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.

A long-headed Cambrian soft-bodied vertebrate from the American Great Basin region

The fossil record suggests that chordates might have been minor components of marine ecosystems during the first major diversification of animal life in the Cambrian. Vertebrates are represented by a handful of rare soft-bodied stem-lineage taxa known from Konservat-Lagerstätten, including Myllokunmingia and Yunnanozoon from the Stage 3 of South China, and Emmonsaspis and Metaspriggina from Stage 4-Drumian deposits of northeast USA and British Columbia. Here, we describe the first soft-bodied vertebrate from the American Great Basin, a region home to a dozen Cambrian Konservat-Lagerstätten. Found in the Drumian Marjum Formation of Utah, Nuucichthys rhynchocephalus gen. et sp. nov. is characterized by a finless torpedo-shaped body that includes a snout-like anterior head bearing anterolateral eyes, approximately 25 thick myomeres, a large branchial chamber with a keel and approximately seven putative dorsal bars and a spiniform caudal process. Using Bayesian inference, our analysis recovers Nuucichthys within the vertebrate stem, closer to the crown than Pikaia, Yunnanozoon and Myllokunmingia, where it forms a polytomy with its Laurentian relatives, Emmonsaspis and Metaspriggina, and a scion consisting of conodonts and crown-group vertebrates. Based on the eye orientation and absence of fins, we tentatively reconstruct Nuucichthys as a pelagic organism with limited swimming abilities (planktonektic).

Colonization of the ocean floor by jawless vertebrates across three mass extinctions

BACKGROUND

The deep (> 200 m) ocean floor is often considered to be a refugium of biodiversity; many benthic marine animals appear to share ancient common ancestry with nearshore and terrestrial relatives. Whether this pattern holds for vertebrates is obscured by a poor understanding of the evolutionary history of the oldest marine vertebrate clades. Hagfishes are jawless vertebrates that are either the living sister to all vertebrates or form a clade with lampreys, the only other surviving jawless fishes.

RESULTS

We use the hagfish fossil record and molecular data for all recognized genera to construct a novel hypothesis for hagfish relationships and diversification. We find that crown hagfishes persisted through three mass extinctions after appearing in the Permian ~ 275 Ma, making them one of the oldest living vertebrate lineages. In contrast to most other deep marine vertebrates, we consistently infer a deep origin of continental slope occupation by hagfishes that dates to the Paleozoic. Yet, we show that hagfishes have experienced marked body size diversification over the last hundred million years, contrasting with a view of this clade as morphologically stagnant.

CONCLUSION

Our results establish hagfishes as ancient members of demersal continental slope faunas and suggest a prolonged accumulation of deep sea jawless vertebrate biodiversity.

Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs

The pharyngeal endoderm, an innovation of deuterostome ancestors, contributes to pharyngeal development by influencing the patterning and differentiation of pharyngeal structures in vertebrates; however, the evolutionary origin of the pharyngeal organs in vertebrates is largely unknown. The endostyle, a distinct pharyngeal organ exclusively present in basal chordates, represents a good model for understanding pharyngeal organ origins. Using Stereo-seq and single-cell RNA sequencing, we constructed aspatially resolved single-cell atlas for the endostyle of the ascidian Styela clava. We determined the cell composition of the hemolymphoid region, which illuminates a mixed ancestral structure for the blood and lymphoid system. In addition, we discovered a cluster of hair cell-like cells in zone 3, which has transcriptomic similarity with the hair cells of the vertebrate acoustico-lateralis system. These findings reshape our understanding of the pharynx of the basal chordate and provide insights into the evolutionary origin of multiplexed pharyngeal organs.

A collagen-rich arch in the urochordate notochord coordinates cell shaping and multi-tissue elongation

Cell and tissue reshaping is crucial for coordinating three-dimensional pattern formation, in which the size and shape of the cells must be accurately regulated via signal transport and communication among tissues. However, the identity of signaling and transportation mechanisms in this process remains elusive. In our study, we identified an extracellular matrix (ECM) structure with a vertebra-like shape surrounding the central notochord tissue in the larval tail of the urochordate Ciona. Additionally, we verified that the ECM structure was formed de novo, mainly from collagens secreted by notochord cells. Fluorescence recovery after photobleaching and simulation results revealed that this structure was formed via diffusional collagen flow from a notochord that was restricted and molded in the spaces among tail tissues. We revealed that the collagen structure was essential for notochord cell arrangement and elongation. Furthermore, we observed that the central notochord connects with the epidermis through this ECM structure. The disruption of this structure by collagen knockdown and loss-of-collagen function caused the failure of notochord elongation. More importantly, the epidermis could not elongate proportionally with notochord, indicating that the collagen-rich structure serves as a scaffold to coordinate the concurrent elongation of the tail tissues. These findings provide insights into how the central tissue forms and molds its surrounding ECM structure, by not only regulating its own morphogenesis but also functioning as a scaffold for signal transmission to orchestrate the coordinated morphologic reshaping of the surrounding tissues.

Ultrastructure of the lamprey head mesoderm reveals evolution of the vertebrate head

The cranial muscle is a critical component in the vertebrate head for a predatory lifestyle. However, its evolutionary origin and possible segmental nature during embryogenesis have been controversial. In jawed vertebrates, the presence of pre-otic segments similar to trunk somites has been claimed based on developmental observations. However, evaluating such arguments has been hampered by the paucity of research on jawless vertebrates. Here, we discovered different cellular arrangements in the head mesoderm in lamprey embryos (Lethenteron camtschaticum) using serial block-face scanning electron and laser scanning microscopies. These cell populations were morphologically and molecularly different from somites. Furthermore, genetic comparison among deuterostomes revealed that mesodermal gene expression domains were segregated antero-posteriorly in vertebrates, whereas such segregation was not recognized in invertebrate deuterostome embryos. These findings indicate that the vertebrate head mesoderm evolved from the anteroposterior repatterning of an ancient mesoderm and developmentally diversified before the split of jawless and jawed vertebrates.

Pre-mandibular pharyngeal pouches in early non-teleost fish embryos

The vertebrate pharynx is a key embryonic structure with crucial importance for the metameric organization of the head and face. The pharynx is primarily built upon progressive formation of paired pharyngeal pouches that typically develop in post-oral (mandibular, hyoid and branchial) domains. However, in the early embryos of non-teleost fishes, we have previously identified pharyngeal pouch-like outpocketings also in the pre-oral domain of the cranial endoderm. This pre-oral gut (POG) forms by early pouching of the primitive gut cavity, followed by the sequential formation of typical (post-oral) pharyngeal pouches. Here, we tested the pharyngeal nature of the POG by analysing expression patterns of selected core pharyngeal regulatory network genes in bichir and sturgeon embryos. Our comparison revealed generally shared expression patterns, including Shh, Pax9, Tbx1, Eya1, Six1, Ripply3 or Fgf8, between early POG and post-oral pharyngeal pouches. POG thus shares pharyngeal pouch-like morphogenesis and a gene expression profile with pharyngeal pouches and can be regarded as a pre-mandibular pharyngeal pouch. We further suggest that pre-mandibular pharyngeal pouches represent a plesiomorphic vertebrate trait inherited from our ancestor's pharyngeal metameric organization, which is incorporated in the early formation of the pre-chordal plate of vertebrate embryos.

Response to Comments on "Ultrastructure reveals ancestral vertebrate pharyngeal skeleton in yunnanozoans"

He et al. dispute our anatomical interpretations on the structures of cellular chambers and microfibrils in yunnanozoan branchial arches and put forward alternative interpretations on these structures. Zhang and Pratt argue that the microfibrils we identified in yunnanozoans are more likely modern organic contamination. Here we provide additional evidence to support our interpretations and dismiss the alternative interpretations.

Comment on "Ultrastructure reveals ancestral vertebrate pharyngeal skeleton in yunnanozoans"

Tian et al. (Research Articles, 8 July 2022, abm2708) hypothesized that yunnanozoans are stem-group vertebrates on the basis of "cellular cartilage", "fibrillin microfibers", and "subchordal rod" associated with the branchial arches of yunnanozoans. However, we reject the presence of cellular cartilage, fibrillin, and the phylogenetic proposal of vertebrate affinities based on ultrastructure and morphology of yunnanozoans from more than 8000 specimens.

Comment on "Ultrastructure reveals ancestral vertebrate pharyngeal skeleton in yunnanozoans"

Tian et al. (Reports, 8 July 2022, p. 218) claim that Cambrian yunnanozoan animals are stem vertebrates, based partly on their observation at the nanometer scale of microfibrillar tissue located in the branchial arches. They interpret this to represent cellular cartilage with an extracellular matrix of microfibrils. Instead, we argue that the 'microfibrils' are more likely modern organic contamination.

Cranial cartilages: Players in the evolution of the cranium during evolution of the chordates in general and of the vertebrates in particular

The present contribution is chiefly a review, augmented by some new results on amphioxus and lamprey anatomy, that draws on paleontological and developmental data to suggest a scenario for cranial cartilage evolution in the phylum chordata. Consideration is given to the cartilage-related tissues of invertebrate chordates (amphioxus and some fossil groups like vetulicolians) as well as in the two major divisions of the subphylum Vertebrata (namely, agnathans, and gnathostomes). In the invertebrate chordates, which can be considered plausible proxy ancestors of the vertebrates, only a viscerocranium is present, whereas a neurocranium is absent. For this situation, we examine how cartilage-related tissues of this head region prefigure the cellular cartilage types in the vertebrates. We then focus on the vertebrate neurocranium, where cyclostomes evidently lack neural-crest derived trabecular cartilage (although this point needs to be established more firmly). In the more complex gnathostome, several neural-crest derived cartilage types are present: namely, the trabecular cartilages of the prechordal region and the parachordal cartilage the chordal region. In sum, we present an evolutionary framework for cranial cartilage evolution in chordates and suggest aspects of the subject that should profit from additional study.

Vertebrate cranial evolution: Contributions and conflict from the fossil record

In modern vertebrates, the craniofacial skeleton is complex, comprising cartilage and bone of the neurocranium, dermatocranium and splanchnocranium (and their derivatives), housing a range of sensory structures such as eyes, nasal and vestibulo-acoustic capsules, with the splanchnocranium including branchial arches, used in respiration and feeding. It is well understood that the skeleton derives from neural crest and mesoderm, while the sensory elements derive from ectodermal thickenings known as placodes. Recent research demonstrates that neural crest and placodes have an evolutionary history outside of vertebrates, while the vertebrate fossil record allows the sequence of the evolution of these various features to be understood. Stem-group vertebrates such as Metaspriggina walcotti (Burgess Shale, Middle Cambrian) possess eyes, paired nasal capsules and well-developed branchial arches, the latter derived from cranial neural crest in extant vertebrates, indicating that placodes and neural crest evolved over 500 million years ago. Since that time the vertebrate craniofacial skeleton has evolved, including different types of bone, of potential neural crest or mesodermal origin. One problematic part of the craniofacial skeleton concerns the evolution of the nasal organs, with evidence for both paired and unpaired nasal sacs being the primitive state for vertebrates.

Vertebrate origins are informed by larval lampreys (ammocoetes): a response to Miyashita et al., 2021

This paper addresses a recent claim by Miyashita and co-authors that the filter-feeding larval lamprey is a new evolutionary addition to the lamprey life-cycle and does not provide information about early vertebrates, in contrast to the traditional view that this ammocoete stage resembles the first vertebrates. The evidence behind this revolutionary claim comes from fossil lampreys from 360–306 Mya that include young stages – even yolk-sac hatchlings – with adult (predacious) feeding structures. However, the traditional view is not so easily dismissed. The phylogeny on which the non-ammocoete theory is based was not tested in a statistically meaningful way. Additionally, the target article did not consider the known evidence for the traditional view, namely that the complex filter-feeding structures are highly similar in ammocoetes and the invertebrate chordates, amphioxus and tunicates. In further support of the traditional view, I show that ammocoetes are helpful for reconstructing the first vertebrates and the jawless, fossil stem gnathostomes called ostracoderms – their pharynx, oral cavity, mouth opening, lips and filter-feeding mode (but, ironically, not their mandibular/jaw region). From these considerations, I offer a scenario for the evolution of vertebrate life-cycles that fits the traditional, ammocoete-informed theory and puts filter feeding at centre stage.

“Arch”-etyping vertebrates

Cellular details of gill arches in Cambrian fossils reignite a centuries-old debate