Decoding the Fossil Record of Early Lophophorates

Home , Bioturbation, Cryptostomata, Cycloneuralia, Evolutionary Fauna, Halkieriid, Linguliformea

Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1284

Decoding the fossil record of early lophophorates

Systematics and phylogeny of problematic Cambrian Lophotrochozoa

AODHÁN D. BUTLER

ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-554-9327-1 UPPSALA urn:nbn:se:uu:diva-261907 2015 Dissertation presented at Uppsala University to be publicly examined in Hambergsalen, Geocentrum, Villavägen 16, Uppsala, Friday, 23 October 2015 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor Maggie Cusack (School of Geographical and Earth Sciences, University of Glasgow).

Abstract Butler, A. D. 2015. Decoding the fossil record of early lophophorates. Systematics and phylogeny of problematic Cambrian Lophotrochozoa. (De tidigaste fossila lofoforaterna. Problematiska kambriska lofotrochozoers systematik och fylogeni). Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1284. 65 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9327-1.

The evolutionary origins of animal phyla are intimately linked with the Cambrian explosion, a period of radical ecological and evolutionary innovation that begins approximately 540 Mya and continues for some 20 million years, during which most major animal groups appear. Lophotrochozoa, a major group of protostome animals that includes molluscs, annelids and brachiopods, represent a significant component of the oldest known fossil records of biomineralised animals, as disclosed by the enigmatic ‘small shelly fossil’ faunas of the early Cambrian. Determining the affinities of these scleritome taxa is highly informative for examining Cambrian evolutionary patterns, since many are supposed stem- group Lophotrochozoa. The main focus of this thesis pertained to the stem-group of the Brachiopoda, a highly diverse and important clade of suspension feeding animals in the Palaeozoic era, which are still extant but with only with a fraction of past diversity. Major findings include adding support for tommotiid affinity as stem-group lophophorates. Determining morphological character homologies vital to reconstructing the brachiopod stem- group was achieved by comparing Cambrian Lagerstätten with the widespread biomineralised record of Cambrian stem-brachiopods and small shelly fossils. Polarising character changes associated with the putative transition from scleritome organisms to crown-group brachiopods was furthered by the description of an enigmatic agglutinated tubular lophophorate Yuganotheca elegans from the Chengjiang Lagerstätte, China, which possesses an unusual combination of phoronid, brachiopod and tommotiid characters. These efforts were furthered by the use of X- ray tomographic techniques that revealed novel anatomical features, including exceptionally preserved setae in the tommotiid Micrina. The evidence for a common origin of columnar brachiopod shell structures in the tommotiids is suggested and critically examined. Enigmatic and problematic early and middle Cambrian lophotrochozoans are newly described or re- described in light of new evidence, namely: the stem-brachiopod Mickwitzia occidens Walcott from the Indian Springs Lagerstätte, Nevada; a putative stem-group entoproct Cotyledion tylodes Luo and Hu from Chengjiang, China; a new enigmatic family of rhynchonelliform brachiopods exemplified by the newly described Tomteluva perturbata from the Stephen Formation, Canada; and the tommotiid Micrina etheridgei (Tate) from the Flinders Ranges, South Australia. Cladistic analyses of fossil morphological data supports a monophyletic Brachiopoda.

Keywords: Brachiopoda, Chengjiang, Lagerstätte, Cambrian Explosion, palaeobiology, stem- group, entoproct, phoronid, tommotiid, exceptional preservation

Aodhán D. Butler, Department of Earth Sciences, Palaeobiology, Villav. 16, Uppsala University, SE-75236 Uppsala, Sweden.

ISSN 1651-6214 ISBN 978-91-554-9327-1 urn:nbn:se:uu:diva-261907 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-261907)

For my family

List of Papers

This thesis is based on the following papers, which are referred to in the text by their Roman numerals.

I Butler, A. D., Streng, M., Holmer, L. E. and Babcock. L. E. Exceptionally preserved Mickwitzia from the Indian Springs Lagerstätte. Manuscript accepted for publication in Journal of Paleontology. II Butler, A. D., Garwood, R. J., Streng, M., Lowe, T., Holmer, L.E. X-ray microtomography of the tommotiid Micrina reveals cellular and ultrastructural preservation, confirming a tommotiid stem-linguliform affinity. Manuscript for submission to Roy- al Society Open Science. III Streng, M., Butler, A. D., Peel, J. S., Garwood, R. J. and Caron, J. B. A new family of Cambrian rhynchonelliformean brachiopods with an aberrant coral-like morphology. Manuscript in review, Palaeontology. IV Zhang, Z.-F., Li, G.-X., Holmer, L. E., Brock, G. A. Balt- hasar, U., Skovsted, C. B., Fu, D-J., Zhang, X.-L., Wang, H.- Z., Butler, A., Zhang, Z.-L., Cao, C.-Q., Han, J., Liu, J.-N. & Shu. D.-G. (2014). An early Cambrian agglutinated tubular lophophorate with brachiopod characters. Scientific Reports, 4 (4682) doi:10.1038/srep04682. V Zhang, Z.; Holmer, L. E.; Skovsted, C. B.; Brock, G. A.; Budd, G. E.; Fu, D.; Zhang, X.; Shu, D.; Han, J.; Liu, J.; Wang, H.; Butler, A. N.; Li, G. (2013). A sclerite-bearing stem group entoproct from the early Cambrian and its implications. Scientific Reports, 3 (1066). doi:10.1038/srep01066

The following popular science article was prepared during the PhD and is included in the kappa, but is not a part of the thesis.

VI Butler, A. D. (2015). Fossil Focus: The place of small shelly fossils in the Cambrian explosion, and the origin of Animals. Palaeontology Online, Volume 5, Article 7, 1-14

Additionally, the following papers were prepared during the course of the PhD but not included in the thesis.

VII Butler, A. D., Cunningham, J. A., Budd, G. E., Donoghue, P. C. J. (2015). Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization. Proceedings of the Royal Society of London B: Biological Sciences 282, 20150476. VIII Lagebro, L., Gueriau, P., Hegna, T. A., Rabet, N., Butler, A. D., Budd, G. E. (2015). The oldest notostracan (Upper Devoni- an Strud locality, Belgium). Palaeontology 58, 497–509. doi:10.1111/pala.12155

Reprints were made with permission from the respective copyright holders. Paper I © by the authors Paper II © by the authors Paper III © by the authors Paper IV is reproduced under a Creative Commons Attribution- NonCommercial-ShareAlike 3.0 Unported License. Paper V is reproduced under the Creative Commons Attribution 3.0 Un- ported License. Paper VI is reproduced under the Creative Commons Attribution 3.0 Un- ported license.

http://creativecommons.org/licenses/by-nc-sa/3.0/ http://creativecommons.org/licenses/by/3.0/

Statement of authorship Paper I and Paper II: A. Butler analysed the material, interpreted the results and wrote the MS with input from all authors. Paper III: A. Butler produced, analysed the CT data and shared writing. Paper IV: A. Butler performed cladistic analyses of data, helped with interpretations of fossils and shared writing. Paper V: A. Butler assisted with discussion and analysis of these fossils and shared writing.

Disclaimer: The papers presented herein are for the purpose of public examination as a doctoral thesis only. They are not considered valid publications for taxonomic or nomenclatural purposes according to ICZN article 8.2. Accordingly, all new taxonomic names and emendations in papers I - VI are void. Authority for taxonomic work is retained by the original publications.

Contents

Introduction ...... 9 The Cambrian as a period of profound biological and geological change...... 9 Introduction to Lophotrochozoa/Spiralia ...... 12 Evolution of the Lophophorata: brachiopod origins ...... 14 Small shelly fossils and their phylogenetic implications for lophophorate origins ...... 16 Fate of the Small Shelly Fossils ...... 18 Aims of this thesis ...... 19 Significance of Cambrian exceptional faunas ...... 20 Taphonomy and preservation ...... 20 Indian Springs Lagerstätte: Mickwitzia from Nevada ...... 22 Chengjiang Lagerstätte stem-lophophorates ...... 23 Early Cambrian exceptional preservation ...... 23 X-ray Microtomographic techniques: a novel tool in recovering character data from early Cambrian lophophorates ...... 25 Phylogeny of early lophophorates...... 28 Influence of fossil organisms and stem-groups for phylogenetic reconstruction ...... 28 Phylogenetic significance of newly described fossil material ...... 29 Future Directions ...... 32 Svensk sammanfattning ...... 36 Acknowledgements ...... 40 References ...... 42 Popular science article: The place of small shelly fossils in the Cambrian explosion, and the origin of Animals ...... 49 Introduction: Darwin, the Cambrian explosion and the origin of animals...... 49 A palaeontological mystery… ...... 49 So where are all the fossils ? ...... 50

Timing of the SSF appearance ...... 51 Types and preservation of SSFs ...... 54 Why did hard parts evolve? ...... 54 Research methods ...... 55 What then are the SSFs? ...... 58 What happens to the SSFs? ...... 62 What does the future hold? ...... 63 Further reading ...... 65

Introduction

The Cambrian as a period of profound biological and geological change. For the majority of geological time on Earth, biological processes have been in effect. The appearance of complex multicellular life that characterises the biosphere of the Phanerozoic Eon on the other hand, has a relatively recent origin. The first putatively metazoan fossils from the Ediacaran biota that appear approximately 580 Ma ago (Narbonne & Gehling, 2003) have remained enigmatic since their discovery and despite much speculation no convincing argument to link them with bilaterian or diploblastic metazoans sensu stricto has been forwarded to date. It is not until we search well into the Cambrian (Stage 2) that direct body fossil evidence for animals in a recognisable sense emerges, although signs of conspicuously metazoan activi- ties much earlier than this are disclosed by the trace fossil record of trackways, burrows (Mángano & Buatois, 2014) and faecal pellets, in addition to inference of molecular clock estimates (e.g., Jensen et al., 2005; Marshall, 2006; Maloof et al., 2010). These findings imply the metazoan and bilaterian body plan had evolved, and was present before evidence of it was preserved in the body fossil record. This thesis focuses on the morphology, phylogeny and evolutionary significance of early lophotrochozoans, a major clade of bilaterian animals whose fossil record spans from the present to the earliest evidence of biomineralised animals in the early Cambrian. The most conspicuous evidence of the Cambrian explosion is apparent in the rapid appearance of almost all known animal phyla (Conway Morris, 1989) and the diversification of biomineralised organisms and their easily fossilisable skeletal remains that dominate the subsequent fossil record of the Phanerozoic. An almost-simultaneous appearance of predatory (i.e. mineralized mouthparts such as teeth) and defensive hard tissues (i.e. spines and armoured shells) is evident across a broad range of animal groups (Murdock et al., 2011). Further evidence of the Cambrian radiation is disclosed by fossil Konservat-Lagerstätten that retain exquisitely preserved soft-tissues and provide a window into the ecology and detailed anatomy normally absent from the fossil record resulting from the normal processes of death, decay and biological recycling. Precisely why the Cambrian explosion occurred is a topic of seemingly endless debate within paleontological research. Explanatory processes for the onset of the Cambrian explosion are

9 manifold and are roughly divided between the camps suggesting abiotic physical drivers and on the other hand those highlighting biological innovation as the main driver. Physical mechanisms suggested have ranged from: rising oxygen levels (Chen et al., 2015), shifts in ocean chemistry from weathering (Peters & Gaines, 2012), to transgressive sea level changes providing suitable habitats (Dalziel, 2014). Biological explanations have included: increases in genome size (Li & Zhang, 2010), the onset of predator/prey interactions (Bengtson, 2002) which in turn were facilitated by morphological innovations such as vision, brains and the through gut (Nielsen & Parker, 2010). A further possibility is raised that the Cambrian explosion is an artefact of reading the imperfect fossil record (an inherently biased source of data) in a literal sense. Runnegar (1982) posed the question whether the Cambrian explosion was an explosive event of metazoan evolution (representing a real diversification event), or rather an explosion of fossilisation potential driven by the innovation of biomineralised skeletons. As of yet, no single causative factor provides a satisfactory explanation as a triggering event for the ‘Cam- brian explosion’, rather, it is likely that a complex series of related biotic and abiotic interacting processes and feedback loops are in effect at this time (Smith & Harper, 2013).

Figure 1. Diagrammatic timescale illustrating fossil record of early complex and skeletonised metazoan animals, in addition to proxy measures (i.e. trace fossils) after Marshal (2006)

A further caveat to interpreting patterns of evolution associated with the earliest Cambrian is that the fundamental basis of stratigraphic correlation has as of yet not been agreed upon by the ISCS (International sub- commission for Cambrian stratigraphy). This is a consequence of long stand- ing issues with satisfactorily correlating and designating type sections for regional stratigraphic sub-divisions into a global timescale, thus the precise chronological position of many faunas of palaeobiological significance remains uncertain. The timescale in Fig. 1 refers to the Siberian nomenclature (from which a significant body of SSF’s have been described) and provi- sional subdivisions as proposed by the ISCS (see also Fig. 5). Lee et al. (2013) inferred relatively rapid rates of molecular and morphological evolution for arthropods during the Cambrian as compared with later times, regardless of whether the length of the diversification event was re-

11 stricted to the early Cambrian or telescoped back into the late Ediacaran with a large missing fossil record sensu Erwin et al. (2011) as has been inferred from molecular clock estimations. This pattern of rapid evolution associated with the Cambrian radiation remains to be tested in a similar fashion for other clades. Although the diversification and biomineralisation of lophotrochozoans is seemingly earlier than that of arthropods (Kouchinsky et al., 2012), if this is indeed demonstrably the case, this places a constraint on simultaneous common causative mechanisms as synchronous drivers of the Cambrian explosion (Lee et al., 2013).

Introduction to Lophotrochozoa/Spiralia Lophotrochozoa (or Spiralia) represents one of the major clades of bilaterian protostome animals encompassing many familiar animal groups such as annelids, molluscs and brachiopods and many less well recognised ‘minor’ phyla, i.e. Platyhelminthes, Cycliophora, Rotifera and Gnathostomulida (Fig. 2). Despite the myriad advances in phylogenetic reconstruction enabled by the advent of molecular systematics the relationships of Spiralia are among the most-problematic and least well resolved groupings within the animal tree (Dunn et al., 2014). Indeed even the name of the clade is debated, depending on the placement of taxa within the tree of spiralians, Lophotrocho- zoa, defined as a clade composed of Mollusca, Annelida, and Lophophorata (Halanych et al., 1995), is either a subclade of Spiralia (Nesnidal et al., 2013; Fig. 2 right) or a synonym of Spiralia (Dunn et al., 2014) (Fig. 2 left).

Figure 2. Patterns of conflicting phylogenetic signal within spiralians in phylogenomic and molecular systematic analyses (Dunn et al. 2014, fig. 2d).

The main focus of investigation within this thesis centres on the spiralian sub-clade Lophophorata (Hyman, 1959), organisms united by the synapo- morphies of a horseshoe shaped tentacular ciliated feeding apparatus, the

12 lophophore that surrounds the oral opening and the epistome, a lobe-shaped structure covering the mouth. Although this clade is contradicted in a number of molecular analyses (Fig. 2 left; Hejnol et al., 2009) a monophyletic Lophophorata is recovered in later analyses (Nesnidal et al., 2013) and the conflict between morphology and the molecular data is apparently an artefact of systematic error related to nucleotide compositional bias, thus reject- ing the ‘polyzoa’ hypothesis. With the implication from this that phoronids are not derived from brachiopods and have not secondarily reduced their shell contra Cohen (2000) and Balthasar & Butterfield (2009) While the indications are that lophophorates are a monophyletic clade (Nesnidal et al., 2013; Laumer et al., 2015) constituent lineages of Lopho- phorata, namely Phoronida, Brachiopoda and Ectoprocta (Bryozoa) as of yet remain unresolved in their phylogenetic position with regard to each other. As a further complication whilst Brachiopoda possess an extremely abundant fossil record tracing back to the early Cambrian, a consequence of both their biomineralised skeleton and ecological success through the Phanerozoic, ectoprocts and phoronids have a much sparser appearance in the fossil record with large ghost ranges and only recently a prospective Cambrian occurrence of both groups being suggested (Landing et al., 2015; Zhang et al., 2014; Zhang & Homer, 2015) and not without controversy in the case of the Bryo- zoa (Ma et al., 2015; Taylor et al., 2013) with the oldest non-disputed occurrence of bryozoans dating from the lower Ordovician. A primary focus of this thesis, brachiopods, were among the most bio- diverse and abundant Palaeozoic groups of animals and were a major component of benthic marine ecosystems. The dramatic disappearance of many major brachiopod clades at the end-Permian extinction event however ended their dominance, they never fully recover in terms of diversity in later periods of earth history. A pattern still evident today, since their extant diversity is a highly pruned remnant when compared with extinct clades. As a result of their past abundance, biomineralised shell with high fossilisation potential and cosmopolitan distribution, brachiopods possess one of the highest fideli- ty fossil records in terms of completeness and stratigraphic congruence of any major fossil animal group (Foote and Sepkoski, 1999). Morphology and the pattern of relationships derived from it in the form of cladistic analyses, have found brachiopods to be monophyletic in an almost universal fashion (Hennig et al., 1966; Rowell, 1982; Carlson, 1995; Holmer et al., 1995; Williams et al., 1996). The exact nature of internal relationships remains much debated however, for example, the monophyly, or not, of cra- niids plus linguliforms (‘Inarticulata’) and their relationship with articulated brachiopods (Rhynchonelliformea) (Fig. 3). Molecular analyses however, have been in conflict with the signal from morphology, Housekeeping gene based phylogeny found phoronids, non-biomineralised lophophorates usually considered a sister group of lophophorates with regard to brachiopods, in fact belong within the Brachiopoda as sister group to the inarticulates (Fig.

13 3; Cohen et al., 1998; Cohen & Weydmann, 2005; Santagata & Cohen, 2009). Sperling et al. (2011) made the observation that a paraphyletic brachiopod tree is consistent with the same unrooted dendrogram as for a monophyletic Brachiopoda. Recovering paraphyly of brachiopods in ribosomal trees was inferred to be the result of a long-branch attraction artefact caused by rapid rates of evolution in Rhynchonelliformea when compared with other brachiopod clades. The main issue with resolving brachiopod (and lophophorate) phylogeny is therefore likely a rooting problem (Fig. 3A-B).

Evolution of the Lophophorata: brachiopod origins Brachiopods are unique in that they are one of the few clades of bilaterian animals in which higher-level relationships are characterised by biomineralised shells of differing biomineral types i.e. calcium carbonate as calcite or calcium phosphate in the form of apatite. However, the myriad patterns of relationships proposed for the major lophophorate groups consequently imply a number of significant evolutionary events relating to, for example, the evolution of the biomineralised shell. Some of these include: the independent evolution of the bivalved shell in sister linguliform and rhynchonelliform brachiopod clades i.e. convergence on the brachiopod body plan (Wright, 1979; Valentine, 1973; Gorjansky & Popov, 1986; Skovsted et al., 2009a; 2011), transitions between biomineralised shell chemistries (Balthasar et al., 2009; Carlson, 1995; Williams & Carlson, 2007) (Fig. 3), or secondary loss of the brachiopod shell and biomineralisation in the phoronid stem-lineage, thus making phoronids, in effect, ‘naked’ brachiopods (Cohen, 2000; Bal- thasar & Butterfield, 2009) (Fig. 3B). An enigmatic group of phosphatic early Cambrian fossils known as tommotiids have been proposed as a stem-lineage to Brachiopoda, if this is indeed the case, then an ancestral phosphatic shell for brachiopods is therefore implied. Although phosphatic brachiopods were thought to have appeared first (Williams & Rowell, 1965) both phosphatic and calcitic early stem- brachiopods are now known from essentially coeval strata, corresponding to Cambrian Stage 2, (Kouchinsky et al. 2012) or possibly even older strata. A tommotiid origin then also presents the evolutionary scenario of the bivalved crown-brachiopod body plan emerging from early Cambrian tube-dwelling scleritome animals (Holmer et al., 2002; 2008a; 2011; Williams & Holmer, 2002; Skovsted et al., 2008, 2009a; Balthasar et al., 2009) (Fig. 4). A ‘tommotiid origin’ model would suggest that these lower Cambrian phosphatic fossils form a paraphyletic stem-lineage to Brachiopoda, with calcitic mineralogy evolving convergently in Rhynchonelliformea and Crani- iformea (Holmer et al., 2002, 2008a, 2008b, 2011; Williams & Holmer, 2002; Skovsted et al., 2008, 2009a, 2011; Balthasar et al., 2009). A number of morphological investigations in a cladistic framework have suggested

14 however, that the tommotiids may be a stem-group of the inarticulate phosphatic clades, rather than a stem-group to all brachiopods (Carlson, 2009) (see also Fig. 9) although it should be stressed that these findings are preliminary at best. One potential avenue for a resolution of brachiopod and lophophorate relationships comes from fossil evidence that can detail the sequence of character acquisition and correctly determine the polarisation of crown and stem- group characters (Smith, 2005; Edgecombe, 2010). Stem-group fossil taxa, have proven vital in constructing the evolutionary history of many clades due to the presence of novel character combinations not seen in extant representatives, thus are vital when homology assessments are evaluated (Patter- son, 1981; Budd & Jensen, 2000; Gauthier, 1988; Edgecombe 2010). A prime example described in this thesis is of the enigmatic organism Yuganotheca elegans (paper IV) as it seemingly possesses characters of both brachiopods and phoronids.

Figure 3. Brachiopods as monophyletic A, or paraphyletic B, with respect to phoronids, after Sperling et al. (2011). Shifting the root position implies different character polarisations (e.g. the loss of a biomineralised shell in the phoronids as implied in B; Carlson, 2007; Cohen 2000). C-F, Hypotheses of relationships and their implications for the evolution of biomineralisation assuming brachiopod monophyly. Within brachiopods, the problematic Craniiformea may be sister to Linguli- formea (the ‘Inarticulata’) or Rhynchonelliformea (the ‘Calciata’). Colours depict character optimisation of biomineralisation in alternative trees assuming a single origin of biomineralisation. Green = calcitic, Red = phosphatic. The ‘tommotiid origin’ hypothesis would correspond to D and E, with at least one change to calcitic mineralogy in craniiforms and rhynchonelliforms and a phosphatic ancestral shell for brachiopods.

Small shelly fossils and their phylogenetic implications for lophophorate origins The first evidence of skeletal putative bilaterians are recovered from the extensive variety of phosphatised problematic sclerite-bearing taxa so called ‘small shelly fossils’ (Matthews & Missarzhevsky, 1975), a major component of the early biomineralised fossil record of the ‘Cambrian explosion’. The first reported occurrences of tommotiids predates the estimated base of the Cambrian Stage 2 (Fig.1) (c. 530 Ma) in Avalonia (Landing et al., 2007; Kouchinsky et al., 2012). Sepkoski (1992) recognised “Tommotian” organ-

16 isms as an evolutionary group distinct from his Cambrian fauna sensu stric- to. The disappearance of many tommotiid taxa during the end-Botoman extinction event marks the transition from fossil biodiversity dominated by biomineralised small shelly ‘problematica’ to the more recognisable (i.e. crown-ward) Cambrian organisms such as brachiopods, trilobites and molluscs. To date these have remained chronically understudied in terms of the evolutionary significance of constituent organisms of these small shelly faunas. Although their relationships are beginning to be understood by the use of the stem and crown-group distinction (Budd & Jensen, 2000). In particular, large numbers of putative lophotrochozoans (i.e. annelids, brachiopods, molluscs and their close relatives) have been described, although their phylogeny is poorly resolved. A central research theme of this thesis (papers I, II, IV and V) is to move towards a more complete understanding of these enigmatic Cambrian faunas and their evolutionary significance, in particular the relationship of tommotiids to the stem-group brachiopods.

Figure 4. Purported phylogenetic relationships of small shelly tommotiid taxa with crown brachiopods and phoronids. The ‘tommotiid origin’ hypothesis after Williams & Holmer (2002), Skovsted et al. (2009c, 2011), Holmer et al. (2008a) and Zhang et al. (2013, 2014) papers IV-V.

17 Fate of the Small Shelly Fossils The abundance and diversity of SSFs decline during a major extinction event at the end Botoman (Porter, 2004) they then progressively disappear later in the Cambrian. Since most SSFs do not form a clade or natural grouping, we cannot say that they became extinct in any meaningful sense. Rather, it seems that they evolved into, and were eventually competitively replaced by, more recognisable forms of the classic ‘Palaeozoic evolutionary faunas’ such as brachiopods, bivalves, arthropods and gastropods. This pattern can be reconciled with the fact many small shelly fossils form stem-groups of recognisable Cambrian and later clades e.g. cap shaped fossils and helcionellids with molluscs, protoconodonts as stem-Chaetognatha (Szaniawski, 2002). An aspect of typological thinking sensu Mayr (1970) also factors in here since many stem-group animals do not fit into recognisable groups they are dubbed ‘problematica’ and treated as ‘waste-basket’ taxa and thus not informative in the context of known animal diversity, the case with many small shelly fossils e.g. Dailyatia. When their affinity can be established these animals become allied to a known group and thus escape the wastebas- ket designation as a SSF, e.g. the sclerites of lobopods and halkierids that were placed in context as stem-ecdysozoans and molluscs.

18 Aims of this thesis

The early Cambrian is clearly a critical time interval for understanding the origin and evolution of metazoans. Nowhere is this more apparent than in the case of the Lophotrochozoa, whose origins are long suspected (Conway Morris, 2006) of being intimately linked with the ‘Cambrian explosion’. Less clear, however, is the precise significance of many enigmatic early Cambrian fossil ‘problematica’ (e.g. many small shelly fossils) that have been described as potential stem-group members of lophotrochozoan clades, but have evaded a solid placement in terms of their phylogenetic and consequently, evolutionary significance. The overall aim of this thesis is to clarify the nature of this purported early origination and radiation of this major animal group. This was tackled through the following objectives. • Description of novel fossil species of suspected phylogenetic significance, from exceptional faunas and normally preserved biomineralised fossils, expanding the known diversity of Cambrian early animals (Papers I-V). • Critical examination of the purported link between tommotiid small shelly fossils and Brachiopoda through comparative anatomy (Paper II). • Searching for possible character homologies that link candidate lophophorate stem-group taxa (Papers I, II, IV and V). • Establishing a cladistic framework to test the hypothesised phylogenetic significance and affinity of these lophophorate ‘problematica’ (Papers IV and V) • Making the significance and findings made in the course of this research accessible to the wider public beyond a technical scientific audience (Palaeontology online article).

Methodological advances through the utilisation of microtomographic techniques are central to the achievement of the fossil description efforts (papers II and III) and retrieving novel character data through in depth anatomical investigation. The ultimate synthesis of these research efforts attempts to provide an in- tegrated framework from which to understand the early evolution of lophophorate animals.

19 Significance of Cambrian exceptional faunas

Taphonomy and preservation An infamous quip from the late Adolf Seilacher “Here we have a fossil: what went wrong?” (Sperling, 2013) elegantly sums up the seeming paradox of fossilisation and even more so, exceptional preservation of soft tissues. The act of fossilisation is an escape of a biological entity from the normal cycles of death, decay, ecological recycling, and into the geological record (Briggs, 2003; Sperling, 2013). Since biomineralised anatomy is more favourably predisposed to entering the rock record it must be recognised that that these shells, bones and teeth present a fundamentally biased (though extremely useful) window into the palaeobiology of fossil organisms. The Cambrian fossil record is deeply biased in favour of shelly fossils, a pattern we can infer from exceptionally preserved Burgess Shale and Chengjiang biotas, where the vast majority of taxa and individuals present are soft bodied (Conway Morris, 1986). Exceptional faunas thus give a ‘snapshot’ of the normally missing soft-bodied component of palaeodiversity in typical fossil assemblages of biomineralised organisms. Incidences of exceptional soft tissue preservation in the Cambrian are anomalously common when compared with later geological periods, some possible explanations include: the unique ocean chemistry of the Cambrian, a possible consequence of through guts increasing the fossilisation potential of bilaterian animals (Butler et al., 2015) and a lack of bioturbators (Orr et al., 2003) that subsequently close the Cambrian Lagerstätte window. Gaines et al. (2012) however surmised that bioturbation alone could not account for the apparent loss of Burgess Shale-type preservation from the fossil record. Instead benthic anoxia, that is implied to have been widespread, and possibly other related geochemical factors enabled the spike in occurrence of exceptional preservation in the Cambrian. In the earliest Cambrian, the BST window is absent in strata predating the Atdabanian (Budd, 2003) and aside some isolated examples such as Markuelia and Olivooides (Dong et al., 2013; Steiner et al., 2014), exceptional faunas in the Fortunian and Cambri- an Stage 2 are all but absent. Much of the current knowledge of stem-group animals in the critical phase of the early evolution of many phyla during the Cambrian radiation is based upon fossils described from these sites of exceptional preservation. A few of the more well-known include the Burgess Shale, Sirius Passet and

20 Chengjiang sites from which a plethora of bizarre and evolutionary critical fossils have been described. These include stem members of Arthropoda, Echinodermata, and Chordata (Budd, 2008) all of which have radically shaped evolutionary thinking in these clades. Exceptionally preserved fossils have also enabled the resolution of seemingly insoluble palaeontological dilemmas including: the nature and reconstruction of the halkierid and lobo- pod animals known only from isolated sclerites until the complete animals were discovered with sclerites in-situ. Linking the comparatively rich record of biomineralised animals with exceptionally preserved examples of the same species allows us to more towards a more complete palaeobiological understanding of the anatomy, ecology and life history of these often enigmatic animals e.g. paper I. Following in a similar vein of investigation, new exceptionally preserved lophophorate fossils are a central focus and are featured in all but one of the papers presented in this thesis (papers I, II, IV and V).

Figure 5. Relative timescale and stratigraphic position of described material from this thesis and major early Cambrian events. Generated with TimeScale Creator, based on The Cambrian, Geologic Time Scale 2012 (Peng et al., 2012). A, Tomteluva perturbata (paper III) B, Mickwitzia occidens (paper I) C, Yuganotheca elegans and Cotyledion tylodes (papers IV-V). D, Micrina etheridgei (paper II).

Indian Springs Lagerstätte: Mickwitzia from Nevada The fauna of the Indian Springs locality (paper I) presents a window of exceptional soft tissue preservation, in this case containing mickwitziid stem-group brachiopods that occur alongside a rich Lagerstätte fauna including arthropods, sponges and hyoliths (English & Babcock, 2010). The records of Mickwitzia with exceptional preservation from this location are significant in that they closely resemble the Chengjiang organism Heliomedusa and provide the first incidence of exceptional soft-tissue preservation that supports a close affinity of these taxa, the resemblance is strong enough that we suggest synonymising these taxa into a single genus in a future taxonomic revision. A further unique feature of the Indian Springs locality is that it

22 contains Mickwitzia from contrasting carbonate and mudstone depositional environments allowing us to directly compare the taphonomic effects on preservation of both biomineralised components of the organism and their soft part anatomy in both settings. With original shell material being well preserved in carbonate levels, whilst being dissolved or weathered away in shale settings where soft-tissue preservation occurred. Implications of these findings serve to inform further descriptions of similar organophosphatic lophotrochozoan fossils from the Cambrian (paper I). This part of project in particular re-examines the phylogenetic importance of soft anatomy and shell structure within the putative brachiopod upper stem group Mickwitzi- idae; another is to critically examine the record of other phosphatic lower stem group brachiopods and brachiopod-allied problematica, with the even- tual aim of clarifying their relationships to the known record of Cambrian Lophotrochozoa.

Chengjiang Lagerstätte stem-lophophorates Continuing on the theme of stem group lophotrochozoans, two enigmatic taxa are also described from collaborative research efforts on the Chengjiang Lagerstätte. The first of these Cotyledion tylodes is reinterpreted here as a stem-group entoproct (paper V). Interestingly this organism bears sclerites on its external surface in a similar fashion to tommotiids and other enigmatic stem-group Cambrian Lophotrochozoa. Comparative homology assessments with the scleritomes of organisms such as Eccentrotheca, Paterimitra, Sun- naginia, Micrina (paper II and figured on cover), and Lapworthella make the case for an expansive grade of stem-lophotrochozoan allied taxa. Evalu- ating hypotheses of tommotiid relationships from the perspective of a cladistic approach has to date only been preliminary (Murdock et al. 2014), and this is addressed in papers (IV-V), in which a subsequent attempt to address this issue is presented. The second organism described from the Chengjiang locality Yuganothe- ca elegans (paper IV) is a profoundly strange animal that displays a novel intermediate morphology, only parsable in a phylogenetic context when viewed through the lens of a stem-group affinity (i.e. a way of reconciling the combination of phoronid and brachiopod characters) since it fails to fit into a single extant clade of lophophorates satisfactorily, rather retaining diagnostic characters of both.

Early Cambrian exceptional preservation Exceptional preservation of fossils prior to the Atdabanian (Stage 3) is all but absent, excepting a limited number of small embryonic animals that in-

23 clude Olivooides and Markuelia (Bengtson & Zhao, 1997). Olivooides was later identified as a likely cnidarian scyphozoan stem group member (Dong et al., 2013), or cycloneuralian (Steiner et al., 2014) while Markuelia was interpreted as a stem-scalidophoran or a stem-priapulid (Dong et al., 2010). It is interesting to note that thus far the only examples of Cambrian Stage 1-2 Lagerstätten are small Orsten-type phosphatised fossils. The observation of phosphatised soft anatomy in the form of setae and the probable secreting follicular cells in the tommotiid Micrina etheridgei (paper II) is of significant interest. The character is of intrinsic value in reconstructing the phylogeny of stem-lophophorates but also implies that similar cryptic soft tissue preservation may be present in other small shelly fossils and assemblages of a similar or older age. The potential to gain access to novel soft-part morphological data in stem-group animals from the Tommotian or earlier would be a hugely important advance in Cambrian palaeobiology with implications for early animal evolution. The taphonomic implications of finding soft-tissue from an otherwise relatively ‘normal’ fossil deposit opens the potential to find soft tissues in other tommotiids. This is an exciting new possibility for trying to solve the position of these early Cambrian problematica.

24 X-ray Microtomographic techniques: a novel tool in recovering character data from early Cambrian lophophorates

Little was known about the internal structure and anatomy of most small shelly fossils, and what was understood had been gathered through random breakage of the fossil, exposing fortuitous surfaces of interest, or by destructively grinding samples into thin sections and analyses by light and electron microscopy. Recent advances in virtual palaeontological techniques (Sutton et al., 2014) have enabled researchers to move beyond these limitations and similar efforts have revolutionised the study of many fossil groups e.g. arthropods from the Silurian Herefordshire Lagerstätte (Sutton et al., 2001). The advent of 3D virtual-palaeontological techniques has been revolutionary in allowing researchers to examine fossil organisms internal structure in great detail and often non-destructively. Building on the initial success of tomographic studies on Cambrian and pre-Cambrian problematica, including a number of small shelly fossils (Murdock et al., 2012) further application of these techniques was explored in this thesis to gain new data on early lophophorates. In brief, CT techniques involve rotation of a specimen between an X-ray source and detector and taking a sequential series of images or projections. The projections are analysed with tomographic reconstruction algorithms to produce a serial sequence of slices. These slice datasets are reconstructed into a 3D model with in this thesis either volumetric rendering in the Drishti package (Limaye, 2012), the most computationally intensive approach that renders every voxel, or alternatively a polygon surface mesh based approach in the SPIERS package (Sutton et al., 2012). To collect the tomographic data a suite of different scanning hardware was employed, depending on the size, composition and resolution required for each sample. Large fossils and those still embedded in matrix were scanned in a Nikon Metris 225/320 kV X-ray CT system in a customised bay, smaller samples for high resolution tomography were scanned on an Xradia MicroXCT-200 system. Scans of selected fossils were also performed within the TOMCAT synchrotron beamline at the Swiss Light Source.

25 The investigation of fossils through the use of X-ray computed tomography enabled visualization of the detailed anatomy of a number of early Cambrian lophotrochozoan organisms namely Micrina (Paper II, Fig. 6), Heliomedusa and the new taxon Tomteluva (Paper III). Since the primary research goals of this thesis were focused on the search for putative morphological homologies and characters of phylogenetic utility in members of the stem-brachiopods and allied lophophorates, the comparative datasets derived from these scans were of great utility in furthering this objective. After acid processing to facilitate removal from the host carbonate rock, phosphatic small shelly fossils are well suited to investigation with tomographic techniques as a result of the high density contrast between the phosphatic skeleton and air spaces vacated by the dissolution of carbonate matrix.

Figure 6. Examples of tomography derived virtual ‘slices’ from the tommotiid Micrina in transverse and planar orientations, lamellar phosphatic fabric of high density is bright. Features visible include setal canals and perpendicular columns D- E (paper II).

Experimental scanning of exceptionally preserved pyritised fossils of Helio- medusa orienta from Chengjiang also proved extremely successful, unex- pectedly, with recovery of 3-dimensional soft tissue anatomy from within samples otherwise not exposed by standard mechanical preparation techniques (Fig. 7B). This is a significant advance in non-destructive imaging of these evolutionary important fossils revealing detailed anatomy including the lophophore, gut, mouth, and mantle and associated internal organs. The stem brachiopod Heliomedusa orienta (Fig. 7A, B) was also scanned at the TOMCAT beamline at SLS revealing for the first time the interaction of tangential to shell surface pyritised setae, and also conical structures perpendicular to the shell surface that resemble the inward pointing cone diagnostic character of the genus Mickwitzia (Paper I). This provides strong evidence

26 Heliomedusa is a mickwitziid and thus its exceptionally preserved soft anatomy can be used to infer the palaeobiology of other closely related species.

Figure 7. Examples of CT scans and reconstructions. B, Heliomedusa a probable mickwitziid showing marginal setae, mantle tissue, visceral area and lophophore. Tubular structure to left is likely an attached scyphozoan similar to Byronia. Scale bar =1mm. (A: light photograph of same specimen). C, Silicified Tomteluva perturbata (paper III) with internal anatomy visible. Scale bar = 500µm (1, 4) and 100µm (2-3). D, Micrina etheridgei with setal canals visible by reducing opacity of the shell surface during volume rendering. Scale bar = 500µm (paper II).

In Paper III the description of Tomteluva pertubata is greatly aided with the use of tomography to reveal the delicately preserved internal anatomy of silicified fossils from the Stephen Formation and enable the direct compari- son with similarly aged enigmatic brachiopod fossils, the naukatids.

27 Phylogeny of early lophophorates

Influence of fossil organisms and stem-groups for phylogenetic reconstruction

“Fossils matter first and foremost as samples of morphology that would not otherwise be known.” Edgecombe, (2010).

Much progress has been achieved in understanding the origin of major clades of metazoan life in and around the Cambrian explosion. Of particular utility has been the recognition of the unique position occupied by species present at this time interval, most evidently when the principles of the stem- and crown-group concept are applied to the seemingly bizarre collection of problematic taxa of uncertain biological affinity (Budd & Jensen, 2000; Budd, 2008). The bold conjecture of Patterson (1981) that fossil data could have no influence on reconstructions of phylogeny of extant organisms, more specifi- cally as a consequence of their incompleteness (Ax, 1987) has since been overturned in a number of real world datasets of diverse clades including amniotes (Gauthier et al. 1988) and crustaceans (Huelsenbeck, 1991). Fur- thermore, fossils have been demonstrated as being able to break long- branches and resolve character conflicts (Forey & Fortey, 2001; Smith, 1998) especially in clades where living diversity is highly pruned. Brachi- opoda is a prime example of this pattern, thus fossil data are of particularly high importance when attempting to reconstruct brachiopod phylogeny. Fos- sils also have the power to remedy a hugely significant misleading systematic artefact, namely long branch attraction (Felsenstein, 1978) when constructing phylogenetic hypothesis, by breaking long branches with intermediate fossil derived morphological transformations. Fossils are a direct source of temporal data for evolutionary events, and in a phylogenetic sense, that data is accessible only through the morphology of an organism. Fossils also sample less-derived character states (plesiomor- phies) as well as morphological variation otherwise pruned from the record of extant diversity by extinction (Edgecombe, 2010). One such group that has proved particularly elusive in terms of its biological affinity is the purported stem-group brachiopods. For example those affiliated with the family Mickwitziidae and their purported close relatives

28 within the tommotiid small shelly fossils (Williams & Holmer 2002; Skovsted et al., 2008, 2009a, 2009b, 2009c). It has been suggested that SSFs are a vital link in the series of character acquisitions involved in assembling the brachiopod plan (Skovsted et al., 2008), although this interpretation has been questioned in recent times (Murdock et al., 2014). Since a significant portion of the biological diversity of the early Cambri- an fossil record is likely comprised of lophotrochozoans (Kouchinsky et al., 2012) and the record of their radiation as disclosed by biomineralised tissues significantly predates that of ecdysozoans and deuterostomes, proper placement of these problematica on the tree of Spiralia/Lophotrochozoa is fundamental to assess their phylogenetic significance and thus evolutionary implications for the nature of animal diversification associated with the Cambrian explosion. Despite the enormous advances in animal phylogeny enabled by modern molecular phylogenetic and phylogenomic methods, the interrelationships of constituent groups within Lophotrochozoa remains unresolved and represents a major gap in our understanding of deep animal phylogeny (Dunn et al., 2014). Morphological and systematic investigations remain critical despite the seemingly overshadowing role molecular systematics (Giribet, 2015), since ultimately the evolution of morphology is what most evolutionary biologists are ultimately drawn to investigate in some capacity. Nowhere is this more evident than with fossils, which can provide a unique temporal signal to bear when investigating evolutionary questions.

Phylogenetic significance of newly described fossil material The description of the taxa Yuganotheca elegans and Cotyledion tylodes (Papers IV and V) as stem-lophotrochozoans has significant implications for the relationships among members of Lophophorata. Whilst as we approach crown brachiopods (Fig. 4), re-examination of Micrina etheridgei (paper II) and Mickwitzia occidens (paper I) provide novel insight into the stem of the linguliform brachiopods. The problematic form Tomteluva perturbata on the other hand is recognized as a probable crown-group rhynchonelliform brachiopod and thus not informative for determining the deep splits between major brachiopod clades. This remains to be tested in a cladistic framework, however. The tree topology of brachiopod relationships is fundamentally the same even in seemingly conflicting molecular and morphological datasets, the main issue identified by Sperling et al. (2011) was that the root position of the tree was an underlying cause of conflicting phylogenetic signals. If phoronids can be independently verified as emerging at a coeval or earlier

29 time to brachiopods this strongly weighs against the case for brachiopod paraphyly, that implies this branching event should occur later in the evolutionary history of brachiopods with the absence of a shell as secondary loss rather than a primitive feature of phoronids. The characters polarized by the anatomy of Yuganotheca elegans (paper IV), namely the combination of supposed brachiopod and phoronid apomorphies in a single organism i.e. the presence of mantle canals, pedicle, a bivalved shell and u-shaped gut, indi- cates that the case for monophyly is supported by the presence of transitional morphologies in the fossil record. The cladistic treatment of morphological data expands the tentative phylogenetic framework previously established (Skovsted et al. 2011; Holmer et al., 2011; Skovsted et al., 2009c) in a testable, reproducible way. The key critique of interpretations as to the stem-brachiopod tommotiid relationship hypothesis (Murdock et al., 2012, 2014) justifiably focused on the scarcity of characters to support the affinities of tommotiids such as Micrina (paper II) with linguliform brachiopods. In addition a number of the purported homologies, such as the presence of a closed filtration chamber, were products of circular reasoning.

Figure 8. Tentative placement of Yuganotheca and Cotyledion (from Zhang et al., 2014, fig. 4; paper IV).

30 A smaller focused dataset was established in papers IV-V as a tool to determine the placement of the enigmatic animals Yuganotheca elegans and Cotyledion tylodes. It should be noted that one obvious limitation with the dataset collected thus far is a focus on phosphatic linguliform brachiopods and small shelly fossils with relatively few taxa sampled from purported stem- rhynchonelliform calcitic representatives. This is partially a sampling issue due to the commonly used acetic acid recovery methods that dissolves calcitic matrix and fossils equally well, resulting in a relative paucity of described material. In paper III a new family of calcitic brachiopods is erected with the description of the new species Tomteluva perturbata and Nasakia thulensis. They are recognised as crown-group members of rhynchonelliform brachiopods. Their affinity with a small group of early and middle Cambrian brachiopods, the naukatids, currently appears to be most parsimonious. These taxa are of interest since they display an unusual morphology, which might represent an early phase of specialisation and adaption of brachiopods. How- ever, their likely highly derived morphology and phylogenetic position gives no additional resolution to the deep nodes of brachiopod phylogeny.

31 Future Directions

This thesis has shed new light on the morphology, phylogenetic significance and evolutionary context of some of the most problematic lophophorate animals, namely the stem-group brachiopod taxa Mickwitzia (paper I), the tommotiid Micrina (paper II), the enigmatic Chengjiang forms Yuganotheca elegans (paper IV) and Cotyledion tylodes (paper V) and the now recognised crown rhynchonelliform Tomteluva (paper III). Since the material described in this thesis is primarily derived from our own field collections, it serves to display the continuing importance of researchers to continue field exploration and as a result enhance museum collections in addition to the research outcomes. Future work to conduct systematic revision of the genus Mickwitzia is now a priority, with a complete global picture of diversity and diagnostic characters in place. This includes a systematic revision of the Chengjiang animal Heliomedusa orienta (Fig.7) of which the preliminary data provides a character based supporting link that this taxon is a constituent of the genus Mickwitzia i.e. the presence of inward pointing cones on the interior shell surface, an up until present recognised autapomorphy of Mickwitzia (paper I). If the designation of Heliomedusa stands up under further scrutiny, it provides a unique opportunity to integrate the data from exceptionally preserved soft part anatomy of the Chengjiang fossils that answers many questions about the ground plan and early evolution of linguliform brachiopods. The columnar structures in Micrina/Mickwitzia (paper I-II) have a close morphological similarity and likely homology with acrotretid columns, these appear to have a wider taxonomic distribution than has been first suspected and are a prime target for recovery of phylogenetically useful data from further tommotiids and stem-brachiopods (Holmer et al., 2008b). A census of shell structure utilising microtomographic techniques would be an ideal way of assessing this. 3D virtual palaeontological techniques also allowed significant advances in deciphering the anatomy and thus systematic position of the enigmatic fossils Heliomedusa and Tomteluva. A solid framework is now established to further investigate character homologies in additional samples of SSF animals and those from Chengjiang similarly preserved in pyrite. Of particular interest to solving the lophophorate origin question would be additional scans of the tommotiids Tannuolina, Patermitra, Kulparina and Sunnaginia.

32 Especially if there is the potential to recover exceptionally preserved soft tissues structure similar to the setae we described in paper II. Reconstructing the scleritome of Micrina presents a continuing palaeobiological dilemma as to whether this organism possesses a bivalved scleritome sensu Holmer et al. (2008a), is a slug like animal with an imbricating row of sclerites (Li & Xiao, 2004) or possibly retains a more tubular scleritome similar to its sister taxon Tannuolina reconstructed in Skovsted et al. (2014). Two possible approaches to shed light on this problem are suggested. Firstly, make attempts to find additional material with articulated sclerites similar to efforts with Eccentrotheca (Skovsted et al., 2011). Secondly, to reconstruct the animal from 3D models of tomographically scanned sclerite specimens in silico with the Blender package (Garwood & Dunlop, 2014), or alternatively with 3D printed models. Applying this technique is possible for other tommotiids with poorly understood scleritome reconstructions including Sunnaginia, Kulparina and Paterimitra. Building a comprehensive phylogeny of the SSF and lophophorate stem- group in a cladistic context is a further priority for unravelling the evolutionary context of these fossil organisms. This is already in motion through the establishment of an online MorphoBank effort (project number 2025), allowing a team of researchers to build a collaborative matrix that is updated on an ongoing basis.

Figure 9. Preliminary results from MorphoBank project 2025 dataset derived from Zhang et al. (2014; paper IV) SplitsTree network diagram showing rhynchonelliform brachiopods in blue, linguliform brachiopods in red and linguliform brachiopods plus stem-linguliforms and tommotiids indicated by dashed red box. Current matrix: 25 taxa, 31 characters. Dendrogram based off 18 most parsimonious trees recovered after a TBR tree search, Length 64 steps, CI=0.65 RI=0.81.

Phylogenetic network diagrams are one potentially useful technique in determining patterns of evolution of lophotrochozoans, especially in poorly sampled areas of the tree and where character support is weak or where re- ticulate events in evolution are suspected, e.g. hybridization during specia- tion (Legendre & Makarenkov, 2002). Preliminary results support the affinity of tommotiids as at least a stem-linguliform sister group (Fig. 9). Other outstanding problems with the early fossil record of lophotrochozoans centre on the camenellans, an informal group of organisms that have been placed at the base of the tommotiid stem-group (Skovsted et al., 2009c, 2011) remain enigmatic. Until it is possible to recognise possible homologous features and establish a character based deductive framework for determining their affinities, it is uncertain they belong to the Lophophorata or are indeed even lophotrochozoan stem-group members. A further issue is that sampling of calcitic stem-group lophophorates in cladistic analyses has been sparse and remains a gap in our understanding of the early evolutionary history of Lophotrochozoa.

34 On the other hand, a more complete synthesis of early Cambrian lophophorate morphological phylogeny in combination with molecular systematics in a total evidence framework is now becoming feasible with the assembly of cladistic matrices for increasing numbers of fossil taxa. The end goal of a more clear reconstruction of the Lophotrochozoan stem-lineage during the critical event of the Cambrian radiation has never been closer.

35 Svensk sammanfattning

Under den senare hälften av nittonhundratalet ledde upptäckten av gåtfulla fossil av sannolika tidiga djur från den geologiska ediacaraperioden (635- 542 miljoner år sedan) till konstaterandet att komplext flercelligt liv föregick den kambriska perioden. Organismerna från ediacaraperioden är förmodlig- en besläktade med moderna djur men på vilket sätt de passar in i på djurens släktskapsträd är fortfarande kontroversiellt. Närapå samtliga av dessa fossil bestod enbart av mjukdelar när de levde och saknade helt hårda skelett, men en tid senare dyker dock små, svagt mineraliserade fossil upp i bergartspro- ver från Sibirien, och ytterligare platser. Dessa lager är äldre än de lager som innehåller fossil såsom trilobiter. Dessa fossil benämns ”Small shelly fossils”, förkortat SSF (små skalbärande fossil), ett informellt uttryck författad av paleontologerna Samuel Crosbie Matthews och Vladimir. V. Missarzhev- sky 1975. Namnet används som en informell klassificering för ett brett spektrum av fossil med skelett, av vilka uppträder in slutet av prekambrium, men den övervägande andelen hittas i tidigaste kambrium (542-490 miljoner år sedan). SSF representerar några av de tidigaste bevisen på biomineralisering och bildandet av skelett hos metazoer (djur och deras nära släktingar), och de dyker först upp en tid innan det plötsliga uppträdandet av välbevarade kroppsfossil vilka ofta förknippas med den kambriska explosionen. I inledningen av kambrium markerar närvaron av SSF en betydelsefull övergång från en värld av mikrobiella mattor, encelliga organismer och enkla former bestående av enbart mjukdelar till en värld dominerad av djurgrupper med skelett, grävande organismer och andra metazoer. Denna över- gång skedde under den terreneuviska epoken; den äldsta delen av kambrium, mellan början av kambrium och uppträdandet av trilobiter (runt 20 miljoner år, inkluderar de geologiska indelningarna fortun och tommot, Fig 1.) I takt med att vi förflyttar oss till yngre lager i kambrium (fortun) uppträ- der små skalförande fossil som Halwaxia, uppbyggda av ett mineral som kallas aragonit; konformade molluskliknande former och hyoliter. Förekomsten av SSF når sin kulmen i och med kambriums andra etage (tommot) (Fig.1). Namnet har sitt ursprung från lager i närheten av Tommot i Sibirien, och dessa innehåller stora ansamlingar av tommotider, en form av SSF. Uppträdandet av dessa fossil har föreslagits som en indikator för basen av denna geologiska tidsperiod. De hittas vid sidan av tidiga och omfattande revlika avsättningar av konliknande archaeocyater, organismer som antas

36 vara svampar. Dessa avsättningar hittas direkt innan uppkomsten av både trilobiter och huvudparten av de berömda exceptionellt välbevarade fossill från Burgess Shale och Chengjiang. Majoriteten av SSF hade skelett uppbyggda av mineralet apatit (en typ av kalciumfosfat, samma material som ben och tänder består utav); de andra formerna, särskilt de tidiga varianterna, bestod utav kalciumkarbonat, som moderna musslor och sniglar. Fosfat är relativt sällsynt i dagens hav. Det är ett av de huvudsakliga nä- ringsämnen som stödjer fotosyntesen i växter och alger och är därför en ständig bristvara. I de kambriska haven förmodas det ha varit en mycket högre halt av fosfat vilket möjliggjorde för de tidiga djuren att mer omfattande använda mineralet för skelettuppbyggnad. Faktum är att flertalet SSF är avgjutningar av det ursprungliga djuret som bevarades genom ett överdrag av fosfat som växte utanpå eller på insidan av djurets skalrester efter döden, istället för att ursprungligen bestå av ett fosfatskelett. Fossil bevarade på detta sätt benämns stenkärnor. På detta sätt kan skelett som ursprungligen bestod av kalciumkarbonat hamna i det geologiska arkivet som en fosfatisk fossil.

Forskningsmetoder Det brukliga sättet att samla in fosfatiska fossil är genom att ta block av kalksten och lösa upp dem i ättiksyra (i stort sett koncentrerad vinäger). Av de torkade rester som kvarstår efter syrabehandlingen plockas eventuella fossil ut för att identifieras under mikroskop. Skalrester som består utav kalciumfosfat löses nämligen inte upp i det relativt milda syrabadet (artikel I- III).Elektron- och ljusmikroskop används för att få fram detaljerade kun- skaper om SSF. Fram till de senaste åren har forskare bokstavligen bara skrapat på ytan av vår kunskap om SSF. Väldigt lite är påvisat beträffande den inre strukturen och anatomin hos flertalet SSF. Den begränsade mängd fakta som finns har samlats in från enstaka fragmentariska fossil, eller där tillfälliga ytor exponerats, alternativt från destruktiva metoder såsom fram- ställandet av tunnslip. Nya paleontologiska tekniker inom 3D har tillåtit oss att kunna skanna fossil och på så sätt skala bort skelettet lager för lager på datorskärmen för att slutligen exponera dess interna struktur i detalj. För att producera en så- dan modell behöver forskarna först skanna fossilet. Den vanligaste metoden är röntgentomografi, eller datortomografi, liknande det du kan hitta på ett sjukhus eller för tandkirurgi. Fossilet placeras i skannern och röntgas upp till 4000 gånger på en snurrande plattform. Ett datorprogram används därefter för att rekonstruera en detaljerad 3D-modell som kan hjälpa forskaren att närmare undersöka fossilets struktur. För modeller med en högre upplösning använder sig forskare av röntgen- strålar från en partikelaccelerator, en synkrotron. Källan för röntgenstrålarna från synkrotronen är avsevärt mer intensiva än en standardkälla, och produ-

37 cerar strålning med endast en väglängd, likt en laser. Slutresultatet är en betydligt snabbare scan än med mindre maskiner och har dessutom en högre detaljnivå. Men att erhålla arbetstid på sådan utrustning är få förunnat då det är kostsamt och eftertraktat. Denna teknik användes i vår forskning för att skapa detaljerade modeller av våra SSF Micrina (artikel II) och Tomteluva (artikel III), deras interna strukturer och deras relation till andra djurgrupper.

Varför har hårda delar utvecklats? Levande djur har många olika typer av hårdvävnader och dessa har i sin tur ett spektrum av funktioner. De fungerar som interna stöd, tänder för föda, externa stöd eller exoskelett (t.ex. skal från sniglar), hudskleriter, eller fjäll, som skydd och även som assistens vid simning. Ursprunget till hårda delar tros vara ett exempel på en evolutionär kapprustning mellan rovdjur och bytesdjur, i konstant försök att vinna fördelar och konkurrera ut varandra. Bytesdjuren försökte bygga kraftigare försvar (skal och taggar) och rovdju- ren utvecklade mineraliserade mundelar och andra strategier (som exempel- vis egenskapen att kunna bryta sönder skal) för att övervinna dessa försvar. Inom biologin kallas detta koncept för ”the Red Queen hypothesis” (Hjärter Dam, efter karaktären från boken ”Alice i Underlandet”). Andra idéer som har föreslagits är att skelettbyggandet var ett sätt för djur att göra sig av med sitt överskott av metaboliskt avfall eller att lagra mineral som kalcium; an- vändandet för försvar, support, utfodring och så vidare, var endast en bief- fekt.

Vad är ”Small Shelly Fossils” (SSF)? Brakiopoderna (armfotingar), är en av de vanligaste fossila grupperna från den paleozoiska eran (541 miljoner till 252 miljoner år sedan), och tros ha sitt ursprung inom någon typ av SSF. Det har föreslagits att dessa djur kan spåras tillbaka till tommotiiderna. Det främsta beviset för detta kommer från släktena Eccentrotheca, Micrina och Tannuolina, samt några andra exempel, alla är så kallade Eccentrothecomorpher. Dessa var ursprungligen kända endast från isolerade skleriter. När några forskare lyckades hitta ett antal välbevarade sammanfogade exempel blev det klart att de kom från stam- gruppen djur, troligen relaterade till brakiopoder. Tommotiiden Micrina (artikel II) har även en uppsättning särdrag karakteristiska för brakiopoder. Dessa innefattar deras tillväxtsätt, övergripande morfologi, skalets mikro- struktur, förekomsten av sammanfogade skalhalvor och fosfatiska skalkemi. Det har föreslagits att vi kan, genom att studera SSFer, börja att rekonstruera det evolutionära ursprunget till brakiopodens kroppsplan - om än i flera etapper. Det förefaller existera flertalet intermediära former mellan tommotiider och brakiopoder, ett exempel är den märkliga och tidiga braki- opoden Mickwitzia (artikel I) som delar ett antal likheter i skalstrukturen med Micrina (artikel II). Även om denna uppfattning är långt ifrån accepte-

38 rad, så erbjuder den en spännande möjlighet att undersöka ursprunget av ett fylum i anknytning till utvecklingen av SSFer. Ytterligare en alternativ modell har tagit upp möjligheten att brakiopoder kan ha utvecklats genom "uppvikning" av ett snigelliknande djur, liknande Halkieria. Djuret skulle ha två motsatta skal med en överlappning för att bilda en sluten filtreringskammare, med andra ord tvåskalig (se Cohen et al. 2003). Nyligen beskrevs ett filtrerande djur, Cotyledion tylodes (artikel V), från kambrium, det är täckt med ett yttre pansar av relativt glesa ovala plattor (skleriter) som påminner om flera SSF tommotiider. Närvaron av en skleritom, ett skelett bestående av isolerade element eller skleriter sammanfogade ungefär som medeltida ringbrynjor, verkar vara ett gemensamt kännetecken för flera av stamgrupper hos djur. Cotyledions skleritom (artikel V) kan närmast jämföras med tommotiiden Eccentrotheca, men skleriternas struktur skiljer sig tillräckligt mycket för att utesluta att de tillhör till tommotiderna. Dock är parallellen i form och funktion slående, och det finns troligen en närbelägen relation mellan dessa fossil. Några av de SSF, som vi har sett, kan identifieras som djurens stamgrupp, som de primitiva molluskernas skal, brakiopodernas skal och tuber från an- nelider (ringmaskar) eller taggar. Flera former förblir gåtfulla, och för till- fället anses de tillhöra "problematica", eller fossil med en osäker relation till andra organismer. Nya släktingar till SSF kan också komma att upptäckas i framtiden, hos djur som är beroende av agglutinering (det vill säga deras skal gjorda av sedimentkorn som sitter ihop likt ett sandslott). Detta är en strategi som an- vänds av moderna ringmaskar och hästskomaskar (Phoronida) för att bygga sina skyddande yttre bokammare i röret. Det kan representera en gammal levnadsstrategi hos några av de tidigaste djuren, inbegripet agglutinerade fossil som Salterella och Volborthella. Nyligen upptäcktes ett ovanligt agglutinerande fossil, det delar några av brakiopodernas egenskaper samt funktioner hos sina närmaste släktingar, hästskomaskarna. Denna organism, Yuganotheca elegans (artikel IV), från Chengjiang, en lokal för exceptionell bevaring av fossil, tyder på att agglutinering kan ha varit mer utbredd hos de tidiga djuren än vad som tidigare visats. Men detta är fortfarande i hög grad en obesvarad fråga. Subtila antydningar från SSF, spårfossil och SCF (”Small Carbonaceous Fossils”) ger oss en föreställning om att ett komplext djurliv hade fått fot- fäste i kambriums början och kan i vissa mer kontroversiella fall eventuellt utvidgades till slutet av Ediacaran (Fig. 1).

Original text translated and adapted from Butler, A.D., 2015. Fossil Focus: The place of small shelly fossils in the Cambrian explosion, and the origin of Animals. Palaeontology Online, Volume 5, Article 7, 1-14.

39 Acknowledgements

First off, massive thanks to my supervisors for encouragement and support throughout the rollercoaster that is a PhD, answering e-mails at unsociable hours, countless crises that needed fixing at the last possible moment and getting this whole thing done somehow! It still amazes me how quickly the last 4.75 years have flown by.

Michi thanks for always being supportive, organised and going the extra mile when it was needed, even letting me crash at your place after arriving in Sweden on a particularly cold January. Knowing when to push and also giving me the freedom to follow my own ideas has been great. I’ve learned a lot and could not have asked for more.

Lars I’m grateful for giving another perspective on things, being more than generous when I thought it would be a good idea to start a CT research program from scratch and entertaining my various scientific flights of fancy, and even agreeing to go along with them on occasion.

Russell for making the CT part of this thesis run so smoothly and have the opportunity to do some cool science in interesting places with a cold bever- age in hand, cheers man!

Graham, the useful discussions and support over the years, help with manu- scripts, explaining how everyone is wrong about the Cambrian (ahem) and various fieldwork misadventures are all much appreciated.

Zhifei Zhang is thanked for kindly allowing me to work with some amazing fossils from China and many insightful discussions about brachiopods and small shelly fossils.

John Peel is thanked for advice on SSF’s, useful discussions about the Cam- brian and the ‘joys’ of fieldwork in Greenland, the current state of premier- ship football and kindly loaning specimens and photographs.

Christian Skovsted kindly loaned samples for scanning and provided photo- micrographs.

40 Many thanks are also in order to the following, in no particular order: Gary Wife for technical support, and countless cups of coffee while using the SEM. My colleagues and friends in Paleobiologi over the years for making this a great place to work: Åsa, Milos, Nick, Mattias, Linda, Giannis, Alba, Manuela, Cissi, Dongjing, Haizhou, Oskar I and II, Anna, Emma, Illiam, Jenny, Steve, Tim, JJ, Malgorzata, Tessa, Luka, Heda, Ralf, Sebbe to name a few. Also friends and colleagues from other programs in Geocen- trum and at TGIF. Special thanks to Linda for lending an ear when it was needed most. I’m grateful to the synchrotron gang Imran, Russell, Alan, Johnny, and Nidia for the chance to work with a great bunch, collect good data and have a few laughs, also Tristan and Alberto for assistance with scanning in Manchester and at SLS respectively. The lads from flogstavägen, Dermot and Torsten, who are responsible for various liquid based distractions and more resultant wasted Sunday mornings than I care to remember… and more importantly the odd cup of Barry’s. Åsa Frisk who kindly translated the Swedish summary and Lars again for tweaking the final language. Rolf, Berrit, Vytautaus, Sarina, Allison, Jenny, Hanna, Miki and the rest of the climbing mob for the semi-regular but much needed session, getting lost in the woods looking for crags, the occasional blister and therapeutic recovery beer afterwards. Friends from EBC, UPK, the Buckland Club and further afield for good times. I hope to see you all again after the thesis-hermit phase is over!

Uppsala University and the Swedish Research Council (VR) for are thanked for funding the PhD studies through grants to Streng (VR grants # 621-2008- 3768, 621-2011-4961), and Holmer (VR grants # 2009-4395, 2012-1658). The Palaeontological Association and C F Liljevalch stipendiefonder are thanked for travel grants to attend IPC4 in Mendoza and the PalAss annual meeting in Leeds, 2014.

In the likely event of omitting someone important, my apologies!

Finally, special thanks to my family, in particular my parents Rosemary and Dermot for being so supportive and encouraging me to follow my interests wherever they took me. Also to my late grandparents who I know would have been delighted and proud to see this finished.

Tack så mycket allihopa!

41 References

Ax, P., 1987. The phylogenetic system: the systematization of organisms on the basis of their phylogenesis. Wiley, Chichester. Balthasar, U., Butterfield, N.J., 2009. Early Cambrian “soft-shelled” brachiopods as possible stem-group phoronids. Acta Palaeontologica Polonica 54, 307–314. Balthasar, U., Skovsted, C.B., Holmer, L.E., Brock, G.A., 2009. Homologous skeletal secretion in tommotiids and brachiopods. Geology 37, 1143–1146. doi:10.1130/G30323A.1 Bengtson, S., 2002. Origins and early evolution of predation. Paleontological Socie- ty Papers 8. Bengtson, S., Zhao, Y., 1997. Fossilized Metazoan Embryos from the Earliest Cam- brian. Science 277, 1645–1648. doi:10.1126/science.277.5332.1645 Briggs, D.E.G., 2003. The role of decay and mineralization in the preservation of soft-bodied fossils. Annual Review of Earth and Planetary Sciences. 31, 275– 301. doi:10.1146/annurev.earth.31.100901.144746 Budd, G.E., 2003. The Cambrian Fossil Record and the Origin of the Phyla. Integra- tive and Comparative Biology 43, 157–165. doi:10.1093/icb/43.1.157 Budd, G.E., 2008. The Earliest Fossil Record of the Animals and Its Significance. Philosophical Transactions of the Royal Society of London B: Biological Sci- ences 363, 1425–1434. Budd, G.E., Jensen, S., 2000. A critical reappraisal of the fossil record of the bilaterian phyla. Biological reviews of the Cambridge Philosophical Society 75, 253–295. Butler, A.D., Cunningham, J.A., Budd, G.E., Donoghue, P.C.J., 2015. Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization. Proceedings of the Royal Society of London B: Biologi- cal Sciences 282, 20150476. doi:10.1098/rspb.2015.0476 Carlson, S.J., 2009. Separating the crown from the stem: defining Brachiopoda and pan-brachiopoda delineates stem-brachiopods, in: 2009 Portland GSA Annual Meeting. Carlson, S.J., 1995. Phylogenetic relationships among extant brachiopods. Cladistics 11, 131–197. doi:10.1016/0748-3007(95)90010-1 Chen, X., Ling, H.-F., Vance, D., Shields-Zhou, G.A., Zhu, M., Poulton, S.W., Och, L.M., Jiang, S.-Y., Li, D., Cremonese, L., Archer, C., 2015. Rise to modern levels of ocean oxygenation coincided with the Cambrian radiation of animals. Na- ture Communications 6. doi:10.1038/ncomms8142 Cohen, B.L., 1998. Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences. Philosophical Transactions of the Royal Society of London B: Biological Sciences 353, 2039– 2061. doi:10.1098/rstb.1998.0351

42 Cohen, B.L., 2000. Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.). Proceedings of the Royal Society of London. Series B: Biological Scienc- es 267, 225 –231. doi:10.1098/rspb.2000.0991 Cohen, B.L., Weydmann, A., 2005. Molecular evidence that phoronids are a subtax- on of brachiopods (Brachiopoda: Phoronata) and that genetic divergence of metazoan phyla began long before the early Cambrian. Organisms Diversity & Evolution 5, 253–273. doi:10.1016/j.ode.2004.12.002 Conway Morris, S., 1986. The community structure of the Middle Cambrian phyllo- pod bed (Burgess Shale). Palaeontology 29, 423–467. Conway Morris, S., 1989. Burgess Shale Faunas and the Cambrian Explosion. Sci- ence 246, 339–346. doi:10.1126/science.246.4928.339 Conway Morris, S., 2006. Darwin’s dilemma: the realities of the Cambrian “explosion.” Philosophical Transactions of the Royal Society B: Biological Sciences 361, 1069–1083. doi:10.1098/rstb.2006.1846 Dalziel, I.W.D., 2014. Cambrian transgression and radiation linked to an Iapetus- Pacific oceanic connection? Geology G35886.1. doi:10.1130/G35886.1 Dong, X.-P., Bengtson, S., Gostling, N.J., Cunningham, J.A., Harvey, T.H., Kouchinsky, A., Val’Kov, A.K., Repetski, J.E., Stampanoni, M., Marone, F., others, 2010. The anatomy, taphonomy, taxonomy and systematic affinity of Markuelia: Early Cambrian to Early Ordovician scalidophorans. Palaeontology 53, 1291–1314. Dong, X.-P., Cunningham, J.A., Bengtson, S., Thomas, C.-W., Liu, J., Stampanoni, M., Donoghue, P.C., 2013. Embryos, polyps and medusae of the Early Cambri- an scyphozoan Olivooides. Proceedings of the Royal Society of London B: Bio- logical Sciences 280, 20130071. Dunn, C.W., Giribet, G., Edgecombe, G.D., Hejnol, A., 2014. Animal Phylogeny and Its Evolutionary Implications. Annual Review of Ecology, Evolution, and Systematics 45, 371–395. doi:10.1146/annurev-ecolsys-120213-091627 Edgecombe, G.D., 2010. Palaeomorphology: fossils and the inference of cladistic relationships. Acta Zoologica 91, 72–80. doi:10.1111/j.1463-6395.2009.00426.x English, A.M., Babcock, L.E., 2010. Census of the Indian Springs Lagerstätte, Poleta Formation (Cambrian), western Nevada, USA. Palaeogeography, Palae- oclimatology, Palaeoecology. 295, 236-244. Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D., Peterson, K.J., 2011. The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals. Science 334, 1091–1097. doi:10.1126/science.1206375 Felsenstein, J., 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Biology 27, 401–410. Foote, M., Sepkoski, J.J., 1999. Absolute measures of the completeness of the fossil record. Nature 398, 415–417. doi:10.1038/18872 Forey, P.L., Fortey, R.A., 2001. Fossils in the Reconstruction of Phylogeny. Pal- aeobiology II 515–519. Gaines, R.R., Droser, M.L., Orr, P.J., Garson, D., Hammarlund, E., Qi, C., Canfield, D.E., 2012. Burgess shale- type biotas were not entirely burrowed away. Geolo- gy 40, 283–286. Garwood, R., Dunlop, J., 2014. The walking dead: Blender as a tool for paleontolo- gists with a case study on extinct arachnids. Journal of Paleontology 88, 735– 746. doi:10.1666/13-088

43 Gauthier, J., Kluge, A.G., Rowe, T., 1988. Amniote phylogeny and the importance of fossils. Cladistics 4, 105–209. doi:10.1111/j.1096-0031.1988.tb00514.x Giribet, G., 2015. Morphology should not be forgotten in the era of genomics–a phylogenetic perspective. Zoologischer Anzeiger - A Journal of Comparative Zoology, Special Issue: Proceedings of the 3rd International Congress on Inver- tebrate Morphology 256, 96–103. doi:10.1016/j.jcz.2015.01.003 Gorjansky, W., Popov, L.E., 1986. On the origin systematic position of the calcare- ous-shelled inarticulate brachiopods. Lethaia 19, 233–240. doi:10.1111/j.1502- 3931.1986.tb00737.x Halanych, K.M., Bacheller, J.D., Aguinaldo, A.M., Liva, S.M., Hillis, D.M., Lake, J.A., 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 267, 1641–1643. Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G.W., Edgecombe, G.D., Mar- tinez, P., Baguñà, J., Bailly, X., Jondelius, U., Wiens, M., Müller, W.E.G., Seaver, E., Wheeler, W.C., Martindale, M.Q., Giribet, G., Dunn, C.W., 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings of the Royal Society of London B: Biological Sciences 276, 4261– 4270. doi:10.1098/rspb.2009.0896 Hennig, W., Davis, D.D., Zangerl, R., 1966. Phylogenetic Systematics. University of Illinois Press. Holmer, L.E., Popov, L.E., Bassett, M.G., Laurie, J., 1995. Phylogenetic analysis and ordinal classification of the Brachiopoda. Palaeontology 38, 713–741. Holmer, L.E., Skovsted, C.B., Williams, A., 2002. A Stem Group Brachiopod From The Lower Cambrian: Support For A Micrina (Halkieriid) Ancestry. Palaeon- tology 45, 875–882. doi:10.1111/1475-4983.00265 Holmer, L.E., Skovsted, C.B., Brock, G.A., Valentine, J.L., Paterson, J.R., 2008a. The Early Cambrian tommotiid Micrina, a sessile bivalved stem group brachiopod. Biology Letters 4, 724–728. doi:10.1098/rsbl.2008.0277 Holmer, L., Popov, L.E., Streng, M., 2008b. Organophosphatic stem group brachiopods : implications for the phylogeny of the subphylum Linguliformea. Fossils and Strata, 54, Wiley-Blackwell, pp. 3–11. Holmer, L.E., Skovsted, C.B., Larsson, C., Brock, G.A., Zhang, Z., 2011. First record of a bivalved larval shell in Early Cambrian tommotiids and its phylogenetic significance. Palaeontology 54, 235-239. doi:10.1111/j.1475- 4983.2010.01030.x Huelsenbeck, J.P., 1991. When are fossils better than extant taxa in phylogenetic analysis? Systematic Biology 40, 458–469. Hyman, L.H., 1959. The Invertebrates: Vol. 5. McGraw-Hill. Jensen, S., Droser, M., Gehling, J., 2005. Trace fossil preservation and the early evolution of animals. Palaeogeography Palaeoclimatology Palaeoecology 220, 19–29. Kouchinsky, A., Bengtson, S., Murdock, D.J.E., 2010. A New Tannuolinid Prob- lematic from the Lower Cambrian of the Sukharikha River in Northern Siberia. Acta Palaeontologica Polonica 55, 321–331. doi:10.4202/app.2009.1102 Kouchinsky, A., Bengtson, S., Runnegar, B., Skovsted, C., Steiner, M., Vendrasco, M., 2012. Chronology of early Cambrian biomineralization. Geological Maga- zine 149, 221–251. doi:10.1017/S0016756811000720 Landing, E., Peng, S., Babcock, L.E., Geyer, G., Moczydlowska-Vidal, M., others, 2007. Global standard names for the lowermost Cambrian series and stage. Epi- sodes 30, 287.

44 Landing, E., Antcliffe, J.B., Brasier, M.D., English, A.B., 2015. Distinguishing Earth’s oldest known bryozoan (Pywackia, late Cambrian) from pennatulacean octocorals (Mesozoic–Recent). Journal of Paleontology 89, 292–317. doi:10.1017/jpa.2014.26 Laumer, C.E., Bekkouche, N., Kerbl, A., Goetz, F., Neves, R.C., Sørensen, M.V., Kristensen, R.M., Hejnol, A., Dunn, C.W., Giribet, G., Worsaae, K., 2015. Spi- ralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biol- ogy 25, 2000–2006. doi:10.1016/j.cub.2015.06.068 Lee, M.S.Y., Soubrier, J., Edgecombe, G.D., 2013. Rates of Phenotypic and Ge- nomic Evolution during the Cambrian Explosion. Current Biology 23, 1889– 1895. doi:10.1016/j.cub.2013.07.055 Legendre, P., Makarenkov, V., 2002. Reconstruction of Biogeographic and Evolu- tionary Networks Using Reticulograms. Systematic Biology 51, 199–216. doi:10.1080/10635150252899725 Li, D.J., Zhang, S., 2010. The Cambrian explosion triggered by critical turning point in genome size evolution. Biochemical and Biophysical Research Communica- tions 392, 240–245. doi:10.1016/j.bbrc.2010.01.032 Li, G., Xiao, S., 2004. Tannuolina and Micrina (Tannuolinidae) from the Lower Cambrian of Eastern Yunnan, South China, and Their Scleritome Reconstruc- tion. Journal of Paleontology 78, 900–913. Limaye, A., 2012. Drishti: a volume exploration and presentation tool, in: SPIE Optical Engineering+ Applications. International Society for Optics and Photon- ics, p. 85060X–85060X. Ma, J., Taylor, P.D., Xia, F., Zhan, R., 2015. The oldest known bryozoan: Prophyl- lodictya (Cryptostomata) from the lower Tremadocian (Lower Ordovician) of Liujiachang, south-western Hubei, central China. Palaeontology 58, 925–934. Maloof, A.C., Porter, S.M., Moore, J.L., Dudás, F.Ö., Bowring, S.A., Higgins, J.A., Fike, D.A., Eddy, M.P., 2010. The earliest Cambrian record of animals and ocean geochemical change. Geological Society of America Bulletin 122, 1731– 1774. doi:10.1130/B30346.1 Mángano, M.G., Buatois, L.A., 2014. Decoupling of body-plan diversification and ecological structuring during the Ediacaran–Cambrian transition: evolutionary and geobiological feedbacks. Proceedings of the Royal Society of London B: Bi- ological Sciences 281, 20140038. doi:10.1098/rspb.2014.0038 Marshall, C.R., 2006. Explaining the Cambrian “explosion” of animals. Annual Review of Earth and Planetary Sciences. 34, 355–384. doi:10.1146/annurev.earth.33.031504.103001 Matthews, S.C., Missarzhevsky, V.V., 1975. Small shelly fossils of late Precambrian and early Cambrian age: a review of recent work. Journal of the Geological So- ciety 131, 289–303. doi:10.1144/gsjgs.131.3.0289 Mayr, E., 1970. Populations, species, and evolution: an abridgment of animal species and evolution. Harvard University Press. Murdock, D.J., Donoghue, P.C., Bengtson, S., Marone, F., 2012. Ontogeny and microstructure of the enigmatic Cambrian tommotiid Sunnaginia Missarzhev- sky, 1969. Palaeontology 55, 661–676. Murdock, D.J., Bengtson, S., Marone, F., Greenwood, J.M., Donoghue, P.C., 2014. Evaluating scenarios for the evolutionary assembly of the brachiopod body plan. Evolution & development 16, 13–24. Murdock, D.J.E., Donoghue, P.C.J., 2011. Evolutionary origins of animal skeletal biomineralization. Cells Tissues Organs (Print) 194, 98–102. doi:10.1159/000324245

45 Narbonne, G.M., Gehling, J.G., 2003. Life after snowball: The oldest complex Edia- caran fossils. Geology 31, 27–30. Nesnidal, M.P., Helmkampf, M., Meyer, A., Witek, A., Bruchhaus, I., Ebersberger, I., Hankeln, T., Lieb, B., Struck, T.H., Hausdorf, B., 2013. New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evolutionary Biology 13, 253. doi:10.1186/1471-2148-13-253 Nielsen, C., Parker, A., 2010. Morphological novelties detonated the Ediacaran- Cambrian “explosion”. Evolution & Development 12, 345–345. doi:10.1111/j.1525-142X.2010.00420.x Orr, P.J., Benton, M.J., Briggs, D.E., 2003. Post-Cambrian closure of the deep-water slope-basin taphonomic window. Geology 31, 769–772. Patterson, C., 1981. Significance of fossils in determining evolutionary relationships. Annual Review of Ecology and Systematics 195–223. Peng, S., Babcock, L.E., Cooper, R.A., 2012. Chapter 19 - The Cambrian Period, in: Gradstein, F.M., Schmitz, J.G.O.D., Ogg, G.M. (Eds.), The Geologic Time Scale. Elsevier, Boston, pp. 437–488. Peters, S.E., Gaines, R.R., 2012. Formation of the /`Great Unconformity/’ as a trig- ger for the Cambrian explosion. Nature 484, 363–366. doi:10.1038/nature10969 Porter, S.M., 2004. Halkieriids in Middle Cambrian phosphatic limestones from Australia. Journal of Paleontology 78, 574–590. Rowell, A.J., 1982. The monophyletic origin of the Brachiopoda. Lethaia 15, 299– 307. doi:10.1111/j.1502-3931.1982.tb01695.x Runnegar, B., 1982. The Cambrian explosion: Animals or fossils? Journal of the Geological Society of Australia 29, 395. doi:10.1080/00167618208729222 Santagata, S., Cohen, B., 2009. Phoronid phylogenetics (Brachiopoda; Phoronata): evidence from morphological cladistics, small and large subunit rDNA sequences, and mitochondrial cox1. Zoological Journal of the Linnean Society 157, 34– 50. doi:10.1111/j.1096-3642.2009.00531.x Sepkoski, J.J., 1992. A compendium of fossil marine animal families, 2nd edition. Contributions in biology and geology 83, 1–156. Skovsted, C.B., Brock, G.A., Paterson, J.R., Holmer, L.E., Budd, G.E., 2008. The scleritome of Eccentrotheca from the Lower Cambrian of South Australia: lophophorate affinities and implications for tommotiid phylogeny. Geology 36, 171–174. Skovsted, C.B., Holmer, L.E., Larsson, C.M., Högström, A.E.., Brock, G.A., Top- per, T.P., Balthasar, U., Stolk, S.P., Paterson, J.R., 2009a. The scleritome of Paterimitra: an Early Cambrian stem group brachiopod from South Australia. Proceedings of the Royal Society B: Biological Sciences 276, 1651. Skovsted, C.B., Brock, G.A., Holmer, L.E., Paterson, J.R., 2009b. First report of the early Cambrian stem group brachiopod Mickwitzia from East Gondwana. Gondwana Research 16, 145–150. Skovsted, C.B., Balthasar, U., Brock, G.A., Paterson, J.R., 2009c. The Tommotiid Camenella reticulosa from the Early Cambrian of South Australia: Morphology, Scleritome Reconstruction, and Phylogeny. Acta Palaeontologica Polonica 54, 525–540. doi:10.4202/app.2008.0082 Skovsted, C.B., Brock, G.A., Topper, T.P., Paterson, J.R., Holmer, L.E., 2011. Scleritome construction, biofacies, biostratigraphy and systematics of the tommotiid Eccentrotheca helenia sp. nov. from the Early Cambrian of South Aus- tralia. Palaeontology 54, 253–286. doi:10.1111/j.1475-4983.2010.01031.x

46 Skovsted, C.B., Clausen, S., Álvaro, J.J., Ponlevé, D., 2014. Tommotiids from the early Cambrian (Series 2, Stage 3) of Morocco and the evolution of the tannuolinid scleritome and setigerous shell structures in stem group brachiopods. Palaeontology 57, 171–192. doi:10.1111/pala.12060 Smith, A.B., 2005. The pre-radial history of echinoderms. Geological Journal 40, 255–280. Smith, A.B., 1998. What does palaeontology contribute to systematics in a molecular world? Molecular phylogenetics and evolution 9, 437–447. Smith, M.P., Harper, D.A.T., 2013. Causes of the Cambrian Explosion. Science 341, 1355–1356. doi:10.1126/science.1239450 Sperling, E.A., Pisani, D., Peterson, K.J., 2011. Molecular paleobiological insights into the origin of the Brachiopoda. Evolution and Development 13, 290–303. doi:10.1111/j.1525-142X.2011.00480.x Sperling, E.A. Tackling the 99%: Can we begin to understand the paleoecology of the small and soft-bodied animal majority? In Ecosystem Paleobiology and Geobiology. The Paleontological Society Papers, Volume 19, Andrew M. Bush, Sara B. Pruss, and Jonathan L. Payne (eds.). p. 77-86. Steiner, M., Qian, Y., Li, G., Hagadorn, J.W., Zhu, M., 2014. The developmental cycles of early Cambrian Olivooidae fam. nov.(? Cycloneuralia) from the Yang- tze Platform (China). Palaeogeography, Palaeoclimatology, Palaeoecology 398, 97–124. Sutton M.D., Briggs D.E.G., Siveter D.J., & Siveter D.J., 2001. Methodologies for the visualization and reconstruction of three-dimensional fossils from the Siluri- an Herefordshire Lagerstätte. Palaeontologica Electronica 4, 1-17. Sutton, M.D., Garwood, R.J., Siveter, D.J., Siveter, D.J., 2012. SPIERS and VAXML; A software toolkit for tomographic visualisation and a format for virtual specimen interchange. Palaeontologia Electronica 15, 1–14. Sutton, M., Rahman, I., Garwood, R., 2014. Techniques for virtual palaeontology. John Wiley & Sons. Szaniawski, H., 2002. New evidence for the protoconodont origin of chaetognaths. Acta Palaeontologica Polonica 47, 405–419. Taylor, P.D., Berning, B., Wilson, M.A., 2013. Reinterpretation of the Cambrian “bryozoan” Pywackia as an octocoral. Journal of Paleontology 87, 984–990. doi:10.1666/13-029 Valentine, J.W., 1973. Evolutionary paleoecology of the marine biosphere. Prentice- Hall. Williams, A., Carlson, S., 2007. Affinities of brachiopods and trends in their evolution, in: Treatise on Invertebrate Paleontology, Part H, Brachiopoda, Revised. Geological Society of America & Paleontological Institute, Boulder, Colorado & Lawrence, Kansas. Williams, A., Carlson, S.J., Brunton, C.H.C., Holmer, L.E., Popov, L., 1996. A Su- pra-Ordinal Classification of the Brachiopoda. Philosophical Transactions of the Royal Society of London B: Biological Sciences 351, 1171–1193. doi:10.1098/rstb.1996.0101 Williams, A. & Rowell, A. J., 1965. Evolution and Phylogeny. In Moore, R. C. (ed.): Treatise on Invertebrate Paleontology, Part H, Brachiopoda, Revised, H164-199. The Geological Society of America and The University of Kansas, Boulder and Lawrence. Wright, 1979. The origin of major invertebrate groups. In: House, M. R. The Sys- tematics Association special volume No. 12. 1979 pp. x + 515 pp.

47 Zhang, Z., Holmer, L.E., Skovsted, C.B., Brock, G.A., Budd, G.E., Fu, D., Zhang, X., Shu, D., Han, J., Liu, J., Wang, H., Butler, A., Li, G., 2013. A sclerite- bearing stem group entoproct from the early Cambrian and its implications. Sci- entific Reports 3. doi:10.1038/srep01066 Zhang, Z.-F., Li, G.-X., Holmer, L.E., Brock, G.A., Balthasar, U., Skovsted, C.B., Fu, D.-J., Zhang, X.-L., Wang, H.-Z., Butler, A., Zhang, Z.-L., Cao, C.-Q., Han, J., Liu, J.-N., Shu, D.-G., 2014. An early Cambrian agglutinated tubular lophophorate with brachiopod characters. Scientific Reports 4. doi:10.1038/srep04682

48 Popular science article: The place of small shelly fossils in the Cambrian explosion, and the origin of Animals

Introduction: Darwin, the Cambrian explosion and the origin of animals. The small shelly fossils (or SSFs) of the early Cambrian period (approximately 541 million to 509 million years ago) could in many ways be described as the world’s worst jigsaw puzzle. This article will attempt to give a brief tour of the significance, history and biology of this humble yet potentially hugely important group of fossil organisms and how they may help in answering fundamental questions about how and when the major groups of animals evolved on Earth.

A palaeontological mystery… “To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer.” Charles Darwin, On the Origin of Species, (1859) A striking observation made by Victorian geologists and naturalists, including Charles Darwin, was that rocks from the Cambrian, Silurian, Ordo- vician and later periods (the Phanerozoic Eon as it would later come to be known, starting approximately 541 million years ago, to the present) were to a greater or lesser degree filled with the remains of bones, shells, animal teeth and plant fossils ranging from leaves to entire fossilized forests. How- ever, in rocks laid down before the Cambrian strata (in the Precambrian Eon), no trace of macroscopic life as we knew it could be found. Geologists had hit on an apparently huge problem with their understanding of geology and the fossil record at the time. Quite simply, where were the plants, animals and other evidence of life?

Butler, A.D., 2015. Fossil Focus: The place of small shelly fossils in the Cambrian explosion, and the origin of Animals. Palaeontology Online, Volume 5, Article 7, 1-14 Article originally appeared online at : http://www.palaeontologyonline.com/articles/2015/fossil-focus-place-small-shelly-fossils-cambrianexplosion-origin-animals/

49 So where are all the fossils ? Charles Walcott (who discovered the Burgess shale fossil field in Canada) proposed the name Lipalian for an interval of time that he thought had come before the Cambrian and was somehow not represented in the fossil record or simply did not preserve any fossilized remains. A few reasons were suggested: there were no animals around, they were soft bodied (non- biomineralized) and so did not preserve well or at all, or conditions were not suited to fossilization until the ‘Laggerstätte windows’ (for more infor- mation, you can read this article). On closer inspection, however, it turned out that the devil is in the details. There is, as it turns out, a rich record of trace fossils — burrows or trackways in early Cambrian rocks — which amounts to indirect evidence of the presence of some kind of complex organisms. Indeed, the start of the Cambrian is defined by the appearance of the trace fossil Treptichnus pedum, thought to be made by an organism similar to modern priapulids, a kind of marine worm. In the latter half of the twentieth century, the discovery of mysterious faunas, or collections of animals, from the Ediacaran period (635 million to 541 million years ago) showed that complex multicellular life predates the Cambrian. Organisms from these faunas may be related to modern animals in some way, but how they fit into the bigger picture of animal evolution is still controversial. They were almost universally soft-bodied. More recently, the presence of small, weakly mineralized fossils was recognized from the rocks in Siberia and other locations earlier than the rocks than contain trilo- bite fossils. These are ‘small shelly fossils’, an informal term coined by pal- aeontologists Samuel Matthews and Vladimir. V. Missarzhevsky in 1975 (see further reading) as a catch-all classification for a vast array of skeletal fossils, some of which appear in the late Precambrian, but most of which are found in the earliest Cambrian period (Fig. 1). These represent some of the first evidence of biomineralization and formation of skeletons by metazoans (animals and their close relatives), and pre-date by some time the sudden appearance of large fossils so often associated with the ‘Cambrian explosion’.

50 text

Figure 1 — A typical assemblage of diverse small shelly fossils from the Cambrian of Greenland. Images from scanning electron microscopy. A. Yochelcionella, a stem-group mollusc with a ‘snorkel’. B. Chancelloria, mysterious fossil organisms thought to be related to molluscs or sponges. C. Microdictyon plate, an armoured ‘worm’. D. Hyolith, small conical shell probably related to molluscs and annelids. E. Pelagiella, a stem-gastropod. F. A small bivalved arthropod or bradoriid. Images courtesy of John S. Peel

Timing of the SSF appearance Small shelly fossils near the start of the Cambrian mark a key transition from a world of microbial mats, single-celled organisms and simple soft-bodied forms, to one dominated by animals with skeletons, burrowing organisms and other metazoans. This transition happened in an epoch dubbed the Ter- reneuvian: the oldest part of the Cambrian, between the start of the Cambrian period and the appearance of trilobites (around 20 million years, including the Fortunian and Tommotian stages in Fig. 2).

Figure 2 — An approximate timeline of the Cambrian period and late Ediacaran period.

One of the first small shelly forms to appear is Cloudina (Fig. 3A), which is made up of stacked conical fossils found initially in the late Precambrian and persisting into the Cambrian. Other early ‘weakly mineralizing’ forms include Namacalathus (Fig. 3B) and Namapoikia from Namibia. Interestingly, Ediacaran organisms and these early shelly organisms are never found together, but they can be found in alternating layers, perhaps indicating that they preferred different environments. As we move to younger rocks, into the Cambrian itself (rocks from the Fortunian epoch), we begin to see small shelly fossils called halwaxiids, made of a mineral called aragonite; mollusc-like forms; and hyoliths (similar to those in Fig. 1).

Figure 3 — Weakly mineralized fossils of uncertain origin from the late Ediacaran period. A. Cloudina reconstruction (Source). B. Namacalathus reconstruction.

The hey-day of small shelly fossil abundance is in ‘Stage 2’ of the Cambri- an, also known as the Tommotian epoch (Fig. 2). This name comes from the strata of Siberia, which contain a large assemblage of SSFs called the tommotiids. The appearance of these fossils has been suggested as the indicator for the onset of this period of geological time. They are found alongside extensive early reef-like deposits of cup-shaped archaeocyaths, organisms thought to be sponges. This is directly before the appearance of trilobites and most of the famous Cambrian exceptional fossil sites such as the Burgess Shale and Chengjiang biotas (Fig. 2). Globally, small shelly fossils have occurred widely, turning up in Cam- brian rocks corresponding to shallow marine environments in many places around the globe, including China, Morocco, Australia (Fig. 4), Estonia, Sweden, the United Kingdom, Russia, Mongolia and even Antarctica.

Figure 4 — Flinders Ranges, South Australia. Prime hunting grounds for Cambrian SSFs.

Types and preservation of SSFs The vast majority of small shelly fossils had skeletons built from a mineral known as apatite (a form of calcium phosphate, the same material as bones and teeth); other forms, particularly the early examples, were made from calcium carbonate, like modern bivalves or snails. Phosphate is relatively rare in the oceans today. It is one of the main nu- trients that support photosynthesis in plants and algae, so it is in constant short supply. Cambrian oceans, however, are thought to have had a much higher phosphate content, enabling early animals to make extensive use of this mineral for their skeletons. Indeed, many SSFs are casts of the original animal that have been preserved by a phosphatic coating that grew on or inside the animals remains after death, rather than being an originally phosphatic skeleton. Fossils preserved this way are called steinkerns. In this way, skeletons originally made of calcium carbonate can end up in the rock record as a phosphatic fossil.

Why did hard parts evolve? “Now, here, you see, it takes all the running you can do, to keep in the same place.” Lewis Carroll, Through the Looking-Glass, and What Alice Found There (1871)

54 Many types of hard tissue with a huge range of functions can be seen in living animals. These act as internal supports (like the vertebrate skeleton inside you!), teeth for feeding, external supports or exoskeletons (snail shells for example) and dermal sclerites, or scales, for protection and to help swimming. The origin of hard parts is thought to be an example of an evolutionary arms race between predator and prey, constantly trying to gain ad- vantage over, and out-compete, each other. Prey animals tried to build better hard defences (shells and spines) and predators developed mineralized mouthparts and other strategies (such as behaviour) to defeat this armour. This concept in biology has been called the Red Queen hypothesis (after the character from Through the Looking-Glass). Other ideas have suggested that building skeletons was a way for animals to dispose of excess metabolic wastes or to store minerals such as calcium; the use for defence, support, feeding and so on was a side effect.

Research methods The usual method of collecting these phosphatic fossils is taking large blocks of limestone and dissolving them in acetic acid (essentially concentrated vinegar, leading to some people calling these fossils ‘small smellies’!), then picking through the dried residues to recover whatever fossil remains are left. Skeletons made of calcium phosphate will not dissolve in the mild acid bath (Fig. 5).

Figure 5 — A typical set up in an acid-processing lab. Samples are sorted, weighed and split mechanically. Carbonate rocks are left in the acid bath until the rock has fully dissolved. The remaining shelly fragments are sieved, washed and then sorted under a microscope.

Traditionally, SSFs were studied using a conventional light microscope to observe thin-sections of rock or whole specimens picked out of the acid residues. The invention of the electron microscope has allowed researchers to analyse the surface features of these animals in much higher detail, enabling them to find exquisitely preserved details such as cellular imprints and im- pressions of microvilli, extremely small features ranging from a few microns to nanometres in size. These are very useful for unravelling the mystery of the relationships of SSFs to more well-known fossil animals. Electron and light microscopy provided a basis of knowledge about SSFs, but until recent years researchers had literally only scratched the surface of SSF anatomy. Little was known about the internal structure and anatomy of most small shelly fossils, and what little was understood had been gathered through random breakage of the fossil, exposing an occasional surface, or by destructively grinding it into thin sections.

Figure 6 — Research techniques used to investigate small shelly fossils. A. Scan- ning electron microscope, Uppsala University, Sweden. B. CT scanner at the Uni- versity of Manchester, UK. C. TOMCAT beam line at the Swiss Light Source for synchrotron tomography. D. Outside panorama of the accelerator-ring building at the Swiss Light Source.

This all changed with the advent of 3D virtual-palaeontological techniques that allowed researchers to scan the fossils (Fig. 6) and peel away the skeleton, layer by layer, on a computer screen, exploring the creatures’ internal structure in great detail (Fig. 7).

Figure 7 — Example of CT reconstruction in progress, for the tommotiid Micrina. Internal structures are clearly visible when the surface layers are removed.

To produce such a model, researchers first need to scan the fossil. The most common technique is X-ray computed tomography, or CT scanning — similar to what you might find in a hospital or dentist surgery. The fossil is placed into the scanner and X-rayed from up to 4,000 positions on a spinning platform. A computer program is then used to reconstruct a detailed 3D model that can help the researcher to investigate the structure of the fossil. For higher-resolution models, researchers have generated X-rays using a particle accelerator called a synchrotron. The X-ray source from the synchrotron is much more intense than a standard source, and it produces radiation of a single wavelength, similar to a laser. The end result is a much faster scan than with smaller machines, at higher levels of detail. However, ma- chine time on such equipment comes at a premium! It is expensive and much sought-after. With these tools at their disposal, researchers move a large step closer to solving the enigma of just what small shelly fossils represent, and how they relate to living animals.

What then are the SSFs?

Putting together the evidence gained so far from such studies, I have outlined a few examples of how some SSFs have found a home in more recognizable animal groups. Mysterious isolated skeletal plates — or sclerites — had long been known from acid residues of an animal dubbed Halkieria. Nearly all known species

58 of this genus were known from such fragments, and reconstructions of the host organism remained elusive for a long time. That was, until the amazing discovery of exceptionally preserved articulated examples from the Sirius Passet Lagerstätte in Greenland. These showed a truly remarkable slug-like animal covered in armoured plates, with bivalved ‘shells’ at either end (Fig. 8).

Figure 8 — Fully articulated Halkieria evangelista from the Lower Cambrian of Greenland (Sirius Passet Formation). Image courtesy John S. Peel.

The isolated sclerites of Microdictyon (Fig. 1C and Fig. 9F) are well known from lower Cambrian small shelly deposits, and are thought to have been shed during moulting. Exceptionally preserved specimens from the Chengjiang locality clearly show the sclerites inside the soft-bodied animal, as muscle supports. It was only when these exceptional fossils were discovered that the nature and source of the isolated sclerites became clear — they belonged to an early worm-like arthropod.

Figure 9 — Scanning electron microscopy of tommotiids and other Cambrian small shelly fossils from South Australia. A. Dailyatia, a tommotiid ‘problematica’. Rela- tionship to other animals and biology not yet clear. B. Micrina, thought to be a stem- group brachiopod. C. Hyolithellus, a probable annelid tube. D. Sponge spicule. E. Lapworthella, an enigmatic tommotiid of unknown origin. F. Microdictyon ‘armoured worm’ sclerite. G. Palaeoscolecid worm. H. A bradoriid spine from a species called Mongolitubulus unispinosa. Scale bars = 200 µm. Images courtesy Tim Topper.

Another example is the origin of brachiopods (lamp shells), one of the most common fossil groups of the Palaeozoic era (541 million to 252 million years ago). It has been suggested that these animals can be traced back to a certain group of tommotiid small shelly fossils. The primary evidence for this comes from genera called Eccentrotheca, Micrina and Tannuolina, and a few other examples, the so-called Eccentrothecomorphs. These were initially known only from isolated sclerites. When researchers were lucky enough to find a number of well-preserved articulated examples, it became clear that they came from stem group animals probably related to brachiopods. The tommotiid Micrina (Fig. 7, 9B) also has a set of features charac- teristic to brachiopods, including their mode of growth, overall morphology, shell microstructure, presence of two articulated shell valves and phosphatic shell chemistry. It has been suggested that by studying the SSFs we can begin to reconstruct the evolutionary origins of the brachiopod body plan — albeit in stages, because there seem to be many intermediate forms between tomotiids and brachiopods. Although this view is far from universally accepted, it offers a tantalizing possibility to investigate the origin of a phylum from within the radiation of the small shelly fossils.

60 One further alternative model has raised the possibility that brachiopods may have evolved through the ‘folding up’ of a slug-like animal similar to Halkieria, with opposed shell plates overlapping to form a closed filtration chamber, or in other words the bivalved shell (see Cohen et al. in further reading).

Figure 10 — Tannuolina from the Cambrian of Morocco and Eccentrotheca from South Australia. A. Rare articulated scleritome of Eccentrotheca consisting of many sclerites. B. Reconstruction of whole animal with feeding organ, or lophophore. C. Isolated sclerites of Tannuolina. D. Reconstruction of Tannuolina based on careful observations of how the sclerites fit together. Images courtesy Christian Skovsted.

A recently described Cambrian filter-feeding animal, Cotyledion tylodes, is covered with an outer armour of relatively sparse oval plates (known as sclerites) that also resemble some tommotiid small shelly fossils (Fig. 11). The presence of a scleritome, a skeleton made of isolated elements or sclerites joined somewhat like medieval chainmail, seems to be a common uniting

61 feature of many animal stem groups. The scleritome of Cotyledion is most comparable to that of the tommotiid Eccentrotheca, but the sclerites differ in structure enough that it is thought not to be a tommotiid. However, the paral- lel in form and function is striking, and there is probably a close relationship between these fossils.

Figure 11 — Cotyledion tylodes fossil (A) and reconstructions (B–C) Adapted from Zhang et al. (2013). Ap, anal papilla; M, mouth; Es, esophagus; St, distended stom- ach. Note that the entire body is covered in oval sclerites, like that of Eccentrotheca (Fig. 10A).

Some additional SSFs, such as the rather beautiful but problematic Dailyatia (Fig. 9A), continue to defy classification, with the scleritome having been reconstructed in contrasting ways. One model suggests that the animal was slug-like, similar to Halkieria; another makes it a tube-dweller with a tightly packed scleritome, like Eccentrotheca (Fig. 10A, B). Pending the discovery of a complete scleritome or of an exceptionally preserved host animal, the jury is still out as to which of these reconstruction models is correct, if indeed either of them is!

What happens to the SSFs?

The occurrence and diversity of SSFs declines as we move later into the Cambrian. The SSFs are not a clade or natural grouping, so we cannot say

62 that they became extinct in any meaningful sense. Rather, it seems that they evolved into, and were eventually replaced by, more recognizable forms of the ‘Palaeozoic evolutionary fauna’ such as brachiopods, bivalves, arthropods and gastropods. As we approach the Ordovician period, most of the remaining small shelly components of the fossil record turn out to be larval gastropods.

What does the future hold?

Some SSFs, as we have seen, are identifiable as stem-group animals such as arthropods; others correspond to primitive mollusc shells, brachiopod valves and annelid tubes or spines. Many more forms remain enigmatic, and for the moment are considered ‘problematica’, or fossils with an uncertain relationship to other organisms. Organic parallels to the SSFs have emerged in the record of small carbonaceous fossils, or SCFs. These are another suite of small mysterious fossils, recovered by hydrofluoric-acid processing of shales and mudrocks. The recovered bits of organic material, made from chitin and other structural pol- ymers, give us further insight into hidden Cambrian diversity. For example, they push back the earliest known mouthparts of some crustaceans by mil- lions of years. These complementary fossil records of early animals help us to flesh out what sort of diversity may have been present early in the history of animal evolution, especially given that SCFs and SSFs preserve in very different environments (deep marine mudstones vs. shallow carbonate rocks, respectively). New relatives of SSFs may also be discovered in the future, in animals that rely on agglutination (that is, their shells are made from grains of sedi- ment stuck together much like a sandcastle). This is a strategy used by modern annelid worms and Phoronida (horseshoe worms) to build their protec- tive outer living tubes. It may represent an ancient life strategy in some of the earliest animals, including the agglutinated fossils Salterella and Vol- borthella. A recently discovered unusual agglutinating fossil organism shows some brachiopod characteristics as well as features of their nearest relatives, the phoronids or horseshoe worms. This organism, Yuganotheca elegans from the Chengjiang site of exceptional fossil preservation, suggests that agglutination may have been more widespread in early animals than has been recognized, but this remains very much an open question (Fig. 12).

Figure 12 — Yuganotheca elegans from Chengjiang, China, showing fossil (A–C), and reconstruction. The paired shell valves are made of agglutinated sand grains. Mouth (M), central lumen (Pc) and the terminal bulb (Dg) of the pedicle. Recon- struction of animal in life position filter feeding with its lophophore organ, on right.

My personal view of what we can tell from this rich record of seemingly insignificant small fossils is that the appearance of animals happened in a more gradual way than was first thought, with an explosion of fossilization potential happening alongside the huge diversification of life in the Cambri- an, a direct result of the evolution of hard parts. Subtle hints from sources such as SSFs, trace fossils and SCFs give us an idea that complex animal life had gained a foothold in the earliest Cambrian and possibly even extended to the late Ediacaran in some more controversial cases (Fig. 2). In conclusion, the hardest jigsaws are usually the most satisfying to finish. It seems likely that further investigation of the hidden diversity within SSFs will turn up a few surprises and — who knows — perhaps the evolutionary roots of a phylum or two along the way!

64 Further reading Cohen, B. L., Holmer, L. E. & Lüter, C. 2003. The brachiopod fold: a ne- glected body plan hypothesis. Palaeontology 46, 59–65. doi: 10.1111/1475- 4983.00287 Marshall, C. R. 2006. Explaining the Cambrian “explosion” of animals. The Annual Review of Earth and Planetary Sciences 34, 355–384. doi: 10.1146/annurev.earth.33.031504.103001 Matthews, S. T. & Missarzhevsky, V. V. 1975. Small shelly fossils of late Precambrian and early Cambrian age: A review of recent work. Journal of the Geological Society 131, 289–303. doi: 10.1144/gsjgs.131.3.0289 Murdock, D. J. E., Bengtson, S., Marone, F., Greenwood, J. M. & Do- noghue, P. C. 2014. Evaluating scenarios for the evolutionary assembly of the brachiopod body plan. Evolution & Development 16, 13–24. doi: 10.1111/ede.12059 Skovsted, C. B., Clausen, S., Álvaro, J. J. & Ponlevé, D. 2014. Tommoti- ids from the early Cambrian (Series 2, Stage 3) of Morocco and the evolution of the tannuolinid scleritome and setigerous shell structures in stem group brachiopods. Palaeontology 57, 171–192. doi: 10.1111/pala.12060 Skovsted, C. B., Brock, G. A., Topper, T. P., Paterson, J. R. & Holmer, L. E. 2011. Scleritome construction, biofacies, biostratigraphy and systematics of the tommotiid Eccentrotheca helenia sp. nov. from the Early Cambrian of South Australia. Palaeontology 54, 253–286. doi: 10.1111/j.1475- 4983.2010.01031.x Zhang, Z. et al. 2013. A sclerite-bearing stem group entoproct from the early Cambrian and its implications. Scientific Reports 3, 1066. doi: 10.1038/srep01066 Zhang, Z-F. et al. 2014. An early Cambrian agglutinated tubular lophophorate with brachiopod characters. Scientific Reports 4, 4682. doi: 10.1038/srep04682

65 Acta Universitatis Upsaliensis Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1284 Editor: The Dean of the Faculty of Science and Technology

A doctoral dissertation from the Faculty of Science and Technology, Uppsala University, is usually a summary of a number of papers. A few copies of the complete dissertation are kept at major Swedish research libraries, while the summary alone is distributed internationally through the series Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology. (Prior to January, 2005, the series was published under the title “Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology”.)

ACTA UNIVERSITATIS UPSALIENSIS Distribution: publications.uu.se UPPSALA urn:nbn:se:uu:diva-261907 2015