Cambrian edrioasteroid reveals new mechanism for secondary reduction of the skeleton in echinoderms

Abstract

Echinoderms are characterized by a distinctive high-magnesium calcite endoskeleton as adults, but elements of this have been drastically reduced in some groups. Herein, we describe a new pentaradial echinoderm, Yorkicystis haefneri n. gen. n. sp., which provides, to our knowledge, the oldest evidence of secondary non-mineralization of the echinoderm skeleton. This material was collected from the Cambrian Kinzers Formation in York (Pennsylvania, USA) and is dated as ca 510 Ma. Detailed morphological observations demonstrate that the ambulacra (i.e. axial region) are composed of flooring and cover plates, but the rest of the body (i.e. extraxial region) is preserved as a dark film and lacks any evidence of skeletal plating. Moreover, X-ray fluorescence analysis reveals that the axial region is elevated in iron. Based on our morphological and chemical data and on taphonomic comparisons with other fossils from the Kinzers Formation, we infer that the axial region was originally calcified, while the extraxial region was non-mineralized. Phylogenetic analyses recover Yorkicystis as an edrioasteroid, indicating that this partial absence of skeleton resulted from a secondary reduction. We hypothesize that skeletal reduction resulted from lack of expression of the skeletogenic gene regulatory network in the extraxial body wall during development. Secondary reduction of the skeleton in Yorkicystis might have allowed for greater flexibility of the body wall.

1. Introduction

Animals are characterized by an enormous diversity of biomineralized skeletons, which perform important functions such as protecting the internal organs or supporting the body structure. Elucidating the origins of animal biomineralization is a major research focus in evolutionary and geobiology; skeletons are thought to have evolved independently in various clades during the latest Ediacaran or early Cambrian through co-option of a conserved ancestral genetic toolkit [1,2], with possible drivers including changing seawater chemistry, oxygen availability or increasing predation pressure [3,4]. However, the pattern and process of skeletal loss, widespread across animal phylogeny [5], is much less well studied, and it remains unclear if commonalities exist in how and why skeletons are reduced among species.

Echinoderms, with their distinctive high-magnesium calcite endoskeleton, are a model system for studying the evolution and development of the skeleton [6]. Calcareous plates or ossicles are ubiquitous in most echinoderm bodies, but the mineralized skeleton has been greatly reduced in some groups. For example, in derived crinoids the ambulacral flooring plates are decalcified [7], whereas in crown-group holothurians, mineralization of the body wall skeleton is mostly reduced to small spicules [8]. Thus, reduction of mineralization primarily affects distinct parts of the body in different classes; in crinoids, the axial region (i.e. parts of the body associated with the water vascular system) is most strongly affected, whereas in holothurians, there is greater loss of mineralization in the extraxial region (i.e. the rest of the body). Although developmental mechanisms associated with skeletal formation are well understood in many echinoderms [9,10], the processes involved in skeletal reduction remain enigmatic. The reasons why some echinoderm groups reduced mineralization in their skeleton are also unclear, with explanations ranging from adaptation to more mobile lifestyles [11] to reducing the energetic cost of skeletogenesis [12].

Here, we describe a new echinoderm from the Cambrian of the USA, which has a unique body plan consisting of a calcified axial skeleton and a non-mineralized extraxial region. This taxon demonstrates that skeletal non-mineralization in echinoderms first occurred during the Cambrian, in a fundamentally different way to all other species.

2. Material and methods

Two specimens (Natural History Museum of London, UK (NHMUK) EE 1659, 1660), preserved as external moulds in laminated brown shale, were collected from the Emigsville Member of the Kinzers Formation in York, Pennsylvania, USA (for more information about this formation and fossil content, see [13]). Specimens were obtained from the south slope of the City View Church yard by Mr Christopher Haefner in November 2018 (with permission from the church community). The coordinates of the exposure are 39.9842302 N, 76.7644671 W. At this locality, the Kinzers Formation crops out in a small tectonic block that includes the Emigsville and York members. Excavation yielded a rich associated fauna of trilobites, echinoderms (Lepidocystis and Camptostroma) and soft-bodied organisms (e.g. radiodontans). Echinoderms from this formation always show three-dimensional preservation of the skeleton. The Kinzers Formation extends from the middle Dyeran Stage to somewhere within the Delamaran Stage of the Laurentian zonation scheme for the Cambrian. The olenelloid trilobites Wanneria walcottana and Olenellus roddyi recovered from the City View Church site are consistent with this age assignment (Webster personal communication 26 March, 2019). This falls within Stage 4 of the Cambrian in the global chronostratigraphic scale, approximately 510 Ma [14,15].

Specimens were photographed under natural light, both dry and submerged in water. To investigate the elemental distribution of the fossils, NHMUK EE 1659 was analysed using a Bruker Tornado M4 + micro X-ray fluorescence (XRF) scanning spectrometer at University College London. Analysis with the Tornado M4 + was performed under a 2 mbar vacuum. The system has an X-ray tube with a rhodium target which was used with a 35 kV accelerating voltage and an 800 µA current. The dwell time was 100 µs, the resolution was 1228 × 888 pixels and the pixel size was 25 µm. The resulting fluorescence signal was detected using two silicon drift detector spectrometers. Lastly, specimens were cast in latex, with the resulting casts whitened with NH₄Cl sublimate prior to photography. Specimens are housed at the NHMUK. Comparative material of other echinoderms from the Kinzers Formation is deposited in the Museum of Comparative Zoology (Harvard University) and National Museum of Natural History (Smithsonian Institution).

To establish the relationships between Yorkicystis and other early echinoderms, parsimony and Bayesian phylogenetic analyses were performed. We chose to focus exclusively on pentaradial forms because all recent phylogenetic analyses [16–21] have recovered these as derived in echinoderm phylogeny. We selected all the major pentaradial morphotypes present in the Cambrian and early Ordovician for which fossil material is sufficiently well known, including a spiral form (Helicocystis), early edrioasteroids (Kailidiscus and Stromatocystites), isorophid edrioasteroids (Isorophus and Argodiscus), plesiomorphic blastozoans (Lepidocystis, Gogia and Vyscystis), an early glyptocystitid (Ridersia) and the earliest crinoids (Titanocrinus and Apektocrinus). Helicoplacus was chosen as the outgroup because it is a triradial form that is widely regarded as the sister group to pentaradial forms [17,22]. Morphological information was obtained from direct observations of fossil specimens and the published literature. Most of the taxa were coded as in previous phylogenetic analyses [23–25]. The final character matrix consisted of 13 taxa and 28 characters (electronic supplementary material, table S1). Parsimony analyses were run using the branch and bound algorithm in the program Paup* v. 4.0a [26]. Bayesian analyses were run using MrBayes v. 3.2 [27] using the Mkv model [28]. Rate variation was modelled using a gamma distribution with a prior of exponential (1.0). Branch lengths were unconstrained with a compound Dirichlet prior. Two differing values of the symmetric Dirichlet hyperprior were used to account for differing transition rate asymmetries. The joint posterior distribution of model parameters, branch lengths, and tree topologies was estimated using Markov chain Monte Carlo (MCMC). Additional details of phylogenetic analyses and MCMC convergence are provided in the electronic supplementary material.

3. Results

(a) . Morphology of Yorkicystis gen. nov

The body of Yorkicystis haefneri gen. et sp. nov. is divided into two main regions that are preserved in different ways and correspond to the extraxial and axial body walls (sensu [29,30]). The extraxial region of Y. haefneri gen. et sp. nov. consists of a globular body (figures 1a,b and 2a,b; electronic supplementary material, figure S3), measuring 23 mm wide and 18 mm long in the most complete specimen (NHMUK EE 1659). It is preserved as a dark film (figure 2a), with no evidence of skeletal plating (figure 1a,b; electronic supplementary material, figure S3). No attachment structure or body openings (e.g. periproct, gonopore, hydropore) are preserved.

Figure 1.

Yorkicystis haefneri from the early Cambrian Kinzers Formation (York, Pennsylvania). (a) NHMUK EE 1659, holotype complete specimen. (b) NHMUK EE 1660, paratype complete specimen. (c,d) NHMUK EE 1660, ambulacrum in lateral view. (e) NHMUK EE 1659, ambulacrum in lateral view. (f–i). NHMUK EE 1659, ambulacrum in plan view, part (f,g) and counterpart (h,i). Colours: red, flooring plates; green, primary of cover plates; yellow, cover plates. amb, ambulacrum; at, ambulacral tip; cp, cover plate; fp, flooring plate; pcp, primary cover plate; pe, peristome; pp, podial pore. All images are photographs of latex casts whitened with NH₄Cl sublimate. (Online version in colour.)

Figure 2.

Yorkicystis haefneri from the early Cambrian Kinzers Formation (York, Pennsylvania). (NHMUK EE 1659). (a) Photograph of specimen submerged in water. (b) False-colour element map generated using X-ray fluorescence analysis showing Fe (green), Si (blue) and P (red); intensity of colour corresponds to element intensity. axp, axial part; exp, extraxial part; pe, peristome. (Online version in colour.)

The axial region is composed of five large, probably straight, recumbent ambulacra that converge in the peristomial region and presumably originate at the centrally located mouth (figures 1a,b and 2a,b). The ambulacra are long (maximum length of 20 mm in the holotype and 24 mm in the paratype), wide in plan view and slightly taper in width distally (figure 1a–e). Each ambulacrum is composed of two series of plates, which we interpret as flooring and cover plates, similar to those in other edrioasteroid-grade echinoderms [31]. Flooring plates are biserially arranged, triangular in shape and very thick (figure 1f–i). Their internal surfaces are smooth, with notches at the lateral margins that we interpret as podial pores (sensu [32]) (figure 1f,i). Externally, these plates have prominent rims converging at a central point that extend to the corners of each plate (figure 1c,d,e,g). These rims are elevated compared to the main body of the plates. Cover plates are tessellate and organized into multiple series of tiny polygonal plates, which decrease in size towards the perradial line (figure 1c–e). The first series of cover plates articulate with the apices of the flooring plates. Ambulacra are preserved in reddish-orange (figure 2a). The peristome is covered by tiny plates with no obvious organization preserved (figure 1a,b).

(b) . Elemental analysis

XRF mapping showed that NHMUK EE 1659 is enriched in P, Fe, Ca, Zn and S and depleted in Si, Al, K and Mg compared to the surrounding matrix (figure 2b; electronic supplementary material, figure S2). Within the fossil, the axial region is especially elevated in Fe (figure 2b; electronic supplementary material, figure S2), with local enrichment of Zn and S in some parts (electronic supplementary material, figure S2); P and Ca are elevated in both the axial and extraxial regions (figure 2b; electronic supplementary material, figure S2).

(c) . Phylogenetic position

In both our Bayesian and parsimony analyses, Yorkicystis was recovered as an edrioasteroid, in a clade with Argodiscus, Isorophus and Kailidiscus (figure 3). This clade of edrioasteroids was part of a larger clade consisting of all pentaradial forms excluding Helicocystis. In both analyses, Helicocystis was retrieved as the earliest-diverging pentaradial echinoderm.

Figure 3.

Phylogenetic position of Yorkicystis. (a) A 50% majority-rule consensus tree resulting from Bayesian analyses. Numbers next to nodes represent the proportion of trees in the post-burn-in posterior sample that contained that node. Analysis performed with a symmetric Dirichelet hyperprior set to ∞, corresponding to symmetric character transition rates. Branch lengths represent the number of expected changes per character. (b) Strict consensus of the four most parsimonious trees resulting from parsimony analyses. Bootstrap support (BS; bold) and decay indices (DI; italics) are shown for each node with BS > 50 and DI > 0. Both trees are rooted on Helicoplacus. (Online version in colour.)

4. Discussion

Variation in the morphology and preservation of the axial and extraxial parts of the body in Yorkicystis demonstrates that these regions had different compositions in life. While the specimens preserve no trace of original calcite, the presence of ambulacra with characteristic flooring and cover plates (figures 1c–i and 4), preserved as three-dimensional moulds elevated in Fe (figure 2b; electronic supplementary material, figure S2), and the relict ‘ghost' stereom microstructure in the external part of flooring plates are clear indicators of a typical echinoderm skeleton. By contrast, the extraxial region is generally preserved as a dark film (figure 2a). This mode of preservation is common among Burgess Shale-type deposits like the Kinzers Formation [33,34], and soft tissues are often preserved in this way [33,35]. This, together with the apparent absence of skeletal plating, as revealed by direct study of the fossils and latex casting (figures 1a,b and 2a,b; electronic supplementary material, figure S3) strongly suggests the extraxial region of Yorkicystis was originally non-mineralized. Although the fossils appear preserved flattened and with curved ambulacra, taphonomic observations indicate that their original shape was globular and probably with straight ambulacra (electronic supplementary material, figure S1).

Figure 4.

Digital reconstruction of the ambulacral construction of Yorkicystis haefneri. (a–d) Single ambulacrum in different views. (e–j) Detail of part of the ambulacrum in different views. (k) Inferred soft tissues of the water vascular system housed within the ambulacrum during life. cp, cover plate; fp, flooring plate; pp, podial pore; tf, tube foot. (Online version in colour.)

Our phylogenetic analyses recover Yorkicystis as an edrioasteroid (figure 3), revealing that the reduction of the skeleton was a derived trait, and not representative of the plesiomorphic condition among pentaradial echinoderms. Yorkicystis is thus interpreted as the oldest echinoderm with a secondarily non-mineralized body wall (figure 5). While a small number of Ediacaran and lower Cambrian fossils have previously been considered as uncalcified echinoderms (e.g. [18,36–38]), their echinoderm affinities are highly dubious and debated [20,22,39,40]. However, comparable patterns of incomplete calcification have been documented in other echinoderm groups based on younger fossil and living forms. For example, in most crinoids, flooring plates are weakly or not calcified, while other elements of the axial skeleton are mineralized [7,41]; in some taxa, components of the extraxial region, such as the anal sac, are also uncalcified [12]. Some edrioasteroids like isorophids and Walcottidiscus also reduce part of the aboral region to attach on substrates [42]. More radical reduction of skeletal mineralization is present among holothurians, in which the skeleton typically consists of small spicules embedded in the body wall and a ring of ossicles surrounding the pharynx [8,43], or is lost entirely [11,44]; skeletal reduction thus affects both the axial and extraxial regions. Consequently, Yorkicystis is unique among echinoderms in having a clear differentiation between calcified axial and uncalcified extraxial regions.

Figure 5.

Life reconstruction of Yorkicystis haefneri. (Online version in colour.)

Developmental mechanisms underpinning the formation of the skeleton in Yorkicystis may shed light on skeletal development in echinoderms more broadly. Transcriptomic comparisons of crinoids, echinoids, asteroids and ophiuroids [10], as well as numerous experimental studies in larval and adult skeletons of extant echinoderm classes, have identified a conserved biomineralization ‘toolkit' of genes and proteins that underlies the process of skeletogenesis. This includes transcription factors such as Alx1 and Ets1, signalling pathways like fibroblast growth factor (FGF) and vascular endothelial growth factor (VEGF) and numerous downstream differentiation genes such as c-lectin protein domain-bearing genes, metalloproteases and cell-surface molecules [9,10,45,46]. The existence of this conserved set of genes across echinoderms points to a distinct genetic regulatory module directing the development of the echinoderm skeleton. During development, aspects of this regulatory network are deployed in distinct spatial contexts based on ectodermal signalling cues, resulting in the growth of skeleton in particular parts of the body [45–48]. Inhibiting these signalling pathways results in downregulation of skeletogenic genes and obstruction of biomineralization in both embryos and adult echinoderms [46–48]. Given the conserved nature of the main components of the echinoderm skeletal biomineralization toolkit, we expect that the echinoderm skeletal gene regulatory network has been expressed during skeletal growth in both axial and extraxial skeletons of all fossil echinoderms. We hypothesize that, where this skeletogenic module is not deployed, skeletal loss or reduction will result. In this context, Yorkicystis, with its uncalcified extraxial body, indicates that components of the skeletogenic gene regulatory network were expressed only in the axial region.

The morphology of Yorkicystis could also indicate that the activation of the skeletogenic gene regulatory network in axial and extraxial tissues is independent and that the expression of this gene network in these tissues may be controlled by different upstream developmental genetic mechanisms, such as differential deployment of signalling pathways. This might imply different molecular mechanisms underlying the development of axial and extraxial tissue [49], although the existence of other echinoderms with varying degrees of calcification across axial and extraxial regions (see above) could point to greater variability in developmental processes between taxa. Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR) genome editing have facilitated functional perturbations of gene expression in adult echinoderms in distinct morphological regions of the adult body plan [50]. Based on the morphology of Yorkicystis, with its calcified axial and uncalcified extraxial skeletons, we hypothesize that functional knockout of transcription factors or signalling genes towards the top of the skeletal gene regulatory network hierarchy, such as Alx1 or VegfR, in the extraxial regions of growing adult echinoderms will result in a distinct loss of skeleton in those regions. Developments in functional perturbations, paired with recent advances in localizing skeletal gene expression in post-metamorphic echinoderms [51], make testing this hypothesis possible.

Early echinoderms displayed great plasticity in terms of their body plan construction, with bilateral, asymmetrical, triradial and pentaradial forms described from the Cambrian [22,52]. Recent phylogenetic analyses [18,20,17,19] place bilateral and asymmetrical forms as stem-group echinoderms, indicating that some of the synapomorphies of crown-group echinoderms, such as pentaradial symmetry and ambulacra with flooring and cover plates, are not plesiomorphic for the phylum [16,22]. Our phylogenetic analyses recover Yorkicystis as a derived pentaradial form, most closely related to Cambrian edrioasteroids such as Kailidiscus, with the absence of skeleton in the extraxial part of the body owing to secondary loss. This represents, to our knowledge, the oldest example of skeletal reduction yet documented in echinoderms. Moreover, the secondary loss of skeleton in the extraxial region alone differs from the situation in all other echinoderms with reduced skeletons (e.g. crinoids and holothurians), and strongly implies a distinct mechanism for reducing the skeleton. The absence of skeleton in the extraxial region suggests that Yorkicystis preferentially directed energy towards skeletogenesis in the axial region. This would have conserved energy for other metabolic requirements, while still ensuring the external soft parts of the water vascular system (i.e. the tube feet, figure 4k) were supported and protected. The absence of plating in the extraxial part would also explain why the ambulacra in Yorkicystis depart morphologically from other edrioasteroids. Loss of the extraxial skeleton might have enabled greater flexibility of the body wall, allowing the animal to vary its body shape in response to changing currents.

5. Systematic palaeontology

Phylum: Echinodermata

Class: Edrioasteroidea

Family: Yorkicystitidae nov. (urn:lsid:zoobank.org:act:62B6B33F-08AC-45E3-8634-CCC9B8B33D13).

Genus: Yorkicystis gen. nov. (urn:lsid:zoobank.org:act:32ADE21F-6738-491E-9B52-E6047205F73F).

Type species: Yorkicystis haefneri sp. nov.

Etymology. Genus name refers to the city of York, Pennsylvania, where specimens were collected.

Diagnosis. Extraxial body uncalcified. Axial body composed of five large, recumbent ambulacra incorporated into the thecal wall. Ambulacra consist of biserially arranged, large triangular adradial flooring plates with external rims; flooring plates internally smooth, with podial pores along lateral margins. Cover plates organized into multiple series.

Discussion. The new family Yorkicystitidae is here created to accommodate the new genus and species Yorkicystis haefneri, which is differentiated from all other edrioasteroids based on its unique body construction (uncalcified extraxial region and ambulacral construction). The ambulacra, consisting of multiple series of cover plates and biserial flooring plates, differ from those of derived isorophid edrioasteroids, which have uniserial flooring plates [23,53], but are more similar to stromatocystitids (i.e. Cambraster and Stromatocystites) and edrioasterids in which flooring plates are biserially arranged [32,42,54,55]. The flooring plate system in Yorkicystis probably corresponds to and is thus homologous with the adradial series of Walcottidiscus [42]. In Cambraster, Stromatocystites and edrioasterids the flooring plates are externally exposed and articulate aborally with the tessellate interambulacral membrane; this is not the case in Yorkicystis because of the absence of calcified elements in the extraxial region. However, the floor plates do not have an externally exposed shelf that would be expected if they were the abradial set. Instead they are strongly rimmed in Yorkicystis.

The cover plate system in Yorkicystis is similar to the multitiered systems in some other Cambrian echinoderms, including the edrioasteroid Kailidiscus and the class Cincta, where larger platelets abradially articulate with tiers of smaller platelets towards the midline. This type of cover plate system is unknown among taxa with biserial abradial floor plates, except for the edrioasterid Pseudedriophus guensburgi, which is otherwise dissimilar [56].

Yorkicystis haefneri sp. nov. (urn:lsid:zoobank.org:act:71EEFF3C-235A-4FE3-A8C0-8B51900319AD)

Etymology. Species name dedicated to Mr Christopher Haefner, who discovered the two known specimens and made them available for research.

Diagnosis. As for genus.

Material. Holotype: NHMUK EE 1659, includes part and counterpart. Paratype: NHMUK EE 1660, is a complete specimen with well-preserved ambulacra.

Locality and horizon. York, Pennsylvania, USA; Stage 4, Series 2, Cambrian.

Description. See above and the electronic supplementary material, information.

Data accessibility

The data are provided in the electronic supplementary material [57].

Authors' contributions

S.Z. conceived the study, cast and photographed specimens, conceived the phylogenetic analysis, analysed and interpreted data and drafted the manuscript. I.A.R. conceived the elemental analysis, helped draft the manuscript, analysed and interpreted data and critically revised the manuscript. C.D.S. conceived the phylogenetic analysis, analysed and interpreted data and critically revised the manuscript. J.R.T. ran the phylogenetic analyses, analysed and interpreted data and critically revised the manuscript. A.P.G. conceived and carried out the elemental analysis, analysed and interpreted data, and critically revised the manuscript.

All authors gave final approval for publication and agree to be held accountable for the work performed therein.

Competing interests

We declare we have no competing interests.

Funding

S.Z. was supported by the Spanish Ministry of Science, Innovation and Universities (grant no CGL2017-87631), co-financed by the European Regional Development Fund and the project ‘Aragosaurus: Recursos Geológicos y Paleoambientales' (E18_17R) funded by the Government of Aragon. I.A.R. was supported by the Oxford University Museum of Natural History. J.R.T. was supported by a Royal Society Newton International Fellowship and a Leverhulme Trust Early Career Fellowship.