Origin Of Chordates Research Articles

Deuterostome Ancestors and Chordate Origins.

The Deuterostomia are a monophyletic group, consisting of the Ambulacraria, with two phyla, Hemichordata and Echinodermata, and the phylum Chordata, containing the subphyla Cephalochordata (lancelets or Amphioxus), Tunicata (Urochordata) and Vertebrata. Hemichordates and echinoderms are sister groups and are critical for understanding the deuterostome ancestor and the origin and evolution of the chordates within the deuterostomes. Enteropneusta, worm-like hemichordates, share many chordate features as adults, including a post-anal tail, gill slits, and a Central Nervous System (CNS) that deploy similar developmental Genetic Regulatory Networks (GRNs). Genomic comparisons show that cephalochordates share synteny and a vermiform body plan similar to vertebrates, but phylogenomic analyses place tunicates as the sister group of vertebrates. Tunicates have a U-shaped gut and a very different adult body plan than the rest of the chordates, and all tunicates have small genomes and many gene losses, although the GRNs underlying specific tissues, such as notochord and muscle, are conserved. Echinoderms and vertebrates have extensive fossil records, with fewer specimens found for tunicates and enteropneusts, or worm-like hemichordates. The data is mounting that the deuterostome ancestor was a complex benthic worm, with gill slits, a cartilaginous skeleton, and a CNS. Two extant groups, echinoderms and tunicates, have evolved highly derived body plans, remarkably different than the deuterostome ancestor. We review the current genomic and GRN data on the different groups of deuterostomes' characters to re-evaluate different hypotheses of chordate origins. Notochord loss in echinoderms and hemichordates is as parsimonious as notochord gain in the chordates but has implications for the deuterostome ancestor. The chordate ancestor lost an ancestral nerve net, retained the central nervous system, and evolved neural crest cells.

Introduction to the 2024 Chordate Origins, Evolution and Development SICB Symposium.

The evolution of the distinct chordate body plan has intrigued scientists for over a hundred and seventy years. Modern genomics and transcriptomics have allowed the elucidation of the Developmental Gene Regulatory Networks (GRNs) underlying the developmental programs for particular tissues and body axes in invertebrates and vertebrates. This has been most revealing in the Deuterostomia, the superphylum in which chordates evolved. The time was ripe to gather those working on deuterostome developmental GRNs to revisit the development and evolution of chordates and discuss the evolution of this unique body plan at the SICB 2024 meetings in Seattle, WA. It has been several years since the genomes of the major deuterostome clades have been sequenced - echinoderms, hemichordates, tunicates, lancelets and vertebrates. Genomic analyses have shown that lancelets have a genome and body plan that closely resemble the vertebrates, although phylogenomic analyses suggest that the tunicates are the sister group of the vertebrates. The evolution of the sessile and sometimes colonial adult tunicates was likely from a motile, lancelet-like ancestor. Scientists from all over the world converged at the SICB meetings in Seattle to discuss the current ideas of how chordates evolved. Some common mechanisms and themes emerged and are captured in this ICB volume on Chordate Origins, Evolution and Development.

"A New Explanation of Nature of Cancer and Question of the Origin of Chordates"

"A New Explanation of Nature of Cancer and Question of the Origin of Chordates"

ScRNA-seq analysis of cells comprising the amphioxus notochord

Cephalochordates occupy a key phylogenetic position for deciphering the origin and evolution of chordates, since they diverged earlier than urochordates and vertebrates. The notochord is the most prominent feature of chordates. The amphioxus notochord features coin-shaped cells bearing myofibrils. Notochord-derived hedgehog signaling contributes to patterning of the dorsal nerve cord, as in vertebrates. However, properties of constituent notochord cells remain unknown at the single-cell level. We examined these properties using Iso-seq analysis, single-cell RNA-seq analysis, and in situ hybridization (ISH). Gene expression profiles broadly categorize notochordal cells into myofibrillar cells and non-myofibrillar cells. Myofibrillar cells occupy most of the central portion of the notochord, and some cells extend the notochordal horn to both sides of the ventral nerve cord. Some notochord myofibrillar genes are not expressed in myotomes, suggesting an occurrence of myofibrillar genes that are preferentially expressed in notochord. On the other hand, non-myofibrillar cells contain dorsal, lateral, and ventral Müller cells, and all three express both hedgehog and Brachyury. This was confirmed by ISH, although expression of hedgehog in ventral Müller cells was minimal. In addition, dorsal Müller cells express neural transmission-related genes, suggesting an interaction with nerve cord. Lateral Müller cells express hedgehog and other signaling-related genes, suggesting an interaction with myotomes positioned lateral to the notochord. Ventral Müller cells also expressed genes for FGF- and EGF-related signaling, which may be associated with development of endoderm, ventral to the notochord. Lateral Müller cells were intermediate between dorsal/ventral Müller cells. Since vertebrate notochord contributes to patterning and differentiation of ectoderm (nerve cord), mesoderm (somite), and endoderm, this investigation provides evidence that an ancestral or original form of vertebrate notochord is present in extant cephalochordates.

Hemichordates' diffuse "skin brain" shows unexpected complexity.

Hemichordates are close relatives of chordates. Their nervous system patterning is chordate-like, but their neural architecture remains unexplored. A new study in PLOS Biology reveals an unexpected neuroanatomical complexity in these animals, also informing chordate origins.

A miniaturized nigrostriatal-like circuit regulating locomotor performance in a protochordate

To gain insight into the evolution of motor control systems at the origin of vertebrates, we have investigated higher-order motor circuitry in the protochordate Oikopleura dioica. We have identified a highly miniaturized circuit in Oikopleura with a projection from a single pair of dopaminergic neurons to a small set of synaptically coupled GABAergic neurons, which in turn exert a disinhibitory descending projection onto the locomotor central pattern generator. The circuit is reminiscent of the nigrostriatopallidal system in the vertebrate basal ganglia, in which disinhibitory circuits release specific movements under the modulatory control of dopamine. We demonstrate further that dopamine is required to optimize locomotor performance in Oikopleura, mirroring its role in vertebrates. A dopamine-regulated disinhibitory locomotor control circuit reminiscent of the vertebrate nigrostriatopallidal system was thus already present at the origin of ancestral chordates and has been maintained in the face of extreme nervous system miniaturization in the urochordate lineage.

Saccoglossus kowalevskii: Evo-devo insights from the mud.

Hemichordates have long been recognized as a critical group for addressing hypotheses of chordate origins. Historically this was due to anatomical traits that resembled those of chordates, most strikingly the dorsolateral gill slits. As molecular data and phylogenetic analyses were found to support a close phylogenetic relationship between hemichordates and chordates within the deuterostomes, interest was revived in hemichordates. In particular, Saccoglossus kowalevskii has been developed as a molecular model to represent hemichordate developmental biology. Herein, we highlight the considerations when choosing a particular species to study and the challenges we encountered when developing S. kowalevskii. We discuss our findings and how method and tool development enabled them, and how we envision expanding our repertoire of molecular tools in the future. Establishing a new model organism comes with many obstacles-from identifying a reliable season to collect animals, to developing modern molecular techniques. The Saccoglossus research community has benefited greatly from the collaborations and teamwork established over the years. As a result, Saccoglossus is well positioned to contribute to a new century of evolutionary developmental (evo-devo) research.

The Enigmatic Reissner's Fiber and the Origin of Chordates.

Reissner’s fiber (RF) is a secreted filament that floats in the neural canal of chordates. Since its discovery in 1860, there has been no agreement on its primary function, and its strong conservation across chordate species has remained a mystery for comparative neuroanatomists. Several findings, including the chemical composition and the phylogenetic history of RF, clinical observations associating RF with the development of the neural canal, and more recent studies suggesting that RF is needed to develop a straight vertebral column, may shed light on the functions of this structure across chordates. In this article, we will briefly review the evidence mentioned above to suggest a role of RF in the origin of fundamental innovations of the chordate body plan, especially the elongation of the neural tube and maintenance of the body axis. We will also mention the relevance of RF for medical conditions like hydrocephalus, scoliosis of the vertebral spine and possibly regeneration of the spinal cord.

Transitional chordates and vertebrate origins: Tunicates.

The Origin of Chordates has fascinated scientists from the time of Charles Darwin's publication "Descent of Man" in 1871. For over 100 years, it was accepted that chordates evolved from tunicates, our sessile invertebrate sister group. However, genomic and embryonic analyses have shown that lancelets have a body plan and genome much more like vertebrates than do tunicates. In 2000, we proposed a worm-like hypothesis of chordate origins, and genomic and embryonic studies in the past 20 years have supported this hypothesis. This hypothesis contends that the deuterostome ancestor was worm-like, with gill slits, very much like a chordate. In contrast, tunicates have a very derived adult body plan that evolved independently. Here, we review the current understanding of deuterostome phylogeny and supporting evidence for the relationships within each phylum. Then we discuss our hypothesis for chordate origins and evidence to support it. We explore some of the evolutionary changes that ascidians have made to their adult body plan and some of the key gene regulatory networks that have been elucidated in Ciona. Finally, we end with insights that we have gained from studying tailless ascidians for the past 30 years. We've found that differentiation genes, at the end of the gene regulatory networks, become pseudogenes and nonfunctional, even though they are still expressed in tailless ascidians. We expect that eventually these pseudogenes will not be expressed and the ascidian larval body plan is abandoned, leaving the embryo to develop directly into an adult.

Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation.

Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and Xenopus the expression domain of one of them, Hotairm1, located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in Xenopus, showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution.

BMP controls dorsoventral and neural patterning in indirect-developing hemichordates providing insight into a possible origin of chordates

A defining feature of chordates is the unique presence of a dorsal hollow neural tube that forms by internalization of the ectodermal neural plate specified via inhibition of BMP signaling during gastrulation. While BMP controls dorsoventral (DV) patterning across diverse bilaterians, the BMP-active side is ventral in chordates and dorsal in many other bilaterians. How this phylum-specific DV inversion occurs and whether it is coupled to the emergence of the dorsal neural plate are unknown. Here we explore these questions by investigating an indirect-developing enteropneust from the hemichordate phylum, which together with echinoderms form a sister group of the chordates. We found that in the hemichordate larva, BMP signaling is required for DV patterning and is sufficient to repress neurogenesis. We also found that transient overactivation of BMP signaling during gastrulation concomitantly blocked mouth formation and centralized the nervous system to the ventral ectoderm in both hemichordate and sea urchin larvae. Moreover, this mouthless, neurogenic ventral ectoderm displayed a medial-to-lateral organization similar to that of the chordate neural plate. Thus, indirect-developing deuterostomes use BMP signaling in DV and neural patterning, and an elevated BMP level during gastrulation drives pronounced morphological changes reminiscent of a DV inversion. These findings provide a mechanistic basis to support the hypothesis that an inverse chordate body plan emerged from an indirect-developing ancestor by tinkering with BMP signaling.

Developmental atlas of appendicularian Oikopleura dioica actins provides new insights into the evolution of the notochord and the cardio-paraxial muscle in chordates

Locomotion by tail beating powered by a system of bilateral paraxial muscle and notochord is likely one of the key evolutionary innovations that facilitated the origin and radiation of chordates. The innovation of paraxial muscle was accompanied by gene duplications in stem chordates that gave rise to muscular actins from cytoplasmic ancestral forms, which acquired contractile capability thanks to the recruitment of the myosin motor-machinery. To better understand the role of actin diversification during the evolution of chordates, in this work we have characterized the complete actin catalogue of the appendicularian Oikopleura dioica, an urochordate that maintains a chordate body plan throughout its life, including the notochord in a muscled tail that confers an active free-living pelagic style. Our genomic survey, phylogenetic analyses and Diagnostic-Actin-Values (DAVs) reveal that O. dioica has four muscular actins (ActnM1–4) and three cytoplasmic actins (ActnC1–3), most of which originated by independent gene duplications during the evolution of the appendicularian lineage. Detailed developmental expression atlas of the complete actin catalogue of O. dioica reveals differences in the temporal-regulation and tissue-specificity of different actin paralogs, suggesting complex processes of subfunctionalization during the evolution of urochordates. Our results suggest the presence of a “cardio-paraxial” muscular actin at least in the last common ancestor of Olfactores (i.e. vertebrates+urochordates). Our results reveal highly dynamic tissue-specific expression patterns for some cytoplasmic actins, including the notochord, ciliated cells and neurons with axonal projections, which challenge the classic housekeeping notion ascribed to these genes. Considering that previous work had demonstrated the existence of notochord-specific actins in cephalochordates, the tissue-specific expression of two cytoplasmic actins in the notochord of O. dioica suggests that this pattern plausibly reflects the ancestral condition of chordates, and provides new insights to better understand the evolutionary origin of the notochord.

Molecular phylogeny of four ascidian species inferred from mitochondrial Cytochrome Oxidase subunit I (COI) sequence

Ascidians is a crucial group for the studies of deuterostome evolution and the origin of chordates, yet little molecular work has been done to determine the evolutionary relationships and largely unexplored beyond a few species. The phylogenetic analysis are presented for four different species of solitary ascidians, Ascidia virginea, Ascidiella aspersa, Clavelina oblonga and Aplidium fuscum, obtained from Great Nicobar Biosphere reserve (GNBR). Mitochondrial Cytochrome Oxidase subunit 1(COI) gene was amplified and the genetic diversity at the phylogenic level was measured. Bar-coded sequences were extracted with BLAST format from NCBI and the genetic diversity of the submitted sequences were compared with the related ascidian species. Maximum divergences measured among the four species were as follows: Ascidia virginea (96%), Ascidiella aspersa (96%), Clavelina oblonga (94%) and Aplidium fuscum (97%). This is the first report of molecular phylogeny of ascidians from Great Nicobar Biosphere Reserve, Andaman and Nicobar Islands. From this study, we found some stable clades on the evolutionary relationships among these ascidian species that may prompt a reevaluation of some morphological characters.

An Evolutionarily Conserved Network Mediates Development of the zona limitans intrathalamica, a Sonic Hedgehog-Secreting Caudal Forebrain Signaling Center.

Recent studies revealed new insights into the development of a unique caudal forebrain-signaling center: the zona limitans intrathalamica (zli). The zli is the last brain signaling center to form and the first forebrain compartment to be established. It is the only part of the dorsal neural tube expressing the morphogen Sonic Hedgehog (Shh) whose activity participates in the survival, growth and patterning of neuronal progenitor subpopulations within the thalamic complex. Here, we review the gene regulatory network of transcription factors and cis-regulatory elements that underlies formation of a shh-expressing delimitated domain in the anterior brain. We discuss evidence that this network predates the origin of chordates. We highlight the contribution of Shh, Wnt and Notch signaling to zli development and discuss implications for the fact that the morphogen Shh relies on primary cilia for signal transduction. The network that underlies zli development also contributes to thalamus induction, and to its patterning once the zli has been set up. We present an overview of the brain malformations possibly associated with developmental defects in this gene regulatory network (GRN).

Leucine-rich repeat containing protein LRRC8A is essential for swelling-activated Cl- currents and embryonic development in zebrafish.

A volume‐regulated anion channel (VRAC) has been electrophysiologically characterized in innumerable mammalian cell types. VRAC is activated by cell swelling and mediates the volume regulatory efflux of Cl− and small organic solutes from cells. Two groups recently identified the mammalian leucine‐rich repeat containing protein LRRC8A as an essential VRAC component. LRRC8A must be coexpressed with at least one of the other four members of this gene family, LRRC8B‐E, to reconstitute VRAC activity in LRRC8 −/− cells. LRRC8 genes likely arose with the origin of chordates. We identified LRRC8A and LRRC8C‐E orthologs in the zebrafish genome and demonstrate that zebrafish embryo cells and differentiated adult cell types express a swelling‐activated Cl− current indistinguishable from mammalian VRAC currents. Embryo cell VRAC currents are virtually eliminated by morpholino knockdown of the zebrafish LRRC8A ortholog lrrc8aa. VRAC activity is fully reconstituted in LRRC8 −/− human cells by coexpression of zebrafish lrrc8aa and human LRRC8C cDNAs. lrrc8aa expression varies during zebrafish embryogenesis and lrrc8aa knockdown causes pericardial edema and defects in trunk elongation and somatogenesis. Our studies provide confirmation of the importance of LRRC8A in VRAC activity and establish the zebrafish as a model system for characterizing the molecular regulation and physiological roles of VRAC and LRRC8 proteins.

Erratum: Cis-regulatory architecture of a brain signaling center predates the origin of chordates.

Erratum: Cis-regulatory architecture of a brain signaling center predates the origin of chordates.

Cis-regulatory architecture of a brain signaling center predates the origin of chordates.

Genomic approaches have predicted hundreds of thousands of tissue specific cis-regulatory sequences, but the determinants critical to their function and evolutionary history are mostly unknown1–4. Here, we systematically decode a set of brain enhancers active in the zona limitans intrathalamica (zli), a signaling center essential for vertebrate forebrain development via the secreted morphogen, Sonic hedgehog (Shh)5,6. We apply a de novo motif analysis tool to identify six position-independent sequence motifs together with their cognate transcription factors that are essential for zli enhancer activity and Shh expression in the mouse embryo. Using knowledge of this regulatory lexicon, we discover novel Shh zli enhancers in mice, and a functionally equivalent element in hemichordates, indicating an ancient origin of the Shh zli regulatory network that predates the chordate phylum. These findings support a strategy for delineating functionally conserved enhancers in the absence of overt sequence homologies, and over extensive evolutionary distances.

Phylostratigraphic profiles in zebrafish uncover chordate origins of the vertebrate brain.

An elaborated tripartite brain is considered one of the important innovations of vertebrates. Other extant chordate groups have a more basic brain organization. For instance, cephalochordates possess a relatively simple brain possibly homologous to the vertebrate forebrain and hindbrain, whereas tunicates display the tripartite organization, but without the specialized brain centers. The difference in anatomical complexity is even more pronounced if one compares chordates with other deuterostomes that have only a diffuse nerve net or alternatively a rather simple central nervous system. To gain a new perspective on the evolutionary roots of the complex vertebrate brain, we made here a phylostratigraphic analysis of gene expression patterns in the developing zebrafish (Danio rerio). The recovered adaptive landscape revealed three important periods in the evolutionary history of the zebrafish brain. The oldest period corresponds to preadaptive events in the first metazoans and the emergence of the nervous system at the metazoan–eumetazoan transition. The origin of chordates marks the next phase, where we found the overall strongest adaptive imprint in almost all analyzed brain regions. This finding supports the idea that the vertebrate brain evolved independently of the brains within the protostome lineage. Finally, at the origin of vertebrates we detected a pronounced signal coming from the dorsal telencephalon, in agreement with classical theories that consider this part of the cerebrum a genuine vertebrate innovation. Taken together, these results reveal a stepwise adaptive history of the vertebrate brain where most of its extant organization was already present in the chordate ancestor.

Chordate evolution and the three-phylum system.

Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics.

Phylogenomic Resolution of the Hemichordate and Echinoderm Clade

Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced transcriptomes for 14 hemichordates as well as 8 echinoderms and complemented these with existing data for a total of 33 ambulacrarian operational taxonomic units (OTUs). Examination of leaf stability values revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus canadensis were unstable in placement; therefore, analyses were also run without these taxa. Analyses of 185 genes resulted in reciprocal monophyly of Enteropneusta and Pterobranchia, placed the deep-sea family Torquaratoridae within Ptychoderidae, and confirmed the position of ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa hypothesis). These results are consistent with earlier perspectives concerning plesiomorphies of Ambulacraria, including pharyngeal gill slits, a single axocoel, and paired hydrocoels and somatocoels. The resolved ambulacrarian phylogeny will help clarify the early evolution of chordate characteristics and has implications for our understanding of major fossil groups, including graptolites and somasteroideans.