Organ systems of a Cambrian euarthropod larva.

The Cambrian radiation of euarthropods can be attributed to an adaptable body plan. Sophisticated brains and specialized feeding appendages, which are elaborations of serially repeated organ systems and jointed appendages, underpin the dominance of Euarthropoda in a broad suite of ecological settings. The origin of the euarthropod body plan from a grade of vermiform taxa with hydrostatic lobopodous appendages ('lobopodian worms')1,2 is founded on data from Burgess Shale-type fossils. However, the compaction associated with such preservation obscures internal anatomy3-6. Phosphatized microfossils provide a complementary three-dimensional perspective on early crown group euarthropods7, but few lobopodians8,9. Here we describe the internal and external anatomy of a three-dimensionally preserved euarthropod larva with lobopods, midgut glands and a sophisticated head. The architecture of the nervous system informs the early configuration of the euarthropod brain and its associated appendages and sensory organs, clarifying homologies across Panarthropoda. The deep evolutionary position of Youti yuanshi gen. et sp. nov. informs the sequence of character acquisition during arthropod evolution, demonstrating a deep origin of sophisticated haemolymph circulatory systems, and illuminating the internal anatomical changes that propelled the rise and diversification of this enduringly successful group.

Protomelission is an early dasyclad alga and not a Cambrian bryozoan.

The animal phyla and their associated body plans originate from a singular burst of evolution occurring during the Cambrian period, over 500 million years ago1. The phylum Bryozoa, the colonial 'moss animals', have been the exception: convincing skeletons of this biomineralizing clade have been absent from Cambrian strata, in part because potential bryozoan fossils are difficult to distinguish from the modular skeletons of other animal and algal groups2,3. At present, the strongest candidate4 is the phosphatic microfossil Protomelission5. Here we describe exceptionally preserved non-mineralized anatomy in Protomelission-like macrofossils from the Xiaoshiba Lagerstätte6. Taken alongside the detailed skeletal construction and the potential taphonomic origin of 'zooid apertures', we consider that Protomelission is better interpreted as the earliest dasycladalean green alga-emphasizing the ecological role of benthic photosynthesizers in early Cambrian communities. Under this interpretation, Protomelission cannot inform the origins of the bryozoan body plan; despite a growing number of promising candidates7-9, there remain no unequivocal bryozoans of Cambrian age.

The Cambrian cirratuliform Iotuba denotes an early annelid radiation.

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

Robust Analysis of Phylogenetic Tree Space.

Phylogenetic analyses often produce large numbers of trees. Mapping trees' distribution in "tree space" can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences between different data sources or phylogenetic methods-but the high-dimensional spaces defined by metric distances are necessarily distorted when represented in fewer dimensions. Here, I explore the consequences of this transformation in phylogenetic search results from 128 morphological data sets, using stratigraphic congruence-a complementary aspect of tree similarity-to evaluate the utility of low-dimensional mappings. I find that phylogenetic similarities between cladograms are most accurately depicted in tree spaces derived from information-theoretic tree distances or the quartet distance. Robinson-Foulds tree spaces exhibit prominent distortions and often fail to group trees according to phylogenetic similarity, whereas the strong influence of tree shape on the Kendall-Colijn distance makes its tree space unsuitable for many purposes. Distances mapped into two or even three dimensions often display little correspondence with true distances, which can lead to profound misrepresentation of clustering structure. Without explicit testing, one cannot be confident that a tree space mapping faithfully represents the true distribution of trees, nor that visually evident structure is valid. My recommendations for tree space validation and visualization are implemented in a new graphical user interface in the "TreeDist" R package. [Multidimensional scaling; phylogenetic software; tree distance metrics; treespace projections.].

Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees.

"Rogue" taxa of uncertain affinity can confound attempts to summarize the results of phylogenetic analyses. Rogues reduce resolution and support values in consensus trees, potentially obscuring strong evidence for relationships between other taxa. Information theory provides a principled means of assessing the congruence between a set of trees and their consensus, allowing rogue taxa to be identified more effectively than when using ad hoc measures of tree quality. A basic implementation of this approach in R recovers reduced consensus trees that are better resolved, more accurate, and more informative than those generated by existing methods. [Consensus trees; information theory; phylogenetic software; Rogue taxa.].

Phylogenetic Signal and Bias in Paleontology.

An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data typically used in paleontology (bones and teeth) from six data sets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological data sets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA data sets usually increases congruence of resulting topologies to the well-corroborated tree, but this varies among morphological data sets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artifacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation. [Concatenation; fossilization; morphology; parsimony; systematics; taphonomy; total-evidence.].

Hyoliths are Palaeozoic lophophorates.

Hyoliths are abundant and globally distributed 'shelly' fossils that appear early in the Cambrian period and can be found throughout the 280 million year span of Palaeozoic strata. The ecological and evolutionary importance of this group has remained unresolved, largely because of their poorly constrained soft anatomy and idiosyncratic scleritome, which comprises an operculum, a conical shell and, in some taxa, a pair of lateral spines (helens). Since their first description over 175 years ago, hyoliths have most often been regarded as incertae sedis, related to molluscs or assigned to their own phylum. Here we examine over 1,500 specimens of the mid-Cambrian hyolith Haplophrentis from the Burgess Shale and Spence Shale Lagerstätten. We reconstruct Haplophrentis as a semi-sessile, epibenthic suspension feeder that could use its helens to elevate its tubular body above the sea floor. Exceptionally preserved soft tissues include an extendable, gullwing-shaped, tentacle-bearing organ surrounding a central mouth, which we interpret as a lophophore, and a U-shaped digestive tract ending in a dorsolateral anus. Together with opposing bilateral sclerites and a deep ventral visceral cavity, these features indicate an affinity with the lophophorates (brachiopods, phoronids and tommotiids), substantially increasing the morphological disparity of this prominent group.

Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees.

MOTIVATION: The Robinson-Foulds (RF) metric is widely used by biologists, linguists and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies the number of bipartition splits that occur in both trees-but this conservative approach ignores potential similarities between almost-identical splits, with undesirable consequences. 'Generalized' RF metrics address this shortcoming by pairing splits in one tree with similar splits in the other. Each pair is assigned a similarity score, the sum of which enumerates the similarity between two trees. The challenge lies in quantifying split similarity: existing definitions lack a principled statistical underpinning, resulting in misleading tree distances that are difficult to interpret. Here, I propose probabilistic measures of split similarity, which allow tree similarity to be measured in natural units (bits). RESULTS: My new information-theoretic metrics outperform alternative measures of tree similarity when evaluated against a broad suite of criteria, even though they do not account for the non-independence of splits within a single tree. Mutual clustering information exhibits none of the undesirable properties that characterize other tree comparison metrics, and should be preferred to the RF metric. AVAILABILITY AND IMPLEMENTATION: The methods discussed in this article are implemented in the R package 'TreeDist', archived at https://dx.doi.org/10.5281/zenodo.3528123. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Hallucigenia's head and the pharyngeal armature of early ecdysozoans.

The molecularly defined clade Ecdysozoa comprises the panarthropods (Euarthropoda, Onychophora and Tardigrada) and the cycloneuralian worms (Nematoda, Nematomorpha, Priapulida, Loricifera and Kinorhyncha). These disparate phyla are united by their means of moulting, but otherwise share few morphological characters--none of which has a meaningful fossilization potential. As such, the early evolutionary history of the group as a whole is largely uncharted. Here we redescribe the 508-million-year-old stem-group onychophoran Hallucigenia sparsa from the mid-Cambrian Burgess Shale. We document an elongate head with a pair of simple eyes, a terminal buccal chamber containing a radial array of sclerotized elements, and a differentiated foregut that is lined with acicular teeth. The radial elements and pharyngeal teeth resemble the sclerotized circumoral elements and pharyngeal teeth expressed in tardigrades, stem-group euarthropods and cycloneuralian worms. Phylogenetic results indicate that equivalent structures characterized the ancestral panarthropod and, seemingly, the ancestral ecdysozoan, demonstrating the deep homology of panarthropod and cycloneuralian mouthparts, and providing an anatomical synapomorphy for the ecdysozoan supergroup.

An algorithm for Morphological Phylogenetic Analysis with Inapplicable Data.

Morphological data play a key role in the inference of biological relationships and evolutionary history and are essential for the interpretation of the fossil record. The hierarchical interdependence of many morphological characters, however, complicates phylogenetic analysis. In particular, many characters only apply to a subset of terminal taxa. The widely used "reductive coding" approach treats taxa in which a character is inapplicable as though the character's state is simply missing (unknown). This approach has long been known to create spurious tree length estimates on certain topologies, potentially leading to erroneous results in phylogenetic searches-but pratical solutions have yet to be proposed and implemented. Here, we present a single-character algorithm for reconstructing ancestral states in reductively coded data sets, following the theoretical guideline of minimizing homoplasy over all characters. Our algorithm uses up to three traversals to score a tree, and a fourth to fully resolve final states at each node within the tree. We use explicit criteria to resolve ambiguity in applicable/inapplicable dichotomies, and to optimize missing data. So that it can be applied to single characters, the algorithm employs local optimization; as such, the method provides a fast but approximate inference of ancestral states and tree score. The application of our method to published morphological data sets indicates that, compared to traditional methods, it identifies different trees as "optimal." As such, the use of our algorithm to handle inapplicable data may significantly alter the outcome of tree searches, modifying the inferred placement of living and fossil taxa and potentially leading to major differences in reconstructions of evolutionary history.

Hallucigenia's onychophoran-like claws and the case for Tactopoda.

The Palaeozoic form-taxon Lobopodia encompasses a diverse range of soft-bodied 'legged worms' known from exceptional fossil deposits. Although lobopodians occupy a deep phylogenetic position within Panarthropoda, a shortage of derived characters obscures their evolutionary relationships with extant phyla (Onychophora, Tardigrada and Euarthropoda). Here we describe a complex feature in the terminal claws of the mid-Cambrian lobopodian Hallucigenia sparsa--their construction from a stack of constituent elements--and demonstrate that equivalent elements make up the jaws and claws of extant Onychophora. A cladistic analysis, informed by developmental data on panarthropod head segmentation, indicates that the stacked sclerite components in these two taxa are homologous-resolving hallucigeniid lobopodians as stem-group onychophorans. The results indicate a sister-group relationship between Tardigrada and Euarthropoda, adding palaeontological support to the neurological and musculoskeletal evidence uniting these disparate clades. These findings elucidate the evolutionary transformations that gave rise to the panarthropod phyla, and expound the lobopodian-like morphology of the ancestral panarthropod.

Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets.

Phylogenetic analysis aims to establish the true relationships between taxa. Different analytical methods, however, can reach different conclusions. In order to establish which approach best reconstructs true relationships, previous studies have simulated datasets from known tree topologies, and identified the method that reconstructs the generative tree most accurately. On this basis, researchers have argued that morphological datasets should be analysed by Bayesian approaches, which employ an explicit probabilistic model of evolution, rather than parsimony methods-with implied weights parsimony sometimes identified as particularly inaccurate. Accuracy alone, however, is an inadequate measure of a tree's utility: a fully unresolved tree is perfectly accurate, yet contains no phylogenetic information. The highly resolved trees recovered by implied weights parsimony in fact contain as much useful information as the more accurate, but less resolved, trees recovered by Bayesian methods. By collapsing poorly supported groups, this superior resolution can be traded for accuracy, resulting in trees as accurate as those obtained by a Bayesian approach. By contrast, equally weighted parsimony analysis produces trees that are less resolved and less accurate, leading to less reliable evolutionary conclusions.

Hyoliths with pedicles illuminate the origin of the brachiopod body plan.

Hyoliths are a taxonomically problematic group of Palaeozoic lophotrochozoans that are among the first shelly fossils to appear in the Cambrian period. On the basis of their distinctive exoskeleton, hyoliths have historically been classified as a separate phylum with possible affinities to the molluscs, sipunculans or lophophorates-but their precise phylogenetic position remains uncertain. Here, we describe a new orthothecide hyolith from the Chengjiang Lagerstätte (Cambrian Series 2 Stage 3), Pedunculotheca diania Sun, Zhao et Zhu gen. et sp. nov., which exhibits a non-mineralized attachment structure that strikingly resembles the brachiopod pedicle-the first report of a peduncular organ in hyoliths. This organ establishes a sessile, suspension feeding ecology for these orthothecides and-together with other characteristics (e.g. bilaterally symmetrical bivalve shell enclosing a filtration chamber and the differentiation of cardinal areas)-identifies hyoliths as stem-group brachiopods. Our phylogenetic analysis indicates that both hyoliths and crown brachiopods derived from a tommotiid grade, and that the pedicle has a single origin within the brachiopod total group.

Onychophoran-like musculature in a phosphatized Cambrian lobopodian.

The restricted, exclusively terrestrial distribution of modern Onychophora contrasts strikingly with the rich diversity of onychophoran-like fossils preserved in marine Cambrian Lagerstätten The transition from these early forebears to the modern onychophoran body plan is poorly constrained, in part owing to the absence of fossils preserving details of the soft anatomy. Here, we report muscle tissue in a new early Cambrian (Stage 3) lobopodian, Tritonychus phanerosarkus gen. et sp. nov., preserved in the Orsten fashion by three-dimensional replication in phosphate. This first report of Palaeozoic onychophoran musculature establishes peripheral musculature as a characteristic of the ancestral panarthropod, but documents an unexpected muscular configuration. Phylogenetic analysis reconstructs T. phanerosarkus as one of a few members of the main onychophoran lineage-which was as rare and as cryptic in the Cambrian period as it is today.

Primitive soft-bodied cephalopods from the Cambrian.

The exquisite preservation of soft-bodied animals in Burgess Shale-type deposits provides important clues into the early evolution of body plans that emerged during the Cambrian explosion. Until now, such deposits have remained silent regarding the early evolution of extant molluscan lineages-in particular the cephalopods. Nautiloids, traditionally considered basal within the cephalopods, are generally depicted as evolving from a creeping Cambrian ancestor whose dorsal shell afforded protection and buoyancy. Although nautiloid-like shells occur from the Late Cambrian onwards, the fossil record provides little constraint on this model, or indeed on the early evolution of cephalopods. Here, we reinterpret the problematic Middle Cambrian animal Nectocaris pteryx as a primitive (that is, stem-group), non-mineralized cephalopod, based on new material from the Burgess Shale. Together with Nectocaris, the problematic Lower Cambrian taxa Petalilium and (probably) Vetustovermis form a distinctive clade, Nectocarididae, characterized by an open axial cavity with paired gills, wide lateral fins, a single pair of long, prehensile tentacles, a pair of non-faceted eyes on short stalks, and a large, flexible anterior funnel. This clade extends the cephalopods' fossil record by over 30 million years, and indicates that primitive cephalopods lacked a mineralized shell, were hyperbenthic, and were presumably carnivorous. The presence of a funnel suggests that jet propulsion evolved in cephalopods before the acquisition of a shell. The explosive diversification of mineralized cephalopods in the Ordovician may have an understated Cambrian 'fuse'.

Beyond the Burgess Shale: Cambrian microfossils track the rise and fall of hallucigeniid lobopodians.

Burgess Shale-type deposits are renowned for their exquisite preservation of soft-bodied organisms, representing a range of animal body plans that evolved during the Cambrian 'explosion'. However, the rarity of these fossil deposits makes it difficult to reconstruct the broader-scale distributions of their constituent organisms. By contrast, microscopic skeletal elements represent an extensive chronicle of early animal evolution--but are difficult to interpret in the absence of corresponding whole-body fossils. Here, we provide new observations on the dorsal spines of the Cambrian lobopodian (panarthropod) worm Hallucigenia sparsa from the Burgess Shale (Cambrian Series 3, Stage 5). These exhibit a distinctive scaly microstructure and layered (cone-in-cone) construction that together identify a hitherto enigmatic suite of carbonaceous and phosphatic Cambrian microfossils--including material attributed to Mongolitubulus, Rushtonites and Rhombocorniculum--as spines of Hallucigenia-type lobopodians. Hallucigeniids are thus revealed as an important and widespread component of disparate Cambrian communities from late in the Terreneuvian (Cambrian Stage 2) through the 'middle' Cambrian (Series 3); their apparent decline in the latest Cambrian may be partly taphonomic. The cone-in-cone construction of hallucigeniid sclerites is shared with the sclerotized cuticular structures (jaws and claws) in modern onychophorans. More generally, our results emphasize the reciprocal importance and complementary roles of Burgess Shale-type fossils and isolated microfossils in documenting early animal evolution.

Evolution: Assembling the deuterostome body plan.

Starfish, graptolites and humans look as different as can be, yet are more closely related to each other than to any other phylum. Disc-shaped Cambrian fossils join the dots between these disparate body plans to plot out their evolutionary origins.

Mouthparts of the Burgess Shale fossils Odontogriphus and Wiwaxia: implications for the ancestral molluscan radula.

The Middle Cambrian lophotrochozoans Odontogriphus omalus and Wiwaxia corrugata have been interpreted as stem-group members of either the Mollusca, the Annelida, or a group containing Mollusca + Annelida. The case for each classification rests on the organisms' unusual mouthparts, whose two to three tooth-rows resemble both the molluscan radula and the jaws of certain annelid worms. Despite their potential significance, these mouthparts have not previously been described in detail. This study examined the feeding apparatuses of over 300 specimens from the 505-million-year-old Burgess Shale, many of which were studied for the first time. Rather than denticulate plates, each tooth row comprises a single axial tooth that is flanked on each side by eight to 16 separate shoehorn-shaped teeth. Tooth rows sat on a grooved basal tongue, and two large lobes flanked the apparatus. New observations--the shape, distribution and articulation of the individual teeth, and the mouthparts' mode of growth--are incompatible with an annelid interpretation, instead supporting a classification in Mollusca. The ancestral molluscan radula is best reconstructed as unipartite with a symmetrical medial tooth, and Odontogriphus and Wiwaxia as grazing deposit-feeders.

A 'hermit' shell-dwelling lifestyle in a Cambrian priapulan worm.

The Cambrian 'explosion', about 530 million years ago, marks a rapid diversification of the major animal lineages1. A concomitant increase in the complexity of ecosystems is believed to have accelerated this evolutionary radiation2, but direct evidence of the ecological modes of Cambrian taxa is nevertheless scarce - even in exceptional Burgess Shale-type deposits3. Here, we present new fossil material from the Cambrian (Stage 4) Guanshan biota in southern China that reveals the consistent occurrence of the priapulan worm ?Eximipriapulus4 within the conical shells of hyoliths. This represents the first direct evidence of a 'hermiting' life strategy - the adoption of a different organism's exoskeleton - in the priapulans and within the Palaeozoic era. It highlights the intense degree of convergent evolution during the Cambrian radiation. Hermiting behaviour has previously been linked with the escalation of predation pressure during the Mesozoic marine revolution5; such intensity of predation may also have characterised early Cambrian oceans.