Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny.

Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.

An open-source, citizen science and machine learning approach to analyse subsea movies.

BACKGROUND: The increasing access to autonomously-operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists who need to apply tools for data management and processing that are efficient, publicly available and easy to use. Such tools are starting to be developed for a wider community and here we present an approach to combine essential analytical functions for analysing large volumes of image data in marine ecological research. NEW INFORMATION: This paper describes the Koster Seafloor Observatory, an open-source approach to analysing large amounts of subsea movie data for marine ecological research. The approach incorporates three distinct modules to: manage and archive the subsea movies, involve citizen scientists to accurately classify the footage and, finally, train and test machine learning algorithms for detection of biological objects. This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. We tested our approach for monitoring cold water corals in a Marine Protected Area in Sweden using videos from remotely-operated vehicles (ROVs). Our study resulted in a machine learning model with an adequate performance, which was entirely trained with classifications provided by citizen scientists. We illustrate the application of machine learning models for automated inventories and monitoring of cold water corals. Our approach shows how citizen science can be used to effectively extract occurrence and abundance data for key ecological species and habitats from underwater footage. We conclude that the combination of open-source tools, citizen science systems, machine learning and high performance computational resources are key to successfully analyse large amounts of underwater imagery in the future.

A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group.

Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air-dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale.

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a 'Big Data' approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence-absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts.

Ascidians are marine filter feeders and harbor diverse microbiota that can exhibit a high degree of host-specificity. Pharyngeal samples of Scandinavian and Mediterranean ascidians were screened for consistently associated bacteria by culture-dependent and -independent approaches. Representatives of the Endozoicomonas (Gammaproteobacteria, Hahellaceae) clade were detected in the ascidian species Ascidiella aspersa, Ascidiella scabra, Botryllus schlosseri, Ciona intestinalis, Styela clava, and multiple Ascidia/Ascidiella spp. In total, Endozoicomonas was detected in more than half of all specimens screened, and in 25-100% of the specimens for each species. The retrieved Endozoicomonas 16S rRNA gene sequences formed an ascidian-specific subclade, whose members were detected by fluorescence in situ hybridization (FISH) as extracellular microcolonies in the pharynx. Two strains of the ascidian-specific Endozoicomonas subclade were isolated in pure culture and characterized. Both strains are chemoorganoheterotrophs and grow on mucin (a mucus glycoprotein). The strains tested negative for cytotoxic or antibacterial activity. Based on these observations, we propose ascidian-associated Endozoicomonas to be commensals, living off the mucus continuously secreted into the pharynx. Members of the ascidian-specific Endozoicomonas subclade were also detected in seawater from the Scandinavian sampling site, which suggests acquisition of the symbionts by horizontal transmission. The combined results indicate a host-specific, yet facultative symbiosis between ascidians and Endozoicomonas.

Description of Endozoicomonas ascidiicola sp. nov., isolated from Scandinavian ascidians.

Two gram-negative, facultative anaerobic, chemoorganoheterotrophic, motile and rod-shaped bacteria, strains AVMART05(T) and KASP37, were isolated from ascidians (Tunicata, Ascidiaceae) of the genus Ascidiella collected at Gullmarsfjord, Sweden. The strains are the first cultured representatives of an ascidian-specific lineage within the genus Endozoicomonas (Gammaproteobacteria, Oceanospirillales, Hahellaceae). Both strains feature three distinct 16S rRNA gene paralogs, with identities of 98.9-99.1% (AVMART05(T)) and 97.7-98.8% (KASP37) between paralogs. The strains are closely related to Endozoicomonas atrinae and Endozoicomonas elysicola, with which they share 97.3-98.0% 16S rRNA gene sequence identity. Digital DNA-DNA hybridization, average nucleotide identity, and tetra-nucleotide correlation analysis indicate that both strains belong to a single species distinct from their closest relatives. Both strains feature similar DNA G+C contents of 46.70mol% (AVMART05(T)) and 44.64mol% (KASP37). The fatty acid patterns of AVMART05(T) and KASP37 are most similar to those of Endozoicomonas euniceicola and Endozoicomonas gorgoniicola. Based on the polyphasic approach, we propose the species Endozoicomonas ascidiicola sp. nov. to accommodate the newly isolated strains. E. ascidiicola sp. nov. is represented by the type strain AVMART05(T) (=DSM 100913(T)=LMG 29095(T)) and strain KASP37 (=DSM 100914=LMG 29096).

Evaluating the potential of ecological niche modelling as a component in marine non-indigenous species risk assessments.

Marine biological invasions have increased with the development of global trading, causing the homogenization of communities and the decline of biodiversity. A main vector is ballast water exchange from shipping. This study evaluates the use of ecological niche modelling (ENM) to predict the spread of 18 non-indigenous species (NIS) along shipping routes and their potential habitat suitability (hot/cold spots) in the Baltic Sea and Northeast Atlantic. Results show that, contrary to current risk assessment methods, temperature and sea ice concentration determine habitat suitability for 61% of species, rather than salinity (11%). We show high habitat suitability for NIS in the Skagerrak and Kattegat, a transitional area for NIS entering or leaving the Baltic Sea. As many cases of NIS introduction in the marine environment are associated with shipping pathways, we explore how ENM can be used to provide valuable information on the potential spread of NIS for ballast water risk assessment.

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control.

The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.

The founding charter of the Genomic Observatories Network.

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

Genomics in marine monitoring: new opportunities for assessing marine health status.

This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.

A decadal view of biodiversity informatics: challenges and priorities.

Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.

Xenoturbella bocki exhibits direct development with similarities to Acoelomorpha.

Xenoturbella bocki, a marine animal with a simple body plan, has recently been suggested to be sister group to the Acoelomorpha, together forming the new phylum Xenacoelomorpha. The phylogenetic position of the phylum is still under debate, either as an early branching bilaterian or as a sister group to the Ambulacraria (hemichordates and echinoderms) within the deuterostomes. Although development has been described for several species of Acoelomorpha, little is known about the life cycle of Xenoturbella. Here we report the embryonic stages of Xenoturbella, and show that it is a direct developer without a feeding larval stage. This mode of development is similar to that of the acoelomorphs, supporting the newly proposed phylum Xenacoelomorpha and suggesting that the last common ancestor of the phylum might have been a direct developer.

The placental analogue and the pattern of sexual reproduction in the cheilostome bryozoan Bicellariella ciliata (Gymnolaemata).

BACKGROUND: Matrotrophy or extraembryonic nutrition - transfer of nutrients from mother to embryo during gestation - is well known and thoroughly studied among vertebrates, but still poorly understood in invertebrates. The current paper focuses on the anatomy and ultrastructure of the oogenesis and placentotrophy as well as formation of the brood chamber (ovicell) in the cheilostome bryozoan Bicellariella ciliata (Linnaeus, 1758). Our research aimed to combine these aspects of the sexual reproduction into an integral picture, highlighting the role of the primitive placenta-like system in the evolution of bryozoan reproductive patterns. RESULTS: Follicular and nutrimentary provisioning of the oocyte occur during oogenesis. Small macrolecithal oocytes are produced, and embryos are nourished in the ovicell via a simple placental analogue (embryophore). Every brooding episode is accompanied by the hypertrophy of the embryophore, which collapses after larval release. Nutrients are released and uptaken by exocytosis (embryophore) and endocytosis (embryo). Embryos lack specialized area for nutrient uptake, which occurs through the whole epidermal surface. The volume increase between the ripe oocyte and the larva is ca. 10-fold. CONCLUSIONS: The ovicell is a complex organ (not a special polymorph as often thought) consisting of an ooecium (protective capsule) and an ooecial vesicle (plugging the entrance to the brooding cavity) that develop from the distal and the fertile zooid correspondingly. Combination of macrolecithal oogenesis and extraembryonic nutrition allows attributing B. ciliata to species with reproductive pattern IV. However, since its oocytes are small, this species represents a previously undescribed variant of this pattern, which appears to represent a transitional state from the insipient matrotrophy (with large macrolecithal eggs) to substantial one (with small microlecithal ones). Altogether, our results substantially added and corrected the data obtained by the previous authors, providing a new insight in our understanding of the evolution of matrotrophy in invertebrates.

Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species.

Horseshoe crabs are marine invertebrates well known for their exceptionally low rates of diversification during their entire evolutionary history. Despite the low species diversity in the group, the phylogenetic relationships among the extant species, especially among the three Asian species are still unresolved. Here we apply a new set of molecular genetic data in combination with a wide geographic sampling of the intra-specific diversity to reinvestigate the evolutionary history among the four living limulid xiphosurans. Our analysis of the intraspecific diversity reveals low levels of connectivity among Carcinoscorpius rotundicauda lineages, which can be explained by the estuarine-bound ecology of this species. Moreover, a clear genetic break across the Thai-Malay Peninsula suggests the presence of cryptic species in C. rotundicauda. The limulid phylogeny finds strong support for a monophyletic genus Tachypleus and a diversification of the three Asian species during the Paleogene period, with speciation events well separated in time by several million years. The tree topology suggests that the three Asian species originated in central South East Asia from a marine stem group that inhabited the shallow coastal waters between the Andaman Sea, Vietnam, and Borneo. In this region C. rotundicauda probably separated from the Tachypleus stem group by invading estuarine habitats, while Tachypleus tridentatus most likely migrated northeast along the Southern coast of China and towards Japan.

Potential for clonal animals in longevity and ageing studies.

Ageing is defined as a decline in reproductive and/or somatic performance over time, and as such is experienced by most organisms. Evolutionary theories explain ageing as a consequence of reduced selection pressure against mutations and reduced allocation to somatic maintenance in post-reproductive individuals. In addition, the fecundity of younger age-groups makes a more significant contribution than infinite maintenance of the parental body to the production of subsequent generations. However, in clonal animals, as well as in plants that reproduce by agametic cloning, the adult body is itself a reproductive unit that increases its fitness as a function of genet size. Given the apparent longevity of many such clonal organisms, species undergoing agametic cloning are often assumed to be non-ageing and even potentially immortal. Here, we present a brief overview of ageing in organisms undergoing agametic cloning, focusing on animals and molecular investigation. We discuss molecular and evolutionary aspects of ageing or non-ageing with respect to selection in clonal species. Of particular relevance to the search for potential mechanistic processes behind longevity is the notion that clonal organisms are frequently smaller than their obligate sexual counterparts. In conclusion, we find that while clonal animals also commonly age, evolutionary arguments together with empirical evidence suggest that they are likely to be long-lived and stress resistant at the genet level. However, theoretical modeling continues to predict the possibility of immortality, if the contribution from sexual reproduction is low. Future in-depth study of long-lived clones should present an excellent opportunity to discover novel mechanisms for renewal and long-term somatic maintenance and health.

Population dynamics of American horseshoe crabs--historic climatic events and recent anthropogenic pressures.

Populations of the American horseshoe crab, Limulus polyphemus, have declined, but neither the causes nor the magnitude are fully understood. In order to evaluate historic demography, variation at 12 microsatellite DNA loci surveyed in 1218 L. polyphemus sampled from 28 localities was analysed with Bayesian coalescent-based methods. The analysis showed strong declines in population sizes throughout the species' distribution except in the geographically isolated southern-most population in Mexico, where a strong increase in population size was inferred. Analyses suggested that demographic changes in the core of the distribution occurred in association with the recolonization after the Ice Age and also by anthropogenic effects, such as the past overharvest of the species for fertilizer or the current use of the animals as bait for American eel (Anguilla rostrata) and whelk (Busycon spp.) fisheries. This study highlights the importance of considering both climatic changes and anthropogenic effects in efforts to understand population dynamics--a topic which is highly relevant in the ongoing assessments of the effects of climate change and overharvest.

The first internal molecular phylogeny of the animal phylum Entoprocta (Kamptozoa).

This article provides the first molecular phylogenetic study of the enigmatic invertebrate phylum Entoprocta and was designed to resolve the internal phylogenetic relationships of the taxon. The study is based on partial and combined analyses of the mitochondrial gene cytochrome c oxidase subunit I (COI), as well as the nuclear ribosomal genes 28S rDNA and 18S rDNA. A short morphological character matrix was constructed to trace character evolution along the combined molecular phylogenetic tree. The combined analyses of all three genes strongly support the monophyly of the phylum Entoprocta and a sister group relationship of Entoprocta and Cycliophora, a result which is consistent with a number of previous morphological and molecular assessments. We find evidence for two separate lineages within the Entoprocta, one lineage leading to all recent colonial taxa, Coloniales, another representing the clade of solitary entoprocts, Solitaria. Our study suggests that Loxosomella is a paraphyletic assembly with regard to the genera Loxomitra, Loxosoma, and Loxocorone. The results imply that the ancestral entoproct was a solitary, marine organism with an epizoic life style. The groundplan of the entoproct adult stage probably included a bilobed centralized nervous system, and the larva was assumedly planktonic, with a gut and a ciliated creeping sole.

Two types of endosymbiotic bacteria in the enigmatic marine worm Xenoturbella bocki.

Two types of endosymbiotic bacteria were identified in the gastrodermis of the marine invertebrate Xenoturbella bocki (Xenoturbellida, Bilateria). While previously described Chlamydia-like endosymbionts were rare, Gammaproteobacteria distantly related to other endosymbionts and pathogens were abundant. The endosymbionts should be considered when interpreting the poorly understood ecology and evolution of Xenoturbella.

Assessing the root of bilaterian animals with scalable phylogenomic methods.

A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.