Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes

The jawless vertebrates (lamprey and hagfish) are the closest extant outgroups to all jawed vertebrates (gnathostomes) and can therefore provide critical insight into the evolution and basic biology of vertebrate genomes. As such, it is notable that the genomes of lamprey and hagfish possess a capacity for rearrangement that is beyond anything known from the gnathostomes. Like the jawed vertebrates, lamprey and hagfish undergo rearrangement of adaptive immune receptors. However, the receptors and the mechanisms for rearrangement that are utilized by jawless vertebrates clearly evolved independently of the gnathostome system. Unlike the jawed vertebrates, lamprey and hagfish also undergo extensive programmed rearrangements of the genome during embryonic development. By considering these fascinating genome biologies in the context of proposed (albeit contentious) phylogenetic relationships among lamprey, hagfish, and gnathostomes, we can begin to understand the evolutionary history of the vertebrate genome. Specifically, the deep shared ancestry and rapid divergence of lampreys, hagfish and gnathostomes is considered evidence that the two versions of programmed rearrangement present in lamprey and hagfish (embryonic and immune receptor) were present in an ancestral lineage that existed more than 400 million years ago and perhaps included the ancestor of the jawed vertebrates. Validating this premise will require better characterization of the genome sequence and mechanisms of rearrangement in lamprey and hagfish.     

Vasoactivity of the ventral aorta of the American eel (Anguilla rostrata), Atlantic hagfish ( Myxine glutinosa), and sea lamprey (Petromyzon marinus)

To determine if vascular smooth muscle from teleost and agnathan fishes expresses receptors for signaling agents that are important in vascular tension in other vertebrates, we exposed rings of aortic vascular smooth muscle from the eel (Anguilla rostrata), the hagfish (Myxine glutinosa), and the lamprey (Petromyzon marinus) to a suite of putative agonists, including: acetylcholine, endothelin, nitric oxide, natriuretic peptides, and prostanoids. Acetylcholine constricted aortic rings from the eel, but had no effect on the rings from lamprey. On the other hand, endothelin constricted rings from all three species. Use of receptor-specific ET agonists demonstrated that only ET(A) receptors are expressed in the eel and lamprey aorta. The nitric oxide donor sodium nitroprusside or nitric oxide itself dilated rings from the eel, but both agonists constricted rings from the hagfish and NO produced a biphasic response (constriction followed by dilation) in the lamprey. Two natriuretic peptides, eel ANP and porcine CNP, produced marginally significant dilation in the eel aorta, human ANP dilated the hagfish rings, and pCNP and eANP dilated the lamprey rings. The prostanoids PGE(1) and PGE(2) both dilated the eel aortic rings, and PGE(1) and carbaprostacyclin (stable PGI(2) agonist) dilated the hagfish and lamprey rings. Our results suggest that receptors for a variety of vasoactive signaling agents are expressed in the aortic smooth muscle of the earliest vertebrates (lamprey and hagfish), as well as the more advanced teleosts (eel).     

Lamprey as an evo-devo model: lessons from comparative embryology and molecular phylogenetics

Lamprey, the living jawless vertebrate, has been regarded as one of the most primitive groups of vertebrates. The evolutionary phylogenetic position of the lamprey promises to provide hints about the origin of the vertebrate genome as well as the origin of the body plan, a part of which may be written in the genome. Since the lamprey split from the gnathostome lineage early in the history of vertebrates, the shared developmental mechanisms in lampreys and gnathostomes can be regarded as possessed by the hypothetical common ancestor of these animals, whereas the gnathostome-specific developmental mechanisms that are absent from lampreys indicate that they are relatively new, added to the developmental program only after the split of gnathostomes. Thus, the sequential establishment of the gnathostome body plan is inherently related to the history of genomic duplication events. In this review, recent molecular developmental and evolutionary molecular research on the living lampreys are summarized and discussed, taking vertebrate comparative morphology and embryology into consideration.     

A Reporter Assay in Lamprey Embryos Reveals Both Functional Conservation and Elaboration of Vertebrate Enhancers

The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.     

The Vertebrate 7S K RNA Separates Hagfish (Myxine glutinosa) and Lamprey (Lampetra fluviatilis)

7S RNA sequences from the hagfish (Myxiniformes) and lamprey (Petromyzontiformes) were cloned and analyzed. In both species, 7S L RNA (also designated SRP RNA, since it represents the RNA constituent of the signal recognition particle) was clearly detectable. The sequence similarity between the two species was 86%, compared with about 75% similarity between either of these species and mammals. 7S K RNA was also cloned from the lamprey. The similarity between the 7S K RNA of the lamprey and that of mammals was 68%. Interestingly, several interspersed elements were found with nearly 100% similarity compared with mammals. In contrast to the lamprey, no 7S K RNA-related sequences were detectable among hagfish RNA, neither in northern blots nor with the PCR assay. In view of the significant conservation between the 7S K RNA of lamprey and that of mammals (human), this unexpected result clearly separates lamprey and hagfish. In addition, the lack of detectable 7S K RNA sequences in an outgroup, such as amphioxus, indicates that these results do not reflect an autapomorphy of hagfish. Therefore, our data provide additional support to the notion of a sister group relationship between Petromyzontiformes and gnathostomous vertebrates to the exclusion of Myxiniformes. Received: 24 September 1999 / Accepted: 9 February 2000     

Hagfish embryos again: the end of a long drought

Hagfishes have long held a key place in discussions of early vertebrate evolution. Frustratingly, one basis for such discussions -- namely hagfish embryology -- is very incompletely known, because the embryos of these animals are notoriously difficult to obtain. Fortunately, a recent publication on a Far Eastern hagfish describes a workable procedure for obtaining embryos and then uses this precious material to show that the hagfish neural crest arises by cell delamination as in other vertebrates -- and not by epithelial outpouchings from the wall of the neural tube as previously claimed. Importantly, because hagfish embryos should now be available on a regular basis, the way is open for additional morphological and developmental genetic investigations to help evaluate existing evolutionary scenarios and perhaps suggest new ones.     

Conservation of engrailed-like homeobox sequences during vertebrate evolution

The Drosophila melanogaster developmental gene engrailed (en) is a member of a distinct subfamily of homeobox genes with a wide phylogenetic distribution. Here we report the use of reduced stringency polymerase chain reaction (PCR) to amplify and clone 8 genes related to en from 5 vertebrate species, including representatives of the most ancient vertebrate lineages. Nucleotide and deduced amino acid sequence comparisons between mouse, toad, zebrafish, lamprey and hagfish genes reveal extensive evolutionary conservation, and suggests that 2 en-like genes have been retained in most vertebrate lineages.     

Developmental anatomy of lampreys

Lampreys are a group of aquatic chordates whose relationships to hagfishes and jawed vertebrates are still debated. Lamprey embryology is of interest to evolutionary biologists because it may shed light on vertebrate origins. For this and other reasons, lamprey embryology has been extensively researched by biologists from a range of disciplines. However, many of the key studies of lamprey comparative embryology are relatively inaccessible to the modern scientist. Therefore, in view of the current resurgence of interest in lamprey evolution and development, we present here a review of lamprey developmental anatomy. We identify several features of early organogenesis, including the origin of the nephric duct, that need to be re-examined with modern techniques. The homologies of several structures are also unclear, including the intriguing subendothelial pads in the heart. We hope that this review will form the basis for future studies into the phylogenetic embryology of this interesting group of animals.     

Evolution of the vertebrate jaw from developmental perspectives

Attainment of the biting jaw is regarded as one of the major novelties in the early history of vertebrates. Based on a comparison between lamprey and gnathostome embryos, evolutionary developmental studies have tried to explain this novelty as changes in the developmental patterning of the mandibular arch, the rostralmost pharyngeal arch, at the molecular and cellular levels. On the other hand, classical theories in the field of comparative morphology assumed the involvement of hypothetical premandibular arch(es) that ancestral animals would have possessed rostral to the mandibular arch, in the transition from agnathan to gnathostome states. These theories are highly biased toward the segmental scheme of the vertebrate head, and the concept of premandibular “arches” is no longer accepted by the current understanding. Instead, the premandibular domain has now become of interest in the understanding of cranial development, especially in its rostral part. As newer theories that consider involvement of the premandibular domain, the neoclassical and heterotopy theories are here compared from evolutionary developmental perspectives, in conjunction with the development of nasal and hypophyseal placodes, in the context of the evolutionary acquisition of the jaw. Given recent advances in understanding of the lamprey development, evolution of the Dlx code is also discussed together with the evolutionary scenario of jaw acquisition.     

Immunochemical evidence that the single lactate dehydrogenase of lampreys is more similar to LDHB4 than to LDHA4 of hagfish

The tetrameric lactate dehydrogenases (LDH) of vertebrates contain several different subunits that arose by gene duplication. While the A and B subunits occur in all classes of gnathostomes, the enzymes of agnathans appear to represent two stages in the evolution of vertebrate LDH. Lampreys of the family Petromyzontidae have a single enzyme classified as LDHA4, while hagfish possess both A and B subunits which form only the two homopolymers LDHA4 and LDHB4. It is generally assumed that the original vertebrate LDH was an A4 type, that duplication to give the B subunit occurred prior to the divergence of lampreys and hagfish, and that modern lampreys subsequently lost expression of the B gene. Lactate dehydrogenases were purified from representatives of all three lamprey families, and it was confirmed that members of the Mordaciidae and Geotriidae also possess single tetrameric LDH enzymes containing one subunit type. The kinetic properties of the lamprey LDH enzymes were compared with the LDH homopolymers of hagfish, skate, and sardine. These properties did not allow the lamprey enzymes to be unequivocally identified as either LDHA4 or LDHB4. Immunochemical titration using antisera against lamprey and hagfish LDH homopolymers demonstrated that the lamprey LDH enzymes showed greater immunochemical similarity to LDHB4 than to LDHA4 of hagfish. It is concluded that there is little evidence for the claim that the original vertebrate LDH was an A4 rather than B4 type.     

Distribution of creatine, guanidinoacetate and the enzymes for their biosynthesis in the animal kingdom. Implications for phylogeny

1. The distribution of creatine and the creatine-synthesizing enzymes in the animal kingdom has been investigated. Creatine was found in tissues of all vertebrates examined, and in various invertebrates from phyla Annelida, Echinodermata, Hemichordata and Chordata, subphylum Cephalochordata. The activities of the creatine-synthesizing enzymes, arginine-glycine transamidinase and guanidinoacetate methylpherase, were not detected in the hagfish or in any of the invertebrates, including those in which creatine was found, with the exception that transamidinase activities were detected in the amphioxus and salt water clam; however, these activities are considered to be artifacts for reasons mentioned in the text. Additional evidence that the hagfish and various creatine-containing invertebrates could not synthesize creatine was the observation that these animals did not convert one or the other of the likely precursors of creatine (arginine and glycine) into creatine, in vivo. Further, the inability of these animals to synthesize creatine is correlated with the observations that all animals tested were able to abstract creatine from their aqueous environment. 2. The activities of the creatine-synthesizing enzymes were detected in the sea lamprey and in all but a few of the other vertebrates examined. Neither activity could be detected in the sharks and rays (cartilaginous fish), buffalo fish (bony fish) or the snapping turtle. Transamidinase or guanidinoacetate methylpherase activity could not be found in the salamander or garter snake, respectively. 3. The results obtained with the lamprey are in direct contrast with those obtained with the hagfish (both subphylum Agnatha, class Cyclostomata). The lamprey had the ability to synthesize creatine and did not abstract creatine from lake water. The hagfish did not have any apparent ability to synthesize creatine and did abstract creatine from sea water. The present report thus supports the theory that the myxinoid (hagfish) and petromyzoid (lamprey) agnathans are only distantly related. 4. The lack of creatine-synthesizing enzyme activities in the cartilaginous fishes may have phylogenetic significance, but may also be explained by the availability of creatine in the diet of these animals. The lack of one or both enzyme activities in vertebrates other than the hagfish and the cartilaginous fish is suggested to be the result of creatine in the diet.     

Embryology of the lamprey and evolution of the vertebrate jaw: insights from molecular and developmental perspectives

Evolution of the vertebrate jaw has been reviewed and discussed based on the developmental pattern of the Japanese marine lamprey, Lampetra japonica. Though it never forms a jointed jaw apparatus, the L. japonica embryo exhibits the typical embryonic structure as well as the conserved regulatory gene expression patterns of vertebrates. The lamprey therefore shares the phylotype of vertebrates, the conserved embryonic pattern that appears at pharyngula stage, rather than representing an intermediate evolutionary state. Both gnathostomes and lampreys exhibit a tripartite configuration of the rostral-most crest-derived ectomesenchyme, each part occupying an anatomically equivalent site. Differentiated oral structure becomes apparent in post-pharyngula development. Due to the solid nasohypophyseal plate, the post-optic ectomesenchyme of the lamprey fails to grow rostromedially to form the medial nasal septum as in gnathostomes, but forms the upper lip instead. The gnathostome jaw may thus have arisen through a process of ontogenetic repatterning, in which a heterotopic shift of mesenchyme-epithelial relationships would have been involved. Further identification of shifts in tissue interaction and expression of regulatory genes are necessary to describe the evolution of the jaw fully from the standpoint of evolutionary developmental biology.     

Actin-related intercellular adhesion junctions in the germinal compartment of the testis in the hagfish (Eptatretus stouti) and lamprey (Lampetra tridentatus)

The germinal epithelium of male vertebrates consists of Sertoli cells and spermatogenic cells. Intercellular junctions formed by Sertoli cells assume critical roles in the normal functions of this epithelium. While Sertoli cell junctions have been well characterized in mammals, similar junctions in nonmammalian vertebrates have received little attention. We examined the intercellular junctions found within the germinal epithelium of the hagfish (Eptatretus stouti) and lamprey (Lampetra tridentatus). Ultrastructurally, Sertoli cells were seen to form filament-associated junctions in both species. Adjacent Sertoli cells formed microfilament-related junctions near their apices. Filaments of these junctions were arranged in loose networks and were not associated with cisterns of endoplasmic reticulum. In fixed, frozen sections of hagfish testis, similar areas labeled with rhodamine phalloidin, indicating the filament type is actin. In the lamprey, desmosomes were observed immediately below the microfilament-related junctions. In appearance and location, the Sertoli cell junctions observed in these species resembled those of the typical junctional complex of other epithelial cell types. No junctions were observed between Sertoli cells and elongating spermatids. In the hagfish, but not the lamprey, an additional zone of microfilaments occurred near the base of Sertoli cells in areas of association with the basal lamina. Our observations are consistent with the proposal that the unique forms of intercellular attachment found in the testes of higher vertebrates evolved from a typical epithelial form of intercellular junction.     

Antigen-specific receptors. Generation of the diversity from lamprey to human

In the last century it was established that the diversity of the antigen-recognizing receptors of Band T-lymphocytes and Ig/antibodies in mice and humans is due to the random recombination of DNA segments organized in clusters and located in fetal genome far apart. During somatic rearrangement of genome these segments combine and form functional V-genes, coding antigen-specific receptors. In birds and some other animals the diversity is provided or increased by gene conversion, which leads to the diversification of nucleotide sequences in pre-rearranged functional V-genes. Recently it was shown that the generation of the diversity might be realized by an entirely different way. In most primitive and living now agnathan vertebrates, lamprey and hagfishes, Ig-genes are absent, and somatic diversification of the antigen-specific receptors is due to a stepwise assembly of functional V-genes from separate modules. These modules coding leucine-rich repeats (LRR) adjust to a single (or two) “incomplete” germ-line V-gene and insert into it by gene conversion. LRR modules lodge in so called DNA “cassettes”. The number of LRR in the agnathan genome reaches 2–3 thousands; primary structure of LRR is very variable. The properties of lamprey and hagfish antibodies differ from that of other vertebrates. It is extremely interesting that similar LRR are found in Toll-like receptors of insects, mollusks and even plants, where they provide the resistance to different diseases. The data obtained are very important for the evolutionary immunology. The review deals with the mechanisms of generation of diversity of the antigen-specific receptors in vertebrates, insects, and plants.     

Distribution of Mammalian-Like Melanopsin in Cyclostome Retinas Exhibiting a Different Extent of Visual Functions

Mammals contain 1 melanopsin (Opn4) gene that is expressed in a subset of retinal ganglion cells to serve as a photopigment involved in non-image-forming vision such as photoentrainment of circadian rhythms. In contrast, most nonmammalian vertebrates possess multiple melanopsins that are distributed in various types of retinal cells; however, their functions remain unclear. We previously found that the lamprey has only 1 type of mammalian-like melanopsin gene, which is similar to that observed in mammals. Here we investigated the molecular properties and localization of melanopsin in the lamprey and other cyclostome hagfish retinas, which contribute to visual functions including image-forming vision and mainly to non-image-forming vision, respectively. We isolated 1 type of mammalian-like melanopsin cDNA from the eyes of each species. We showed that the recombinant lamprey melanopsin was a blue light-sensitive pigment and that both the lamprey and hagfish melanopsins caused light-dependent increases in calcium ion concentration in cultured cells in a manner that was similar to that observed for mammalian melanopsins. We observed that melanopsin was distributed in several types of retinal cells, including horizontal cells and ganglion cells, in the lamprey retina, despite the existence of only 1 melanopsin gene in the lamprey. In contrast, melanopsin was almost specifically distributed to retinal ganglion cells in the hagfish retina. Furthermore, we found that the melanopsin-expressing horizontal cells connected to the rhodopsin-containing short photoreceptor cells in the lamprey. Taken together, our findings suggest that in cyclostomes, the global distribution of melanopsin in retinal cells might not be related to the melanopsin gene number but to the extent of retinal contribution to visual function.     

Hagfish (cyclostomata, vertebrata): searching for the ancestral developmental plan of vertebrates

The phylogenetic position of the hagfish remains enigmatic. In contrast to molecular data that suggest monophyly of the cyclostomes, several morphological features imply a more ancestral state of this animal compared with the lampreys. To resolve this question requires an understanding of the embryology of the hagfish, especially of the neural crest. The early development of the hagfish has long remained a mystery. We collected a shallow-water-dwelling hagfish, Eptatretus burgeri, set up an aquarium tank designed to resemble its habitat, and successfully obtained several embryos. By observing the histology and expression of genes known to play fundamental roles in the neural crest, we found that the hagfish crest develops as delaminating migratory cells, as in other vertebrates. We conclude that the delaminating neural crest is a vertebrate synapomorphy that seems to have appeared from the beginning of their evolutionary history, before the splitting away of the hagfish lineage.     

The origin of developmental mechanisms underlying vertebral elements: implications from hagfish evo-devo

The origins of the vertebral elements and the underlying developmental mechanisms have so far remained unclear, largely due to the unusual axial skeletal morphology of hagfish, one of two extant jawless vertebrate clades. Hagfish axial supporting tissue is generally believed to consist of the notochord and cartilaginous fin rays only. However, careful investigations of whether vertebral elements are truly absent in hagfish are scarce, and it is also unclear whether the axial skeletal morphology of the hagfish is an ancestral or a derived condition. To address these questions, we re-examined the axial skeletal morphology of the Japanese inshore hagfish (Eptatretus burgeri). Based on a report published a century ago which implied the existence of vertebral elements in hagfish, we conducted anatomical and histological analyses of the hagfish axial skeletal systems and their development. Through this analysis, we demonstrate that hagfish possesses sclerotome-derived cartilaginous vertebral elements at the ventral aspect of the notochord. Based on (i) molecular phylogenetic evidence in support of the monophyly of cyclostomes (hagfish and lampreys) and jawed vertebrates (gnathostomes), and (ii) the morphology of the vertebral elements in extant gnathostomes and cyclostomes, we propose that the embryos of the common ancestor of all vertebrates would have possessed sclerotomal cells that formed the segmentally arranged vertebral elements attached to the notochord. We also conclude that the underlying developmental mechanisms are likely to have been conserved among extinct jawless vertebrates and modern gnathostomes.