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.

Contingent interactions among biofilm-forming bacteria determine preservation or decay in the first steps toward fossilization of marine embryos.

Fossils of soft tissues provide important records of early animals and embryos, and there is substantial evidence for a role for microbes in soft tissue fossilization. We are investigating the initial events in interactions of bacteria with freshly dead tissue, using marine embryos as a model system. We previously found that microbial invasion can stabilize embryo tissue that would otherwise disintegrate in hours or days by generating a bacterial pseudomorph, a three dimensional biofilm that both replaces the tissue and replicates its morphology. In this study, we sampled seawater at different times and places near Sydney, Australia, and determined the range and frequency of different taphonomic outcomes. Although destruction was most common, bacteria in 35% of seawater samples yielded morphology­preserving biofilms. We could replicate the taphonomic pathways seen with seawater bacterial communities using single cultured strains of marine gammaproteobacteria. Each given species reproducibly generated a consistent taphonomic outcome and we identified species that yielded each of the distinct pathways produced by seawater bacterial communities. Once formed,bacterial pseudomorphs are stable for over a year and resist attack by other bacteria and destruction by proteases and other lytic enzymes. Competition studies showed that the initial action of a pseudomorphing strain can be blocked by a strain that destroys tissues. Thus embryo preservation in nature may depend on contingent interactions among bacterial species that determine if pseudomorphing occurs.We used Artemia nauplius larvae to show that bacterial biofilm replacement of tissue is not restricted to embryos, but is relevant for preservation of small multicellular organisms. We present a model for bacterial self­assembly of large­scale three­dimensional tissue pseudomorphs, based on smallscaleinteractions among individual bacterial cells to form local biofilms at structural boundaries within the tissue. Localbiofilms then conjoin to generate the pseudomorph.

Written in stone: fossils, genes and evo-devo.

Fossils give evo-devo a past. They inform phylogenetic trees to show the direction of evolution of developmental features, and they can reveal ancient body plans. Fossils also provide the primary data that are used to date past events, including divergence times needed to estimate molecular clocks, which provide rates of developmental evolution. Fossils can set boundaries for hypotheses that are generated from living developmental systems, and for predictions of ancestral development and morphologies. Finally, although fossils rarely yield data on developmental processes directly, informative examples occur of extraordinary preservation of soft body parts, embryos and genomic information.

Embryo fossilization is a biological process mediated by microbial biofilms.

Fossilized embryos with extraordinary cellular preservation appear in the Late Neoproterozoic and Cambrian, coincident with the appearance of animal body fossils. It has been hypothesized that microbial processes are responsible for preservation and mineralization of organic tissues. However, the actions of microbes in preservation of embryos have not been demonstrated experimentally. Here, we show that bacterial biofilms assemble rapidly in dead marine embryos and form remarkable pseudomorphs in which the bacterial biofilm replaces and exquisitely models details of cellular organization and structure. The experimental model was the decay of cleavage stage embryos similar in size and morphology to fossil embryos. The data show that embryo preservation takes place in 3 distinct steps: (i) blockage of autolysis by reducing or anaerobic conditions, (ii) rapid formation of microbial biofilms that consume the embryo but form a replica that retains cell organization and morphology, and (iii) bacterially catalyzed mineralization. Major bacterial taxa in embryo decay biofilms were identified by using 16S rDNA sequencing. Decay processes were similar in different taphonomic conditions, but the composition of bacterial populations depended on specific conditions. Experimental taphonomy generates preservation states similar to those in fossil embryos. The data show how fossilization of soft tissues in sediments can be mediated by bacterial replacement and mineralization, providing a foundation for experimentally creating biofilms from defined microbial species to model fossilization as a biological process.

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.

Morphogenetic mechanisms of coelom formation in the direct-developing sea urchin Heliocidaris erythrogramma.

Indirect development via a feeding pluteus larva represents the ancestral mode of sea urchin development. However, some sea urchin species exhibit a derived form of development, called direct development, in which features of the feeding larva are replaced by accelerated development of the adult. A major difference between these two developmental modes is the timing of the formation of the left coelom and initiation of adult development. These processes occur much earlier in developmental and absolute time in direct developers and may be underlain by changes in morphogenetic processes. In this study, we explore whether differences in the cellular mechanisms responsible for the development of the left coelom and adult structures are associated with the change in the timing of their formation in the direct-developing sea urchin Heliocidaris erythrogramma. We present evidence that left coelom formation in H. erythrogramma, which differs in major aspects of coelom formation in indirect developers, is not a result of cell division. Further, we demonstrate that subsequent development of adult structures requires cell division.

Axial patterning of the pentaradial adult echinoderm body plan.

Adult echinoderms possess a highly diverged, pentaradial body plan. Developmental mechanisms underlying this body plan are completely unknown, but are critical in understanding how echinoderm pentamery evolved from bilateral ancestors. These mechanisms are difficult to study in indirect-developing species; in this study, we use the direct-developing sea urchin Heliocidaris erythrogramma, whose accelerated adult development can be perturbed by NiCl(2). We introduce a new nomenclature for the adult echinoderm axes to facilitate discussion of the radially symmetric body plan and the events required to pattern it. In sea urchins, the adult oral-aboral axis is often conflated with the long axes of the five rays; we identify these as distinct body axes, the proximodistal (PD). In addition, we define a circular axis, the circumoral (CO), along which the division into five sectors occurs. In NiCl(2)-treated larvae, aspects of normal PD pattern were retained, but CO pattern was abolished. Milder treatments resulted in relatively normal juveniles ranging from biradial to decaradial. NiCl(2) treatment had no effect either on mesodermal morphology or on the ectodermal gene expression response to an inductive mesodermal signal. This suggests that the mesoderm does not mediate the disruption of CO patterning by NiCl(2). In contrast, mesodermal signaling may explain the presence of PD pattern in treated larvae. However, variations in appendage pattern suggest that ectodermal signals are also required. We conclude that CO patterning in both germ layers is dependent on ectodermal events and PD patterning is controlled by mutual ectoderm-mesoderm signaling.

Co-option and dissociation in larval origins and evolution: the sea urchin larval gut.

The origin of marine invertebrate larvae has been an area of controversy in developmental evolution for over a century. Here, we address the question of whether a pelagic "larval" or benthic "adult" morphology originated first in metazoan lineages by testing the hypothesis that particular gene co-option patterns will be associated with the origin of feeding, indirect developing larval forms. Empirical evidence bearing on this hypothesis is derivable from gene expression studies of the sea urchin larval gut of two closely related but differently developing congenerics, Heliocidaris tuberculata (feeding indirect-developing larva) and H. erythrogramma (nonfeeding direct developer), given two subsidiary hypotheses. (1) If larval gut gene expression in H. tuberculata was co-opted from an ancestral adult expression pattern, then the gut expression pattern will remain in adult H. erythrogramma despite its direct development. (2) Genes expressed in the larval gut of H. tuberculata will not have a coordinated expression pattern in H. erythrogramma larvae due to loss of a functional gut. Five structural genes expressed in the invaginating archenteron of H. tuberculata during gastrulation exhibit substantially different expression patterns in H. erythrogramma with only one remaining endoderm specific. Expression of these genes in the adult of H. erythrogramma and larval gut of H. tuberculata, but not in H. erythrogramma larval endoderm, supports the hypothesis that they first played roles in the formation of adult structures and were subsequently recruited into larval ontogeny during the origin and evolution of feeding planktotrophic deuterostome larvae.

Deciphering the fossil record of early bilaterian embryonic development in light of experimental taphonomy.

Experimental analyses of decay in a tunicate deuterostome and three lophotrochozoans indicate that the controls on decay and preservation of embryos, identified previously based on echinoids, are more generally applicable. Four stages of decay are identified regardless of the environment of death and decay. Embryos decay rapidly in oxic and anoxic conditions, although the gross morphology of embryos is maintained for longer under anoxic conditions. Under anoxic reducing conditions, the gross morphology of the embryos is maintained for the longest period of time, compatible with the timescale required for bacterially mediated mineralization of soft tissues. All four stages of decay were encountered under all environmental conditions, matching the spectrum of preservational qualities encountered in all fossil embryo assemblages. The preservation potential of embryos of deuterostomes and lophotrochozoans is at odds with the lack of such embryos in the fossil record. Rather, the fossil record of embryos, as sparse as it is, is dominated by forms interpreted as ecdysozoans, cnidarians, and stem-metazoans. The dearth of deuterostome and lophotrochozoan embryos may be explained by the fact that ecdysozoans, at least, tend to deposit their eggs in the sediment rather than through broadcast spawning. However, fossil embryos remain very rare and the main controlling factor on their fossilization may be the unique conspiracy of environmental conditions at a couple of sites. The preponderance of fossilized embryos of direct developers should not be used in evidence against the existence of indirect development at this time in animal evolutionary history.

Nodal expression and heterochrony in the evolution of dorsal-ventral and left-right axes formation in the direct-developing sea urchin Heliocidaris erythrogramma.

To understand the role of body axes in the evolution of larval form, we use the two sea urchins in the genus Heliocidaris, which have distinctly different larval morphologies. Heliocidaris tuberculata is an indirect-developing sea urchin, which forms a pluteus larva, whereas its sister species, Heliocidaris erythrogramma, exhibits direct development and forms a nonfeeding, ovoid larva. Changes along all three larval axes underlie the differences in larval form associated with each developmental mode. Nodal signaling has recently been implicated as important in establishing the dorsal-ventral (D-V) and left-right (L-R) axes in the indirect-developing sea urchin Paracentrotus lividus. However, because of changes in morphology and timing of morphogenetic events associated with the D-V and L-R axes, respectively, in H. erythrogramma, it was unclear whether nodal played the same roles during direct development. We show that the expression patterns and functions of nodal during H. erythrogramma development are similar to its roles in indirect-developing sea urchins in both D-V and L-R axes formation. However, there are profound changes in gene expression downstream of nodal signaling along the D-V axis and major heterochronies in the execution of the function of nodal along the L-R axis. These highly modified events are linked to the dramatic modifications of larval morphology that have occurred during the evolution of direct development in H. erythrogramma.

Egg energetics, fertilization kinetics, and population structure in echinoids with facultatively feeding larvae.

Larvae of marine invertebrates either arise from small eggs and feed during their development or arise from large eggs that proceed to metamorphosis sustained only from maternal provisioning. Only a few species are known to possess facultatively feeding larvae. Of about 250 echinoid species with known mode of development, only two, Brisaster latifrons and Clypeaster rosaceus, are known to develop through facultatively planktotrophic larvae. To obtain more information on this form of development and its consequences, we determined egg size and egg energetic and protein content of these two species. We found that eggs of B. latifrons resemble those of species with nonfeeding larvae in these characteristics more than those of C. rosaceus. We also compared DNA sequences of the cytochrome oxidase (COI) gene from the Caribbean C. rosaceus to those of the sympatric planktotrophic developer C. subdepressus and also to those of the eastern Pacific species C. europacificus to estimate the degree of divergence between species with different developmental modes. Comparison of COI sequences of C. rosaceus from Panama and Florida revealed that there is no geographic differentiation in this species. Cross-fertilization experiments between C. rosaceus and C. subdepressus indicated that bidirectional gametic incompatibility has evolved between the two species.

Tinkering: new embryos from old--rapidly and cheaply.

Marine embryos and larvae reflect distinct life histories and body plans from their adults, and are relatively simple in morphology and genetic regulation. Evolution of development to produce highly modified larval forms can be rapid among closely related species. We have studied the mechanisms by which the non-feeding direct-developing larva of the sea urchin Heliocidaris erythrogramma evolved from an indirect-developing feeding larva, the pluteus. H. erythrogramma diverged within 4 million years from its sister species, H. tuberculata, which has a typical pluteus larva. Radical evolution of H. erythrogramma early development allows it to reach metamorphosis in three to four days versus the several weeks required for the pluteus. We have used embryology, cross species hybrids, and manipulation of gene expression in embryos to dissect developmental changes and the genic controls that underlie these changes. Evolution of a new larval form resulted largely from several heterochronies in which conserved regulatory pathways are shifted in timing, producing new temporal relationships to other developmental events. Other changes in gene regulation also have contributed to rapid evolution of larval features, including the origin of unexpected and novel tissue identities that transcend changes within homologous features.

Who came first--larvae or adults? origins of bilaterian metazoan larvae.

There is a classic controversy in zoology over whether the common ancestor of living bilaterian phyla was a benthic animal with a bilaterian body plan, or was a pelagic larva-like animal similar to what we see today in the primary larvae of indirect-developing bilaterians. We examine the current larva-like adult hypothesis, and present an alternate model for the evolution of complex life histories by intercalation of larval features into the ontogeny of an ancestral direct-developing bilaterian. This gradual accumulation of larval features results in a developmental regulatory program that produces a larva distinct in body plan from the adult. The evolution of a rapid and complete metamorphosis is made possible by the convergent evolution of set aside cells in the final stages of the emergence of indirect developing larval forms. Although convergences abound either hypothesis for the evolution of developmental pathways and life histories, the bilaterian first hypothesis is consistent with all stages of evolution of a complex life history being selectively advantageous, with the rapid evolution of larval forms, and with the frequent co-option of genes from the adult phase of the life cycle prevalent in the evolution of embryos and larvae.

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.

Adaptive evolution of bindin in the genus Heliocidaris is correlated with the shift to direct development.

Sea urchins are widely used to study both fertilization and development. In this study we combine the two fields to examine the evolution of reproductive isolation in the genus Heliocidaris. Heliocidaris tuberculata develops indirectly via a feeding larva, whereas the only other species in the genus, H. erythrogramma, has evolved direct development through a nonfeeding larva. We estimated the time of divergence between H. erythrogramma and H. tuberculata from mitochondrial DNA divergence, quantified levels of gametic compatibility between the two species in cross-fertilization assays, and examined the mode of evolution of the sperm protein bindin by sequencing multiple alleles of the two species. Bindin is the major component of the sea urchin sperm acrosomal vesicle, and is involved in sperm-egg attachment and fusion. Based on our analyses, we conclude that: the two species of Heliocidaris diverged less than five million years ago, indicating that direct development can evolve rapidly in sea urchins; since their divergence, the two species have become gametically incompatible; Heliocidaris bindin has evolved under positive selection; and this positive selection is concentrated on the branch leading to H. erythrogramma. Three hypotheses can explain the observed pattern of selection on bindin: (1) it is a correlated response to the evolution of direct development in H. erythrogramma; (2) it is the result of an intraspecific process acting in H. erythrogramma but not in H. tuberculata; or (3) it is the product of reinforcement on the species that invests more energy into each egg to avoid hybridization.

Evolutionary Conservation of the Larval Serotonergic Nervous System in a Direct Developing Sea Urchin: (sea urchin development/larval nervous systems/heterochrony/direct development/Heliocidaris erythrogramma).

Development of the larval serotonergic nervous system is examined by indirect immunofluorescence in two congeneric species of sea urchins that exhibit divergent embryonic and larval development. Heliocidar is tuberculata undergoes indirect planktotrophic development via a pluteus larva, whereas Heliocidaris erythrogramma develops directly, passing through a brief, highly derived lecithotrophic larval stage. We have cleared the opaque embryos of H. erythrogramma and discuss internal features of its development. The serotonergic nervous system of H. tuberculata arises in the apical plate at the end of gastrulation and develops into a bilaterally symmetric ganglion lying between the anterolateral arms in the preoral hood. Putatively homologous neurons appear at the apical end of the modified larva of H. erythrogramma well after the completion of gastrulation, coincident with development of the primary podia of the adult rudiment. The neurons form a bilaterally symmetric ganglion whose orientation relative to the vestibule is conserved with respect to that found in planktotrophic larvae. This allows us to define a left and right side for this larva which lacks external points of asymmetry such as a larval mouth. The alteration in the time of nervous system development in H. erythrogramma relative to that of H. tuberculata, and other indirect developers, implicates heterochronies in cellular differentiation as an important component of the evolution of direct development.

Mechanism of an Alternate Type of Echinoderm Blastula Formation: The Wrinkled Blastula of the Sea Urchin Heliocidaris erythrogramma: (direct development/echinoderm development/morphogenesis/sea urchin embryos/wrinkled blastula).

While most indirect-developing echinoderms (possessing a feeding larval stage) form a hollow, smooth-walled blastula, most direct-developing species form a wrinkled blastula. The process of wrinkled blastula formation was examined in the direct-developing sea urchin, Heliocidaris erythrogramma. Approximately 5 hrs after fertilization the blastula epithelium contains folds along one, two or three orthogonal planes, which superficially appear like 2-, 4- or 8-cell stages, respectively. Microinjection of fluorescent dye into individual blastomeres of 2-, 4- and 8-cell embryos revealed that the wrinkles correspond with the first, second and third cleavage planes. Two factors appear to generate the wrinkled blastula epithelium. First, blastomeres undergo a partial separation along the first, second and third cleavage planes during early cleavage. Subsequent cell divisions are oriented such that the blastula epithelium is constructed with deep creases along these planes of cell separation. Second, there is no room for the expansion of the developing blastoderm within the tightly fitting fertilization envelope. Prior to hatching from the fertilization envelope, wrinkles in the blastula epithelium disappear, due to an increased packing and elongation of the cells. In addition, a substantial volume of cellular material is removed as lipids are secreted into the blastocoel in an apocrine fashion.

Evolutionary Modification of Echinoid Sperm Correlates with Developmental Mode: (direct development/evolution of development/sea urchins/sperm morphology/genome size).

A significant fraction of living sea urchin species have completely or partially eliminated the pluteus larval stage and instead develop directly from embryo to adult. Direct developing sea urchins develop from large buoyant eggs. We present data to show that evolution of these large eggs is accompanied by the evolution of spermatozoa with elogate heads, in contrast with the conical sperm heads typical of most echinoids. Two congeneric Australian species, Heliocidaris tuberculata, which develops via a pluteus, and H. erythogramma, a direct developer, were investigated in detail. The sperm of H. erythrogramma have an elongate head (11 µm in length) as compared to the conical sperm head (5.6 µm) of H. tuberculata. Electrophoretic analysis of the sperm histones indicates that no unusual histones or protamines are associated with modified head morphology. Genome sizes were determined by flow cytometry. H. erythrogramma has a haploid genome size of 1.3 pg as compared to a haploid genome size of 0.95 pg for H. tuberculata. Other direct developing echinoids have elongate sperm heads, and co-evolution of gametes is indicated as a common feature of evolution of direct development in echinoids. The most extreme case, the direct developing cidaroid sea urchin, Phyllacanthus parvispinus, possesses the longest and narrowest sperm head (20 µm × 1 µm) ever observed in an echinoid.

A shift in germ layer allocation is correlated with large egg size and facultative planktotrophy in the echinoid Clypeaster rosaceus.

Egg size is a correlate of larval evolution in marine embryos. Comparing species with different egg sizes that develop via similar larvae reveals the flexibility and the constraints underlying larval forms. Clypeaster rosaceus is an echinoid that develops via a facultatively planktotrophic pluteus larva. Unlike most echinoids that develop via plutei, C. rosaceus (1) has a larger egg, with a correspondingly smaller ratio of surface area to volume, and (2) forms a large left coelom early in development. Given these characteristics, we predicted underlying changes in the allocation of embryonic tissues to germ layers. With a low surface-to-volume ratio, the C. rosaceus pluteus likely requires relatively less ectoderm than a typical pluteus, whereas the early formation of a large left coelom likely requires relatively more mesoderm than a typical pluteus. We tested this hypothesis by examining the cell lineage of C. rosaceus. We found that the boundary between ectoderm and endoderm in C. rosaceus has shifted relative to echinoids with more typical planktotrophic plutei and extends to or above the third cleavage plane at the equator of the embryo. This indicates a smaller proportional allocation to ectoderm and a larger proportional allocation to endomesoderm compared to echinoids with smaller egg sizes. On the basis of this observation, we develop a new model for the transition from obligate planktotrophy to lecithotrophy. We argue that species with larger eggs may allocate proportionally more tissue to structures selected for accelerated development. In the case of C. rosaceus, the larval cell lineage apportions more cells to endomesoderm and less to ectoderm due to the smaller surface-to-volume ratio of its larger eggs and the early formation of a large left coelom.