Re-evaluating the phylogenetic position of the enigmatic early Cambrian deuterostome Yanjiahella

Echinoderms are a diverse clade of marine invertebrates with a distinctive body plan. Extant forms are characterized by a calcite skeleton with a mesh-like microstructure (stereom), pentaradial symmetry as adults developed after metamorphosis from a bilateral larva, and a water vascular system with tube feet1. These characters differentiate echinoderms from their sister group, the bilaterally symmetric hemichordates2. The morphological gulf between these phyla means that key questions, such as when and how echinoderms diverged from the latest common ancestor shared with hemichordates, have no immediate answer. Topper et al.3 report Yanjiahella biscarpa from the Fortunian (~541.0–534.6 Ma) of Hubei Province, China claiming it to be the oldest, most plesiomorphic echinoderm yet discovered. Yanjiahella is ~15–20 million years older than the earliest unequivocal echinoderms reported to date4. Topper et al.3 interpret it as a hemichordate-like echinoderm bridging the gap between these two morphologically disparate sister phyla, with important implications for understanding the origin and early evolution of echinoderms. However, this paper fails to identify a single echinoderm synapomorphy in the fossil material they describe. Moreover, our re-analysis of their phylogenetic character matrix demonstrates that placement of Yanjiahella is ambiguous. Affinities of Yanjiahella and its potential significance for understanding deuterostome evolution are unclear. Topper et al.3 report no trace of stereom in Yanjiahella biscarpa, claiming its absence in the 35 studied specimens results from their preservation as natural molds in gray-black silty-shale, rather than evidence of absence. Most Cambrian echinoderms are preserved as molds, with the original calcite skeleton dissolved during weathering and/or diagenesis. Yet presence of stereom can typically be inferred by direct observations following removal of iron oxides and calcite residues using oxalic acid solutions or latex cast series. Subsequent casting of these molds using latex often reveals relic “ghost” surface textures typical of echinoderms (Fig. 1). Even when these textures are not preserved, latex casting can still provide critical information allowing recognition of skeletal plate arrangements and the position of major apertures. If Yanjiahella originally had stereom microstructure in its skeleton, we would expect to see evidence of this in latex casts of the fossils or on the surfaces of the fossils under SEM, once the specimens had been properly prepared, but Topper et al.3 carried out no such work. Indeed, many of the morphological uncertainties about Yanjiahella expressed in Topper et al.3 including the original composition, shape and arrangement of plates, and https://doi.org/10.1038/s41467-020-14920-x OPEN

Nature Research wishes to improve the reproducibility of the work that we publish. This form provides structure for consistency and transparency in reporting. For further information on Nature Research policies, seeAuthors & Referees and theEditorial Policy Checklist .

Statistics
For all statistical analyses, confirm that the following items are present in the figure legend, table legend, main text, or Methods section.

n/a Confirmed
The exact sample size (n) for each experimental group/condition, given as a discrete number and unit of measurement A statement on whether measurements were taken from distinct samples or whether the same sample was measured repeatedly The statistical test(s) used AND whether they are one-or two-sided Only common tests should be described solely by name; describe more complex techniques in the Methods section.
A description of all covariates tested A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons A full description of the statistical parameters including central tendency (e.g. means) or other basic estimates (e.g. regression coefficient) AND variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals) For null hypothesis testing, the test statistic (e.g. F, t, r) with confidence intervals, effect sizes, degrees of freedom and P value noted Give P values as exact values whenever suitable.

For Bayesian analysis, information on the choice of priors and Markov chain Monte Carlo settings
For hierarchical and complex designs, identification of the appropriate level for tests and full reporting of outcomes Estimates of effect sizes (e.g. Cohen's d, Pearson's r), indicating how they were calculated Our web collection on statistics for biologists contains articles on many of the points above.

Software and code
Policy information about availability of computer code Data collection

Data analysis
For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors/reviewers. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research guidelines for submitting code & software for further information.

Data
Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A list of figures that have associated raw data -A description of any restrictions on data availability 2 nature research | reporting summary

October 2018
For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study design
All studies must disclose on these points even when the disclosure is negative.

Palaeontology
Specimen provenance

Specimen deposition
Describe how sample size was determined, detailing any statistical methods used to predetermine sample size OR if no sample-size calculation was performed, describe how sample sizes were chosen and provide a rationale for why these sample sizes are sufficient.
Describe any data exclusions. If no data were excluded from the analyses, state so OR if data were excluded, describe the exclusions and the rationale behind them, indicating whether exclusion criteria were pre-established.
Describe the measures taken to verify the reproducibility of the experimental findings. If all attempts at replication were successful, confirm this OR if there are any findings that were not replicated or cannot be reproduced, note this and describe why.
Describe how samples/organisms/participants were allocated into experimental groups. If allocation was not random, describe how covariates were controlled OR if this is not relevant to your study, explain why.
Describe whether the investigators were blinded to group allocation during data collection and/or analysis. If blinding was not possible, describe why OR explain why blinding was not relevant to your study.
Describe all antibodies used in the study; as applicable, provide supplier name, catalog number, clone name, and lot number.
Describe the validation of each primary antibody for the species and application, noting any validation statements on the manufacturer's website, relevant citations, antibody profiles in online databases, or data provided in the manuscript.
State the source of each cell line used.
Describe the authentication procedures for each cell line used OR declare that none of the cell lines used were authenticated.
Confirm that all cell lines tested negative for mycoplasma contamination OR describe the results of the testing for mycoplasma contamination OR declare that the cell lines were not tested for mycoplasma contamination.
Name any commonly misidentified cell lines used in the study and provide a rationale for their use.
n/a n/a 3 nature research | reporting summary

October 2018
Dating methods Tick this box to confirm that the raw and calibrated dates are available in the paper or in Supplementary Information.

Animals and other organisms
Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research Laboratory animals

Wild animals
Field-collected samples

Ethics oversight
Note that full information on the approval of the study protocol must also be provided in the manuscript.

Human research participants
Policy information about studies involving human research participants Population characteristics

Recruitment
Ethics oversight Note that full information on the approval of the study protocol must also be provided in the manuscript.

Clinical data Policy information about clinical studies
All manuscripts should comply with the ICMJEguidelines for publication of clinical research and a completedCONSORT checklist must be included with all submissions.

Clinical trial registration
Study protocol

Data collection
Outcomes ChIP-seq

Data deposition
Confirm that both raw and final processed data have been deposited in a public database such as GEO.
Confirm that you have deposited or provided access to graph files (e.g. BED files) for the called peaks.

Data access links
May remain private before publication.

Files in database submission
Genome browser session (e.g. UCSC)

Methodology
Replicates n/a For laboratory animals, report species, strain, sex and age OR state that the study did not involve laboratory animals.
Provide details on animals observed in or captured in the field; report species, sex and age where possible. Describe how animals were caught and transported and what happened to captive animals after the study (if killed, explain why and describe method; if released, say where and when) OR state that the study did not involve wild animals.
For laboratory work with field-collected samples, describe all relevant parameters such as housing, maintenance, temperature, photoperiod and end-of-experiment protocol OR state that the study did not involve samples collected from the field.
Identify the organization(s) that approved or provided guidance on the study protocol, OR state that no ethical approval or guidance was required and explain why not.
Describe the covariate-relevant population characteristics of the human research participants (e.g. age, gender, genotypic information, past and current diagnosis and treatment categories). If you filled out the behavioural & social sciences study design questions and have nothing to add here, write "See above." Describe how participants were recruited. Outline any potential self-selection bias or other biases that may be present and how these are likely to impact results.
Identify the organization(s) that approved the study protocol.
Provide the trial registration number from ClinicalTrials.gov or an equivalent agency.
Note where the full trial protocol can be accessed OR if not available, explain why.
Describe the settings and locales of data collection, noting the time periods of recruitment and data collection.
Describe how you pre-defined primary and secondary outcome measures and how you assessed these measures.
For "Initial submission" or "Revised version" documents, provide reviewer access links. For your "Final submission" document, provide a link to the deposited data.