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Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

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Abstract

Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic [1, 2]; alternatively, they have been linked to the complex Ambulacraria (echinoderms and hemichordates) in a clade called the Xenambulacraria [3, 4, 5], suggesting their simplicity evolved by reduction from a complex ancestor. The difficulty resolving this problem implies the phylogenetic signal supporting the correct solution is weak and affected by inadequate modeling, creating a misleading non-phylogenetic signal. The idea that the Nephrozoa hypothesis might be an artifact is prompted by the faster molecular evolutionary rate observed within the Acoelomorpha. Unequal rates of evolution are known to result in the systematic artifact of long branch attraction, which would be predicted to result in an attraction between long-branch acoelomorphs and the outgroup, pulling them toward the root [6]. Other biases inadequately accommodated by the models used can also have strong effects, exacerbated in the context of short internal branches and long terminal branches [7]. We have assembled a large and informative dataset to address this problem. Analyses designed to reduce or to emphasize misleading signals show the Nephrozoa hypothesis is supported under conditions expected to exacerbate errors, and the Xenambulacraria hypothesis is preferred in conditions designed to reduce errors. Our reanalyses of two other recently published datasets [1, 2] produce the same result. We conclude that the Xenacoelomorpha are simplified relatives of the Ambulacraria.

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... This contrasts with consistent, strong support for the monophyly of the protostomes. To study the support for the deuterostome clade in the context of the well-supported protostome clade, we use five recent, independently generated, phylogenomic datasets covering the diversity of animal phyla [i.e., (2)(3)(4)(5)(6)]. We investigate the support for different topologies relating the Chordata, Xenambulacraria, Ecdysozoa, and Lophotrochozoa. ...
... Last, while two datasets support paraphyletic deuterostomes under complex site heterogeneous models (4,5), which account for across-site amino acid preference variability (8), all five datasets support monophyletic deuterostomes when using simpler and less well-fitting site homogeneous models. Unequal rates, faster-evolving loci, and inadequate site homogeneous models are all known to promote LBA artifacts, especially in the context of short internal nodes (1,7,9). ...
... Systematic error is especially likely to affect our ability to reconstruct relationships between taxa separated by the very short branches we have described. Recent work has shown that Xenacoelomorpha are very likely to be the sister group of the Ambulacraria (4,5,18); nevertheless, experiments in which we removed the contentious Xenacoelomorpha did not change the results showing that this controversy should not affect our interpretation of the findings. ...
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The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.
... CAT/CATGTR offers improved resilience to long-branch attraction artefacts (LBA) 22 and is almost always better fitting than standard site-homogeneous amino acid substitution models (e.g. WAG) [8][9][10][23][24][25][26][27][28][29] . This is because, by accommodating sitespecific biochemical constraints, CAT/CATGTR can better detect saturation (i.e. ...
... Recoding is believed to reduce both saturation and compositional heterogeneity 30,31 , and possibly other biasing factors 32 , in amino acid datasets. In fact, when applied to resolve difficult phylogenetic questions, the level of heterogeneity present in recoded data can often be better accommodated by available models than that in the original amino acid data 9,24,33 . As such, recoding is thought to offer improved resilience to both LBA and compositional artefacts. ...
... Taken together, these results indicate that standard partitioned phylogenomics is highly susceptible to LBA, but that both amino acid recoding and better-fitting site-heterogeneous models can mitigate LBA in partitioned phylogenomics. The RL2 findings also support recent efforts pairing recoding and site-heterogeneous models to resolve difficult, ancient nodes in animal phylogeny 5,9,24,33 , despite the erosion of data relevant to more shallow nodes. ...
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Resolving the relationships between the major lineages in the animal tree of life is necessary to understand the origin and evolution of key animal traits. Sponges, characterized by their simple body plan, were traditionally considered the sister group of all other animal lineages, implying a gradual increase in animal complexity from unicellularity to complex multicellularity. However, the availability of genomic data has sparked tremendous controversy as some phylogenomic studies support comb jellies taking this position, requiring secondary loss or independent origins of complex traits. Here we show that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models. Testing on real datasets, we show a great improvement in model-fit that attenuates branching artefacts induced by systematic error. We reanalyse key datasets and show that partitioned phylogenomics does not support comb jellies as sister to other animals at either the supermatrix or partition-specific level.
... While the Ctenophora-first and the Nephrozoa topologies ( Fig. 1) have gained support in independent analyses of large datasets (1)(2)(3)(4)(5)(6), supporters of the alternative topologies (Porifera-first and Xenambulacraria; Fig. 1) have suggested that there is an expectation of a long-branch attraction (LBA) artifact (7)(8)(9). LBA is a systematic error that falsely groups long branches (10), such as those leading to the outgroups and to both the Ctenophora and Xenacoelomorpha. LBA can be exacerbated by the use of substitution models that do not account for heterogeneities in sequence evolution such as nonhomogeneous rates of substitution between alignment sites or heterogeneities in the frequencies of amino acids across the alignment (11)(12)(13)(14). ...
... Attraction between the long branches leading to the Ctenophora and Xenacoelomorpha and to their respective outgroups could result in the Ctenophora-first and Nephrozoa trees. The support seen for Ctenophora-first and Nephrozoa topologies, however, is generally stronger than for the alternatives (8,9). ...
... We have used recently published phylogenomic datasets that were designed to place either the ctenophores [Simion et al. (8); dataset "Simion-all"] or the xenacoelomorphs [Philippe et al. (9) and Cannon et al. (5); datasets "Philippe-all" and " Cannon"] in the animal tree. We ask whether unaccounted-for across-site heterogeneity in amino acid composition might have resulted in model violations that could lead to the underestimation of the prevalence of convergent evolution. ...
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The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives.
... Traditionally, this group of small marine worms have been placed as the primary emerging bilaterian lineage ( Figure 1A), implying a less complex body plan of the most recent common ancestor of Bilateria, with a simple brain, blind gut, and lacking excretory and vascular systems (Ruiz-Trillo et al. 2004;Paps et al. 2009;Ruiz-Trillo & Paps 2016;Hejnol & Pang 2016;Rouse et al. 2016;Cannon et al. 2016). The alternative placements within Deuterostomia ( Figure 1B and C) suggest a secondary simplification of a large number of significant morphological traits in the Xenacoelomorph clade which are considered to be present in the last common ancestor of deuterostomes, i.e. the loss such as complex organ systems, a digestive system with mouth and anus, coeloms, and body compartmentalisation (Bourlat et al. 2003(Bourlat et al. , 2006Philippe, Brinkmann, Copley, et al. 2011;Philippe et al. 2019;Kapli & Telford 2020). More recently, the placement of Xenacoelomorpha within Bilateria has brought into question whether Deuterostomia should be considered monophyletic at all Kapli et al. 2021). ...
... Empirical analyses of newly generated genomic and transcriptomic data continue to produce conflicting placements for Xenacoelomorpha, with support garnered for both the Nephrozoa ( Figure 1A) (Cannon et al. 2016;Rouse et al. 2016) Finding the definitive placement of Xenacoelomorpha is complicated by biological and systematic features of the phylum including high rates of sequence evolution and gene loss within Xenacoelomorpha (particularly within Acoelomorpha), and short internal branches in the deep splitting lineages of Bilateria Kapli et al. 2021). Careful analyses of novel and previously published datasets (Cannon et al. 2016;Rouse et al. 2016) by Philippe et al (2019) attempted to address some of these features by using site heterogeneous models, data re-coding, and the 'best' gene sets based on signal within the gene trees. In doing so they recovered Xenacoelomorpha sister to Ambulacraria plus a paraphyletic Deuterostomia (T3, Figure 1C). ...
... Assessing how various biases in data such as rate and compositional heterogeneity may affect resulting topology has seen model adequacy and fit receive a justifiable level of attention (Morgan et al. 2013;Feuda et al. 2017;Philippe et al. 2019;Kapli & Telford 2020;Redmond & McLysaght 2021). However, the underlying signal within large datasets for phylogeny reconstruction warrants further exploration. ...
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Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum, or within Deuterostomia, sister to Ambulacraria. While their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral Bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. More recently, further studies have brought into question whether Deuterostomia should be considered monophyletic at all. Hidden paralogy presents a major challenge for reconstructing species phylogenies. Here we assess whether hidden paralogy has contributed to the conflict over the placement of Xenacoelomorpha. Our approach assesses previously published datasets, enriching for orthogroups whose gene trees support well resolved clans elsewhere in the animal tree of life. We find that the majority of constituent genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy is rife at this depth. We demonstrate that enrichment for genes with orthologous signal alters the final topology that is inferred, whilst simultaneously improving fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our orthology enriched set of genes. At a time when we are steadily progressing towards sequencing all of life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modelled adequately.
... However, modeling the evolution of amino acid sequences is difficult (Philippe, Brinkmann, Lavrov, et al., 2011;Tihelka et al., 2021). Deep metazoan phylogenies reconstructed from alternative amino acid datasets, or even the same amino acid dataset analysed using different substitution models (Cannon et al., 2016;Philippe et al., 2019;Pisani et al., 2015;Whelan et al., 2015), as well as using different taxon samplings of the ingroup (Dunn et al., 2008;Pick et al., 2010) and the outgroup (Pisani et al., 2015;Whelan et al., 2015), are frequently incongruent. This acknowledged model-and data dependency of phylogenomic analyses underpins the phylogenetic instability observed towards the root of the animal tree (e.g., Dunn et al., 2014). ...
... With a few exceptions (Rouse et al., 2016), Xenacoelomorpha are millimeter-sized and primarily benthic or sediment dwelling bilaterians devoid of a true body cavity and an anus. Xenacoelomorpha has been recovered in different positions in the animal tree: as the sister group of all other bilaterian animals (Nephrozoa) (Cannon et al., 2016;Rouse et al., 2016), or as the sister group of the Ambulacraria (Echinodermata+Hemichordata) constituting the clade Xenambulacraria (Kapli & Telford, 2020;Philippe et al., 2019). ...
... Previous gene content analyses have focussed on the root of the animals. Accordingly, here we primarily focus our LBA assessment on the Xenacoelomorpha by performing taxon exclusion experiments in an approach similar to Philippe et al. (2019). ...
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An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.
... Among the latter, common approaches include the selection of loci with high levels of phylogenetic signal (e.g., Salichos and Rokas 2013) and the removal of those potentially affected by systematic biases (e.g., Nesnidal et al. 2010). However, multiple sources of bias are known (KapLi et al. 2021) and different proxies for signal have been employed (Salichos and Rokas 2013;Salichos et al. 2014;Arcila et al. 2017;Philippe et al. 2019;Vankan et al. 2020), and the downstream consequences of choosing among these are largely unknown. This is further complicated by the fact that sources of bias and proxies for signal can be strongly correlated (Mongiardino Koch and Thompson 2021), such that the optimization of either dimension individually modifies the other in potentially unintended ways. ...
... In case the species tree for the lineages sampled is highly uncertain, an option is available to run the analysis without using RF similarities as input for the PCA. Alternatively, uncertain nodes can be collapsed in the tree used to measure topological distances; taken further this would converge on the approach used by Philippe et al. (2019) to focus only on the recovery of a handful of uncontroversial monophyletic groups. A few different sets of variables were explored, as well as alternative metrics for some of them (such as different tree distances); these changes did not improve the proportion of variance captured by the first two PCs and were not further explored. ...
Article
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Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different datasets. Here, I calculate multiple gene properties for a range of phylogenomic datasets spanning animal, fungal and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared to alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties, and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
... Three acoel genomes with different degrees of completeness have been produced in the last few yearsthose of species Hofstenia miamia ( Gehrke et al. 2019 ), Praesagittifera naikaiensis ( Arimoto et al. 2019 ) and Symsagittifera roscoffensis ( Philippe et al. 2019 ). While the first is quite complete, that of our species is only a preliminary draft. ...
... Strikingly, many of these sequences show specifi c patterns of divergence with respect to the putative orthologs in other bilaterian clades (i.e. Wnts), corroborating the well-known fast rate of evolution of acoel, and in particular Symsagittifera , genomes ( Philippe et al. 2019 ). Moreover, these gene family characterizations provide a source of sequences necessary for the design of probes used in downstream experiments by situ hybridization ( Perea-Atienza et al. 2018 ) or in the identifi cation of BAC clones used in studies of chromosomal mapping ( Moreno et al. 2009 ). ...
... These results suggest that ASICs emerged during early bilaterian evolution, and we next sought evidence for potential biological roles by investigating the expression of ASIC genes in the different bilaterian lineages. The precise relationships between these lineages are under debate, but Xenacoelomorpha forms a putative sister group to all remaining Bilateria [27][28][29][30]. Therefore, we investigated ASIC expression in Xenacoelomorpha, utilizing the acoels Isodiametra pulchra, Hofstenia miamia, and Convolutriloba macropyga. ...
... Excitatory proton-gated currents and broad neuronal expression of ASICs in xenacoelomorphs is reminiscent of vertebrate ASICs. However, whether the ancestral bilaterian ASIC had this role remains unclear, as the position of Xenacoelomorpha as sister taxon of all other bilaterians or as part of a group with hemichordates and echinoderms within Deuterostomia is debated [27][28][29][30]. We therefore turned to the third major lineage of bilaterians and investigated previously unidentified ASICs in Protostomia. ...
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Acid-sensing ion channels (ASICs) are membrane proteins that endow vertebrate neurons with fast excitatory responses to decreases in extracellular pH. Although previous studies suggest that ASICs are found in certain invertebrates, the lineage in which ASICs emerged and the functional role of ASICs beyond the vertebrates is unknown. We reconstructed ASIC evolution by surveying metazoan ASICs and performing a phylogenetic analysis, which suggests that ASICs evolved in an early bilaterian. This was supported by electrophysiological measurements of proton-gated currents at heterologous channels from diverse bilaterians. This also revealed substantial variation in biophysical properties of broadly related ASICs, with selective sodium/potassium ion permeability ranging from 3-to 36-fold and half-maximal activating pH from 4.2 to 8.1. Furthermore, we studied the expression of ASICs in species outside the vertebrates and found expression in the central nervous system of certain bilaterian lineages but in the periphery, including nervous system, digestive system, and motile ciliated epithelia, of most lineages. The loss of such epithelial cells in Ecdysozoa might explain the loss of ASICs from this major animal lineage. Our results suggest that ASICs emerged in an early bilaterian, and expression in the central nervous system was accompanied or even pre-dated by expression in the periphery.
... Such a short deuterostome branch has important consequences for our understanding of character evolution at the base of the Bilateria as (assuming it exists) it implies a short period of time separating the last bilaterian common ancestor (Urbilateria) and the last deuterostome common ancestor (Urdeuterostomia) 4,20 . Hybridisation between lineages following speciation is another process that would blur the distinction between these ancestral taxa. ...
... In all our analyses, we kept the full set of taxa apart from the fast evolving Acoelomorpha species that have been shown to be prone to phylogenetic inference errors 4 ...
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The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia and Deuterostomia. Protostomia contains the Ecdysozoa and the Lophotrochozoa; Deuterostomia contains the Chordata and the Xenambulacraria (Hemichordata, Echinodermata and Xenacoelomorpha). Their names refer to a supposed distinct origin of the mouth (stoma) in the two clades, but these groups have been differentiated by other embryological characters including embryonic cleavage patterns and different ways of forming their mesoderm and coeloms. Deuterostome monophyly is not consistently supported by recent studies. Here we compare support for Protostomia and Deuterostomia using five recently published, phylogenomic datasets. Protostomia is always strongly supported, especially by longer and higher quality genes. Support for Deuterostomia is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that can cause tree reconstruction errors - inadequate models, short internal branch, faster evolving genes, and unequal branch lengths - correlate with statistical support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. A survey of molecular characters supposedly diagnostic of deuterostomes shows many are not valid synapomorphies. The branch between bilaterian and deuterostome common ancestors, if real, is very short. This finding fits with growing evidence suggesting the common ancestor of all Bilateria had many deuterostome characteristics. This finding has important implications for our understanding of early animal evolution and for the interpretation of some enigmatic Cambrian fossils such as vetulicolians and banffiids.
... Thus, a substantial proportion (43%) of the microsyntenic blocks found in the BLCA emerged after the cnidarian-bilaterian split. Given the disputed position of the ctenophore and xenacoelomorpha phyla [21,22,24,25], we calculated the amount of microsyntenic blocks novelties under various phylogenetic hypotheses. Regardless of the hypothesis, we obtained similar results regarding the counts of MLCA, PLCA and BLCA novel blocks ( Supplementary Fig. 3). ...
... Syntenic gains at various points in evolution were associated with different molecular functions. Among the 212 Gene Ontology (GO) terms enriched in the genes within the BLCA novel syntenies (Supplementary Table 1 [19], polytomy at the root of Metazoa and Bilateria due to the disputed position of Ctenophora [20], and Xenacoelomorpha [21,22], respectively. Number of species surveyed for each group is indicated in brackets. ...
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Background Animal genomes are strikingly conserved in terms of local gene order (microsynteny). While some of these microsyntenies have been shown to be coregulated or to form gene regulatory blocks, the diversity of their genomic and regulatory properties across the metazoan tree of life remains largely unknown. Results Our comparative analyses of 49 animal genomes reveal that the largest gains of synteny occurred in the last common ancestor of bilaterians and cnidarians and in that of bilaterians. Depending on their node of emergence, we further show that novel syntenic blocks are characterized by distinct functional compositions (Gene Ontology terms enrichment) and gene density properties, such as high, average and low gene density regimes. This is particularly pronounced among bilaterian novel microsyntenies, most of which fall into high gene density regime associated with higher gene coexpression levels. Conversely, a majority of vertebrate novel microsyntenies display a low gene density regime associated with lower gene coexpression levels. Conclusions Our study provides first evidence for evolutionary transitions between different modes of microsyntenic block regulation that coincide with key events of metazoan evolution. Moreover, the microsyntenic profiling strategy and interactive online application (Syntenic Density Browser, available at: http://synteny.csb.univie.ac.at/ ) we present here can be used to explore regulatory properties of microsyntenic blocks and predict their coexpression in a wide-range of animal genomes.
... Excretory organs are thought to be one of the key evolutionary innovations of the emergence of complex body plans 8,9 and are believed to facilitate the conquest of new habitats, such as freshwater and terrestrial environments. 3,10 Specialized excretory organs are a common feature of protostomes and deuterostomes ( Figure 1A), sometimes united in the clade Nephrozoa 8,9,11 (however, see Kapli and Telford 12 and Philippe et al. 13 and references therein for the recent discussion on the topic whether Nephrozoa is not simply synonymous with Bilateria). The diverse excretory organs can be grouped into secretory organs (e.g., Malpighian tubules of insects), in which primary urine is produced by the means of active, transcellular transport 3,4,10 and organs that are based on the principle of ultrafiltration (UF). ...
... These data support the idea that the conserved set of nephridial developmental TFs has been inherited from the last common ancestor of protostomes and deuterostomes (Figure 4A). Although recently the basal position of Xenacoelomorpha in the bilaterian tree of life has been challenged again 12,13 and monophyly of deuterostomes has been questioned, 51 these ambiguities do not directly influence our reconstruction of the ancestral set of nephridia-related transcription factors. Regardless of the topological controversies, the demonstrated molecular similarities could be traced back to the last common ancestor of protostomes and Ambulacraria ( Figure 4A), in which the ancestral excretory organs were already present. ...
Article
Excretion is an essential physiological process, carried out by all living organisms, regardless of their size or complexity. Both protostomes (e.g., flies and flatworms) and deuterostomes (e.g., humans and sea urchins) possess specialized excretory organs serving that purpose. Those organs exhibit an astonishing diversity, ranging from units composed of just few distinct cells (e.g., protonephridia) to complex structures, built by millions of cells of multiple types with divergent morphology and function (e.g., vertebrate kidneys). Although some molecular similarities between the development of kidneys of vertebrates and the regeneration of the protonephridia of flatworms have been reported, the molecular underpinnings of the development of excretory organs have never been systematically studied in a comparative context. Here, we show that a set of transcription factors (eya, six1/2, pou3, sall, lhx1/5, and osr) and structural proteins (nephrin, kirre, and zo1) is expressed in the excretory organs of a phoronid, brachiopod, annelid, onychophoran, priapulid, and hemichordate that represent major protostome lineages and non-vertebrate deuterostomes. We demonstrate that the molecular similarity observed in the vertebrate kidney and flatworm protonephridia is also seen in the developing excretory organs of those animals. Our results show that all types of ultrafiltration-based excretory organs are patterned by a conserved set of developmental genes, an observation that supports their homology. We propose that the last common ancestor of protostomes and deuterostomes already possessed an ultrafiltration-based organ that later gave rise to the vast diversity of extant excretory organs, including both proto- and metanephridia.
... [38,39] showing evolutionary relationships of the main animal phyla. The dashed lines indicate that the position of the Xenacoelomorpha is still a matter of debate [40][41][42], which might potentially affect the monophyly of the deuterostomes [43]. The earliest branches of the tree are currently also unresolved, with different phylogenies placing either the Ctenophora or the Porifera as the sister group to all other animals [44][45][46] ...
... Sexually mature specimens of the European amphioxus (Branchiostoma lanceolatum) were collected at the previously described site in Argelès-sur-Mer, France, transported to [38,39] showing evolutionary relationships of the main animal phyla. The dashed lines indicate that the position of the Xenacoelomorpha is still a matter of debate [40][41][42], which might potentially affect the monophyly of the deuterostomes [43]. The earliest branches of the tree are currently also unresolved, with different phylogenies placing either the Ctenophora or the Porifera as the sister group to all other animals [44][45][46], as indicated by the orange arrow and question mark. ...
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Glycine is an important neurotransmitter in vertebrates, performing both excitatory and inhibitory actions. Synaptic levels of glycine are tightly controlled by the action of two glycine transporters, GlyT1 and GlyT2, located on the surface of glial cells and neurons, respectively. Only limited information is available on glycinergic neurotransmission in invertebrates, and the evolution of glycinergic neurotransmission is poorly understood. Here, by combining phylogenetic and gene expression analyses, we characterized the glycine transporter complement of amphioxus, an important invertebrate model for studying the evolution of chordates. We show that amphioxus possess three glycine transporter genes. Two of these (GlyT2.1 and GlyT2.2) are closely related to GlyT2 of vertebrates, whereas the third (GlyT) is a member of an ancestral clade of deuterostome glycine transporters. GlyT2.2 expression is predominantly non-neural, whereas GlyT and GlyT2.1 are widely expressed in the amphioxus nervous system and are differentially expressed, respectively, in neurons and glia. Vertebrate glycinergic neurons express GlyT2 and glia GlyT1, suggesting that the evolution of the chordate glycinergic system was accompanied by a paralog-specific inversion of gene expression. Despite this genetic divergence between amphioxus and vertebrates, we found strong evidence for conservation in the role glycinergic neurotransmission plays during larval swimming, the implication being that the neural networks controlling the rhythmic movement of chordate bodies may be homologous.
... Acoels are part of Xenacoelomorpha, a group of worms that has been proposed to be the sister-group of all remaining bilaterians [79]. This view remains however challenged as they are also proposed to belong with the deuterostomes [80]. Choanoflagellates are a group of eukaryots closely related to metazoans, that had been reported to possess neuroglobin-like proteins [18]. ...
... Acoela belongs to the phylum Xenacoelomorpha (Philippe et al. 2011;Cannon et al. 2016); however, the phylogenetic position of Xenacoelomorpha is still unclear. Several phylogenetic analyses have suggested that Xenacoelomorpha is a sister group to Nephrozoa or Ambulacraria (Cannon et al. 2016;Marlétaz et al. 2019;Philippe et al. 2019). Thus, it is suggested that the simplicity of Acoela represents ancient bilaterian characteristics or secondary losses from a complex ancestor. ...
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Acoel statocysts are fluid-filled chambers formed by two parietal cells underlying basal lamina as a capsule and contain a movable statolith cell called a lithocyte. The statocyst is needed for geotaxis; however, the mechanism of the gravity receptor system has not been elucidated. We focused on the geotactic ability of the acoel Praesagittifera naikaiensis, acquired during the development of the statocyst and its nervous system after hatching, and examined the three-dimensional relationship between the statocyst and its nervous system. Acoel geotactic ability was acquired between 0 and 7 days after hatching. No major changes in neural structures, namely a commissural brain, nerve cords, and commissures, were observed between juveniles and adults. The statocyst-associated commissure (stc), a commissural brain component, was circular and was located ventral to the statocyst but was not observed in neural connections to the capsule’s lumen. Fine structures of the statocyst revealed that the statolith developed after hatching. We hypothesized that geotactic ability needs the following conditions: (1) a sufficient concentration of calcium salt in the statolith; (2) stc must work as afferent neurons; and (3) a ventral polar cell, which is present outside the capsule, must be a sensory cell stimulated by the lithocyte.
... Genomes of malacosporeans would be of particular interest in this respect, as similarities and differences in gene family expansions can help to gain further insights into the adaptations characterizing their independent historic invertebrate and vertebrate host acquisition events. To further confirm or refute a common origin of the Endocnidozoa and decipher their origins within the Cnidaria, a complete genome of Polypodium is required, and solutions for dealing with varying evolutionary rates across different cnidarian lineages must be developed and applied [10,65,66]. ...
Article
Myxozoans are highly diverse and globally distributed cnidarian endoparasites in freshwater and marine habitats. They have adopted a heteroxenous life cycle, including invertebrate and fish hosts, and have been associated with diseases in aquaculture and wild fish stocks. Despite their importance, genomic resources of myxozoans have proven difficult to obtain due to their miniaturized and derived genome character and close associations with fish tissues. The first ‘omic’ datasets have now become the main resource for a better understanding of host–parasite interactions, virulence, and diversity, but also the evolutionary history of myxozoans. In this review, we discuss recent genomic advances in the field and outline outstanding questions to be answered with continuous and improved efforts of generating myxozoan genomic data.
... Both are elongated, bilaterally symmetrical, nearly half a millimeter long, and densely covered in motile cilia. Acoel worms are minute animals of extreme simplicity (long believed to be flatworms, but now known to belong to a separate bilaterian lineage (Ruiz-Trillo et al., 1999;Cannon et al., 2016;Marlétaz, 2019;Philippe et al., 2019). They lack excretory organs, an anus, and even a proper gut. ...
... Acoels are part of Xenacoelomorpha, a group of worms that has been proposed to be the sister-group of all remaining bilaterians [79]. This view remains however challenged as they are also proposed to belong with the deuterostomes [80]. Choanoflagellates are a group of eukaryots closely related to metazoans, that had been reported to possess neuroglobin-like proteins [18]. ...
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Background How vascular systems and their respiratory pigments evolved is still debated. While many animals present a vascular system, hemoglobin exists as a blood pigment only in a few groups (vertebrates, annelids, a few arthropod and mollusk species). Hemoglobins are formed of globin sub-units, belonging to multigene families, in various multimeric assemblages. It was so far unclear whether hemoglobin families from different bilaterian groups had a common origin. Results To unravel globin evolution in bilaterians, we studied the marine annelid Platynereis dumerilii, a species with a slow evolving genome. Platynereis exhibits a closed vascular system filled with extracellular hemoglobin. Platynereis genome and transcriptomes reveal a family of 19 globins, nine of which are predicted to be extracellular. Extracellular globins are produced by specialized cells lining the vessels of the segmental appendages of the worm, serving as gills, and thus likely participate in the assembly of a previously characterized annelid-specific giant hemoglobin. Extracellular globin mRNAs are absent in smaller juveniles, accumulate considerably in growing and more active worms and peak in swarming adults, as the need for O 2 culminates. Next, we conducted a metazoan-wide phylogenetic analysis of globins using data from complete genomes. We establish that five globin genes (stem globins) were present in the last common ancestor of bilaterians. Based on these results, we propose a new nomenclature of globins, with five clades. All five ancestral stem-globin clades are retained in some spiralians, while some clades disappeared early in deuterostome and ecdysozoan evolution . All known bilaterian blood globin families are grouped in a single clade (clade I) together with intracellular globins of bilaterians devoid of red blood. Conclusions We uncover a complex “pre-blood” evolution of globins, with an early gene radiation in ancestral bilaterians. Circulating hemoglobins in various bilaterian groups evolved convergently, presumably in correlation with animal size and activity. However, all hemoglobins derive from a clade I globin, or cytoglobin, probably involved in intracellular O 2 transit and regulation. The annelid Platynereis is remarkable in having a large family of extracellular blood globins, while retaining all clades of ancestral bilaterian globins.
... Three acoel genomes with different degrees of completeness have been produced in the last few years-those of species Hofstenia miamia (Gehrke et al. 2019), Praesagittifera naikaiensis (Arimoto et al. 2019), and Symsagittifera roscoffensis (Philippe et al. 2019). While the first is quite complete, that of our species is only a preliminary draft. ...
... Finally, the EDM models may help resolve open phylogenetic problems involving large data sets and distantly related species (Simion et al. 2017;Philippe et al. 2019). Further, dissimilarities in compositional heterogeneity may be detected by applying EDCluster to specific species groups. ...
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Biochemical demands constrain the range of amino acids acceptable at specific sites resulting in across-site compositional heterogeneity of the amino acid replacement process. Phylogenetic models that disregard this heterogeneity are prone to systematic errors, which can lead to severe long branch attraction artifacts. State-of-the-art models accounting for across-site compositional heterogeneity include the CAT model, which is computationally expensive, and empirical distribution mixture models estimated via maximum likelihood (C10 to C60 models). Here, we present a new, scalable method EDCluster for finding empirical distribution mixture models involving a simple cluster analysis. The cluster analysis utilizes specific coordinate transformations which allow the detection of specialized amino acid distributions either from curated databases, or from the alignment at hand. We apply EDCluster to the HOGENOM and HSSP databases in order to provide universal distribution mixture (UDM) models comprising up to 4096 components. Detailed analyses of the UDM models demonstrate the removal of various long branch attraction artifacts and improved performance compared to the C10 to C60 models. Ready-to-use implementations of the UDM models are provided for three established software packages (IQ-TREE, Phylobayes, and RevBayes).
... Although it has been hypothesized that transient suppression of the repressor must occur to enable Wnt3 activation at oralfacing wound sites (Nakamura et al., 2011) and expression analysis shows a corresponding absence of Sp5 before Wnt3 acoels such as Hofstenia (red text) as a sister lineage to all other bilaterians, with regenerative capacity and prior knowledge of Wnt utilization in this process. The dashed line indicates a putative relationship between acoels and echinoderms based on an alternative phylogenetic position of acoels as a sister to Ambulacraria, proposed by some studies (Philippe et al., 2007(Philippe et al., , 2011Philippe, 2019). The black circle indicates a trait is present in at least one species of the lineage shown. ...
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Whole-body regeneration relies on the re-establishment of body axes for patterning of new tissue. Wnt signaling is required to correctly regenerate tissues along the primary axis in many animals. However, the causal mechanisms that first launch Wnt signaling during regeneration are poorly characterized. We use the acoel worm Hofstenia miamia to identify processes that initiate Wnt signaling during posterior regeneration and find that the ligand wnt-3 is upregulated early in posterior-facing wounds. Functional studies reveal that wnt-3 is required to regenerate posterior tissues. wnt-3 is expressed in stem cells, it is needed for their proliferation, and its function is stem cell dependent. Chromatin accessibility data reveal that wnt-3 activation requires input from the general wound response. In addition, the expression of a different Wnt ligand, wnt-1, before amputation is required for wound-induced activation of wnt-3. Our study establishes a gene regulatory network for initiating Wnt signaling in posterior tissues in a bilaterian.
... In particular, functional studies of neural specification and patterning in xenacoelomorphs are needed to infer how genetic pathways underlying these processes have evolved. These studies would also inform the evolution of animal nervous systems [28][29][30] in the alternative scenario that places xenacoelomorphs as sister to Ambulacraria [31,32]. ...
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The origin of bilateral symmetry, a major transition in animal evolution, coincided with the evolution of organized nervous systems that show regionalization along major body axes. Studies of Xenacoelomorpha, the likely outgroup lineage to all other animals with bilateral symmetry, can inform the evolutionary history of animal nervous systems. Here, we characterized the neural anatomy of the acoel Hofstenia miamia. Our analysis of transcriptomic data uncovered orthologues of enzymes for all major neurotransmitter synthesis pathways. Expression patterns of these enzymes revealed the presence of a nerve net and an anterior condensation of neural cells. The anterior condensation was layered, containing several cell types with distinct molecular identities organized in spatially distinct territories. Using these anterior cell types and structures as landmarks, we obtained a detailed timeline for regeneration of the H. miamia nervous system, showing that the anterior condensation is restored by eight days after amputation. Our work detailing neural anatomy in H. miamia will enable mechanistic studies of neural cell type diversity and regeneration and provide insight into the evolution of these processes.
... It is claimed that they are a sister group of Ambulacraria (hemichordates + echinoderms) (Philippe et al., 2011). However, the phylogenetic position of Xenacoelomorpha remains controversial and inconclusive (Cannon et al., 2016;Brauchle et al., 2018;Philippe et al., 2019). As the systematic position of acoels changes the overall view of metazoan evolution, it is an important, open question in evolutionary biology (Hejnol and Pang, 2016;Ruiz-Trillo and Paps, 2016). ...
Article
Acoel flatworms are simple bilaterians that lack digestive lumens and coelomic cavities. Although they are a significant taxon for evaluating the evolution of metazoans, suitable species for biological experiments are not available in Japan. We recently focused on Praesagittifera naikaiensis, which inhabits the sandy shores of intertidal zones in the Seto Inland Sea in Japan, as a candidate for a representative acoel species to be used in experiments. However, reports on its distribution range remain limited. Here, we surveyed the habitats of P. naikaiensis on 108 beaches along the Seto Inland Sea. Praesagittifera naikaiensis is reported here from 37 sites (six previously known and 31 newly discovered sites) spread over a wide area of the Seto Inland Sea, from Awaji Island in Hyogo Prefecture to Fukuoka Prefecture (364 km direct distance). Based on the mitochondrial cytochrome oxidase subunit I (COI) gene haplotypes, we evaluated the genetic diversity of 145 individuals collected from 33 sites. Out of 42 COI haplotypes, 13 haplotypes were shared by multiple individuals. The most frequent haplotype was observed in 67 individuals collected from 31 sites. Eight other haplotypes were detected at geographically distant locations (maximum of 299 km direct distance). Multiple haplotypes were found at 32 sites. These results demonstrate that sufficient genetic flow exists among P. naikaiensis populations throughout the Seto Inland Sea. Molecular phylogenetic analysis of the COI haplotypes of P. naikaiensis revealed that all specimens were grouped into one clade. The genetic homogeneity of the animals in this area favors their use as an experimental animal.
... A later study taking into account supplementary genomic and transcriptomic data from several species and refined evolutionary models placed Xenacoelomorpha as a sister group to all other Bilaterians (Nephrozoa) making it a candidate phylum to better understand bilaterian origins (Cannon et al. 2016). The use of alternative models of gene evolution has questioned that phylogenetic position (Philippe et al. 2019). In fact, these alternative suggestions of phylogenetic affinities reflect general methodological problems involved in the use of phylogenomic tools and models to reconstruct early diverging clades (Kapli et al. 2020), a problematic that remains unsolved with current approaches. ...
Article
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Bilaterian animals display a wide variety of cell types, organized into defined anatomical structures and organ systems, which are mostly absent in pre-bilaterian animals. Xenacoelomorpha are an early-branching bilaterian phylum displaying an apparently relatively simple anatomical organization that have greatly diverged from other bilaterian clades. In this study, we use whole-body single-cell transcriptomics on the acoel Isodiametra pulchra to identify and characterize different cell types. Our analysis identifies the existence of ten major cell type categories in acoels all contributing to main biological functions of the organism: metabolism, locomotion and movements, behavior, defense and development. Interestingly, while most cell clusters express core fate markers shared with other animal clades, we also describe a surprisingly large number of clade-specific marker genes, suggesting the emergence of clade-specific common molecular machineries functioning in distinct cell types. Together, these results provide novel insight into the evolution of bilaterian cell types and open the door to a better understanding of the origins of the bilaterian body plan and their constitutive cell types.
... Acoelomorpha are now assigned to their own clade together with Xenoturbellida and no longer considered platyhelminths (Ruiz-Trillo and Paps 2016;Philippe et al. 2011). Xenacoelomorpha are now considered simplified relatives of the Ambulacraria (Philippe et al. 2019). To our knowledge, there is no fossil record of parasitic acoelomorphs. ...
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The fossil record of parasitic helminths is often stated to be severely limited. Many studies have therefore used host constraints to constrain molecular divergence time estimates of helminths. Here we review direct fossil evidence for several of these parasitic lineages belong to various phyla (Acanthocephala, Annelida, Arthropoda, Nematoda, Nematomorpha, Pentastomida, Platyhelminthes). Our compilation shows that the fossil record of soft-bodied helminths is patchy, but more diverse than commonly assumed. The fossil record provides evidence that ectoparasitic helminths (e.g., worm-like pentastomid arthropods) have been around since the early Paleozoic, while endoparasitic helminths (cestodes) arose at least during, or possibly even before the late Paleozoic. Nematode lineages parasitizing terrestrial plant and animal hosts have been in existence at least since the Devonian and Triassic, respectively. All major phyla (Acanthocephala, Annelida, Platyhelminthes. Nematoda, Nematomorpha) had evolved endoparasitic lineages at least since the Mesozoic. Interestingly, although parasitism is considered derived within Metazoa, the oldest evidence for Nematoda and Platyhelminthes includes body fossils of parasitic representatives. Furthermore, the oldest fossil evidence of these parasitic lineages often falls within molecular divergence time estimates based on host co-evolution suggesting the fossil record of helminths themselves might be just as good or at least complementary (and less circular in justification) to calibration based on host associations. Data also provide evidence for obvious host switches or extinctions, which cautions against models of pure co-divergence where use of host calibrations to constrain divergence time estimates may be considered.
... Among non-bilateral clades, ctenophores were controversially placed to be basal to the Porifera, sister to the Eumetazoan (Laumer et al. 2019), or together with the Cnidaria, revive the Coelenterata (Pett et al. 2019); the Placazoa was placed as a sister clade to the Eumetazoa (which together comprise the Epitheliozoa) or to the Cnidaria (Laumer et al. 2019). Within the Bilateria, the Xenoacoelomorpha was either basal to the Nephrozoa (protostomes and deuterostomes) or at a basal position within deuterostomes (Laumer et al. 2019;Philippe et al. 2019); there are other uncertainties within the three major bilateral clades that are beyond the scope of this discussion. ...
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The Cambrian Explosion by nature is a three-phased explosion of animal body plans alongside episodic biomineralization, pulsed change of generic diversity, body size variation, and progressive increase of ecosystem complexity. The Cambrian was a time of crown groups nested by numbers of stem groups with a high-rank taxonomy of Linnaean system (classes and above). Some stem groups temporarily succeeded while others were ephemeral and underrepresented by few taxa. The high number of stem groups in the early history of animals is a major reason for morphological gaps across phyla that we see today. Most phylum-level clades achieved their maximal disparity (or morphological breadth) during the time interval close to their first appearance in the fossil record during the early Cambrian, whereas others, principally arthropods and chordates, exhibit a progressive exploration of morphospace in subsequent Phanerozoic. The overall envelope of metazoan morphospace occupation was already broad in the early Cambrian though it did not reach maximal disparity nor has diminished significantly as a consequence of extinction since the Cambrian. Intrinsic and extrinsic causes were extensively discussed but they are merely prerequisites for the Cambrian Explosion. Without the molecular evolution, there could be no Cambrian Explosion. However, the developmental system is alone insufficient to explain Cambrian Explosion. Time-equivalent environmental changes were often considered as extrinsic causes, but the time coincidence is also insufficient to establish causality. Like any other evolutionary event, it is the ecology that make the Cambrian Explosion possible though ecological processes failed to cause a burst of new body plans in the subsequent evolutionary radiations. The Cambrian Explosion is a polythetic event in natural history and manifested in many aspects. No simple, single cause can explain the entire phenomenon.
... stomes (Philippe et al., 2011(Philippe et al., , 2019Kapli and Telford, 2020) or a sister group to the Nephrozoa (Hejnol et al., 2009;Cannon et al., 2016). Therefore, acoels are an important group of animals to questions of the origin and evolutionary history of bilaterians. ...
Article
Acoels, belonging to Xenacoelomorpha, are small worms with a relatively simple body plan and are considered a critical clade for understanding the evolution of bilaterians. Despite acoels' importance, however, many undiscovered species are predicted to be present worldwide. Here, we describe a new marine acoel species, Amphiscolops oni sp. nov., based on materials collected from the intertidal and subtidal zones of rocky shores at several localities along the Japanese Pacific coast. The new species is approximately 3 mm long and shows typical characteristics of the family Convolutidae, such as the presence of eyespots, symbiosis with algae, position of the gonopores, morphology of the bursal nozzles, lack of central singlet microtubules in the axonemes of spermatozoa, and funnel-like posture of the anterior end. Based on morphology and the results of molecular phylogenetic analyses, we assign this species to the genus Amphiscolops. Interestingly, these worms show unique behaviors such as swimming by flapping the lateral sides and actively capturing prey by swinging the anterior funnel. Furthermore, they possess a dorsal appendage-a characteristic previously unreported in Xenacoelomorpha-representing an evolutionary novelty acquired by this species.
... (a) A schematic phylogenetic tree shows the relationships of major animal lineages [spiralian relationships shown based on Marletaz et al. (2019)]. The red dashed line indicates uncertainty in the placement of xenacoelomorphs, as some studies suggest placement in the clade with echinoderms and hemichordates (Cannon et al. 2016, Kapli & Telford 2020, Philippe et al. 2019. Purple and gold circles next to the tree indicate the presence of at least one species capable of whole-body regeneration or of structural regeneration, respectively. ...
Article
The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells are discussed as examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
... Indeed, the seisonid branch was the longest in trees in which the lineage diverged basally [38,59]. However, it is getting increasingly clear that attraction of a long ingroup branch to the outgroup or root leads to systematic error in phylogenetic analyses (e.g., [60]). We found a strong indication of this phenomenon in the unrooted tree derived from 100 concatenated BUSCO Metazoa genes (Fig. 12A): Here, S. nebaliae grouped together with the outgroup representative S. mediterranea. ...
Article
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Background: Seisonidea (also Seisonacea or Seisonidae) is a group of small animals living on marine crustaceans (Nebalia spec.) with only four species described so far. Its monophyletic origin with mostly free-living wheel animals (Monogononta, Bdelloidea) and endoparasitic thorny-headed worms (Acanthocephala) is widely accepted. However, the phylogenetic relationships inside the Rotifera-Acanthocephala clade (Rotifera sensu lato or Syndermata) are subject to ongoing debate, with consequences for our understanding of how genomes and lifestyles might have evolved. To gain new insights, we analyzed first drafts of the genome and transcriptome of the key taxon Seisonidea. Results: Analyses of gDNA-Seq and mRNA-Seq data uncovered two genetically distinct lineages in Seison nebaliae Grube, 1861 off the French Channel coast. Their mitochondrial haplotypes shared only 82% sequence identity despite identical gene order. In the nuclear genome, distinct linages were reflected in different gene compactness, GC content and codon usage. The haploid nuclear genome spans ca. 46 Mb, of which 96% were reconstructed. According to~23,000 SuperTranscripts, gene number in S. nebaliae should be within the range published for other members of Rotifera-Acanthocephala. Consistent with this, numbers of metazoan core orthologues and ANTP-type transcriptional regulatory genes in the S. nebaliae genome assembly were between the corresponding numbers in the other assemblies analyzed. We additionally provide evidence that a basal branching of Seisonidea within Rotifera-Acanthocephala could reflect attraction to the outgroup. Accordingly, rooting via a reconstructed ancestral sequence led to monophyletic Pararotatoria (Seisonidea+Acanthocephala) within Hemirotifera (Bdelloidea+Pararotatoria).
... However, the main result of taxon sampling variations was the evidence for a major impact of model violations with LG4X, especially for the nuclear compartment. These observations are in agreement with the sensitivity to MBE LBA of models that do not fully incorporate the heterogeneity of the substitution process across sites (Lartillot et al. 2007;Philippe et al. 2011Philippe et al. , 2019Simion et al. 2017). They further suggest that neither the PC nor the NC hypothesis is correct and that we need to use a better model to get insights into the ochrophyte radiation. ...
Article
It is commonly assumed that increasing the number of characters has the potential to resolve evolutionary radiations. Here, we studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous origin mitochondrion, plastid and nucleus). Surprisingly while statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion (6,762 sites) and plastid (21,692 sites) trees, it decreases in the nuclear (209,105 sites) tree. Statistical support is not simply related to the dataset size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that this ability for current phylogenetic methods is limited, because conflicting results were obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid dataset provided higher statistical support for the ochrophyte radiation than the larger nucleus dataset. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear dataset. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of datasets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.
... [37,38] showing evolutionary relationships of the main animal phyla. The dashed lines indicate that the position of the Xenacoelomorpha is still a matter of debate [39][40][41], which might potentially affect the monophyly of the deuterostomes [42]. The earliest branches of the tree are currently also unresolved, with different phylogenies placing either the Ctenophora or the Porifera as the sister group to all other animals [43][44][45], as indicated by the orange arrow and question mark. ...
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Glycine is an important neurotransmitter in vertebrates, performing both excitatory and inhibitory actions. Synaptic levels of glycine are tightly controlled by the action of two glycine transporters, GlyT1 and GlyT2, located on the surface of glial cells and glycinergic or glutamatergic neurons, respectively. Glycinergic neurotransmission in invertebrates has so far only been investigated in a very limited number of species, and, although it was suggested that its functions are to some extent conserved with vertebrates, the evolution of glycinergic neurotransmission remains very poorly understood. Here, by combining phylogenetic and gene expression analyses, we characterized the glycine transporter complement of amphioxus, an important invertebrate model for studying the evolution of chordates. We show that amphioxus possesses three glycine transporter genes, two of which (GlyT2.1 and GlyT2.2) are closely related to GlyT2 of vertebrates, while the other (GlyT) is a member of an ancestral clade of deuterostome glycine transporters. While expression of GlyT2.2 is predominantly non-neural, GlyT and GlyT2.1 are widely expressed in the amphioxus nervous system and are characterized by differential expression in neurons and glia, respectively. However, in vertebrates, glycinergic neurons express GlyT2 and glia GlyT1, suggesting that the evolution of the chordate glycinergic system was accompanied by complex genetic remodeling leading to the paralog-specific inversion of gene expression. Albeit this genetic divergence between amphioxus and vertebrates, we found strong evidence for a general conservation of the role of glycinergic neurotransmission during larval swimming, allowing us to hypothesize that the neural networks controlling the rhythmic movement of chordate bodies are homologous.
... Firstly, Placozoa and Cnidaria are sister groups, resolving a longstanding controversy (15)(16)(17)(18)(19)(20)(21). Secondly, Xenacoelomorpha is nested within Bilateria and is the sister group to Protostomia, rejecting three out of four hypotheses in the field (22)(23)(24)(25)(26)(27)(28)(29). ...
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Invertebrates, animals (metazoans) without backbones, encompass ~97% of all animal yet remains understudied. They have provided insights into molecular mechanisms underlying fundamentally identical mechanisms in phylogenetically diverse animals, including vertebrates. Marine invertebrates have long fascinated researchers due to their abundance, diversity, adaptations, and impact on ecosystems and human economies. Here, we report a compendium and appraisal of 190 marine invertebrate genomes spanning 21 phyla, 43 classes, 92 orders, and 134 families. We identify a high proportion and long unit size of tandem repeats, likely contributing to reported difficulties in invertebrate genome assembly. A well-supported phylogenetic tree of marine invertebrates from 974 single-copy orthologous genes resolved topological controversies. We show that Ctenophora is at the basal phylum and Porifera is the sister group of Parahoxozoa; that Xenacoelomorpha is within Bilateria and is the sister group to Protostomia, rejecting three out of four hypotheses in the field; and that Bryozoa is at the basal position of Lophotrochozoa, not grouped into Lophophorata. We also present insights into the genetic underpinnings of metazoans from Hox genes, innate immune gene families, and nervous system gene families. Our marine invertebrate genome compendium provides a unified foundation for studies on their evolution and effects on ecological systems and human life.
... Therefore, discovery of the receptor(s) that mediate the excitatory effects of ArSS1 in A. rubens represents a fascinating objective for future work. Furthermore, from an evolutionary perspective, it will also be of interest to determine the occurrence and characteristics of SS/ASTC-type neuropeptides in hemichordates and xenacoelomorphs, phyla recognized as being closely related to echinoderms within the proposed deuterostome clade Xenambulacraria (48). SS/ASTC-type receptors are present in species belonging to these phyla (e.g., GenBank accession no. ...
Article
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Somatostatin (SS) and allatostatin-C (ASTC) are inhibitory neuropeptides in chordates and protostomes, respectively, which hitherto were identified as orthologs. However, echinoderms have two SS/ASTC-type neuropeptides (SS1 and SS2), and here, our analysis of sequence data indicates that SS1 is an ortholog of ASTC and SS2 is an ortholog of SS. The occurrence of both SS-type and ASTC-type neuropeptides in echinoderms provides a unique context to compare their physiological roles. Investigation of the expression and actions of the ASTC-type neuropeptide ArSS1 in the starfish Asterias rubens revealed that it causes muscle contraction (myoexcitation), contrasting with myoinhibitory effects of the SS-type neuropeptide ArSS2. Our findings suggest that SS-type and ASTC-type neuropeptides are paralogous and originated by gene duplication in a common ancestor of the Bilateria, with only one type being retained in chordates (SS) and protostomes (ASTC) but with both types being retained in echinoderms. Loss of ASTC-type and SS-type neuropeptides in chordates and protostomes, respectively, may have been due to their functional redundancy as inhibitory regulators of physiological processes. Conversely, the retention of both neuropeptide types in echinoderms may be a consequence of the evolution of a myoexcitatory role for ASTC-type neuropeptides mediated by as yet unknown signaling mechanisms.
... This suggests that the HGT took place either at the root of the deuterostomes, or possibly at the root of bilateria. Note that this part of the tree of life remains poorly resolved, with an extremely short branch between the bilaterian common ancestor and the deuterostomes (Philippe et al. 2019). ...
Article
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Protein post-translational modifications (PTMs) add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than one billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared to products of likely endosymbiont gene transfer, mitochondrial proteins and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.
... In most deuterostomes, it is difficult to untangle the roles of ß-catenin and Nodal signaling in primary (animal-vegetal) and secondary (dorsoventral) axis specification. Nodal signaling is an evolutionary novelty of the Bilateria [68], the last common ancestor of which may have been very similar to the last common ancestor of deuterostomes [69][70][71]. Nodal signaling functions in parallel with the BMP pathway through paralogous receptor and effector proteins [68,72,73]. In non-chordate deuterostomes, such as sea urchins, the roles of ß-catenin, Nodal, and BMP signaling can be discerned more readily than in other deuterostomes. ...
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Mechanisms and evolution of primary axis specification in insects are discussed in the context of the roles of ß-catenin and TCF in polarizing metazoan embryos. Three hypotheses are presented. First, insects with sequential segmentation and posterior growth use cell-autonomous mechanisms for establishing embryo polarity via the nuclear ratio of ß-catenin and TCF. Second, TCF homologs establish competence for anterior specification. Third, the evolution of simultaneous segmentation mechanisms, also known as long-germ development, resulted in primary axis specification mechanisms that are independent of ß-catenin but reliant on TCF, a condition that preceded the frequent replacement of anterior determinants in long germ insects.
Chapter
Xenacoelomorpha are a phylogenetically and biologically interesting, but severely understudied group of worm-like animals. Among them, the acoel Isodiametra pulchra has been shown to be amenable to experimental work, including the study of stem cells and regeneration. The animal is capable of regenerating the posterior part of the body, but not its head. Here, methods such as nucleic acid extractions, in situ hybridisation, RNA interference, antibody and cytochemical stainings, and the general handling of the animals are presented.
Conference Paper
Members of at least 15 animal phyla have a bi-phasic lifecycle composed of a pelagic larval stage which metamorphoses into a benthic adult. This lifecycle enables larvae to disperse in the ocean to colonise new environments. Although bi-phasic life cycles are widespread across Metazoa, it is unclear if marine larvae were present in the common ancestor or have evolved multiple times as an adaptation to a common selective pressure. Answering this question is fundamental if we are to reconstruct the lifecycle of the last common ancestor of animals. Many marine larvae are at least superficially similar, they are small, swim through beating of ciliated bands and sense the environment with an apical organ structure. Most animals with such larvae belong to the superclade of Lophotrochozoa and this thesis will concentrate on this group. To assess the homology of larvae, authors have compared the early development and expression profile of similar larval organs across phyla and shown that, generally, these are conserved. However, these studies only compared a handful of species and genes and a more thorough approach is needed. In this work I have used single cell sequencing to characterise the cells present in two lophotrochozoan marine larvae (mollusc’s trochophore larva and polyclad flatworms’ Mueller’s larva). I have performed in situ hybridisation and hybridisation chain reaction to identify cells belonging to different structures (including the ciliary bands and apical organ). Subsequently, I have compared the expression of orthologous genes in cell types of the two larvae. I have found that ciliary cells, neurons, muscles and proliferative cells co-express a large number of orthologous genes (>600) of which many are transcription factors (>30). 4 These results hint at a likely homology of lophotrochozoan larvae and set the basis to expand comparative work to more larvae across Bilateria and possibly Metazoa.
Chapter
Acoel worms represent an enigmatic lineage of animals (Acoelomorpha) that has danced around the tree of animal life. Morphology-based classification placed them as flatworms (Phylum Platyhelminthes), with much of their biology being interpreted as a variation on what is observed in better-studied members of that phylum. However, molecular phylogenies suggest that acoels belong to a clade (Xenacoelomorpha) that could be a sister group to other animals with bilateral symmetry (Bilateria) or could belong within deuterostomes, closely related to a group that includes sea stars (Ambulacraria). This change in phylogenetic position has led to renewed interest in the biology of acoels, which can now offer insights into the evolution of many bilaterian traits. The acoel Hofstenia miamia has emerged as a powerful new research organism that enables mechanistic studies of xenacoelomorph biology, especially of developmental and regenerative processes. This article explains the motivation for developing Hofstenia as a new model system, describes Hofstenia biology, highlights the tools and resources that make Hofstenia a good research organism, and considers the questions that Hofstenia is well-positioned to answer. Finally, looking to the future, this article serves as an invitation to new and established scientists to join the growing community of researchers studying this exciting model system.
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The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration. Since the last review of this resource in 2012, it has undergone several improvements. Most notable is the shift from a single SQL database to a series of linked databases tied to a framework of data called NameBank. This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking of publications tied to names and improved annotation of scientific authorities and types. Additionally, practices utilized by NCBI Taxonomy curators specific to major taxonomic groups are described, terms peculiar to NCBI Taxonomy are explained, external resources are acknowledged and updates to tools and other resources are documented. Database URL: https://www.ncbi.nlm.nih.gov/taxonomy
Article
Volvocales forms a species‐rich clade with wide morphological variety and is regarded as an ideal model for tracing the evolutionary transitions in multicellularity. The phylogenetic relationships among the colonial volvocine algae and its relatives are important for investigating the origin of multicellularity in the clade Reinhardtinia. Therefore, a robust phylogenetic framework of the unicellular and colonial volvocine algae with broad taxon and gene sampling is essential for illuminating the evolution of multicellularity. Recent chloroplast phylogenomic studies have uncovered five major orders in the Chlorophyceae, but the family‐level relationships within Sphaeropleales and Volvocales remain elusive due to the uncertain positions of some incertae sedis taxa. In this study, we contributed six newly sequenced chloroplast genomes in the Volvocales and analyzed a dataset with 91 chlorophycean taxa and 58 protein‐coding genes. Conflicting phylogenetic signals were detected among chloroplast genes that resulted in discordant tree topologies among different analyses. We compared the phylogenetic trees inferred from original nucleotide, RY‐coding, codon‐degenerate, and amino acid datasets, and improved the robustness of phylogenetic inference in the Chlorophyceae by reducing base compositional bias. Our analyses indicate that the unicellular Chlamydomonas and Vitreochlamys are close to or nested within the colonial taxa, and all the incertae sedis taxa are nested within the monophyletic Sphaeropleales s.l. We propose that the colonial taxa in the Reinhardtinia are paraphyletic and multicellularity evolved once in the volvocine green algae and might be lost in Chlamydomonas and Vitreochlamys. We assessed base compositional bias among 91 volvocine algae in the nt dataset and each of the three codon positions, and the percentage GC content of each species was plotted to visualize compositional heterogeneity. We compared the phylogenies inferred from different datasets with decreasing compositional biases (original nucleotide, RY‐coding, codon‐degenerate and amino acid datasets) and Robinson–Foulds (RF) algorithm was used for tree distance calculations. Conflicting phylogenetic signals among 58 plastid genes were detected and quantified through the calculation of genewise log‐likelihood support, which resulted in discordant tree topologies at key nodes among different datasets. We hypothesize that the colonial taxa in the Reinhardtinia are paraphyletic and multicellularity has evolved once in the colonial clade, but was subsequently lost in Vitreochlamys and Chlamydomonas based on the phylogeny and ancestral state reconstruction analysis. We supplemented the chloroplast genomes and improved the robustness of phylogenetic inference in the Volvocales, which are crucial for studying the fundamental processes that shaped the initial advent of multicellularity.
Article
Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and error prone if done ad hoc . This tutorial provides protocols to make use of OMA Orthologous Groups, a set of genes all orthologous to each other, to infer a phylogenetic species tree. It is designed to be user-friendly and computationally inexpensive, by providing two options: (1) Using only precomputed groups with species available on the OMA Browser, or (2) Computing orthologs using OMA Standalone for additional species, with the option of using precomputed orthology relations for those present in OMA. A protocol for downstream analyses is provided as well, including creating a supermatrix, tree inference, and visualization. All protocols use publicly available software, and we provide scripts and code snippets to facilitate data handling. The protocols are accompanied with practical examples.
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It is commonly assumed that increasing the number of characters has the potential to resolving radiations. We studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous size and origin (6,762 sites for mitochondrion, 21,692 sites for plastid and 209,105 sites for nucleus). While statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion and plastid trees, it decreases in the nuclear tree. Statistical support is not simply related to the dataset size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that proper signal extraction is difficult to attain, as demonstrated by conflicting results obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid dataset provided higher statistical support for the ochrophyte radiation than the larger nucleus dataset. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear dataset. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of datasets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.
Article
The acoel worm Hofstenia miamia, which can replace tissue lost to injury via differentiation of a population of stem cells, has emerged as a new research organism for studying regeneration. To enhance the depth of mechanistic studies in this system, we devised a protocol for microinjection into embryonic cells that resulted in stable transgene integration into the genome and generated animals with tissue-specific fluorescent transgene expression in epidermis, gut, and muscle. We demonstrate that transgenic Hofstenia are amenable to the isolation of specific cell types, investigations of regeneration, tracking of photoconverted molecules, and live imaging. Further, our stable transgenic lines revealed insights into the biology of Hofstenia, including a high-resolution three-dimensional view of cell morphology and the organization of muscle as a cellular scaffold for other tissues. Our work positions Hofstenia as a powerful system with multiple toolkits for mechanistic investigations of development, whole-body regeneration, and stem cell biology.
Chapter
Hemichordates, along with echinoderms and chordates, belong to the lineage of bilaterians called the deuterostomes. Their phylogenetic position as an outgroup to chordates provides an opportunity to investigate the evolutionary origins of the chordate body plan and reconstruct ancestral deuterostome characters. The body plans of the hemichordates and chordates are organizationally divergent making anatomical comparisons very challenging. The developmental underpinnings of animal body plans are often more conservative than the body plans they regulate, and offer a novel data set for making comparisons between morphologically divergent body architectures. Here I review the hemichordate developmental data generated over the past 20 years that further test hypotheses of proposed morphological affinities between the two taxa, but also compare the conserved anteroposterior, dorsoventral axial patterning programs and germ layer specification programs. These data provide an opportunity to determine which developmental programs are ancestral deuterostome or bilaterian innovations, and which ones occurred in stem chordates or vertebrates representing developmental novelties of the chordate body plan.
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The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy - identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs which experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction which mimic expected patterns of gene evolution.
Article
Animal phylogeny has always been controversial, but a new study brings some much-needed order for two infamous wandering groups, the ctenophores and the Xenacoelomorphs. The study introduces an innovative approach to dissect systematic errors in the underlying methodology of molecular phylogenies.
Thesis
Nervous systems in metazoans range from simple nerve nets to complex centralized organs. Because of such diversity, the evolutionary history of nervous system in metazoans has been heavily debated. Echinoderms are a large group of metazoans that constitute with the hemichordates the clade of the ambulacrarians, within the deuterostomes. So far, adult echinoderms have been largely ignored in comparative biology because they exhibit a large set of anatomical oddities. However, a careful examination of neural patterning and organization in adult echinoderms is needed to decipher nervous system evolution in deuterostomes. To achieve this goal, we first improved the husbandry protocol for the sea urchin species Paracentrotus lividus to obtain suitable quantities of post-metamorphic individuals for experimentations. Then, we facilitated the study of post-metamorphic echinoids by staging the development of P. lividus from fertilization to post-metamorphic juvenile stages. Finally, we yielded an exhaustive body-wide description of the neuromuscular anatomy of post-metamorphic P. lividus juveniles which indicated that the nervous system of adult echinoids is not strictly centralized as it also includes elements that are typical of nerve nets. Similar investigation in post-metamorphic specimens of the sea star Patiria miniata and the sea cucumber Parastichopus parvimensis revealed a similar organization. Finally, we started a molecular screening of neural patterning genes in post-metamorphic P. lividus and P. miniata juveniles, suggesting that a genetic program similar to the one found in hemichordates is also used to pattern the ectoderm of adult echinoderms.
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Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform 6-state recoding approaches. Our results suggest that 6-state recoding strategies are not effective in the face of high saturation. Further, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies 6-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform 6-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than 6 states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated 6-state recoding, many of which have significant bearing on relationships across the tree of life.
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Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes. Chlamydiae are strictly intracellular bacteria that exist in a wide variety of environments but the diversity of the phylum is not well described. Here, the authors analyze 82 metagenome-assembled genomes, identify seven new families, and describe genomic signals of metabolic diversity.
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Acoels are marine worms that belong to the phylum Xenacoelomorpha, a deep-diverging bilaterian lineage. This makes acoels an attractive system for studying the evolution of major bilaterian traits. Thus far, acoel development has not been described in detail at the morphological and transcriptomic levels in a species in which functional genetic studies are possible. We present a set of developmental landmarks for embryogenesis in the highly regenerative acoel Hofstenia miamia. We generated a developmental staging atlas from zygote to hatched worm based on gross morphology, with accompanying bulk transcriptome data. Hofstenia embryos undergo a stereotyped cleavage program known as duet cleavage, which results in two large vegetal pole 'macromeres' and numerous small animal pole 'micromeres'. These macromeres become internalized as micromere progeny proliferate and move vegetally. We also noted a second, previously undescribed, cell-internalization event at the animal pole, following which we detected major body axes and tissues corresponding to all three germ layers. Our work on Hofstenia embryos provides a resource for mechanistic investigations of acoel development, which will yield insights into the evolution of bilaterian development and regeneration.
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The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circulatory system. Two conflicting hypotheses are under debate: Xenacoelomorpha is the sister group to all remaining Bilateria (= Nephrozoa, namely protostomes and deuterostomes) or is a clade inside Deuterostomia. Thus, determining the phylogenetic position of this clade is pivotal for understanding the early evolution of bilaterian features, or as a case of drastic secondary loss of complexity. Here we show robust phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa. Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes and using different models of evolution under maximum likelihood and Bayesian inference analyses, strongly corroborate this result. Rigorous testing of 25 experimental data sets designed to exclude data partitions and taxa potentially prone to reconstruction biases indicates that long-branch attraction, saturation, and missing data do not influence these results. The sister group relationship between Nephrozoa and Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.
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The discovery of four new Xenoturbella species from deep waters of the eastern Pacific Ocean is reported here. The genus and two nominal species were described from the west coast of Sweden1,2, but their taxonomic placement remains unstable3,4. Limited evidence placed Xenoturbella with molluscs5,6, but the tissues can be contaminated with prey7,8. They were then considered deuterostomes9–13. Further taxon sampling and analysis have grouped Xenoturbella with acoelomorphs (=Xenacoelomorpha) as sister to all other Bilateria (=Nephrozoa)14,15, or placed Xenacoelomorpha inside Deuterostomia with Ambulacraria (Hemichordata + Echinodermata)16. Here we describe four new species of Xenoturbella and reassess those hypotheses. A large species (>20 cm long) was found at cold-water hydrocarbon seeps at 2,890 m depth in Monterey Canyon and at 1,722 m in the Gulf of California (Mexico). A second large species (~10 cm long) also occurred at 1,722 m in the Gulf of California. The third large species (~15 cm long) was found at ~3,700 m depth near a newly discovered carbonate-hosted hydrothermal vent in the Gulf of California. Finally, a small species (~2.5 cm long), found near a whale carcass at 631 m depth in Monterey Submarine Canyon (California), resembles the two nominal species from Sweden. Analysis of whole mitochondrial genomes places the three larger species as a sister clade to the smaller Atlantic and Pacific species. Phylogenomic analyses of transcriptomic sequences support placement of Xenacoelomorpha as sister to Nephrozoa or Protostomia.
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Xenoturbellida and Acoelomorpha are marine worms with contentious ancestry. Both were originally associated with the flatworms (Platyhelminthes), but molecular data have revised their phylogenetic positions, generally linking Xenoturbellida to the deuterostomes and positioning the Acoelomorpha as the most basally branching bilaterian group(s). Recent phylogenomic data suggested that Xenoturbellida and Acoelomorpha are sister taxa and together constitute an early branch of Bilateria. Here we assemble three independent data sets-mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions and new microRNA (miRNA) complements-and show that the position of Acoelomorpha is strongly affected by a long-branch attraction (LBA) artefact. When we minimize LBA we find consistent support for a position of both acoelomorphs and Xenoturbella within the deuterostomes. The most likely phylogeny links Xenoturbella and Acoelomorpha in a clade we call Xenacoelomorpha. The Xenacoelomorpha is the sister group of the Ambulacraria (hemichordates and echinoderms). We show that analyses of miRNA complements have been affected by character loss in the acoels and that both groups possess one miRNA and the gene Rsb66 otherwise specific to deuterostomes. In addition, Xenoturbella shares one miRNA with the ambulacrarians, and two with the acoels. This phylogeny makes sense of the shared characteristics of Xenoturbellida and Acoelomorpha, such as ciliary ultrastructure and diffuse nervous system, and implies the loss of various deuterostome characters in the Xenacoelomorpha including coelomic cavities, through gut and gill slits.
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The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other.
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Deuterostomes comprise vertebrates, the related invertebrate chordates (tunicates and cephalochordates) and three other invertebrate taxa: hemichordates, echinoderms and Xenoturbella. The relationships between invertebrate and vertebrate deuterostomes are clearly important for understanding our own distant origins. Recent phylogenetic studies of chordate classes and a sea urchin have indicated that urochordates might be the closest invertebrate sister group of vertebrates, rather than cephalochordates, as traditionally believed. More remarkable is the suggestion that cephalochordates are closer to echinoderms than to vertebrates and urochordates, meaning that chordates are paraphyletic. To study the relationships among all deuterostome groups, we have assembled an alignment of more than 35,000 homologous amino acids, including new data from a hemichordate, starfish and Xenoturbella. We have also sequenced the mitochondrial genome of Xenoturbella. We support the clades Olfactores (urochordates and vertebrates) and Ambulacraria (hemichordates and echinoderms). Analyses using our new data, however, do not support a cephalochordate and echinoderm grouping and we conclude that chordates are monophyletic. Finally, nuclear and mitochondrial data place Xenoturbella as the sister group of the two ambulacrarian phyla. As such, Xenoturbella is shown to be an independent phylum, Xenoturbellida, bringing the number of living deuterostome phyla to four.
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Xenoturbella bocki, first described in 1949 (ref. 1), is a delicate, ciliated, marine worm with a simple body plan: it lacks a through gut, organized gonads, excretory structures and coelomic cavities. Its nervous system is a diffuse nerve net with no brain. Xenoturbella's affinities have long been obscure and it was initially linked to turbellarian flatworms. Subsequent authors considered it variously as related to hemichordates and echinoderms owing to similarities of nerve net and epidermal ultrastructure, to acoelomorph flatworms based on body plan and ciliary ultrastructure (also shared by hemichordates), or as among the most primitive of Bilateria. In 1997 two papers seemed to solve this uncertainty: molecular phylogenetic analyses placed Xenoturbella within the bivalve molluscs, and eggs and larvae resembling those of bivalves were found within specimens of Xenoturbella. This molluscan origin implies that all bivalve characters are lost during a radical metamorphosis into the adult Xenoturbella. Here, using data from three genes, we show that the samples in these studies were contaminated by bivalve embryos eaten by Xenoturbella and that Xenoturbella is in fact a deuterostome related to hemichordates and echinoderms.