Xenoturbella is a deuterostome that eats molluscs

Xenoturbella bocki, first described in 1949 (ref. 1), is a delicate, ciliated, marine worm with a simple body plan: it lacks a through gut, organized gonads, excretory structures and coelomic cavities. Its nervous system is a diffuse nerve net with no brain. Xenoturbella's affinities have long been obscure and it was initially linked to turbellarian flatworms. Subsequent authors considered it variously as related to hemichordates and echinoderms owing to similarities of nerve net and epidermal ultrastructure, to acoelomorph flatworms based on body plan and ciliary ultrastructure (also shared by hemichordates), or as among the most primitive of Bilateria. In 1997 two papers seemed to solve this uncertainty: molecular phylogenetic analyses placed Xenoturbella within the bivalve molluscs, and eggs and larvae resembling those of bivalves were found within specimens of Xenoturbella. This molluscan origin implies that all bivalve characters are lost during a radical metamorphosis into the adult Xenoturbella. Here, using data from three genes, we show that the samples in these studies were contaminated by bivalve embryos eaten by Xenoturbella and that Xenoturbella is in fact a deuterostome related to hemichordates and echinoderms.     

Acoelomorph flatworms are deuterostomes related to Xenoturbella

Xenoturbellida and Acoelomorpha are marine worms with contentious ancestry. Both were originally associated with the flatworms (Platyhelminthes), but molecular data have revised their phylogenetic positions, generally linking Xenoturbellida to the deuterostomes and positioning the Acoelomorpha as the most basally branching bilaterian group(s). Recent phylogenomic data suggested that Xenoturbellida and Acoelomorpha are sister taxa and together constitute an early branch of Bilateria. Here we assemble three independent data sets-mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions and new microRNA (miRNA) complements-and show that the position of Acoelomorpha is strongly affected by a long-branch attraction (LBA) artefact. When we minimize LBA we find consistent support for a position of both acoelomorphs and Xenoturbella within the deuterostomes. The most likely phylogeny links Xenoturbella and Acoelomorpha in a clade we call Xenacoelomorpha. The Xenacoelomorpha is the sister group of the Ambulacraria (hemichordates and echinoderms). We show that analyses of miRNA complements have been affected by character loss in the acoels and that both groups possess one miRNA and the gene Rsb66 otherwise specific to deuterostomes. In addition, Xenoturbella shares one miRNA with the ambulacrarians, and two with the acoels. This phylogeny makes sense of the shared characteristics of Xenoturbellida and Acoelomorpha, such as ciliary ultrastructure and diffuse nervous system, and implies the loss of various deuterostome characters in the Xenacoelomorpha including coelomic cavities, through gut and gill slits.     

Tunicates and not cephalochordates are the closest living relatives of vertebrates

Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.     

Ancient deuterostome origins of vertebrate brain signalling centres

Neuroectodermal signalling centres induce and pattern many novel vertebrate brain structures but are absent, or divergent, in invertebrate chordates. This has led to the idea that signalling-centre genetic programs were first assembled in stem vertebrates and potentially drove morphological innovations of the brain. However, this scenario presumes that extant cephalochordates accurately represent ancestral chordate characters, which has not been tested using close chordate outgroups. Here we report that genetic programs homologous to three vertebrate signalling centres-the anterior neural ridge, zona limitans intrathalamica and isthmic organizer-are present in the hemichordate Saccoglossus kowalevskii. Fgf8/17/18 (a single gene homologous to vertebrate Fgf8, Fgf17 and Fgf18), sfrp1/5, hh and wnt1 are expressed in vertebrate-like arrangements in hemichordate ectoderm, and homologous genetic mechanisms regulate ectodermal patterning in both animals. We propose that these genetic programs were components of an unexpectedly complex, ancient genetic regulatory scaffold for deuterostome body patterning that degenerated in amphioxus and ascidians, but was retained to pattern divergent structures in hemichordates and vertebrates.     

On the Phylum Vetulicolia

1 The Chengjiang Fauna and the four greatest inno- vations in the evolutionary history of animals In 1837, i.e. 22 years before the formal publication of Origin of Species, by comprehending the finch story in the Galapagos, Charles Darwin understood that an animal species could be transformed into another species bygradual modifications and for the first time drew the fa- mous “branching tree”[1]. A century later, passing through two major revisions, i.e. the so-called Neo-Darwinism and …     

Ancestral echinoderms from the Chengjiang deposits of China

Deuterostomes are a remarkably diverse super-phylum, including not only the chordates (to which we belong) but groups as disparate as the echinoderms and the hemichordates. The phylogeny of deuterostomes is now achieving some degree of stability, especially on account of new molecular data, but this leaves as conjectural the appearance of extinct intermediate forms that would throw light on the sequence of evolutionary events leading to the extant groups. Such data can be supplied from the fossil record, notably those deposits with exceptional soft-part preservation. Excavations near Kunming in southwestern China have revealed a variety of remarkable early deuterostomes, including the vetulicolians and yunnanozoans. Here we describe a new group, the vetulocystids. They appear to have similarities not only to the vetulicolians but also to the homalozoans, a bizarre group of primitive echinoderms whose phylogenetic position has been highly controversial.     

Conservation and elaboration of Hox gene regulation during evolution of the vertebrate head

The comparison of Hox genes between vertebrates and their closest invertebrate relatives (amphioxus and ascidia) highlights two derived features of Hox genes in vertebrates: duplication of the Hox gene cluster, and an elaboration of Hox expression patterns and roles compared with non-vertebrate chordates. We have investigated how new expression domains and their associated developmental functions evolved, by testing the cis-regulatory activity of genomic DNA fragments from the cephalochordate amphioxus Hox cluster in transgenic mouse and chick embryos. Here we present evidence for the conservation of cis-regulatory mechanisms controlling gene expression in the neural tube for half a billion years of evolution, including a dependence on retinoic acid signalling. We also identify amphioxus Hox gene regulatory elements that drive spatially localized expression in vertebrate neural crest cells, in derivatives of neurogenic placodes and in branchial arches, despite the fact that cephalochordates lack both neural crest and neurogenic placodes. This implies an elaboration of cis-regulatory elements in the Hox gene cluster of vertebrate ancestors during the evolution of craniofacial patterning.     

An Early Cambrian tunicate from China

Like the Burgess Shales of Canada, the Chengjiang Lagerst?tte from the Lower Cambrian of China is renowned for the detailed preservation as fossils of delicate, soft-bodied creatures, providing an insight into the Cambrian explosion. The fossils of possible hemichordate chordates and vertebrates have attracted particular attention. Tunicates, or urochordates, comprise the most basal chordate clade, and details of their evolution could be important in understanding the sequence of character acquisition that led to the emergence of chordates and vertebrates. However, definitive fossils of tunicates from the Cambrian are scarce or debatable. Here we report a probable tunicate Cheungkongella ancestralis from the Chengjiang fauna. It resembles the extant ascidian tunicate genus Styela whose morphology could be useful in understanding the origin of the vertebrates.     

Broad phylogenomic sampling improves resolution of the animal tree of life

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.     

Paired gill slits in a fossil with a calcite skeleton

The chordates, hemichordates (such as acorn worms) and echinoderms (such as starfish) comprise the group Deuterostomia, well established as monophyletic. Among extant deuterostomes, a skeleton in which each plate has the crystallographic structure of a single crystal of calcite is characteristic of echinoderms and is always associated with radial symmetry and never with gill slits. Among fossils, however, such a skeleton sometimes occurs without radial symmetry. This is true of Jaekelocarpus oklahomensis, from the Upper Carboniferous of Oklahoma, USA, which, being externally almost bilaterally symmetrical, is traditionally placed in the group Mitrata (Ordovician to Carboniferous periods, 530-280 million years ago), by contrast with the bizarrely asymmetrical Cornuta (Cambrian to Ordovician periods, 540 to 440 million years ago). Using computer X-ray microtomography, we describe the anatomy of Jaekelocarpus in greater detail than formerly possible, reveal evidence of paired gill slits internally and interpret its functional anatomy. On this basis we suggest its phylogenetic position within the deuterostomes.     

Reproduction: widespread cloning in echinoderm larvae

Asexual reproduction by free-living invertebrate larvae is a rare and enigmatic phenomenon and, although it is known to occur in sea stars and brittle stars, it has not been detected in other echinoderms despite more than a century of intensive study. Here we describe spontaneous larval cloning in three species from two more echinoderm classes: a sea cucumber (Holothuroidea), a sand dollar and a sea urchin (Echinoidea). Larval cloning may therefore be an ancient ability of echinoderms and possibly of deutero-stomes - the group that includes echinoderms, acorn worms, sea squirts and vertebrates.     

Migratory neural crest-like cells form body pigmentation in a urochordate embryo

The neural crest, a source of many different cell types in vertebrate embryos, has not been identified in other chordates. Current opinion therefore holds that neural crest cells were a vertebrate innovation. Here we describe a migratory cell population resembling neural crest cells in the ascidian urochordate Ecteinascidia turbinata. Labelling of embryos and larvae with the vital lipophilic dye DiI enabled us to detect cells that emerge from the neural tube, migrate into the body wall and siphon primordia, and subsequently differentiate as pigment cells. These cells express HNK-1 antigen and Zic gene markers of vertebrate neural crest cells. The results suggest that migratory cells with some of the features of neural crest cells are present in the urochordates. Thus, we propose a hypothesis for neural crest evolution beginning with the release of migratory cells from the CNS to produce body pigmentation in the common ancestor of the urochordates and vertebrates. These cells may have gained additional functions or were joined by other cell types to generate the variety of derivatives typical of the vertebrate neural crest.     

A paleontological perspective of vertebrate origin

The Early Cambrian Haikouichthys and Haikouella have been claimed to be related to contribute in an important way to our understanding of vertebrate origin,but there have been heated debates about how exactly they are to be interpreted. New discoveries of numerous specimens of Haikouichthys not only confirm the identity of previously described structures such as the dorsal and the ventral fins, and chevron-shaped myomeres, but also reveal many new important characteristics, including sensory organs of the head (e.g. large eyes), and a prominent notochord with differentiated vertebral elements. This “first fish” appears, however, to retain primitive reproductive features of acraniates, suggesting that it is a stem-group craniates. A new order (Myllokunmingiida) and a new family (Myllokunmingiidae) are erected, and a new species, Zhongjianichthys rostratus (gen. et sp. nov.), is described herein. Over 1400 newly-discovered specimens of Haikouella provide a wealth of anatomical information on this organism. It differs from chordates in many organs and organ systems, including the skin, muscles, respiratory, circulatory and nervous systems.In contrast, its body-design resembles that of vetulicolians,and the presence of a “transitional” nervous system with both dorsal and ventral nerve cords suggests an affinity with living hemichordates. On the basis of these and other recent findings of fossil deuterostomes, a five-step hypothesis for vertebrate origin is proposed, intended to bridge the long-standing gap between protostomes and vertebrates. Four of the five steps accord with established ideas current in modern evolutionary zoology. Evidence for the first step is obtainable only from fossils, and specifically from fossils found from South China, hence the crucial importance of S. China sites for our understanding of early vertebrate origins and evolution. Accordingly, South China is suggested as the oldest-known birthplace of the whole vertebrates.     

Yunnanozoon是半索动物的远祖

对澄江化石库中Ｙｕｎｎａｎｏｚｏｏｎ（云南虫）重新研究表明，其身体由吻、邻和躯干三部发构成；躯干前段为具有成对鳃孔的咽腔，后段为消化区这种独特的身体造型与现生肠鳃类半索动物几无二致，从鸸 有明这个早寒武世动物是地球上半索动物门中书已知最古老的祖先类型。     

Mitochondrial protein phylogeny joins myriapods with chelicerates

The animal phylum Arthropoda is very useful for the study of body plan evolution given its abundance of morphologically diverse species and our profound understanding of Drosophila development. However, there is a lack of consistently resolved phylogenetic relationships between the four extant arthropod subphyla, Hexapoda, Myriapoda, Chelicerata and Crustacea. Recent molecular studies have strongly supported a sister group relationship between Hexapoda and Crustacea, but have not resolved the phylogenetic position of Chelicerata and Myriapoda. Here we sequence the mitochondrial genome of the centipede species Lithobius forficatus and investigate its phylogenetic information content. Molecular phylogenetic analysis of conserved regions from the arthropod mitochondrial proteome yields highly resolved and congruent trees. We also find that a sister group relationship between Myriapoda and Chelicerata is strongly supported. We propose a model to explain the apparently parallel evolution of similar head morphologies in insects and myriapods.     

Machaeridians are Palaeozoic armoured annelids

The systematic affinities of several Palaeozoic skeletal taxa were only resolved when their soft-tissue morphology was revealed by the discovery of exceptionally preserved specimens. The conodonts provide a classic example, their tooth-like elements having been assigned to various invertebrate and vertebrate groups for more than 125 years until the discovery of their soft tissues revealed them to be crown-group vertebrates. Machaeridians, which are virtually ubiquitous as shell plates in benthic marine shelly assemblages ranging from Early Ordovician (Late Tremadoc) to Carboniferous, have proved no less enigmatic. The Machaeridia comprise three distinct families of worm-like animals, united by the possession of a dorsal skeleton of calcite plates that is rarely found articulated. Since they were first described 150 years ago machaeridians have been allied with barnacles, echinoderms, molluscs or annelids. Here we describe a new machaeridian with preserved soft parts, including parapodia and chaetae, from the Upper Tremadoc of Morocco, demonstrating the annelid affinity of the group. This discovery shows that a lineage of annelids evolved a dorsal skeleton of calcareous plates early in their history; it also resolves the affinities of a group of problematic Palaeozoic invertebrates previously known only from isolated elements and occasional skeletal assemblages.     

Arthropod phylogeny based on eight molecular loci and morphology

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.     

Molecular evidence regarding the origin of echolocation and flight in bats

Bats (order Chiroptera) are one of the few orders of mammals that echolocate and the only group with the capacity for powered flight. The order is subdivided into Microchiroptera and Megachiroptera, with an array of characteristics defining each group, including complex laryngeal echolocation systems in microbats and enhanced visual acuity in megabats. The respective monophylies of the two suborders have been tacitly assumed, although microbat monophyly is uncorroborated by molecular data. Here we present a phylogenetic analysis of bat relationships using DNA sequence data from four nuclear genes and three mitochondrial genes (total of 8,230 base pairs), indicating that microbat families in the superfamily Rhinolophoidea are more closely related to megabats than they are to other microbats. This implies that echolocation systems either evolved independently in rhinolophoids and other microbats or were lost in the evolution of megabats. Our data also reject flying lemur (order Dermoptera) as the bat sister group, indicating that presumed shared derived characters for flying lemurs and bats are convergent features that evolved in association with gliding and flight, respectively.     

Energetic constraints on the diet of terrestrial carnivores

Species in the mammalian order Carnivora exhibit a huge diversity of life histories with body sizes spanning more than three orders of magnitude. Despite this diversity, most terrestrial carnivores can be classified as either feeding on invertebrates and small vertebrates or on large vertebrates. Small carnivores feed predominantly on invertebrates probably because they are a superabundant resource (sometimes 90% of animal biomass); however, intake rates of invertebrate feeders are low, about one tenth of those of vertebrate feeders. Although small carnivores can subsist on this diet because of low absolute energy requirements, invertebrate feeding appears to be unsustainable for larger carnivores. Here we show, by reviewing the most common live prey in carnivore diets, that there is a striking transition from feeding on small prey (less than half of predator mass) to large prey (near predator mass), occurring at predator masses of 21.5-25 kg. We test the hypothesis that this dichotomy is the consequence of mass-related energetic requirements and we determine the predicted maximum mass that an invertebrate diet can sustain. Using a simple energetic model and known invertebrate intake rates, we predict a maximum sustainable mass of 21.5 kg, which matches the point where predators shift from small to large prey.