A Silurian armoured aplacophoran and implications for molluscan phylogeny

A Cambrian spiny stem mollusk and the deep homology of lophotrochozoan scleritomes

Mollusks encompass enormous disparity, including familiar clams and snails alongside less familiar aculiferans (chitons and vermiform aplacophorans) with complex multicomponent skeletons. Paleozoic fossils trace crown mollusks to forms exhibiting a combination of biomineralized shells and sclerites (e.g., scales, spines, and spicules). We describe a shell-less, Cambrian stem mollusk, Shishania aculeata gen. et sp. nov., with conical, hollow chitinous sclerites and a smooth girdle, broad foot, and mantle cavity. The sclerites have a microstructure of narrow canals consistent with the impressions of chaetal microvilli found in annelids and brachiopods. Shishania sclerites provide a morphological stepping stone between typical chaetae (chitinous bristles) and the external organic part of aculiferan sclerites that encloses a mineralized body. This discovery reinforces a common origin of lophotrochozoan chaetae and the biomineralized aculiferan sclerites, suggesting that the mollusk ancestor was densely covered with hollow chitinous chaetae.

Vestigial organs alter fossil placements in an ancient group of terrestrial chelicerates

Vestigial organs provide a link between ancient and modern traits and therefore have great potential to resolve the phylogeny of contentious fossils that bear features not seen in extant species. Here we show that extant daddy-longlegs (Arachnida, Opiliones), a group once thought to possess only one pair of eyes, in fact additionally retain a pair of vestigial median eyes and a pair of vestigial lateral eyes. Neuroanatomical gene expression surveys of eye-patterning transcription factors, opsins, and other structural proteins in the daddy-longlegs Phalangium opilio show that the vestigial median and lateral eyes innervate regions of the brain positionally homologous to the median and lateral eye neuropils, respectively, of chelicerate groups like spiders and horseshoe crabs. Gene silencing of eyes absent shows that the vestigial eyes are under the control of the retinal determination gene network. Gene silencing of dachshund disrupts the lateral eyes, but not the median eyes, paralleling loss-of-function phenotypes in insect models. The existence of lateral eyes in extant daddy-longlegs bears upon the placement of the oldest harvestmen fossils, a putative stem group that possessed both a pair of median eyes and a pair of lateral eyes. Phylogenetic analysis of harvestman relationships with an updated understanding of lateral eye incidence resolved the four-eyed fossil group as a member of the extant daddy-longlegs suborder, which in turn resulted in older estimated ages of harvestman diversification. This work underscores that developmental vestiges in extant taxa can influence our understanding of character evolution, placement of fossils, and inference of divergence times.

The Cambrian cirratuliform Iotuba denotes an early annelid radiation

The principal animal lineages (phyla) diverged in the Cambrian, but most diversity at lower taxonomic ranks arose more gradually over the subsequent 500 Myr. Annelid worms seem to exemplify this pattern, based on molecular analyses and the fossil record: Cambrian Burgess Shale-type deposits host a single, early-diverging crown-group annelid alongside a morphologically and taxonomically conservative stem group; the polychaete sub-classes diverge in the Ordovician; and many orders and families are first documented in Carboniferous Lagerstätten. Fifteen new fossils of the 'phoronid' Iotuba (=Eophoronis) chengjiangensis from the early Cambrian Chengjiang Lagerstätte challenge this picture. A chaetal cephalic cage surrounds a retractile head with branchial plates, affiliating Iotuba with the derived polychaete families 'Flabelligeridae' and Acrocirridae. Unless this similarity represents profound convergent evolution, this relationship would pull back the origin of the nested crown groups of Cirratuliformia, Sedentaria and Pleistoannelida by tens of millions of years-indicating a dramatic unseen origin of modern annelid diversity in the heat of the Cambrian 'explosion'.

A Cambrian tommotiid preserving soft tissues reveals the metameric ancestry of lophophorates

Among extant animals, Lophotrochozoa accounts for the majority of phyla.¹ This bilaterian clade radiated rapidly during the Cambrian explosion, obfuscating its phylogenetic relationships and rendering many aspects of its early evolution uncertain. Many early lophotrochozoans are known only from isolated skeletal microfossils, "small shelly fossils," often derived from larger animals with complex multi-element skeletons.² The discovery of articulated fossils has revealed surprising insights into the animals from which these skeletal pieces were derived, such as paired shells in the mollusc Halkieria.³ Tommotiids are a key group of phosphatic early skeletal fossils that first appear in the late early Cambrian.^4,5 Although their affinities were previously obscure, discoveries of partial scleritomes and investigations of growth and microstructure⁶ provide links with Brachiopoda^7,8 and Phoronida,⁹ two of the lophophorate phyla. By contrast, the body plan of camenellan tommotiids remains a palaeontological mystery, with hypothetical reconstructions representing motile, benthic, dorsally armored worms.^4,10 Here, we describe an articulated camenellan (Wufengella bengtsoni gen. et sp. nov.) from the Cambrian Chengjiang Biota, China, revealing the morphology of the scleritome and the first soft tissues from an adult tommotiid. Wufengella carries two dorsal rows of sclerites in a highly asymmetric arrangement, flanked by smaller, cap-shaped sclerites. The scleritome was fringed by iterated fascicles of chaetae and two layers of flattened lobes. Phylogenetic analysis confirms that camenellans occupy a deep branch in lophophorate phylogeny, prior to the acquisition of a sessile lifestyle. Wufengella reveals direct evidence for a metameric body plan reminiscent of annelids early in the evolutionary history of lophophorates.^11,12.

Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster without a foot

Recent molecular phylogenetic investigations strongly supported the placement of the shell-less, worm-shaped aplacophoran molluscs (Solenogastres and Caudofoveata) and chitons (Polyplacophora) in a clade called Aculifera, which is the sister taxon of all other molluscs. Thus, understanding the evolutionary history of aculiferan molluscs is important for understanding early molluscan evolution. In particular, fundamental questions about evolutionary relationships within Aplacophora have long been unanswered. Here, we supplemented the paucity of available data with transcriptomes from 25 aculiferans and conducted phylogenomic analyses on datasets with up to 525 genes and 75 914 amino acid positions. Our results indicate that aplacophoran taxonomy requires revision as several traditionally recognized groups are non-monophyletic. Most notably, Cavibelonia, the solenogaster taxon defined by hollow sclerites, is polyphyletic, suggesting parallel evolution of hollow sclerites in multiple lineages. Moreover, we describe Apodomenia enigmatica sp. nov., a bizarre new species that appears to be a morphological intermediate between Solenogastres and Caudofoveata. This animal is not a missing link, however; molecular and morphological studies show that it is a derived solenogaster that lacks a foot, mantle cavity and radula. Taken together, these results shed light on the evolutionary history of Aplacophora and reveal a surprising degree of morphological plasticity within the group.

A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

BACKGROUND

Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, particularly those addressing the relationships among the major chiton lineages.

RESULTS

Here, we present a mitogenomic phylogeny of chitons based on 13 newly sequenced mitochondrial genomes along with eight available ones and RNAseq-derived mitochondrial sequences from four additional species. Reconstructed phylogenies largely agreed with the latest advances in chiton systematics and integrative taxonomy but we identified some conflicts that call for taxonomic revisions. Despite an overall conserved gene order in chiton mitogenomes, we described three new rearrangements that might have taxonomic utility and reconstructed the most likely scenario of gene order change in this group. Our phylogeny was time-calibrated using various fossils and relaxed molecular clocks, and the robustness of these analyses was assessed with several sensitivity analyses. The inferred ages largely agreed with previous molecular clock estimates and the fossil record, but we also noted that the ambiguities inherent to the chiton fossil record might confound molecular clock analyses.

CONCLUSIONS

In light of the reconstructed time-calibrated framework, we discuss the evolution of key morphological features and call for a continued effort towards clarifying the phylogeny and evolution of chitons.

Ultrastructural Analysis of Human Gallstones using Synchrotron Radiation µCT

OBJECTIVE

Gallstone formation is a pathological process of mineralization in the human body. Determination of the morphology and ultrastructure of gallstones holds the key to understanding the pathophysiology of gallbladder disease. Synchrotron radiation phase-contrast Xray microtomography is a novel technology, which is designed for comprehensive analysis of gallstone ultrastructure.

MATERIALS AND METHODS

Nine human gallstones were obtained from the Department of Pathology, Qingpu branch of Zhongshan Hospital Affiliated to Fudan University (China), and scanned by synchrotron radiation µCT (SR µCT). The imaging data generated by SR µCT scan were analyzed.

RESULTS

The three-dimensional ultrastructure of human gallstones corresponding to their cholesterol and bile pigment composition was determined.

CONCLUSIONS

The ultrastructure of gallstones exhibits considerable diversity and complexity. The synchrotron radiation phase-contrast X-ray microtomography is a valuable tool for in-depth study of human gallstones.

The evolution of molluscs

Molluscs are extremely diverse invertebrate animals with a rich fossil record, highly divergent life cycles, and considerable economical and ecological importance. Key representatives include worm-like aplacophorans, armoured groups (e.g. polyplacophorans, gastropods, bivalves) and the highly complex cephalopods. Molluscan origins and evolution of their different phenotypes have largely remained unresolved, but significant progress has been made over recent years. Phylogenomic studies revealed a dichotomy of the phylum, resulting in Aculifera (shell-less aplacophorans and multi-shelled polyplacophorans) and Conchifera (all other, primarily uni-shelled groups). This challenged traditional hypotheses that proposed that molluscs gradually evolved complex phenotypes from simple, worm-like animals, a view that is corroborated by developmental studies that showed that aplacophorans are secondarily simplified. Gene expression data indicate that key regulators involved in anterior-posterior patterning (the homeobox-containing Hox genes) lost this function and were co-opted into the evolution of taxon-specific novelties in conchiferans. While the bone morphogenetic protein (BMP)/decapentaplegic (Dpp) signalling pathway, that mediates dorso-ventral axis formation, and molecular components that establish chirality appear to be more conserved between molluscs and other metazoans, variations from the common scheme occur within molluscan sublineages. The deviation of various molluscs from developmental pathways that otherwise appear widely conserved among metazoans provides novel hypotheses on molluscan evolution that can be tested with genome editing tools such as the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein9) system.

Molecular phylogeny of Caudofoveata (Mollusca) challenges traditional views

The shell-less, worm-shaped Caudofoveata (=Chaetodermomorpha) is one of the least known groups of molluscs. The taxon consists of 141 recognized species found from intertidal environments to the deep-sea where they live burrowing in sediment. Evolutionary relationships of the group have been debated, but few studies based on morphological or molecular data have investigated the phylogeny of the group. Here we use molecular phylogenetics to resolve relationships among and within families of Caudofoveata. Phylogenetic analyses were performed using selected mitochondrial and nuclear genes from species from all recognized families of Caudofoveata. In resulting trees and contrary to traditional views, Prochaetodermatidae forms the sister clade to a clade containing the other two currently recognized families, Chaetodermatidae and Limifossoridae. The monophyly of Prochaetodermatidae is highly supported, but Limifossoridae and Chaetodermatidae are not recovered as monophyletic. Most of the caudofoveate genera are also not recovered as monophyletic in our analyses. Thus results from our molecular data suggest that the current classification of Caudofoveata is in need of revision, and indicate evolutionary scenarios that differ from previously proposed hypotheses based on morphology.

Mitogenomics reveals phylogenetic relationships of caudofoveate aplacophoran molluscs

The worm-shaped, shell-less aplacophoran molluscs Caudofoveata and Solenogastres have recently received attention as part of the clade Aculifera, but relationships within these two lineages are still largely unknown. Here, we use complete mitochondrial genomes to shed light on higher-level relationships within Caudofoveata. Mitochondrial genomes have been sequenced for many diverse molluscs, but only two mitochondrial genomes from aplacophoran molluscs (the caudofoveates Scutopus ventrolineatus and Chaetoderma nitidulum) are available to date. We sequenced and assembled complete or near complete mitochondrial genomes of five additional species of Caudofoveata (Falcidens acutargatus, Falcidens halanychi, Scutopus robustus, Psilodens balduri and Spathoderma clenchi) and one species of Solenogastres (Neomenia carinata) for comparison to available mitochondrial genomes of aculiferans. Comparison of mitochondrial gene order among different lineages revealed a highly conserved order of protein coding genes corresponding to the hypothesized ancestral gene order for Mollusca. Unique arrangements of tRNAs were found among lineages of aculiferan molluscs as well as among caudofoveate taxa. Phylogenetic analyses of amino acid sequences for the 13 protein-coding genes recovered a monophyletic Aplacophora. Within Caudofoveata, Chaetodermatidae, but not Limifossoridae, was recovered monophyletic. Taken together, our results suggest that mitochondrial genomes can serve as useful molecular markers for aculiferan phylogenetics, especially for more recent phylogenetic events.

Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data

Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.

Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data

Fossil taxa are critical to inferences of historical diversity and the origins of modern biodiversity, but realizing their evolutionary significance is contingent on restoring fossil species to their correct position within the tree of life. For most fossil species, morphology is the only source of data for phylogenetic inference; this has traditionally been analysed using parsimony, the predominance of which is currently challenged by the development of probabilistic models that achieve greater phylogenetic accuracy. Here, based on simulated and empirical datasets, we explore the relative efficacy of competing phylogenetic methods in terms of clade support. We characterize clade support using bootstrapping for parsimony and Maximum Likelihood, and intrinsic Bayesian posterior probabilities, collapsing branches that exhibit less than 50% support. Ignoring node support, Bayesian inference is the most accurate method in estimating the tree used to simulate the data. After assessing clade support, Bayesian and Maximum Likelihood exhibit comparable levels of accuracy, and parsimony remains the least accurate method. However, Maximum Likelihood is less precise than Bayesian phylogeny estimation, and Bayesian inference recaptures more correct nodes with higher support compared to all other methods, including Maximum Likelihood. We assess the effects of these findings on empirical phylogenies. Our results indicate probabilistic methods should be favoured over parsimony.

Orthrozanclus elongata n. sp. and the significance of sclerite-covered taxa for early trochozoan evolution

Orthrozanclus is a shell-bearing, sclerite covered Cambrian organism of uncertain taxonomic affinity, seemingly representing an intermediate between its fellow problematica Wiwaxia and Halkieria. Attempts to group these slug-like taxa into a single ‘halwaxiid’ clade nevertheless present structural and evolutionary difficulties. Here we report a new species of Orthrozanclus from the early Cambrian Chengjiang Lagerstätte. The scleritome arrangement and constitution in this material corroborates the link between Orthrozanclus and Halkieria, but not with Wiwaxia — and calls into question its purported relationship with molluscs. Instead, the tripartite construction of the halkieriid scleritome finds a more compelling parallel in the camenellan tommotiids, relatives of the brachiopods and phoronids. Such a phylogenetic position would indicate the presence of a scleritome in the common ancestor of the three major trochozoan lineages, Mollusca, Annelida and Brachiozoa. On this view, the absence of fossil Ediacaran sclerites is evidence against any ‘Precambrian prelude’ to the explosive diversification of these phyla in the Cambrian, c. 540–530 million years ago.

A new crustacean from the Herefordshire (Silurian) Lagerstätte, UK, and its significance in malacostracan evolution

Cascolus ravitis gen. et sp. nov. is a three-dimensionally preserved fossil crustacean with soft parts from the Herefordshire (Silurian) Lagerstätte, UK. It is characterized by a head with a head shield and five limb pairs, and a thorax (pereon) with nine appendage-bearing segments followed by an apodous abdomen (pleon). All the appendages except the first are biramous and have a gnathobase. The post-mandibular appendages are similar one to another, and bear petal-shaped epipods that probably functioned as a part of the respiratory-circulatory system. Cladistic analysis resolves the new taxon as a stem-group leptostracan (Malacostraca). This well-preserved arthropod provides novel insights into the evolution of appendage morphology, tagmosis and the possible respiratory-circulatory physiology of a basal malacostracan.

Inferring muscular ground patterns in Bivalvia: Myogenesis in the scallop Nodipecten nodosus

Background

Myogenesis is currently investigated in a number of invertebrate taxa using combined techniques, including fluorescence labeling, confocal microscopy, and 3D imaging, in order to understand anatomical and functional issues and to contribute to evolutionary questions. Although developmental studies on the gross morphology of bivalves have been extensively pursued, organogenesis including muscle development has been scarcely investigated so far.

Results

The present study describes in detail myogenesis in the scallop Nodipecten nodosus (Linnaeus, 1758) during larval and postmetamorphic stages by means of light, electron, and confocal microscopy. The veliger muscle system consists of an anterior adductor muscle, as well as four branched pairs of striated velum retractors and two pairs of striated ventral larval retractors. The pediveliger stage exhibits a considerably elaborated musculature comprising the velum retractors, the future adult foot retractor, mantle (pallial) muscles, and the anterior and posterior adductors, both composed of smooth and striated portions. During metamorphosis, all larval retractors together with the anterior adductor degenerate, resulting in the adult monomyarian condition, whereby the posterior adductor retains both myofiber types. Three muscle groups, i.e., the posterior adductor, foot retractor, and pallial muscles, have their origin prior to metamorphosis and are subsequently remodeled.

Conclusions

Our data suggest a dimyarian condition (i.e., the presence of an anterior and a posterior adductor in the adult) as the basal condition for pectinids. Comparative analysis of myogenesis across Bivalvia strongly argues for ontogenetic and evolutionary independence of larval retractors from the adult musculature, as well as a complex set of larval retractor muscles in the last common bivalve ancestor.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-015-0125-x) contains supplementary material, which is available to authorized users.

New reconstruction of the Wiwaxia scleritome, with data from Chengjiang juveniles

Wiwaxiids are a problematic group of scale-covered lophotrochozoans known from Cambrian Stages 3-5. Their imbricating dorsal scleritome of leaf-like scales has prompted comparison with various annelids and molluscs, and has been used as a template to reconstruct the articulation pattern of isolated Small Shelly Fossils. The first articulated specimens of Wiwaxia from the Cambrian Stage 3 Chengjiang Konservat-Lagerstätte show that the Wiwaxia scleritome comprised nine equivalent transverse rows associated with outgrowths of soft tissue, but did not possess a separate zone of anterior sclerites. This serial construction is fundamentally incompatible with the circumferential disposition of sclerites in early molluscs, but does closely resemble the armature of certain annelids. A deep homology with the annelid scleritome must be reconciled with Wiwaxia's mollusc-like mouthparts and foot; together these point to a deep phylogenetic position, close to the common ancestor of annelids and molluscs.

From complex to simple: myogenesis in an aplacophoran mollusk reveals key traits in aculiferan evolution

Background

Recent studies suggest a bifurcation at the base of Mollusca, resulting in the primarily single-shelled Conchifera (Bivalvia, Gastropoda, Scaphopoda, Monoplacophora, Cephalopoda) and the spicule-bearing Aculifera (Polyplacophora, Neomeniomorpha, Chaetodermomorpha). A recent study revealed a complex larval musculature exclusively shared by Neomeniomorpha and Polyplacophora, supporting a close relationship of both taxa. However, the ontogenetic transition from the complex larval to the simple adult neomeniomorph musculature, which mainly consists of a three-layered body-wall musculature and serially iterated dorsoventral muscles, remains unknown. To close this gap in knowledge, we studied remodeling of the larval musculature during metamorphosis in the neomeniomorph Wirenia argentea. A comparative analysis with a novel data set of a polyplacophoran, Leptochiton asellus, allows us to infer the morphology of the last common ancestor of Aculifera and the evolution of its subclades therefrom.

Results

The complex larval musculature of Wirenia argentea persists through metamorphosis and becomes modified to form two of the three muscle layers of the adult body wall. The innermost longitudinal layer of the three-layered body wall musculature is generated by transformation and expansion of distinct larval longitudinal muscle bundles. The larval ventrolateral muscle strands are remodeled and eventually become the most ventral part of the adult longitudinal layer of the body wall musculature. The paired larval enrolling muscle forms the lateral parts and the former rectus muscle is destined to become the most dorsal part of the longitudinal layer of the body wall musculature. The transient ventromedian muscle is lost during postmetamorphic development.

Conclusions

Postmetamorphic remodeling in W. argentea supports the hypothesis of a complex myoanatomy rather than a three-layered body wall musculature at the base of Aculifera, and thus argues against homology of the body wall musculature of adult Neomeniomorpha and other potential molluscan sister groups. Our data show that the neomeniomorph body wall musculature is a derived condition and not an aculiferan or molluscan plesiomorphy.

Unexpected co-linearity of Hox gene expression in an aculiferan mollusk

BACKGROUND

Mollusca is an extremely diverse animal phylum that includes the aculiferans (worm-like aplacophorans and eight-shelled polyplacophorans) and their sister group, the conchiferans, comprising monoplacophorans, bivalves (clams, mussels), gastropods (snails, slugs), scaphopods (tusk shells) and cephalopods (squids, octopuses). Studies on mollusks have revealed an overall number of 11 Hox genes in seven out of eight molluscan "class"-level taxa, but expression data of key developmental regulators such as homeotic genes are only available for three gastropod and two cephalopod species. These show that Hox genes are involved in the formation of specific features including shell, foot, funnel or tentacles and not in antero-posterior body plan patterning as in most other bilaterian animals. The role of Hox genes in non-conchiferan (i.e., aculiferan) mollusks remains entirely unknown.

RESULTS

Here we present the first data on the expression of seven Hox genes in apolyplacophoran mollusk, Acanthochitona crinita. In A. crinita the Hox genes Acr-Hox1-5, Hox7 and Post2 are expressed in a co-linear pattern along the antero-posterior axis, but not in molluscan-specific features such as the shell or the foot. The expression pattern is restricted to the post-trochal region and the transcripts are present in ecto-, endo- and mesodermal cell layers. Contrary to the situation in gastropods and cephalopods, we did neither find Hox gene expression in distinct neural subsets of A. crinita, nor in its developing shell plates.

CONCLUSIONS

Our analysis and comparison with other lophotrochozoans indicate that the basal role of Hox genes is in antero-posterior axis patterning in mollusks, similar to the vast majority of bilaterian animals, and that this role has been conserved in polyplacophorans, while co-option into patterning of evolutionary novelties emerged either at the base of Conchifera or independently in gastropods and cephalopods. These morphological innovations most likely contributed to the evolutionary success of its representatives, as exemplified by, e.g., the wide ecological range and species richness of gastropods.

The complete mitochondrial genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis

Background

With more than 100000 living species, mollusks are the second most diverse metazoan phylum. The current taxonomic classification of mollusks recognizes eight classes (Neomeniomorpha, Chaetodermomorpha, Polyplacophora, Monoplacophora, Cephalopoda, Gastropoda, Bivalvia, and Scaphopoda) that exhibit very distinct body plans. In the past, phylogenetic relationships among mollusk classes have been contentious due to the lack of indisputable morphological synapomorphies. Fortunately, recent phylogenetic analyses based on multi-gene data sets are rendering promising results. In this regard, mitochondrial genomes have been widely used to reconstruct deep phylogenies. For mollusks, complete mitochondrial genomes are mostly available for gastropods, bivalves, and cephalopods, whereas other less-diverse lineages have few or none reported.

Results

The complete DNA sequence (14662 bp) of the mitochondrial genome of the chaetodermomorph Scutopus ventrolineatus Salvini-Plawen, 1968 was determined. Compared with other mollusks, the relative position of protein-coding genes in the mitochondrial genome of S. ventrolineatus is very similar to those reported for Polyplacophora, Cephalopoda and early-diverging lineages of Bivalvia and Gastropoda (Vetigastropoda and Neritimorpha; but not Patellogastropoda). The reconstructed phylogenetic tree based on combined mitochondrial and nuclear sequence data recovered monophyletic Aplacophora, Aculifera, and Conchifera. Within the latter, Cephalopoda was the sister group of Gastropoda and Bivalvia + Scaphopoda.

Conclusions

Phylogenetic analyses of mitochondrial sequences showed strong among-lineage rate heterogeneity that produced long-branch attraction biases. Removal of long branches (namely those of bivalves and patellogastropods) ameliorated but not fully resolved the problem. Best results in terms of statistical support were achieved when mitochondrial and nuclear sequence data were concatenated.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0197-9) contains supplementary material, which is available to authorized users.

Mollusc evolution: seven shells on the sea shore

Recent phylogenies unite two seemingly very different groups of mollusc: the Polyplacophora with multiple shells and the shell-less Aplacophora. The finding of seven muscle rows in larvae of both classes suggests that polyplacophoran-like shell rows have been lost in adult Aplacophora.

A virtual world of paleontology

Computer-aided visualization and analysis of fossils has revolutionized the study of extinct organisms. Novel techniques allow fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into their anatomy, development, and preservation. New protocols allow more objective reconstructions of fossil organisms, including soft tissues, from incomplete remains. The resulting digital reconstructions can be used in functional analyses, rigorously testing long-standing hypotheses regarding the paleobiology of extinct organisms. These approaches are transforming our understanding of long-studied fossil groups, and of the narratives of organismal and ecological evolution that have been built upon them.

A new sensory organ in "primitive" molluscs (Polyplacophora: Lepidopleurida), and its context in the nervous system of chitons

Introduction

Chitons (Polyplacophora) are molluscs considered to have a simple nervous system without cephalisation. The position of the class within Mollusca is the topic of extensive debate and neuroanatomical characters can provide new sources of phylogenetic data as well as insights into the fundamental biology of the organisms. We report a new discrete anterior sensory structure in chitons, occurring throughout Lepidopleurida, the order of living chitons that retains plesiomorphic characteristics.

Results

The novel “Schwabe organ” is clearly visible on living animals as a pair of streaks of brown or purplish pigment on the roof of the pallial cavity, lateral to or partly covered by the mouth lappets. We describe the histology and ultrastructure of the anterior nervous system, including the Schwabe organ, in two lepidopleuran chitons using light and electron microscopy. The oesophageal nerve ring is greatly enlarged and displays ganglionic structure, with the neuropil surrounded by neural somata. The Schwabe organ is innervated by the lateral nerve cord, and dense bundles of nerve fibres running through the Schwabe organ epithelium are frequently surrounded by the pigment granules which characterise the organ. Basal cells projecting to the epithelial surface and cells bearing a large number of ciliary structures may be indicative of sensory function. The Schwabe organ is present in all genera within Lepidopleurida (and absent throughout Chitonida) and represents a novel anatomical synapomorphy of the clade.

Conclusions

The Schwabe organ is a pigmented sensory organ, found on the ventral surface of deep-sea and shallow water chitons; although its anatomy is well understood, its function remains unknown. The anterior commissure of the chiton oesophagial nerve ring can be considered a brain. Our thorough review of the chiton central nervous system, and particularly the sensory organs of the pallial cavity, provides a context to interpret neuroanatomical homology and assess this new sense organ.

The continuing debate on deep molluscan phylogeny: evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora)

Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial. We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of five markers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. The recovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages.

Aplacophoran mollusks evolved from ancestors with polyplacophoran-like features

Mollusca is an animal phylum with vast morphological diversity and includes worm-shaped aplacophorans, snails, bivalves, and the complex cephalopods [1]. The interrelationships of these class-level taxa are still contentious [2, 3], but recent phylogenomic analyses suggest a dichotomy at the base of Mollusca, resulting in a monophyletic Aculifera (comprising the shell-less, sclerite-bearing aplacophorans and the eight-shelled polyplacophorans) and Conchifera (all other, primarily univalved groups) [4, 5]. The Aculifera concept has recently gained support via description of the fossil Kulindroplax, which shows both aplacophoran- and polyplacophoran-like features and suggests that the aplacophorans originated from a shelled ancestor [6], but the overall morphology of the last common aculiferan ancestor remains obscure. Here we show that larvae of the aplacophoran Wirenia argentea have several sets of muscles previously known only from polyplacophoran mollusks. Most of these are lost during metamorphosis, and we interpret them as ontogenetic remnants of an ancestor with a complex, polyplacophoran-like musculature. Moreover, we find that the first seven pairs of dorsoventral muscles develop synchronously in Wirenia, similar to juvenile polyplacophorans [7], which supports the conclusions based on the seven-shelled Kulindroplax. Accordingly, we argue that the simple body plan of recent aplacophorans is the result of simplification and does not represent a basal molluscan condition.

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Myoanatomy of aplacophoran larvae is much more complex than that of adults

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Homologous polyplacophoran and aplacophoran muscles support the Aculifera hypothesis

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The last aculiferan ancestor had seven shell plates and associated dorsoventral muscles

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The simple body plan of adult aplacophorans evolved by secondary simplification

Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea?

BACKGROUND

Two theories for the origin of animal life cycles with planktotrophic larvae are now discussed seriously: The terminal addition theory proposes a holopelagic, planktotrophic gastraea as the ancestor of the eumetazoans with addition of benthic adult stages and retention of the planktotrophic stages as larvae, i.e. the ancestral life cycles were indirect. The intercalation theory now proposes a benthic, deposit-feeding gastraea as the bilaterian ancestor with a direct development, and with planktotrophic larvae evolving independently in numerous lineages through specializations of juveniles.

RESULTS

Information from the fossil record, from mapping of developmental types onto known phylogenies, from occurrence of apical organs, and from genetics gives no direct information about the ancestral eumetazoan life cycle; however, there are plenty of examples of evolution from an indirect development to direct development, and no unequivocal example of evolution in the opposite direction. Analyses of scenarios for the two types of evolution are highly informative. The evolution of the indirect spiralian life cycle with a trochophora larva from a planktotrophic gastraea is explained by the trochophora theory as a continuous series of ancestors, where each evolutionary step had an adaptational advantage. The loss of ciliated larvae in the ecdysozoans is associated with the loss of outer ciliated epithelia. A scenario for the intercalation theory shows the origin of the planktotrophic larvae of the spiralians through a series of specializations of the general ciliation of the juvenile. The early steps associated with the enhancement of swimming seem probable, but the following steps which should lead to the complicated downstream-collecting ciliary system are without any advantage, or even seem disadvantageous, until the whole structure is functional. None of the theories account for the origin of the ancestral deuterostome (ambulacrarian) life cycle.

CONCLUSIONS

All the available information is strongly in favor of multiple evolution of non-planktotrophic development, and only the terminal addition theory is in accordance with the Darwinian theory by explaining the evolution through continuous series of adaptational changes. This implies that the ancestor of the eumetazoans was a holopelagic, planktotrophic gastraea, and that the adult stages of cnidarians (sessile) and bilaterians (creeping) were later additions to the life cycle. It further implies that the various larval types are of considerable phylogenetic value.

A Silurian myodocope with preserved soft-parts: cautioning the interpretation of the shell-based ostracod record

Ostracod crustaceans are the most abundant fossil arthropods. The Silurian Pauline avibella gen. et sp. nov., from the Herefordshire Lagerstätte, UK, is an extremely rare Palaeozoic example with soft-part preservation. Based on its soft-part morphology, especially the exceptionally preserved limbs and presence of lateral eyes, it is assigned to the myodocopid myodocopes. The ostracod is very large, with an epipod on the fifth limb pair, as well as gills implying the presence of a heart and an integrated respiratory-circulatory system as in living cylindroleberidid myodocopids. Features of its shell morphology, however, recall halocyprid myodocopes and palaeocopes, encouraging caution in classifying ostracods based on the carapace alone and querying the interpretation of their shell-based fossil record, especially for the Palaeozoic, where some 500 genera are presently assigned to the Palaeocopida.