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 …     

Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida

Deuterostomes comprise vertebrates, the related invertebrate chordates (tunicates and cephalochordates) and three other invertebrate taxa: hemichordates, echinoderms and Xenoturbella. The relationships between invertebrate and vertebrate deuterostomes are clearly important for understanding our own distant origins. Recent phylogenetic studies of chordate classes and a sea urchin have indicated that urochordates might be the closest invertebrate sister group of vertebrates, rather than cephalochordates, as traditionally believed. More remarkable is the suggestion that cephalochordates are closer to echinoderms than to vertebrates and urochordates, meaning that chordates are paraphyletic. To study the relationships among all deuterostome groups, we have assembled an alignment of more than 35,000 homologous amino acids, including new data from a hemichordate, starfish and Xenoturbella. We have also sequenced the mitochondrial genome of Xenoturbella. We support the clades Olfactores (urochordates and vertebrates) and Ambulacraria (hemichordates and echinoderms). Analyses using our new data, however, do not support a cephalochordate and echinoderm grouping and we conclude that chordates are monophyletic. Finally, nuclear and mitochondrial data place Xenoturbella as the sister group of the two ambulacrarian phyla. As such, Xenoturbella is shown to be an independent phylum, Xenoturbellida, bringing the number of living deuterostome phyla to four.     

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.     

Palaeoanatomy and biological affinities of a Cambrian deuterostome (Stylophora)

Stylophora are a peculiar extinct group of asymmetrical deuterostomes whose biological affinity has been fiercely debated. Disarticulated skeletal elements of a ceratocystid stylophoran recovered from the earliest Middle Cambrian of Morocco are not only the oldest stylophorans in the fossil record, but their exceptional preservation provides crucial data on the microstructure of its skeleton. Stylophoran plates are constructed of a three-dimensional mesh, termed 'stereom', identical to that of living echinoderms in which stereom microstructure provides a reliable guide to the nature of the investing soft tissues. Using modern echinoderm anatomy to interpret stereom microstructure of stylophoran elements, here we show that the large proximal lumen of their appendage was filled with muscle and that ligamentary tissues bound distal elements firmly together. We find no evidence for a mouth in the proximal lumen and no evidence that the covering plates of the appendage were articulated. Thus, although skeletal structure suggests that stylophorans are echinoderms, their appendage was not a feeding arm but a muscular locomotory organ.     

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.     

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.     

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.     

'Lophenteropneust' hypothesis refuted by collection and photos of new deep-sea hemichordates

The deep ocean is home to a group of broad-collared hemichordates--the so-called 'lophenteropneusts'--that have been photographed gliding on the sea floor but have not previously been collected. It has been claimed that these worms have collar tentacles and blend morphological features of the two main hemichordate body plans, namely the tentacle-less enteropneusts and the tentacle-bearing pterobranchs. Consequently, lophenteropneusts have been invoked as missing links to suggest that the former evolved into the latter. The most significant aspect of the lophenteropneust hypothesis is its prediction that the fundamental body plan within a basal phylum of deuterostomes was enteropneust-like. The assumption of such an ancestral state influences ideas about the evolution of the vertebrates from the invertebrates. Here we report on the first collected specimen of a broad-collared, deep-sea enteropneust and describe it as a new family, genus and species. The collar, although disproportionately broad, lacks tentacles. In addition, we find no evidence of tentacles in the available deep-sea photographs (published and unpublished) of broad-collared enteropneusts, including those formerly designated as lophenteropneusts. Thus, the lophenteropneust hypothesis was based on misinterpretation of deep-sea photographs of low quality and should no longer be used to support the idea that the enteropneust body plan is basal within the phylum Hemichordata.     

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.     

Primitive deuterostomes from the Chengjiang Lagerst?tte (Lower Cambrian, China).

Cambrian fossil-Lagerst?tten (sites of exceptional fossil preservation), such as those from Chengjiang (Lower Cambrian) and the Burgess Shale (Middle Cambrian), provide our best window into the Cambrian 'explosion'. Such faunas are known from about 40 localities, and have yielded a widely disparate series of taxa ranging from ctenophores to agnathan fish. Recent excavations of the Chengjiang fossil-Lagerst?tte, known from a series of sites near Kunming in Yunnan, south China, have resulted in the discovery of several new forms. In conjunction with material described earlier, these provide evidence for a new group of metazoans, the vetulicolians. Several features, notably a series of gill slits, suggest that this group can throw light on an early stage of deuterostome diversification.     

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.     

Computing Skyline Groups:An Experimental Evaluation

Skyline group, also named as combinational skyline or group-based skyline, has attracted more attention recently. The concept of skyline groups is proposed to address the problem in the inadequacy of the traditional skyline to answer queries that need to analyze not only individual points but also groups of points. Skyline group algorithms aim at finding groups of points that are not dominated by any other same-size groups. Although two types of dominance relationship exist between the groups defined in existing works, they have not been compared systematically under the same experimental framework. Thus, practitioners face difficulty in selecting an appropriate definition. Furthermore, the experimental evaluation in most existing works features a weakness,that is, studies only experimented on small data sets or large data sets with small dimensions. For comprehensive comparisons of the two types of definition and existing algorithms, we evaluate each algorithm in terms of time and space on various synthetic and real data sets. We reveal the characteristics of existing algorithms and provide guidelines on selecting algorithms for different situations.     

Efficient Processing of Skyline Group Queries over a Data Stream

In this paper, we study the skyline group problem over a data stream. An object can dominate another object if it is not worse than the other object on all attributes and is better than the other object on at least one attribute. If an object cannot be dominated by any other object, it is a skyline object. The skyline group problem involves finding k-item groups that cannot be dominated by any other k-item group. Existing algorithms designed to find skyline groups can only process static data. However, data changes as a stream with time in many applications,and algorithms should be designed to support skyline group queries on dynamic data. In this paper, we propose new algorithms to find skyline groups over a data stream. We use data structures, namely a hash table, dominance graph, and matrix, to store dominance information and update results incrementally. We conduct experiments on synthetic datasets to evaluate the performance of the proposed algorithms. The experimental results show that our algorithms can efficiently find skyline groups over a data stream.     

Larval stages of a living sea lily (stalked crinoid echinoderm)

The embryos and larvae of stalked crinoids, which are considered the most basal group of extant echinoderms, have not previously been described. In contrast, much is known about the development of the more accessible stalkless crinoids (feather stars), which are phylogenetically derived from stalked forms. Here we describe the development of a sea lily from fertilization to larval settlement. There are two successive larval stages: the first is a non-feeding auricularia stage with partly longitudinal ciliary bands (similar to the auricularia and bipinnaria larvae of holothurian and asteroid echinoderms, respectively); the second is a doliolaria larva with circumferential ciliary bands (similar to the earliest larval stage of stalkless crinoids). We suggest that a dipleurula-type larva is primitive for echinoderms and is the starting point for the evolution of additional larval forms within the phylum. From a wider evolutionary viewpoint, the demonstration that the most basal kind of echinoderm larva is a dipleurula is consistent with Garstang's auricularia theory for the phylogenetic origin of the chordate neural tube.     

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.     

Eocrinoids from the Cambrian Mantou Formation of Dalian, Liaoning

Cambrian echinoderms,especially eocrinoids,have been reported recently from Guizhou and Yunnan provinces of China,such as the Kaili,Balang,and Guanshan faunas.The present paper reports abundant well-preserved eocrinoids from the Cambrian Mantou Formation of Dalian,Liaoning Province.This new discovery provides additional data on the early evolution of Echinodermata.It also gives us a clue as to where to seek the Cambrian soft-bodied fauna on the margin of the North China Platform.     

Origin of a gene regulatory mechanism in the evolution of echinoderms

A rich diversity of ancient sea urchin lineages survives to the present. These include several advanced orders as well as the cidaroids, which represent the group ancestral to all other sea urchins. Here we show that all advanced groups of sea urchins examined possess in their eggs a class of maternal messenger RNA (mRNA) encoded by the evolutionarily highly conserved alpha-subtype histone genes. The maternal histone mRNAs are unique in their time of accumulation in oogenesis, their localization in the egg nucleus and their delayed timing of translation after fertilization. Cidaroid sea urchins as well as other echinoderm classes, such as starfish and sea cucumbers, possess the genes but do not have maternal alpha-subtype histone mRNAs in their eggs. Thus, although all the echinoderms examined transcribe alpha-subtype histone genes during embryogenesis, the expression of these genes as maternal mRNAs is confined to advanced sea urchins. The fossil record allows us to pinpoint the evolution of this mode of expression of alpha-histone genes to the time of the splitting of advanced sea urchin lineages from the ancestral cidaroids in a radiation which occurred in a relatively brief interval of time approximately 190-200 Myr ago. The origin of a unique gene regulatory mechanism can thus be correlated with a set of macroevolutionary events.     

将Kohonen网络用于估计O－D矩阵的算法研究

Ｏ－Ｄ矩阵通常被看成常数．本文将它作为随机矩阵来研究．在Ｏ－Ｄ矩阵有几种可能取值的假设下，用神经网络中的Ｋｏｈｏｎｅｎ网络及相应的竞争学习算法，估计了Ｏ－Ｄ矩阵的值，并用模拟数据作了验证．结果表明，该算法不仅可以估计Ｏ－Ｄ分布的数值．还可以将交通流量按Ｏ－Ｄ分布的不同来分类，从而为交通控制和交通规划的研究提供了有效的途径．     

Effective leadership and decision-making in animal groups on the move

For animals that forage or travel in groups, making movement decisions often depends on social interactions among group members. However, in many cases, few individuals have pertinent information, such as knowledge about the location of a food source, or of a migration route. Using a simple model we show how information can be transferred within groups both without signalling and when group members do not know which individuals, if any, have information. We reveal that the larger the group the smaller the proportion of informed individuals needed to guide the group, and that only a very small proportion of informed individuals is required to achieve great accuracy. We also demonstrate how groups can make consensus decisions, even though informed individuals do not know whether they are in a majority or minority, how the quality of their information compares with that of others, or even whether there are any other informed individuals. Our model provides new insights into the mechanisms of effective leadership and decision-making in biological systems.     

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.