A critical reappraisal of the fossil record of the bilaterian phyla

A new interpretation of Pikaia reveals the origins of the chordate body plan

Our understanding of the evolutionary origin of Chordata, one of the most disparate and ecologically significant animal phyla, is hindered by a lack of unambiguous stem-group relatives. Problematic Cambrian fossils that have been considered as candidate chordates include vetulicolians,1Yunnanozoon,2 and the iconic Pikaia.3 However, their phylogenetic placement has remained poorly constrained, impeding reconstructions of character evolution along the chordate stem lineage. Here we reinterpret the morphology of Pikaia, providing evidence for a gut canal and, crucially, a dorsal nerve cord-a robust chordate synapomorphy. The identification of these structures underpins a new anatomical model of Pikaia that shows that this fossil was previously interpreted upside down. We reveal a myomere configuration intermediate between amphioxus and vertebrates and establish morphological links between Yunnanozoon, Pikaia, and uncontroversial chordates. In this light, we perform a new phylogenetic analysis, using a revised, comprehensive deuterostome dataset, and establish a chordate stem lineage. We resolve vetulicolians as a paraphyletic group comprising the earliest diverging stem chordates, subtending a grade of more derived stem-group chordates comprising Yunnanozoon and Pikaia. Our phylogenetic results reveal the stepwise acquisition of characters diagnostic of the chordate crown group. In addition, they chart a phase in early chordate evolution defined by the gradual integration of the pharyngeal region with a segmented axial musculature, supporting classical evolutionary-developmental hypotheses of chordate origins4 and revealing a "lost chapter" in the history of the phylum.

New insights into mesoderm and endoderm development, and the nature of the onychophoran blastopore

BACKGROUND

Early during onychophoran development and prior to the formation of the germ band, a posterior tissue thickening forms the posterior pit. Anterior to this thickening forms a groove, the embryonic slit, that marks the anterior-posterior orientation of the developing embryo. This slit is by some authors considered the blastopore, and thus the origin of the endoderm, while others argue that the posterior pit represents the blastopore. This controversy is of evolutionary significance because if the slit represents the blastopore, then this would support the amphistomy hypothesis that suggests that a slit-like blastopore in the bilaterian ancestor evolved into protostomy and deuterostomy.

RESULTS

In this paper, we summarize our current knowledge about endoderm and mesoderm development in onychophorans and provide additional data on early endoderm- and mesoderm-determining marker genes such as Blimp, Mox, and the T-box genes.

CONCLUSION

We come to the conclusion that the endoderm of onychophorans forms prior to the development of the embryonic slit, and thus that the slit is not the primary origin of the endoderm. It is thus unlikely that the embryonic slit represents the blastopore. We suggest instead that the posterior pit indeed represents the lips of the blastopore, and that the embryonic slit (and surrounding tissue) represents a morphologically superficial archenteron-like structure. We conclude further that both endoderm and mesoderm development are under control of conserved gene regulatory networks, and that many of the features found in arthropods including the model Drosophila melanogaster are likely derived.

Evolution of homology: From archetype towards a holistic concept of cell type

The concept of homology lies in the heart of comparative biological science. The distinction between homology as structure and analogy as function has shaped the evolutionary paradigm for a century and formed the axis of comparative anatomy and embryology, which accept the identity of structure as a ground measure of relatedness. The advent of single-cell genomics overturned the classical view of cell homology by establishing a backbone regulatory identity of cell types, the basic biological units bridging the molecular and phenotypic dimensions, to reveal that the cell is the most flexible unit of living matter and that many approaches of classical biology need to be revised to understand evolution and diversity at the cellular level. The emerging theory of cell types explicitly decouples cell identity from phenotype, essentially allowing for the divergence of evolutionarily related morphotypes beyond recognition, as well as it decouples ontogenetic cell lineage from cell-type phylogeny, whereby explicating that cell types can share common descent regardless of their structure, function or developmental origin. The article succinctly summarizes current progress and opinion in this field and formulates a more generalistic view of biological cell types as avatars, transient or terminal cell states deployed in a continuum of states by the developmental programme of one and the same omnipotent cell, capable of changing or combining identities with distinct evolutionary histories or inventing ad hoc identities that never existed in evolution or development. It highlights how the new logic grounded in the regulatory nature of cell identity transforms the concepts of cell homology and phenotypic stability, suggesting that cellular evolution is inherently and massively network-like, with one-to-one homologies being rather uncommon and restricted to shallower levels of the animal tree of life.

Molecular dating of the blood pigment hemocyanin provides new insight into the origin of animals

The Neoproterozoic included changes in oceanic redox conditions, the configuration of continents and climate, extreme ice ages (Sturtian and Marinoan), and the rise of complex life forms. A much-debated topic in geobiology concerns the influence of atmospheric oxygenation on Earth and the origin and diversification of animal lineages, with the most widely popularized hypotheses relying on causal links between oxygen levels and the rise of animals. The vast majority of extant animals use aerobic metabolism for growth and homeostasis; hence, the binding and transportation of oxygen represent a vital physiological task. Considering the blood pigment hemocyanin (Hc) is present in sponges and ctenophores, and likely to be present in the common ancestor of animals, we investigated the evolution and date of Hc emergence using bioinformatics approaches on both transcriptomic and genomic data. Bayesian molecular dating suggested that the ancestral animal Hc gene arose approximately 881 Ma during the Tonian Period (1000-720 Ma), prior to the extreme glaciation events of the Cryogenian Period (720-635 Ma). This result is corroborated by a recently discovered fossil of a putative sponge ~890 Ma and modern molecular dating for the origin of metazoans of ~1,000-650 Ma (but does contradict previous inferences regarding the origin of Hc ~700-600 Ma). Our data reveal that crown-group animals already possessed hemocyanin-like blood pigments, which may have enhanced the oxygen-carrying capacity of these animals in hypoxic environments at that time or acted in the transport of hormones, detoxification of heavy metals, and immunity pathways.

Ancient life and moving fluids

Over 3.7 billion years of Earth history, life has evolved complex adaptations to help navigate and interact with the fluid environment. Consequently, fluid dynamics has become a powerful tool for studying ancient fossils, providing insights into the palaeobiology and palaeoecology of extinct organisms from across the tree of life. In recent years, this approach has been extended to the Ediacara biota, an enigmatic assemblage of Neoproterozoic soft‐bodied organisms that represent the first major radiation of macroscopic eukaryotes. Reconstructing the ways in which Ediacaran organisms interacted with the fluids provides new insights into how these organisms fed, moved, and interacted within communities. Here, we provide an in‐depth review of fluid physics aimed at palaeobiologists, in which we dispel misconceptions related to the Reynolds number and associated flow conditions, and specify the governing equations of fluid dynamics. We then review recent advances in Ediacaran palaeobiology resulting from the application of computational fluid dynamics (CFD). We provide a worked example and account of best practice in CFD analyses of fossils, including the first large eddy simulation (LES) experiment performed on extinct organisms. Lastly, we identify key questions, barriers, and emerging techniques in fluid dynamics, which will not only allow us to understand the earliest animal ecosystems better, but will also help to develop new palaeobiological tools for studying ancient life.

Anoxia can increase the rate of decay for cnidarian tissue: Using Actinia equina to understand the early fossil record

An experimental decay methodology is developed for a cnidarian model organism to serve as a comparison to the many previous such studies on bilaterians. This allows an examination of inherent bias against the fossilisation of cnidarian tissue and their diagnostic characters, under what conditions these occur, and in what way. The decay sequence of Actinia equina was examined under a series of controlled conditions. These experiments show that cnidarian decay begins with an initial rupturing of the epidermis, followed by rapid loss of recognisable internal morphological characters. This suggests that bacteria work quicker on the epidermis than autolysis does on the internal anatomy. The data also show that diploblastic tissue is not universally decayed more slowly under anoxic or reducing conditions than under oxic conditions. Indeed, some cnidarian characters decay more rapidly under anoxic conditions than they do under oxic conditions. This suggests the decay pathways acting may be different to those affecting soft bilaterian tissue such as soft epidermis and internal organs. What is most important in the decay of soft polyp anatomy is the microbial community, which can be dominated by oxic or anoxic bacteria. Different Lagerstätte, even of the same type, will inevitably have subtle difference in their bacterial communities, which among other factors, could be a control on soft polyp preservation leading to either an absence of compelling soft anthozoans (Burgess Shale) or an astonishing abundance (Qingjiang biota).

Predation and the origin of neurones

The core design of spiking neurones is remarkably similar throughout the animal kingdom. Their basic function as fast-signalling thresholding cells might have been established very early in their evolutionary history. Identifying the selection pressures that drove animals to evolve spiking neurones could help us interpret their design and function today. We review fossil, ecological and molecular evidence to investigate when and why animals evolved spiking neurones. Fossils suggest that animals evolved nervous systems soon after the advent of animal-on-animal predation, 550 million years ago (MYa). Between 550 and 525 MYa, we see the first fossil appearances of many animal innovations, including eyes. Animal behavioural complexity increased during this period as well, as evidenced by their traces, suggesting that nervous systems were an innovation of that time. Fossils further suggest that, before 550 MYa, animals were either filter feeders or microbial mat grazers. Extant sponges and Trichoplax perform these tasks using energetically cheaper alternatives than spiking neurones. Genetic evidence testifies that nervous systems evolved before the protostome-deuterostome split. It is less clear whether nervous systems evolved before the cnidarian-bilaterian split, so cnidarians and bilaterians might have evolved their nervous systems independently. The fossil record indicates that the advent of predation could fit into the window of time between those two splits, though molecular clock studies dispute this claim. Collectively, these lines of evidence indicate that animals evolved spiking neurones soon after they started eating each other. The first sensory neurones could have been threshold detectors that spiked in response to other animals in their proximity, alerting them to perform precisely timed actions, such as striking or fleeing.

The disparity of priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data

Priapulids and their extinct relatives, the archaeopriapulids and palaeoscolecids, are vermiform, carnivorous ecdysozoans with an armoured, extensible proboscis. These worms were an important component of marine communities during the Palaeozoic, but were especially abundant and diverse in the Cambrian. Today, they comprise just seven genera in four families. Priapulids were among the first groups used to test hypotheses concerning the morphological disparity of Cambrian fossils relative to the extant fauna. A previous study sampled at the generic level, concluding that Cambrian genera embodied marginally less morphological diversity than their extant counterparts. Here, we sample predominantly at the species level and include numerous fossils and some extant forms described in the last fifteen years. Empirical morphospaces for priapulids, archaeopriapulids and palaeoscolecids are relatively insensitive to changes in the taxon or character sample: their overall form has altered little, despite the markedly improved sampling. Cambrian and post-Cambrian genera occupy adjacent rather than broadly overlapping regions of these spaces, and Cambrian species still show lower morphological disparity than their post-Cambrian counterparts. Crucially, the significance of this difference has increased with improved taxon sampling over research time. In contrast with empirical morphospaces, the phylogeny of priapulids, archaeopriapulids and palaeoscolecids derived from morphological characters is extremely sensitive to details of taxon sampling and the manner in which characters are weighted. However, the extant Priapulidae and Halicryptidae invariably resolve as sister families, with this entire clade subsequently being sister group to the Maccabeidae. In our most inclusive trees, the extant Tubiluchidae are separated from these other living taxa by a number of small, intervening fossil clades.

Phosphatized multicellular algae in the Neoproterozoic Doushantuo Formation, China, and the early evolution of florideophyte red algae

Phosphatic sediments of the Late Neoproterozoic (ca. 600 million years old [Myr]) Doushantuo Formation at Weng'an, South China, contain fossils of multicellular algae preserved in anatomical detail. As revealed by light microscopy and scanning electron microscopy, these fossils include both simple pseudoparenchymatous thalli with apical growth but no cortex-medulla differentiation and more complex thalli characterized by cortex-medulla differentiation and structures interpretable as carposporophytes, suggesting a multiphasic life cycle. Simple pseudoparenchymatous thalli, represented by Wengania, Gremiphyca, and Thallophycoides, are interpreted as stem group florideophytes. In contrast, complex pseudoparenchymatous thalli, such as Thallophyca and Paramecia, compare more closely to fossil and living corallinaleans than to other florideophyte orders, although they also differ in some important aspects (e.g., lack of biocalcification). These more complex thalli are interpreted as early stem group corallinaleans that diverged before Paleozoic stem groups such as Arenigiphyllum, Petrophyton, Graticula, and Archaeolithophyllum. This phylogenetic interpretation implies that (1) the phylogenetic divergence between the Florideophyceae and its sister group, the Bangiales, must have taken place before Doushantuo time-an inference supported by the occurrence of bangialean fossils in Mesoproterozoic rocks; (2) the initial diversification of the florideophytes occurred no later than the Doushantuo time; and (3) the corallinalean clade had a "soft" (uncalcified) evolutionary history in the Neoproterozoic before evolving biocalcification in the Paleozoic and undergoing crown group diversification in the Mesozoic.