Direct-developing sea urchins and the evolutionary reorganization of early development

Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins

Biphasic lifecycles are widespread among animals, but little is known about how the developmental transition between larvae and adults is regulated. Sea urchins are a unique system for studying this phenomenon because of the stark differences between their bilateral larval and pentaradial adult body plans. Here, we use single-cell RNA sequencing to analyze the development of Heliocidaris erythrogramma (He), a sea urchin species with an accelerated, non-feeding mode of larval development. The sequencing time course extends from embryogenesis to roughly a day before the onset of metamorphosis in He larvae, which is a period that has not been covered by previous datasets. We find that the non-feeding developmental strategy of He is associated with several changes in the specification of larval cell types compared to sea urchins with feeding larvae, such as the loss of a larva-specific skeletal cell population. Furthermore, the development of the larval and adult body plans in sea urchins may utilize largely different sets of regulatory genes. These findings lay the groundwork for extending existing developmental gene regulatory networks to cover additional stages of biphasic lifecycles.

A Novel Expression Domain of extradenticle Underlies the Evolutionary Developmental Origin of the Chelicerate Patella

Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2, suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2, disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio, which lacks dachshund-2. Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle. Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.

A novel expression domain of extradenticle underlies the evolutionary developmental origin of the chelicerate patella

Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2 , suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2 , disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio , which lacks dachshund-2 . Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle . Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.

Characterization of thyrotropin-releasing hormone producing neurons in sea urchin, from larva to juvenile

Most sea urchin species are indirect developers, going through a larval stage called pluteus. The pluteus possesses its own nervous system, consisting mainly of the apical organ neurons (controlling metamorphosis and settlement) and ciliary band neurons (controlling swimming behavior and food collection). Additional neurons are located in various areas of the gut. In recent years, the molecular complexity of this apparently "simple" nervous system has become apparent, with at least 12 neuronal populations identified through scRNA-sequencing in the species Strongylocentrotus purpuratus. Among these, there is a cluster of neurosecretory cells that produce a thyrotropin-releasing hormone-type neuropeptide (TRHergic) and that are also photosensory (expressing a Go-Opsin). However, much less is known about the organization of the nervous system in other sea urchin species. The aim of this work was to thoroughly characterize the localization of the TRHergic cells from early pluteus to juvenile stages in the Mediterranean sea urchin species Paracentrotus lividus combining immunostaining and whole mount in situ hybridization. We also compared the localization of TRHergic cells in early plutei of two other sea urchin species, Arbacia lixula and Heliocidaris tuberculata. This work provides new information on the anatomy and development of the nervous system in sea urchins. Moreover, by comparing the molecular signature of the TRHergic cells in P. lividus and S. purpuratus, we have obtained new insights how TRH-type neuropeptide signaling evolved in relatively closely related species.

Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins

Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on regulatory interactions remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyse genomes, epigenomes and transcriptomes during early development in two Heliocidaris sea urchin species that exhibit highly divergent life histories and in an outgroup species. Positive selection and chromatin accessibility modifications within putative regulatory elements are enriched on the branch leading to the derived life history, particularly near dGRN genes. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near conserved cell fate specification genes. Experimentally perturbing key transcription factors reveals profound evolutionary changes to early embryonic patterning events, disrupting regulatory interactions previously conserved for ~225 million years. These results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change. More broadly, even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances.

Emerging models: The "development" of the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis as useful experimental models

The goal of this chapter is to explain the reasoning for developing two understudied invertebrate animal species for asking specific biological questions. The first is the ctenophore (comb jelly) Mnemiopsis leidyi and the second is the anthozoan cnidarian (starlet sea anemone) Nematostella vectensis. Although these two taxa belong to some of the earliest branching extant metazoan clades, their developmental features could hardly be more different from one another. This should serve as a general warning to be careful when extrapolating comparisons of one species to another. Two-taxon comparisons are especially flawed; and to interpret features in a phylogenetic context one must sample carefully within a given taxon to determine how representative certain features are before comparing with other clades. The other benefit of this comparison is to identify key practical factors when attempting to develop new species for experimental investigation.

Extreme phenotypic divergence and the evolution of development

As analyses of developmental mechanisms extend to ever more species, it becomes important to understand not just what is conserved or altered during evolution, but why. Closely related species that exhibit extreme phenotypic divergence can be uniquely informative in this regard. A case in point is the sea urchin genus Heliocidaris, which contains species that recently evolved a life history involving nonfeeding larvae following nearly half a billion years of prior evolution with feeding larvae. The resulting shift in selective regimes produced rapid and surprisingly extensive changes in developmental mechanisms that are otherwise highly conserved among echinoderm species. The magnitude and extent of these changes challenges the notion that conservation of early development in echinoderms is largely due to internal constraints that prohibit modification and instead suggests that natural selection actively maintains stability of inherently malleable trait developmental mechanisms over immense time periods. Knowing how and why natural selection changed during the evolution of nonfeeding larvae can also reveal why developmental mechanisms do and do not change in particular ways.

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history

Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life history transition from planktotrophy (feeding) to lecithotrophy (nonfeeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds with a reduction in microbial community diversity and abundance as well as the association with a diet-specific microbiome. We also determine that the lecithotroph vertically transmits a Rickettsiales that may complement host nutrition through amino acid biosynthesis and influence host reproduction. Our results indicate that the evolutionary loss of a functional gut correlates with a reduction in the microbiome and the association with an endosymbiont. Symbiotic transitions can therefore accompany life history transitions in the evolution of developmental strategies.

Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors

The Echinodermata is characterized by a secondarily evolved pentameral body plan. While the evolutionary origin of this body plan has been the subject of debate, the molecular mechanisms underlying its development are poorly understood. We assembled a de novo developmental transcriptome from the embryo through metamorphosis in the sea star Parvulastra exigua. We use the asteroid model as it represents the basal-type echinoderm body architecture. Global variation in gene expression distinguished the gastrula profile and showed that metamorphic and juvenile stages were more similar to each other than to the pre-metamorphic stages, pointing to the marked changes that occur during metamorphosis. Differential expression and gene ontology (GO) analyses revealed dynamic changes in gene expression throughout development and the transition to pentamery. Many GO terms enriched during late metamorphosis were related to neurogenesis and signalling. Neural transcription factor genes exhibited clusters with distinct expression patterns. A suite of these genes was up-regulated during metamorphosis (e.g. Pax6, Eya, Hey, NeuroD, FoxD, Mbx, and Otp). In situ hybridization showed expression of neural genes in the CNS and sensory structures. Our results provide a foundation to understand the metamorphic transition in echinoderms and the genes involved in development and evolution of pentamery.

Transcriptomic analysis of Nodal - and BMP- associated genes during development to the juvenile seastar in Parvulastra exigua (Asterinidae)

The molecular mechanisms underlying development of the pentameral body of adult echinoderms are poorly understood but are important to solve with respect to evolution of a unique body plan that contrasts with the bilateral body plan of other deuterostomes. As Nodal and BMP2/4 signalling is involved in axis formation in larvae and development of the echinoderm body plan, we used the developmental transcriptome generated for the asterinid seastar Parvulastra exigua to investigate the temporal expression patterns of Nodal and BMP2/4 genes from the embryo and across metamorphosis to the juvenile. For echinoderms, the Asteroidea represents the basal-type body architecture with a distinct (separated) ray structure. Parvulastra exigua has lecithotrophic development forming the juvenile soon after gastrulation providing ready access to the developing adult stage. We identified 39 genes associated with the Nodal and BMP2/4 network in the P. exigua developmental transcriptome. Clustering analysis of these genes resulted in 6 clusters with similar temporal expression patterns across development. A co-expression analysis revealed genes that have similar expression profiles as Nodal and BMP2/4. These results indicated genes that may have a regulatory relationship in patterning morphogenesis of the juvenile seastar. Developmental RNA-seq analyses of Parvulastra exigua show changes in Nodal and BMP2/4 signalling genes across the metamorphic transition. We provide the foundation for detailed analyses of this cascade in the evolution of the unusual pentameral echinoderm body and its deuterostome affinities.

Evolutionary modification of gastrulation in Parvulastra exigua, an asterinid seastar with holobenthic lecithotrophic development

Gastrulation is a fundamental morphogenetic process in development. In echinoderms with ancestral-type development through feeding larvae, gastrulation involves radially symmetrical invagination of cells around the blastopore. Gastrulation in the seastar Parvulastra exigua, a species with non-feeding larvae deviates from this pattern. Microinjection of cells with fluorescent lineage tracer dye revealed that early blastomeres contribute unequally to ectoderm and endoderm. In embryos injected at the two-cell stage, asymmetry was evident in the fluorescence at the top of the archenteron and animal pole ectoderm. Archenteron elongation is driven by asymmetrical involution of cells with more cells crossing the blastopore on one side. Lineages of cells injected at the four-cell stage also differed in allocation to endoderm and ectoderm. In embryos injected at the eight-cell stage ectodermal and endodermal fates were evident reflecting the animal and vegetal fates determined by third cleavage as typical of echinoderms. Modification of gastrulation associated with evolution of development in P. exigua shows that this foundational morphogenetic process can be altered despite its importance for subsequent development. However, observations of slight asymmetry in the lineage fates of blastomeres in asterinids with planktotrophic development indicates that gastrulation by asymmetrical involution in P. exigua may be a hypertrophic elaboration of a pre-existing state in ancestral-type development. As for echinoids with lecithotrophic development, involution as a mechanism to contribute to archenteron elongation may be associated with the impact of extensive maternal nutritive reserves on the mechanics of cell movement and a novel innovation to facilitate early development of the adult rudiment.

Genetic basis for divergence in developmental gene expression in two closely related sea urchins

The genetic basis for divergence in developmental gene expression among species is poorly understood, despite growing evidence that such changes underlie many interesting traits. Here we quantify transcription in hybrids of Heliocidaris tuberculata and Heliocidaris erythrogramma, two closely related sea urchins with highly divergent developmental gene expression and life histories. We find that most expression differences between species result from genetic influences that affect one stage of development, indicating limited pleiotropic consequences for most mutations that contribute to divergence in gene expression. Activation of zygotic transcription is broadly delayed in H. erythrogramma, the species with the derived life history, despite its overall faster premetamorphic development. Altered expression of several terminal differentiation genes associated with the derived larval morphology of H. erythrogramma is based largely on differences in the expression or function of their upstream regulators, providing insights into the genetic basis for the evolution of key life history traits.

A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins

A dramatic life history switch that has evolved numerous times in marine invertebrates is the transition from planktotrophic (feeding) to lecithotrophic (nonfeeding) larval development-an evolutionary tradeoff with many important developmental and ecological consequences. To attain a more comprehensive understanding of the molecular basis for this switch, we performed untargeted lipidomic and proteomic liquid chromatography-tandem mass spectrometry on eggs and larvae from three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph Heliocidaris tuberculata, and the distantly related planktotroph Lytechinus variegatus. We identify numerous molecular-level changes possibly associated with the evolution of lecithotrophy in H. erythrogramma. We find the massive lipid stores of H. erythrogramma eggs are largely composed of low-density, diacylglycerol ether lipids that, contrary to expectations, appear to support postmetamorphic development and survivorship. Rapid premetamorphic development in this species may instead be powered by upregulated carbohydrate metabolism or triacylglycerol metabolism. We also find proteins involved in oxidative stress regulation are upregulated in H. erythrogramma eggs, and apoB-like lipid transfer proteins may be important for echinoid oogenic nutrient provisioning. These results demonstrate how mass spectrometry can enrich our understanding of life history evolution and organismal diversity by identifying specific molecules associated with distinct life history strategies and prompt new hypotheses about how and why these adaptations evolve.

The development and metamorphosis of the indirect developing acorn worm Schizocardium californicum (Enteropneusta: Spengelidae)

Background

Enteropneusts are benthic marine invertebrates that belong to the deuterostome phylum Hemichordata. The two main clades of enteropneusts are defined by differences in early life history strategies. In the Spengelidae and Ptychoderidae, development is indirect via a planktotrophic tornaria larva. In contrast, development in the Harrimanidae is direct without an intervening larval life history stage. Most molecular studies in the development and evolution of the enteropneust adult body plan have been carried out in the harrimanid Saccoglossus kowalevskii. In order to compare these two developmental strategies, we have selected the spengelid enteropneust Schizocardium californicum as a suitable indirect developing species for molecular developmental studies. Here we describe the methods for adult collecting, spawning and larval rearing in Schizocardium californicum, and describe embryogenesis, larval development, and metamorphosis, using light microscopy, immunocytochemistry and confocal microscopy.

Results

Adult reproductive individuals can be collected intertidally and almost year-round. Spawning can be triggered by heat shock and large numbers of larvae can be reared through metamorphosis under laboratory conditions. Gastrulation begins at 17 h post-fertilization (hpf) and embryos hatch at 26 hpf as ciliated gastrulae. At 3 days post-fertilization (dpf), the tornaria has a circumoral ciliary band, mouth, tripartite digestive tract, protocoel, larval muscles and a simple serotonergic nervous system. The telotroch develops at 5 dpf. In the course of 60 days, the serotonergic nervous system becomes more elaborate, the posterior coeloms develop, and the length of the circumoral ciliary band increases. At the end of the larval stage, larval muscles disappear, gill slits form, and adult muscles develop. Metamorphosis occurs spontaneously when the larva reaches its maximal size (ca. 3 mm), and involves loss and reorganization of larval structures (muscles, nervous system, digestive tract), as well as development of adult structures (adult muscles, tripartite body organization).

Conclusions

This study will enable future research in S. californicum to address long standing questions related to the evolution of axial patterning mechanisms, germ layer induction, neurogenesis and neural patterning, the mechanisms of metamorphosis, the relationships between larval and adult body plans, and the evolution of metazoan larval forms.

HETEROCHRONY AND DEVELOPMENTAL INNOVATION: EVOLUTION OF FEMALE GAMETOPHYTE ONTOGENY IN GNETUM, A HIGHLY APOMORPHIC SEED PLANT

Seed plant female gametophytes are focal points for the evolutionary modification of development. From a structural perspective, the most divergent female gametophytes among all seed plants are found in Gnetum, a clade within Gnetales. Coenocytic organization at sexual maturity, absence of defined egg cells (free nuclei are fertilized), lack of centripetal cellularization, and postfertilization development of embryo-nourishing tissues are features of the female gametophytes of Gnetum unparalleled among seed plants. Although the female gametophyte of Gnetum retains the three basic phases of somatic development common to female gametophytes of plesiomorphic seed plants (free nuclear development, cellularization, cellular growth), the timing of fertilization has been accelerated relative to the rate of somatic development. As a consequence, the female gametophyte of Gnetum matures sexually (is fertilized) at a juvenile (compared with the ancestral somatic ontogeny) and free nuclear stage of somatic development, thereby precluding differentiation of egg cells. Unlike progenetic animals, where truncation of somatic ontogeny evolves in tandem with acceleration in the timing of sexual maturation, the female gametophyte of Gnetum completes the entire ancestral somatic ontogeny after precocious sexual maturation. This results in the evolution of postfertilization development of embryo-nourishing female gametophyte tissues, a phenomenon unique among seed plants. Nonheterochronic developmental innovations have also played important roles in the evolution of the female gametophyte of Gnetum. Centripetal cellularization, which is always associated with the phase change from coenocytic to cellular organization among plesiomorphic seed plant female gametophytes, is lacking in Gnetum. Instead, during early phases of development, apomorphic free nuclear organization is coupled with a highly anomalous pattern of cellularization. Stage-specific innovations during early development in the female gametophyte of Gnetum do not affect plesiomorphic aspects of later phases of development. Thus, a complex array of heterochronic and nonheterochronic developmental innovations have played critical roles in the ontogenetic evolution of the highly apomorphic female gametophyte of Gnetum.

Cleavage modification did not alter blastomere fates during bryozoan evolution

BACKGROUND

Stereotypic cleavage patterns play a crucial role in cell fate determination by precisely positioning early embryonic blastomeres. Although misplaced cell divisions can alter blastomere fates and cause embryonic defects, cleavage patterns have been modified several times during animal evolution. However, it remains unclear how evolutionary changes in cleavage impact the specification of blastomere fates. Here, we analyze the transition from spiral cleavage - a stereotypic pattern remarkably conserved in many protostomes - to a biradial cleavage pattern, which occurred during the evolution of bryozoans.

RESULTS

Using 3D-live imaging time-lapse microscopy (4D-microscopy), we characterize the cell lineage, MAPK signaling, and the expression of 16 developmental genes in the bryozoan Membranipora membranacea. We found that the molecular identity and the fates of early bryozoan blastomeres are similar to the putative homologous blastomeres in spiral-cleaving embryos.

CONCLUSIONS

Our work suggests that bryozoans have retained traits of spiral development, such as the early embryonic fate map, despite the evolution of a novel cleavage geometry. These findings provide additional support that stereotypic cleavage patterns can be modified during evolution without major changes to the molecular identity and fate of embryonic blastomeres.

The Adult Body Plan of Indirect Developing Hemichordates Develops by Adding a Hox-Patterned Trunk to an Anterior Larval Territory

Many animals are indirect developers with distinct larval and adult body plans [1]. The molecular basis of differences between larval and adult forms is often poorly understood, adding a level of uncertainty to comparative developmental studies that use data from both indirect and direct developers. Here we compare the larval and adult body plans of an indirect developing hemichordate, Schizocardium californicum [2]. We describe the expression of 27 transcription factors with conserved roles in deuterostome ectodermal anteroposterior (AP) patterning in developing embryos, tornaria larvae, and post-metamorphic juveniles and show that the tornaria larva of S. californicum is transcriptionally similar to a truncated version of the adult. The larval ectoderm has an anterior molecular signature, while most of the trunk, defined by the expression of hox1-7, is absent. Posterior ectodermal activation of Hox is initiated in the late larva prior to metamorphosis, in preparation for the transition to the adult form, in which the AP axis converges on a molecular architecture similar to that of the direct developing hemichordate Saccoglossus kowalevskii. These results identify a molecular correlate of a major difference in body plan between hemichordate larval and adult forms and confirm the hypothesis that deuterostome larvae are "swimming heads" [3]. This will allow future comparative studies with hemichordates to take into account molecular differences caused by early life history evolution within the phylum. Additionally, comparisons with other phyla suggest that a delay in trunk development is a feature of indirect development shared across distantly related phyla.

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris

The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.

Transcriptomic analysis of the highly derived radial body plan of a sea urchin

With their complex life cycle and highly derived body plan, echinoderms are unique among bilaterians. Although early development has been intensively studied, the molecular mechanisms underlying development of the adult echinoderm and its unusual radial body plan are largely unknown. To investigate the evolution of developmental changes in gene expression underlying radial body plan development and metamorphosis, we assembled a reference transcriptome de novo and used RNA-seq to measure gene expression profiles across larval, metamorphic, and postmetamorphic life cycle phases in the sea urchin Heliocidaris erythrogramma. Our results present a high-resolution view of gene expression dynamics during the complex transition from pre- to postmetamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases. These analyses provide an important foundation for more detailed analyses of the evolution of the radial adult body of echinoderms.

SeaBase: a multispecies transcriptomic resource and platform for gene network inference

Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide-ranging capabilities. Genomics tools are essential for taking advantage of these "free lessons" of nature. However, genomics and transcriptomics are challenging in emerging model systems. Here, we present SeaBase, a tool for helping to meet these needs. Specifically, SeaBase provides a platform for sharing and searching transcriptome data. More importantly, SeaBase will support a growing number of tools for inferring gene network mechanisms. The first dataset available on SeaBase is a developmental transcriptomic profile of the sea anemone Nematostella vectensis (Anthozoa, Cnidaria). Additional datasets are currently being prepared and we are aiming to expand SeaBase to include user-supplied data for any number of marine and aquatic organisms, thereby supporting many potentially new models for gene network studies. SeaBase can be accessed online at: http://seabase.core.cli.mbl.edu.

Causes and consequences of the evolution of reproductive mode in Caenorhabditis nematodes

Reproduction is directly connected to the suite of developmental and physiological mechanisms that enable it, but how it occurs also has consequences for the genetics, ecology and longer term evolutionary potential of a lineage. In the nematode Caenorhabditis elegans, anatomically female XX worms can self-fertilize their eggs. This ability evolved recently and in multiple Caenorhabditis lineages from male-female ancestors, providing a model for examining both the developmental causes and longer term consequences of a novel, convergently evolved reproductive mode. Here, we review recent work that implicates translation control in the evolution of XX spermatogenesis, with different selfing lineages possessing both reproducible and idiosyncratic features. We also discuss the consequences of selfing, which leads to a rapid loss of variation and relaxation of natural and sexual selection on mating-related traits, and may ultimately put selfing lineages at a higher risk of extinction.

Molluscan larvae: Pelagic juveniles or slowly metamorphosing larvae?

Asking the right questions about evolution of development, larval morphology, and life history requires knowledge of ancestral state. Two hypotheses dominate current opinion about the ancestral life cycle of bilaterians: the "larva-first" and the "intercalation" hypotheses. Until recently, the larva-first hypothesis was preeminent. This proposes that the original indirect life cycle of bilaterians included a planktotrophic larva followed by a benthic adult. Phylogenetic evidence suggests that a planktotrophic larva is plesiomorphic for echinoderms. A preponderance of developmental studies on echinoderms may have fostered a tendency to extrapolate conclusions about echinoderm development to other clades, particularly the concept that larval and juvenile/adult bodies are mostly separate entities. However, some of the recent reconstructions of bilaterian phylogeny suggest that nonfeeding larvae may have been ancestral for bilaterians, and these may have been intercalated into a life cycle that was originally direct. I review comparative data on molluscan development that suggests the trochophore-like stage is little more than a gastrula with transient structures (prototroch and apical sensory organ) to allow a temporary planktonic phase during development. Most lineage founder cells of molluscan embryos generate progeny that develop through the veliger stage into structures of the juvenile, which becomes benthic when the prototroch and apical sensory organ are lost. In light of this, the model of separate larval and juvenile bodies with the latter developing from nests of multipotent cells within the larva is inappropriate for molluscs. The intercalation hypothesis may be a better model for interpreting development of molluscs and other lophotrochozoans.

The bilaterally asymmetrical larval form of Stomopneustes variolaris (Lamarck)

This study describes the echinopluteus and juveniles of the Indo-Pacific echinoid Stomopneustes variolaris. Late 4-armed larvae had left postoral arms that were longer and more deeply red pigmented than the right arms. Two weeks into development, the sixth pair of arms, the posterolaterals, began to form as these larvae achieved an arbacioid form. The right posterolateral arm grew long, was heavily pigmented at the tip, and was oriented perpendicularly or obliquely to the main body axis. The left posterolateral arm was relatively short, with little pigment. Two of several hundred larvae examined showed different patterns. One, with a juvenile rudiment on the right side, had arms that were a mirror image of those of typical larvae. A second larva, without a rudiment, had equal postoral arms and long, deeply pigmented posterolateral arms. These patterns suggest a developmental link between the asymmetry of the larval arms and the formation of the juvenile rudiment. Adult Stomopneustes also often showed a fixed asymmetry, with the test higher and spines shorter on the side toward interambulacrum 3 and the test lower and spines longer on the opposite side (ambulacrum I). Cleared 1- and 2-day juveniles did not show any obvious asymmetry in the location of apical plates that form from the larval spicules, so there is no evidence for a morphological link between asymmetrical larvae and adults.

Evolvability as the proper focus of evolutionary developmental biology

Research conducted under the label of evolutionary developmental biology has tended to revolve around a few central issues such as modularity, integration, and canalization. Yet, as the field has grown, it has become increasingly difficult to define in terms of its central question and relation to broader evolutionary concerns. We argue that these central issues of evo-devo gain their currency from connections to a central question that defines the field, and we propose that this central question is about the nature of evolvability. However, not all research currently carried out under the label of "evo-devo" speaks to this focal concern. The aim of this article is therefore to argue for a precise formulation of evolutionary developmental biology's core question.

Gene expression patterns in a novel animal appendage: the sea urchin pluteus arm

The larval arms of echinoid plutei are used for locomotion and feeding. They are composed of internal calcite skeletal rods covered by an ectoderm layer bearing a ciliary band. Skeletogenesis includes an autonomous molecular differentiation program in primary mesenchyme cells (PMCs), initiated when PMCs leave the vegetal plate for the blastocoel, and a patterning of the differentiated skeletal units that requires molecular cues from the overlaying ectoderm. The arms represent a larval feature that arose in the echinoid lineage during the Paleozoic and offers a subject for the study of gene co-option in the evolution of novel larval features. We isolated new molecular markers in two closely related but differently developing species, Heliocidaris tuberculata and Heliocidaris erythrogramma. We report the expression of a larval arm-associated ectoderm gene tetraspanin, as well as two new PMC markers, advillin and carbonic anhydrase. Tetraspanin localizes to the animal half of blastula stage H. tuberculata and then undergoes a restriction into the putative oral ectoderm and future location of the postoral arms, where it continues to be expressed at the leading edge of both the postoral and anterolateral arms. In H. erythrogramma, its expression initiates in the animal half of blastulae and expands over the entire ectoderm from gastrulation onward. Advillin and carbonic anhydrase are upregulated in the PMCs postgastrulation and localized to the leading edge of the growing larval arms of H. tuberculata but do not exhibit coordinated expression in H. erythrogramma larvae. The tight spatiotemporal regulation of these genes in H. tuberculata along with other ontogenetic and phylogenetic evidence suggest that pluteus arms are novel larval organs, distinguishable from the processes of skeletogenesis per se. The dissociation of expression control in H. erythrogramma suggest that coordinate gene expression in H. tuberculata evolved as part of the evolution of pluteus arms, and is not required for larval or adult development.

The active evolutionary lives of echinoderm larvae

Echinoderms represent a researchable subset of a dynamic larval evolutionary cosmos. Evolution of echinoderm larvae has taken place over widely varying time scales from the origins of larvae of living classes in the early Palaeozoic, approximately 500 million years ago, to recent, rapid and large-scale changes that have occurred within living genera within a span of less than a million years to a few million years. It is these recent evolutionary events that offer a window into processes of larval evolution operating at a micro-evolutionary level of evolution of discrete developmental mechanisms. We review the evolution of the diverse larval forms of living echinoderms to outline the origins of echinoderm larval forms, their diversity among living echinoderms, molecular clocks and rates of larval evolution, and finally current studies on the roles of developmental regulatory mechanisms in the rapid and radical evolutionary changes observed between closely related congeneric species.

Larval ectoderm, organizational homology, and the origins of evolutionary novelty

Comprehending the origin of marine invertebrate larvae remains a key domain of research for evolutionary biologists, including the repeated origin of direct developmental modes in echinoids. In order to address the latter question, we surveyed existing evidence on relationships of homology between the ectoderm territories of two closely related sea urchin species in the genus Heliocidaris that differ in their developmental mode. Additionally, we explored a recently articulated idea about homology called 'organizational homology' (Müller 2003. In: Müller GB, Newman SA, editors. Origination of organismal form: beyond the gene in developmental and evolutionary biology. Cambridge, MA: A Bradford Book, The MIT Press. p 51-69. ) in the context of this specific empirical case study. Applying the perspective of organizational homology to our experimental system of congeneric echinoids has led us to a new hypothesis concerning the ectoderm evolution in these species. The extravestibular ectoderm of the direct developer Heliocidaris erythrogramma is a novel developmental territory that arose as a fusion of the oral and aboral ectoderm territories found in indirect developing echinoids such as Heliocidaris tuberculata. This hypothesis instantiates a theoretical principle concerning the origin of developmental modules, 'integration', which has been neglected because the opposite theoretical principle, 'parcellation', is more readily observable in events such as gene duplication and divergence (Wagner 1996. Am Zool 36:36-43).

Dissociation of expression patterns of homeodomain transcription factors in the evolution of developmental mode in the sea urchins Heliocidaris tuberculata and H. erythrogramma

The direct-developing sea urchin species Heliocidaris erythrogramma has a radically modified ontogeny. Along with gains of novel features, its entire ectoderm has been reorganized, resulting in the apparent absence of a differentiated oral ectoderm, a major module present in the pluteus of indirect-developing species, such as H. tuberculata. The restoration of an obvious oral ectoderm in H. erythrogrammaxH. tuberculata hybrids, indicates the action of dominant regulatory factors from the H. tuberculata genome. We sought candidate regulatory genes based on the prediction that they should include genes that govern development of the oral ectoderm in the pluteus, but play different roles in H. erythrogramma. Such genes may have a large effect in the evolution of development. Goosecoid (Gsc), Msx, and the sea urchin Abd-B-like gene (Hox11/13b) are present and expressed in both species and the hybrid embryos. Both Gsc and Msx are oral ectoderm specific in H. tuberculata, and show novel and distinct expression patterns in H. erythrogramma. Gsc assumes a novel ectodermal pattern and Msx shifts to a novel and largely mesodermal pattern. Both Gsc and Msx show a restoration of oral ectoderm expression in hybrids. Hox11/13b is not expressed in oral ectoderm in H. tuberculata, but is conserved in posterior spatial expression among H. tuberculata, H. erythrogramma and hybrids, serving as a control. Competitive RT-PCR shows that Gsc, Msx, and Hox11/13b are under different quantitative and temporal controls in the Heliocidaris species and the hybrids. The implications for the involvement of these genes in the rapid evolution of a direct developing larva are discussed.

Heterochrony and the evolution of poecilogony: generating larval diversity

Poecilogony is the production of more than one type of young within a single species of marine invertebrate. We chose a poecilogonous polychaete to investigate potential differences in morphogenesis among offspring that are polymorphic in dispersal potentials (planktonic, benthic) and trophic modes (planktotrophy, adelphophagy). Differences in morphogenesis occur and are strongly influenced by maternal type. Females that provide extra-embryonic nutrition (as nurse eggs; type III females) also produce offspring with an accelerated onset of juvenile traits, relative to planktotrophic offspring of females that do not provide extra-embryonic nutrition (type I females). Thus, progeny of some females appear morphologically preadapted for a benthic lifestyle. Surprisingly, differences in phenotype among offspring do not parallel offspring ecotype, as offspring with early onset of juvenile traits (III) are ecologically bimodal. Some Type III offspring eat the nurse eggs (adelphophagy), have accelerated development, and hatch as benthic juveniles. In contrast, their siblings hatch as small, planktotrophic, dispersive larvae that are morphologically similar to their type III siblings, but ecologically similar to Type I planktotrophic larvae. We propose that poecilogony evolved through sequence heterochrony in morphogenesis with accelerated onset of juvenile traits in type III offspring. In addition, we suggest that heterochrony in life-history events (hatching, metamorphosis) also occurs, thereby generating offspring that are dimorphic in both phenotype and ecotype. Over time, selection acting on different levels of ontogeny (morphogenesis vs. dispersal) may balance this polymorphism and allow poecilogony to persist.

Gastropod ontogenetic torsion: developmental remnants of an ancient evolutionary change in body plan

A dramatic morphogenetic movement ('ontogenetic torsion') during the development of gastropods has been proposed as a recapitulation of the original developmental departure that established the novel gastropod body plan. Nevertheless, speculative literature about ontogenetic torsion and its evolutionary significance has far outstripped empirical observations and recent results suggest that the developmental process may be somewhat different than the traditional description. I used scanning electron microscopy, immunohistochemistry, phalloidin labeling, and histological sections to monitor displacements of five components of the visceropallium with respect to axial coordinates of the cephalopodium in developing embryos of the caenogastropod, Trichotropis cancellata. Embryos of this species achieve a transient stage of anatomical organization that also arises during development of a vetigastropod (Haliotis kamtschatkana), although morphogenetic processes that generate this stage are different in these two species. At the stage of similarity, the embryonic shell has achieved its definitive orientation with respect to the cephalopodium, but the developing mantle cavity, sensory osphradium, and anus are confined to the right side. I also show that this stage of anatomical organization is recognizable during the development of other gastropods, which collectively represent three major gastropod clades. I propose that ontogenetic torsion should be viewed as a conserved stage of anatomical organization during development, rather than a conserved process of 180 degrees rotation between the visceropallium and cephalopodium. The results lead to the suggestion that the mantle cavity of extant gastropods evolved by enlargement of the right side of the mantle cavity in a monoplacophoran-like ancestor. Under this interpretation, there is no need for a hypothetical pre-gastropod with a mantle cavity that was restricted to the posterior end.

Development of calcareous skeletal elements in invertebrates

Most metazoans require skeletal support systems. While the formation of bones and teeth in vertebrates has been well studied, endo- and exoskeleton development of non-vertebrates, especially calcification during terminal differentiation, has been neglected. Biomineralization of skeletons in invertebrates presents interesting research opportunities. We undertake here to survey some of the better understood examples of skeletal development in selected invertebrates. The differentiation of the skeletal spicules of euechinoid larvae and other non-vertebrate deuterostomes, the shells of molluscs, and the calcification of crustacean carapaces are surveyed. The diversity of these different kinds of animals and our present limited understanding make it difficult to identify unifying themes, but there certainly are unifying questions: How is the mineral precursor secreted? What is the nature of the interaction of mineral with the matrix proteins of the skeleton? Is there any conservation of protein domains in matrix proteins found in skeletal elements from different phyla? Are there common strategies in the development of organs that form mineralized structures?

Developmental constraints in a comparative framework: a test case using variations in phalanx number during amniote evolution

Constraints are factors that limit evolutionary change. A subset of constraints is developmental, and acts during embryonic development. There is some uncertainty about how to define developmental constraints, and how to formulate them as testable hypotheses. Furthermore, concepts such as constraint-breaking, universal constraints, and forbidden morphologies present some conceptual difficulties. One of our aims is to clarify these issues. After briefly reviewing current classifications of constraint, we define developmental constraints as those affecting morphogenetic processes in ontogeny. They may be generative or selective, although a clear distinction cannot always be drawn. We support the idea that statements about constraints are in fact statements about the relative frequency of particular transformations (where 'transformation' indicates a change from the ancestral condition). An important consequence of this is that the same transformation may be constrained in one developmental or phylogenetic context, but evolutionarily plastic in another. In this paper, we analyse developmental constraints within a phylogenetic framework, building on similar work by previous authors. Our approach is based on the following assumptions from the literature: (1) constraints are identified when there is a discrepancy between the observed frequency of a transformation, and its expected frequency; (2) the 'expected' distribution is derived by examining the phylogenetic distribution of the transformation and its associated selection pressures. Thus, by looking for congruence between these various phylogenetic distribution patterns, we can test hypotheses about constraint. We critically examine this approach using a test case: variation in phalanx-number in the amniote limb.

Convergent maternal provisioning and life-history evolution in echinoderms

In marine invertebrates, the frequent evolution of lecithotrophic nonfeeding development from a planktotrophic feeding ancestral developmental mode has involved the repeated, independent acquisition of a large, lipid-rich, usually buoyant egg. To investigate the mechanistic basis of egg-size evolution and the role of maternally provisioned lipids in lecithotrophic development, we identified and quantified the egg lipids in six sea urchin species and five sea star species encompassing four independent evolutionary transformations to lecithotrophy. The small eggs of species with planktotrophic development were dominated by triglycerides with low levels of wax esters, whereas the larger eggs of lecithotrophs contain measurable triglycerides but were dominated by wax ester lipids, a relatively minor egg component of planktotrophs. Comparative analysis by independent contrasts confirmed that after removing the influence of phylogeny, the evolution of a large egg by lecithotrophs was correlated with the conspicuous deposition of wax esters. Increases in wax ester abundance exceeded expectations based solely on changes in egg volume. Wax esters may have roles in providing buoyancy to the egg and for postmetamorphic provisioning. Experimentally reducing the amount of wax esters in blastula stage embryos of the lecithotroph Heliocidaris erythrogramma resulted in a viable but nonbuoyant larvae. During normal development for H. erythrogramma, wax ester biomass remained constant during development to metamorphosis (five days postfertilization), but decreased during juvenile development before complete mouth formation (12 days postfertilization) and was further reduced at 18 days postfertilization. The function of wax esters may be specific to the lecithotrophic developmental mode because there were negligible wax esters present in competent pluteus larvae of Strongylocentrotus drobachiensis, a planktotrophic species. These data suggest that this seminal evolutionary modification, the production of a large egg, has been accomplished in part by the elaboration of a preexisting oogenic component, wax esters. The modification of preexisting oogenic processes may facilitate the observed high frequency of transformations in larval mode in marine invertebrates.

Gene expression and larval evolution: changing roles of distal-less and orthodenticle in echinoderm larvae

We describe the expression of the homeobox genes orthodenticle (Otx) and distal-less (Dlx) during the larval development of seven species representing three classes of echinoderms: Holothuroidea, Asteroidea, and Echinoidea. Several expression domains are conserved between species within a single class, including Dlx expression within the brachiolar arms of asteroid larvae and Otx expression within the ciliated bands of holothuroid larvae. Some expression domains are apparently conserved between classes, such as the expression of Dlx within the hydrocoel (left mesocoel) in all three classes. However, several substantial differences in expression domains among taxa were also evident for both genes. Some autapomorphic (unique derived) features of gene expression are phylogenetically associated with autapomorphic structures, such as Dlx expression within the invaginating rudiment of euechinoids. Other autapomorphic gene expression domains are associated with evolutionary shifts in life history from feeding to nonfeeding larval development, such as Otx expression within the ciliated bands of a nonfeeding holothuroid larva. Similar associations between evolutionary changes in morphology and life history mode with changes in regulatory gene expression have also been observed in arthropods, urochordates, and chordates. We predict that recruitment of regulatory genes to a new developmental role is commonly associated with evolutionary changes in morphology and may be particularly common in clades with complex life cycles and diversity of life history modes. Caution should be used when making generalizations about gene expression and function based on a single species, which may not accurately reflect developmental processes and life histories of the phyla to which it belongs.

Variation, plasticity and modularity in anuran development

Although anuran development is generally thought to be relatively conservative, a great deal of variation is evident when different species are compared. This report summarizes the results of comparative analyses of different aspects of anuran development. These include differences in sequence and timing of developmental events, the effects of genome size, and the effects of different life history strategies on anuran embryogenesis. The results show that anuran development is plastic at the evolutionary level, and many changes can occur in the developmental processes of anurans throughout their evolution. Changes are apparently rapid, and are as common as cladogenic events. This evolutionary plasticity can be attributed to the modular nature of anuran development. Different modules can shift relative to one another in time or in space, creating variations in the observed developmental patterns. However, shifts in modules can occur even without having a significant effect on the ultimate outcome of the process. I discuss the implications of the modular nature of development on the evolution of anuran development, and of the group in general.