Unsegmented annelids? Possible origins of four lophotrochozoan worm taxa

In traditional classification schemes, the Annelida consists of the Polychaeta and the Clitellata (the latter including the Oligochaeta and Hirudinida). However, recent analyses suggest that annelids are much more diverse than traditionally believed, and that polychaetes are paraphyletic. Specifically, some lesser-known taxa (previously regarded as separate phyla) appear to fall within the annelid radiation. Abundant molecular, developmental, and morphological data show that the Siboglinidae, which includes the formerly recognized Pogonophora and Vestimentifera, are derived annelids; recent data from the Elongation Factor-1α (EF-1α) gene also suggest that echiurids are of annelid ancestry. Further, the phylogenetic origins of two other lesser-known groups of marine worms, the Myzostomida and Sipuncula, have recently been called into question. Whereas some authors advocate annelid affinities, others argue that these taxa do not fall within the annelid radiation. With advances in our understanding of annelid phylogeny, our perceptions of body plan evolution within the Metazoa are changing. The evolution of segmentation probably is more plastic than traditionally believed. However, as our understanding of organismal evolution is being revised, we are also forced to reconsider the specific characters being examined. Should segmentation be considered a developmental process or an ontological endpoint?     

Parasegmental appendage allocation in annelids and arthropods and the homology of parapodia and arthropodia

The new animal phylogeny disrupts the traditional taxon Articulata (uniting arthropods and annelids) and thus calls into question the homology of the body segments and appendages in the two groups. Recent work in the annelid Platynereis dumerilii has shown that although the set of genes involved in body segmentation is similar in the two groups, the body units of annelids correspond to arthropod parasegments not segments. This challenges traditional ideas about the homology of "segmental" organs in annelids and arthropods, including their appendages. Here I use the expression of engrailed, wingless and Distal-less in the arthropod Artemia franciscana to identify the parasegment boundary and the appendage primordia. I show that the early body organization including the appendage primordia is parasegmental and thus identical to the annelid organization and by deriving the different adult appendages from a common ground plan I suggest that annelid and arthropod appendages are homologous structures despite their different positions in the adult animals. This also has implications for the new animal phylogeny, because it suggests that Urprotostomia was not only parasegmented but also had parasegmental appendages similar to extant annelids, and that limb-less forms in the Protostomia are derived from limb-bearing forms.     

Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach

Even though relationships within Annelida are poorly understood, Eunicida is one of only a few major annelid lineages well supported by morphology. The seven recognized eunicid families possess sclerotized jaws that include mandibles and a maxillary apparatus. The maxillary apparatuses vary in shape and number of elements, and three main types are recognized in extant taxa: ctenognath, labidognath, and prionognath. Ctenognath jaws are usually considered to represent the plesiomorphic state of Eunicida, whereas taxa with labidognath and prionognath are thought to form a derived monophyletic assemblage. However, this hypothesis has never been tested in a statistical framework even though it holds considerable importance for understanding annelid phylogeny and possibly lophotrochozoan evolution because Eunicida has the best annelid fossil record. Therefore, we used maximum likelihood and Bayesian inference approaches to reconstruct Eunicida phylogeny using sequence data from nuclear 18S and 28S rDNA genes and mitochondrial 16S rDNA and cytochrome c oxidase subunit I genes. Additionally, we conducted three different tests to investigate suitability of combining data sets. Incongruence length difference (ILD) and Shimodaira-Hasegawa (SH) test comparisons of resultant trees under different data partitions have been widely used previously but do not give a good indication as to which nodes may be causing the conflict. Thus, we developed a partition addition bootstrap alteration (PABA) approach that evaluates congruence or conflict for any given node by determining how bootstrap scores are altered when different data partitions are added. PABA shows the contribution of each partition to the phylogeny obtained in the combined analysis. Generally, the ILD test performed worse than the other approaches in detecting incongruence. Both PABA and the SH approach indicated the 28S and COI data sets add conflicting signal, but PABA is more informative for elucidating which data partition may be misleading at a given node. All our analyses indicate that the monophyly of the labidognath/prionognath taxa and even a labidognath clade (i.e., a "Eunicidae"/Onuphidae/Lumbrineridae clade) is significantly rejected. We show that the definition of both the labidognath and ctenognath jaw type does not address adequately the variation within Eunicida and thus misleads our current evolutionary understanding. Based on the presented results a symmetric maxillary apparatus with a carrier and four to six maxillae is most likely the plesiomorphic condition for Eunicida. [COI; conflicting data; fossil record; ILD; Jaw Evolution; molecular phylogeny; rDNA; SH test.].     

Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes

Background  

Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. SThe "total-evidence" analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole.     

蜱类系统学研究进展

本文介绍了近年来蜱的编目和分类及系统发育和演化等方面的研究进展。对软蜱科(Argasidae)说明了属的变动;硬蜱科(Ixodidae)介绍了璃眼蜱亚科(Hyalomminae)和凹沟蜱亚科(Bothriocrotoninae)以及相应变动的属(新建的凹沟蜱属Bothriocroton和须角蜱属Cornupalpatum,合并的牛蜱属Boophilus、暗眼蜱属Anocentor和盲花蜱属Aponomma)。根据新的分类变更对已知种类进行了分析。至2006年,世界已知蜱类有3科18属897种,中国有2科10属119种。阐明了有关蜱类系统发育研究的主要观点,并讨论了其不足和有待深入研究的问题。目前,把形态学和分子生物学数据结合在一起的全证据方法,并结合蜱类和不同宿主之间的关系、动物地理学、古生物学以及比较寄生虫学的资料,成为解决蜱类系统发育问题的有效途径。     

The origin of annelids

Annelids are a phylum of segmented bilaterian animals that have become important components of ecosystems spanning terrestrial realms to the deep sea. Annelids are remarkably diverse, possessing high taxonomic diversity and exceptional morphological disparity, and have evolved numerous feeding strategies and ecologies. Their interrelationships and evolution have been the source of much controversy over the past century with the composition of the annelid crown group, the relationship of major groups and the body plan of the ancestral annelid having undergone major recent revisions. There is a convincing body of molecular evidence that polychaetes form a paraphyletic grade and that clitellates are derived polychaetes. The earliest stem group annelids from Cambrian Lagerstätten are errant, epibenthic polychaetes, confirming that biramous parapodia, head appendages and diverse, simple chaetae are primitive for annelids. Current evidence from molecular clocks and the fossil record suggest that crown group annelids are a Late Cambrian – Ordovician radiation, with clitellates radiating in the Late Palaeozoic. Their body fossil record is largely confined to deposits showing exceptional preservation and is punctuated by the acquisition of hard parts in major groups. The discovery of an Ordovician fossil with soft tissues has shown that machaeridians are in fact a clade of crown polychaetes. They were in existence for more than 200 million years and possess unique calcitic dorsal armour, allowing their mode of life and phylogeny to be interpreted in the context of the annelid body plan. We identify a novel clade of machaeridians, the Cuniculepadida, which exhibit a series of adaptations for burrowing.     

果蝇Drosophila saltans种亚组(双翅目:果蝇科)系统发育关系:形态学能否解决分子冲突?(英文)

正确的系统发生重建对于理解进化事件至关重要。尽管分子系统学对于解决此类问题取得了极大的成功,由于一些诸如密码子使用偏性等的内在约束,来源于DNA的信息可能仍然存在着局限。因为发生在祖先的替代性转换,果蝇Drosophila saltans 5个种亚组由不同基因构建的分子系统树之间存在着冲突（在以往发表的分子系统学研究中,这些种组的每一个种亚组至少有一个代表）。本文用40个形态学特征重新分析了这些种组。不同于以前发表的大多数假说,本研究支序分类学的结果表明,果蝇sturtevanti种亚组是一个较早的分支, 而剩下的4个亚组形成一个支持度较高的类群;后者又可以再分为两个姐妹群：一个包含cordata 和elliptica 亚组,另一个包含parasaltans和saltans亚组。本研究结果修正了果蝇saltans种组的分子进化（密码子使用偏性）,并强调形态学对于系统发生重建和理解分子进化现象的重要作用。     

Annelids in evolutionary developmental biology and comparative genomics

Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.     

Phylogeny of Vestimentifera (Siboglinidae, Annelida) inferred from morphology

Vestimentifera, formerly considered a phylum, are here included in the annelid clade Siboglinidae which also encompasses Frenulata and Sclerolinum . All Siboglinidae inhabit reducing habitats, mostly in the deep sea. Vestimentifera are known from hydrothermal vents and cold seeps. Cladistic analyses of vestimentiferan relationships are performed on three levels: (1) among the vestimentiferan species, (2) among the reconstructed ancestral vestimentiferan and other siboglinids and (3) on the level of the families included in the annelidan clade Sabellida. The monophyly of vestimentiferans is confirmed in all analyses. A group of exclusively vent-inhabiting species forms a derived monophyletic clade. The sister group to the vent clade is the Escarpia complex. Lamellibrachia appears to be paraphyletic. Except for the paraphyly of Lamellibrachia , the reconstructed pattern agrees with the molecular phylogeny based on cytochrome c oxidase subunit I. Ancient ridge systems can be invoked to explain modern day geographical distributions. The Pacific Kula Ridge that spanned the Pacific in an east–west direction during the Early Tertiary, may have been a pathway for the ancestor of the vent clade to reach the eastern Pacific. The biogeography is consistent with the recent divergence of Vestimentifera as inferred from molecular data. The reconstructed phylogeny of the Siboglinidae supports the monophyly of the Frenulata and within those, the Thecanephria and Athecanephria. In contrast to molecular and other morphological analyses, Sclerolinum appears as the sister group to the Frenulata. The family level analysis supports the sister group relationship of the Siboglinidae to a clade formed by Sabellariidae, Sabellidae and Serpulidae. Hypothesized homologies of the vestimentiferan obturaculum and vestimentum to structures in related taxa need further investigation.     

One hundred years of instability in ensiferan relationships

Although Ensifera is a major insect model group, its phylogenetic relationships have been understudied so far. Few phylogenetic hypotheses have been proposed, either with morphological or molecular data. The largest dataset ever used for phylogeny reconstruction on this group is molecular (16S rRNA, 18S rRNA and 28S rRNA sequences for 51 ensiferan species), which has been used twice with different resultant topologies. However, only one of these hypotheses has been adopted commonly as a reference classification. Here we re‐analyse this molecular dataset with different methods and parameters to test the robustness and the stability of the adopted phylogeny. Our study reveals the instability of phylogenetic relationships derived from this dataset, especially for the deepest nodes of the group, and suggests some guidelines for future studies. The comparison between the different classifications proposed in the past 70 years for Ensifera and our results allows the identification of potential monophyletic clades (katydids, mole crickets, scaly crickets + Malgasia, true crickets, leaf roller crickets, cave crickets) and the remaining unresolved clades (wetas, Jerusalem crickets and most of the highest rank clades) in Ensifera phylogeny.     

Current status of annelid phylogeny

Annelida is an ecologically and morphologically diverse phylum within the Lophotrochozoa whose members occupy a wide range of environments and show diverse life styles. The phylogeny of this group comprising more than 17,000 species remained controversial for a long time. By using next-generation sequencing and phylogenomic analyses of huge data matrices, it was finally possible to reach a well-supported and resolved annelid backbone tree. Most annelid diversity is comprised in two reciprocal monophyletic groups, Sedentaria and Errantia, which are named after the predominant life style of their members. Errantia include Aciculata (Phyllodocida?+?Eunicida) and Protodriliformia, which is a taxon of interstitial polychaetes. Sedentaria comprise most of the polychaete families formerly classified as Canalipalpata or Scolecida, as well as the Clitellata. Six taxa branch as a basal grade outside of this major radiation: Oweniidae, Magelonidae, Chaetopteridae, Sipuncula, Amphinomida, and Lobatocerebrum. Oweniidae and Magelonidae form a monophyletic group which we name Palaeoannelida, which constitutes the sister taxon of the remaining annelids. The early splits of annelid phylogeny date back to the Cambrian. The new annelid phylogeny highlights the variability and lability of annelid body plans, and many instances of simplifications of body plan as adaptations to new life styles can be found. Therefore, annelids will be an appropriate model to understand major transitions in the evolution of Bilateria in general. Evolutionary developmental studies are one way to investigate macroevolutionary transition in annelids. We briefly summarize the state of developmental model organisms in Annelida and also propose new candidates on the background of the phylogeny.     

The Taxonomy of Sphacelaria cirrosa (Roth.) Ag., Sphacelaria fusca (Huds.) Ag., and Sphacelaria furcigera (Kutz.) Sauv: A Simple Statistical Approach

An attempt has been made to apply some simple statistical techniquesto the taxonomy of a problematical group of species within thegenus Sphacelaria Lyngb. Measurements were carried out on materialcollected from the field, material made available from Herbariumcollections and on material grown under experimental conditionsThe main characteristics considered are cell and filament dimensions,although certain reproductive structures have also been measured. It has been found that the number of longitudinal divisionsin each segment of the main axes and the primary branches hasa profound effect on the over-all appearance of the fronds ofthe three species investigated. Segment length breadth ratioand frond stiffness have been shown to be dependent on the numberof longitudinal walls. This characteristic has enabled one ofthe species, S. cirrosa (Roth) Ag., to be readily distinguishedfrom the other two. Another factor shown to be important is the determinate patternof growth displayed by S. cirrosa as opposed to the indeterminatepattern displayed by S. fusca (Huds ) Ag. and S. furcigera (Kutz.)Sauv. The pattern of growth affects the number of longitudinalwalls, filament width, and the relative lengths of the primarybranches. The angle at which branches emanate from the main axes has beenshown to be a useful characteristic in this group of species. The variability in the number of arms produced by each propagulepresents an interesting problem which has only been described,experimental work suggesting no explanation for this phenomenon.The degree of variability is clearly different in each speciesand is useful taxonomically if a large enough sample is availablefor examination.     

Evolution of the Toxoglossa venom apparatus as inferred by molecular phylogeny of the Terebridae

Toxoglossate marine gastropods, traditionally assigned to thefamilies Conidae, Terebridae, and Turridae, are one of the mostpopulous animal groups that use venom to capture their prey.These marine animals are generally characterized by a venomapparatus that consists of a muscular venom bulb and a tubularvenom gland. The toxoglossan radula, often compared with a hypodermicneedle for its use as a conduit to inject toxins into prey,is considered a major anatomical breakthrough that assistedin the successful initial radiation of these animals in theCretaceous and early Tertiary. The pharmacological success oftoxins from cone snails has made this group a star among biochemistsand neuroscientists, but very little is known about toxins fromthe other Toxoglossa, and the phylogeny of these families islargely in doubt. Here we report the first molecular phylogenyfor the Terebridae and use the results to infer the evolutionof the venom apparatus for this group. Our findings indicatethat most of the genera of terebrids are polyphyletic, and onespecies ("Terebra" (s.l.) jungi) is the sister group to allother terebrids. Molecular analyses combined with mapping ofvenom apparatus morphology indicate that the Terebridae havelost the venom apparatus at least twice during their evolution.Species in the genera Terebra and Hastula have the typical venomapparatus found in most toxoglossate gastropods, but all otherterebrid species do not. For venomous organisms, the dual analysisof molecular phylogeny and toxin function is an instructivecombination for unraveling the larger questions of phylogenyand speciation. The results presented here suggest a paradigmshift in the current understanding of terebrid evolution, whilepresenting a road map for discovering novel terebrid toxins,a largely unexplored resource for biomedical research and potentialtherapeutic drug development.     

How our view of animal phylogeny was reshaped by molecular approaches: lessons learned

In the late 1980s, researchers began applying molecular sequencing tools to questions of deep animal phylogeny. These advances in sequencing were accompanied with improvements in computation and phylogenetic methods, and served to significantly reshape our understanding of metazoan evolution. Prior to this time, researchers asserted phylogenetic hypotheses based on their experience with taxa and to some degree, their authority. Molecular phylogenetic tools provided discrete methods and objective characters for reconstructing phylogeny. Nonetheless, major changes to widely accepted views, such as animal phylogeny, take time to be accepted. Development and acceptance of our current understanding of animal evolution occurred in three main phases: initial hypotheses based on 18S data, confirmation with additional molecular markers, and continued refinement with phylogenomics. With the advent of ideas such as Lophotrochozoa and Ecdysozoa, flaws in the traditional view became apparent. We now understand that complex morphological and embryological features (e.g., segmentation, coelom formation, development of body cavities) are much more evolutionarily plastic than previously recognized. Here, I explore how the transition from the traditional to the modern phylogenetic understanding of animal phylogeny occurred and examine some implications of this change in understanding. As the field moves forward, the utility of morphological and embryological characters for reconstruction of deep animal phylogeny should be discouraged. Instead, these characters should be interpreted in the light of independent phylogeny.     

Molecular Genetic Analysis of Ethanol Intoxication in Drosophila melanogaster

Recently, the fruit fly Drosophila melanogaster has been introducedas a model system to study the molecular bases of a varietyof ethanol-induced behaviors. It became immediately apparentthat the behavioral changes elicited by acute ethanol exposureare remarkably similar in flies and mammals. Flies show signsof acute intoxication, which range from locomotor stimulationat low doses to complete sedation at higher doses and they developtolerance upon intermittent ethanol exposure. Genetic screensfor mutants with altered responsiveness to ethanol have beencarried out and a few of the disrupted genes have been identified.This analysis, while still in its early stages, has alreadyrevealed some surprising molecular parallels with mammals. Theavailability of powerful tools for genetic manipulation in Drosophila,together with the high degree of conservation at the genomiclevel, make Drosophila a promising model organism to study themechanism by which ethanol regulates behavior and the mechanismsunderlying the organism's adaptation to long-term ethanol exposure.     

The genus Cervus in eastern Eurasia

In 2004, Christian Pitra and co-workers published the first molecular phylogeny of Old World deer which advanced our understanding of the Cervinae immeasurably by demonstrating the non-monophyletic status of the red deer/wapiti group, the chital/hog deer group and the swamp deer/Eld's deer group. Therefore, many conspicuous external features—antler complexity, mane and rump-patch development—turned out to be related not to phylogeny as much as to climatic-related lifestyle factors. At a lower level, molecular genetics has reinforced some conclusions drawn on the basis of morphology or behaviour. Striking examples are the divisions between mainland and Japanese sika and between northern and southern forms of Japanese sika. In this paper, I will look at the species living in what Pitra et al. (Evolution and phylogeny of old world deer. Mol Phylogenet Evol 33:880–895, 2004) identified as the heartland of cervine evolution: eastern Eurasia. I will consider the two species groups in this region that seem to crystallize both the problems of cervine classification and the ways in which the new sources of evidence have opened up new avenues of inquiry.     

Monoplacophorans and the Origin and Relationships of Mollusks

The story of the discovery and study of the Monoplacophora (or Tryblidia) and how they have contributed to our understanding of the evolution of the Mollusca highlights the importance of integrating data from the fossil record with the study of living forms. Monoplacophora were common in the early Paleozoic and were thought to have become extinct during the Devonian Period, approximately 375 Mya. In the mid 1950s, they were recovered from abyssal depths off of Costa Rica and were immediately heralded as a “living fossil.” The living specimens confirmed that some of the organs (kidneys, heart, and gills) were repeated serially, just like the shell muscles that had been observed in fossil specimens. This supported the hypothesis that they were closely related to other segmented organisms such as annelids and arthropods. Today, there are 29 described living species and a growing body of work examining their anatomy, phylogeny, and ecology. Additional fossil specimens have also been discovered, and what was once thought to be a possible missing link between annelid worms and mollusks now appears to be a highly specialized branch of the molluscan tree that tells us little about the ancestral mollusk condition. However, some assumptions and generalizations from those early days still remain—such as the abyssal nature of the living species. A large part of the evolutionary history of the lineage remains to be discovered and will likely prove more complicated and interesting than afforded by the living fossil designation.     

Challenging received wisdoms: Some contributions of the new microscopy to the new animal phylogeny

Inspired by the emerging new view of animal phylogeny, recentcomparative morphological studies have applied the range ofavailable new and established microscopical techniques to shednew light on many received wisdoms about animal evolution. HereI review some illustrative recent work of the participants inthe symposium "The New Microscopy: Toward a Phylogenetic Synthesis"held at the annual Society for Integrative and Comparative Biologymeeting in San Diego in January 2005. I will discuss 6 casestudies. Of these, 3 have generated new morphological insightsthat are significantly at odds with received wisdom about high-levelanimal phylogeny but congruent with emerging molecular phylogenies.These examples examine the value of characteristics of arthropodneurogenesis in supporting a controversial new hypothesis ofhigh-level arthropod phylogeny, the insights into annelid phylogenyprovided by studies on central nervous system development inclitellates, and how new data on the source of mesoderm in phoronidscorroborates their placement in the Lophotrochozoa. The remaining3 case studies shed new light particularly on the evolutionof important innovations that are at the base of successfulclades. The examples deal with the evolution of torsion as amajor synapomorphy of the gastropods, illustrate how the originof gastrulation could be studied in sponges, and show that trochophorelarvae may characterize a larger clade of spiralians than hithertosuspected.     

基于mtDNA COⅠ基因的十种长小蠹分子系统进化研究（鞘翅目：长小蠹科）

全世界记录的长小蠹（鞘翅目：长小蠹科）有1 500余种,其分类地位一直存在争议。本研究通过分子基因信息探讨长小蠹科昆虫的分子系统进化关系,测定了中对长小蠹Euplatypus parallelus（Fabricius）、希氏长小蠹E. hintzi Schaufuss、散对长小蠹E. solutus Schedl、杯长小蠹Dinoplatypus cupulatus Chapuis、小杯长小蠹D. cupulatulus Schedl、芦苇黄截尾长小蠹D. calamus Blandford、五棘长小蠹Diapus quinquespinatus Chapuis、锥长小蠹Treptoplatypus solidus Walk、栎长小蠹Platypus quercivorus Murayama和东亚长小蠹P. lewisi Blandford等长小蠹科5属10种mtDNA COⅠ基因部分序列（549 bp）;采用MEGA3.1分析了序列组成及遗传距离,应用PAUP4.0分别构建了长小蠹NJ,MP和ML等3种分子系统树,同时结合长小蠹的形态分类,探讨10 种长小蠹及其所在属的系统进化。结果表明：长小蠹科昆虫在碱基使用频率上有很大的偏向性;长小蠹科与外群小蠹科松瘤小蠹Orthotomicus erosus Wollaston之间的遗传距离（0.288～0.338）远大于科内种间距离（0～0.226）;Diapus属分化最早,Euplatypus属独成一支,Treptohlatypus, Dinoplatypus和Platypus 3属分化为一支。长小蠹科分子系统进化研究结果与Wood（1993）新修订的分类系统基本一致,说明长小蠹科的分类系统更趋于合理。