other genes must be involved in lophotrochozoan mesoderm differentiation. It therefore remains a question if the mesoderm of all bilaterians is homologous.     

Comparative biology of calcium signaling during fertilization and egg activation in animals.

During animal fertilizations, each oocyte or egg must produce a proper intracellular calcium signal for development to proceed normally. As a supplement to recent synopses of fertilization-induced calcium responses in mammals, this paper reviews the spatiotemporal properties of calcium signaling during fertilization and egg activation in marine invertebrates and compares these patterns with what has been reported for other animals. Based on the current database, fertilization causes most oocytes or eggs to generate multiple wavelike calcium oscillations that arise at least in part from the release of internal calcium stores sensitive to inositol 1,4,5-trisphosphate (IP3). Such calcium waves are modulated by upstream pathways involving oolemmal receptors and/or soluble sperm factors and in turn regulate calcium-sensitive targets required for subsequent development. Both "protostome" animals (e.g., mollusks, annelids, and arthropods) and "deuterostomes" (e.g., echinoderms and chordates) display fertilization-induced calcium waves, IP3-mediated calcium signaling, and the ability to use a combination of external calcium influx and internal calcium release. Such findings fail to support the dichotomy in calcium signaling modes that had previously been proposed for protostomes vs deuterostomes and instead suggest that various features of fertilization-induced calcium signals are widely shared throughout the animal kingdom.     

Mitochondrial COI sequences of brachiopods: genetic code shared with protostomes and limits of utility for phylogenetic reconstruction

A 1230-bp region of the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA of each of 16 brachiopod species, representing all five living orders, was amplified by polymerase chain reaction and sequenced. Pairwise comparisons of sequence differences plotted against divergence times estimated from the brachiopod fossil record revealed that, although there are considerable variations in the expected substitution rate among different lineages, amino acid substitutions of the COI sequences may largely become saturated in 100 Ma, due mostly to multiple substitutions at the same site. Coinciding with this result, phylogenetic analysis indicated low bootstrap values for nodes corresponding to divergence events that occurred before 100 Ma, suggesting that COI sequences are suitable only for inference of phylogenetic events subsequent to the Mesozoic. Examination of brachiopod codons corresponding to invariant amino acids in the COI of various other animals suggest the nonuniversal codon relationships UGA = Trp, AUA = Met, AAA/G = Lys, and AGA/G = Ser. These are identical to those in mollusks, annelids, and arthropods, consistent with the conclusion that brachiopods are protostomes, as indicated by previous molecular analyses.     

The mushroom bodies – prominent brain centres of arthropods and annelids with enigmatic evolutionary origin

Loesel, R. and Heuer, C.M. 2010. The mushroom bodies – prominent brain centres of arthropods and annelids with enigmatic evolutionary origin. —Acta Zoologica (Stockholm) 91 : 29–34 Mushroom bodies (MBs) are the most prominent and conspicuous neuropils in the brain of arthropods, onychophorans and vagile polychaete annelids but have not been described in any other animal group with complex brain architecture. Due to a number of unique neuroanatomical characters MBs can easily be identified and distinguished from other brain centres. However, their evolutionary origin and the question whether MBs are homologous structures is still under debate. This paper will briefly summarize the available morphological data and their implications with respect to the molecular evidence on early metazoan radiation. Unraveling the origin of MBs is an example of the challenges neurophylogenists will face in the future, especially so since it will signify a major step towards reconstructing early metazoan brain evolution.     

The complete mitochondrial genome sequence of Whitmania pigra (Annelida, Hirudinea): the first representative from the class Hirudinea

The mitochondrial genome is a significant tool for investigating the evolutionary history of metazoan animals. The currently available mitochondrial genome data in GenBank is limited to understand the detail evolutionary relationship among the metazoan animals, especially in the phylum Annelida. Here we present the mitochondrial gene organization, gene order and codon usage of the leech Whitmania pigra (Annelida), which is the first representative from the class Hirudinea. It is a circular molecule of 14,426bp, and encodes 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. All 37 genes of W. pigra mitochondrial genome are transcribed from the same strand, which is identical to studied annelids, two echiurans, two sipunculans and many other lophotrochozoans. Five conserved gene clusters can be found in mitochondrial genomes of nine studied annelids, including (1) cox1-N-cox2; (2) cox3-Q-nad6-cob-W-atp6; (3) H-nad5-F-E-P-T-nad4L-nad4; (4) srRNA-V-lrRNA; and (5) nad3-S(1)-nad2. Compared with that of other studied annelids, translocations of transfer RNAs were found in the gene arrangement of W. pigra mitochondrial genome. Phylogenetic analysis strongly support that the species from Hirudinina and Oligochaeta form a monophyletic group Clitellata (BPM=100, BPP=100), which is consistent with previous research based on morphological and other molecular data. Both gene order data and amino acid sequences reveal that echiurans are derived annelids and sipunculans should be clustered with annelids and echiurans.     

Analysis of the complete mitochondrial DNA sequence of the brachiopod terebratulina retusa places Brachiopoda within the protostomes

Brachiopod phylogeny is still a controversial subject. Analyses using nuclear 18SrRNA and mitochondrial 12SrDNA sequences place them within the protostomes but some recent interpretations of morphological data support a relationship with deuterostomes. In order to investigate brachiopod affinities within the metazoa further, we compared the gene arrangement on the brachiopod mitochondrial genome with several metazoan taxa. The complete (15 451 bp) mitochondrial DNA (mtDNA) sequence of the articulate brachiopod Terebratulina retusa was determined from two overlapping long polymerase chain reaction products. All the genes are encoded on the same strand and gene order comparisons showed that.only one major rearrangement is required to interconvert the T. retusa and Katharina tunicata (Mollusca: Polvplacophora) mitochondrial genomes. The partial mtDNA sequence of the prosobranch mollusc Littorina saxatilis shows complete congruence with the T. rehtusa gene arrangement with regard to the ribosomal and protein coding genes. This high similarity in gene arrangement is the first to be reported within the protostomes. Sequence analyses of mitochondrial protein coding genes also support a close relationship of the brachiopod with molluscs and annelids, thus supporting the clade Lophotrochozoa. Though being highly informative, sequence analyses of the mitochondrial protein coding genes failed to resolve the branching order within the lophotrochozoa.     

Arthropod-like expression patterns of engrailed and wingless in the annelid Platynereis dumerilii suggest a role in segment formation

The origin of animal segmentation, the periodic repetition of anatomical structures along the anteroposterior axis, is a long-standing issue that has been recently revived by comparative developmental genetics. In particular, a similar extensive morphological segmentation (or metamerism) is commonly recognized in annelids and arthropods. Mostly based on this supposedly homologous segmentation, these phyla have been united for a long time into the clade Articulata. However, recent phylogenetic analysis dismissed the Articulata and thus challenged the segmentation homology hypothesis. Here, we report the expression patterns of genes orthologous to the arthropod segmentation genes engrailed and wingless in the annelid Platynereis dumerilii. In Platynereis, engrailed and wingless are expressed in continuous ectodermal stripes on either side of the segmental boundary before, during, and after its formation; this expression pattern suggests that these genes are involved in segment formation. The striking similarities of engrailed and wingless expressions in Platynereis and arthropods may be due to evolutionary convergence or common heritage. In agreement with similarities in segment ontogeny and morphological organization in arthropods and annelids, we interpret our results as molecular evidence of a segmented ancestor of protostomes.     

Evolutionary aspects of octopaminergic systems with emphasis on arthropods

We review current knowledge on octopaminergic systems in all major phyla with emphasis on arthropods. Octopaminergic systems occur in all triploblastic animals investigated. Close relationships of the octopamine-receptors in protostomes to vertebrate alpha-adrenergic receptors suggest an ancient common origin. Some evidence suggests that the octopaminergic system may be younger than the vertebrate adrenergic system. All octopaminergic systems are constructed from comparatively few neurons, and the cell populations in different representatives of a given phylum are clearly similar. Current data do not allow any conclusions on the relationships between molluscs and annelids (Lophotrochozoa) to nematodes and arthropods (Ecdysozoa).In chelicerates, including Limulus as a remaining xiphosuran, and crustaceans, octopaminergic neurons occur in pairs. All investigated winged insects (Pterygota) possess similar arrangements of octopaminergic cell populations, suggesting that their octopaminergic systems have been largely conserved during evolution. Unpaired octopaminergic neurons, with symmetrical, bilaterally projecting efferent axons in insects do not appear to have counterparts in other arthropods. Unpaired-octopaminergic neurons may thus be an autapomorphic feature of winged insects. Octopamine acts as an inhibitory neurotransmitter in gastropods, and as an excitatory transmitter controlling bioluminescence in fireflies. Octopamine is also implicated in controlling bioluminescence in other phyla. All critically examined triploblastic invertebrates release octopamine as a hormone, as a peripheral modulator and as a central neuromodulator in the nervous system, which exerts its action via evolutionary related G-protein-coupled receptors that activate cAMP. The evolution of the octopaminergic system seems fundamental for the evolution of efficient locomotory mechanisms, complex social interactions, and cognitive abilities of arthropods.     

The evolution of the Hox cluster: insights from outgroups

Two burgeoning research trends are helping to reconstruct the evolution of the Hox cluster with greater detail and clarity. First, Hox genes are being studied in a broader phylogenetic sampling of taxa: the past year has witnessed important new data from teleost fishes, onychophorans, myriapods, polychaetes, glossiphoniid leeches, ribbon worms, and sea anemones. Second, commonly accepted notions of animal relationships are being challenged by alternative phylogenetic hypotheses that are causing us to rethink the evolutionary relationships of important metazoan lineages, especially arthropods, annelids, nematodes, and platyhelminthes.     

The Hox gene complement of a pelagic chaetognath, Flaccisagitta enflata

Chaetognaths are transparent marine animals that are ubiquitous and abundant members of oceanic zooplanktonic communities. Their phylogenetic position within the Metazoa, however, has remained obscure since their discovery. Morphology and embryology have traditionally allied chaetognaths with deuterostomes, but molecular evidence suggests otherwise. Two recent multigene expressed sequence tag (EST) molecular phylogenomic studies suggest that chaetognaths are either sister to the Lophotrochozoa (Matus et al. 2006) or to all protostomes (Marlétaz et al. 2006). We have isolated eight Hox genes, one Parahox gene, and Mox, a related homeodomain gene, from the pelagic chaetognath, Flaccisagitta enflata. Although chaetognath central class Hox genes lack the Lox5 or "spiralian" parapeptide, a diagnostic amino-acid motif that has been utilized previously to assign lophotrochozoan affinity, they do possess a central class Hox gene that has a partial "Ubd-A peptide" found in both ecdysozoan and lophotrochozoan Ubx/Abd-A/Lox2/Lox4 genes. Additionally, we report the presence of two distinct chaetognath posterior Hox genes that possess both ecdysozoan and lophotrochozoan signature amino-acid motifs. The phylogenetic position of chaetognaths, as well as the evolution of the Hox cluster, is discussed in light of these data.