Mary E. Andrews

Fibropellins, products of an EGF repeat-containing gene, form a unique extracellular matrix structure that surrounds the sea urchin embryo☆

The sea urchin SpEGF 1 gene belongs to a growing family of developmentally important genes which encode proteins that contain repeated epidermal growth factor-like motifs. To characterize the embryonic expression of the protein products of this gene from Strongylocentrotus purpuratus, we generated polyclonal antisera from SpEGF I fusion proteins. These antibodies recognize two glycoproteins of 145 and 185 kDa, which we have named fibropellins. These proteins are present in unfertilized oocytes and throughout early development. The fibropellins are stored in cytoplasmic vesicles in the oocyte and are released soon after fertilization in a distinct secretory event following the exocytosis of cortical granule contents. Following secretion the proteins are localized in the basal surface of the hyaline layer. At the blastula stage the fibropellins become organized into distinct fibers which form a mesh-like network over the surface of the embryo. During subsequent development to the pluteus larva stage this network increases in overall morphological complexity and becomes regionally distinct. The molecular weights of the fibropellins and their pattern of embryonic localization indicate that these proteins form a component of the hyaline layer previously described as the apical lamina.

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

Summary 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. erythrogramma×H. 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.

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

SUMMARY 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.

Evolution of the fibropellin gene family and patterns of fibropellin gene expression in sea urchin phylogeny

This study documents evolutionary modifications in the expression patterns of the sea urchin EGF I and EGF III genes, which encode a family of extracellular matrix proteins, the fibropellins. We show that the sea urchin apical lamina, a macromolecular extracellular matrix that surrounds the sea urchin embryo and is made up of the fibropellins, has been conserved through at least 250 million years of echinoid evolution. The contribution of different fibropellin family members to this structure has, however, changed over the course of sea urchin phylogeny, and between two congeneric species that exhibit different developmental modes. Mapping the evolutionary history of the EGF genes on a cladogram of relationships among sea urchins reveals that EGF I is present in all echinoids examined, while EGF III appears to have arisen by duplication and divergence from EGF I during the radiation of a suborder of the camarodont sea urchins some 35–45 million years ago. Alterations in the temporal expression patterns of these genes as well as the loss of one of the two EGF I transcripts and encoded protein are coincident with the evolution of a direct-developing larval form in Heliocidaris erythrogramma. H. erythrogramma and its congener Heliocidaris tuberculata, which develops via a typical echinopluteus larva, shared a common ancestor about 10 million years ago. The differences in fibropellin representation within the apical lamina of the various taxa indicate that a homologous embryonic structure can undergo substantial changes in composition during its evolutionary history.

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

SUMMARY 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.

Microbial ecology and biofilms in the taphonomy of soft tissues

ABSTRACT Authigenic mineralization of embryos (and potentially other soft-bodied organisms) requires first stabilization of cells against rapid self-autolytic destruction, and secondly a role for bacterial biofilms that preserve rather than destructively consume tissue. We predict that the ecology of the second stage in preservation will depend on environmental effects on the bacterial species present, coupled with mutual interactions between the bacteria themselves. We have created a simple experimental model made up of two antagonistic marine bacterial species, tested on a taphonomic target of autolysis-inhibited killed marine embryos. Pseudoalteromonas tunicata forms a three-dimensional preserving biofilm with killed embryos, whereas P. luteoviolacea destroys embryo tissue. Our model system allows controlled laboratory tests of microbial interactions under taphonomic conditions selected to test inferred paleoenvironments present in Lagerstätten. We varied environmental conditions one at a time, and observed the taphonomic outcome for killed embryos in the presence of each species alone, and with both species present in direct competition. Parameters tested include temperature, pH, oxygen level, salinity, and nutrient state. Pseudoalteromonas tunicata was robust in generating preserving biofilm pseudomorphs over a wide range of conditions. In competition, P. luteoviolacea destruction dominated in most conditions. However, we identified conditions of temperature, pH, and salinity where P. luteoviolacea grows poorly and preservation by P. tunicata dominates. Elevated external nutrients reduced the fidelity of P. tunicata pseudomorphs. In low oxygen, P. tunicata physiology was altered and it switched to become a destroyer, dramatically showing the extent to which environment can determine taphonomic outcomes.

Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process

Domestication has had a strong impact on the development of modern societies. We sequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first time to our knowledge that a single population, the Criollo population, underwent strong domestication ~3600 years ago (95% CI: 2481–13,806 years ago). We also show that during the process of domestication, there was strong selection for genes involved in the metabolism of the colored protectants anthocyanins and the stimulant theobromine, as well as disease resistance genes. Our analyses show that domesticated populations of T. cacao (Criollo) maintain a higher proportion of high-frequency deleterious mutations. We also show for the first time the negative consequences of the increased accumulation of deleterious mutations during domestication on the fitness of individuals (significant reduction in kilograms of beans per hectare per year as Criollo ancestry increases, as estimated from a GLM, P = 0.000425).Omar Cornejo et al. report a genomic analysis of 200 cacao plants (Theobroma cacao L.) representing more than 10 genetically distinct populations. They identify metabolic and disease resistance genes as contributing to the domestication of cacao and show that domesticated populations maintain a high proportion of deleterious mutations.

IDENTIFICATION AND MODES OF ACTION OF ENDOGENOUS BACTERIA IN TAPHONOMY OF EMBRYOS AND LARVAE

Abstract: We use experimental taphonomy of embryos and larvae to determine the mechanisms by which endogenous bacteria stabilize rather than destroy soft tissues. Here, we show that bacteria can rapidly move from one dead organism to another through the surrounding medium—donor and recipient tissue need not be touching. In most cases tissue destruction results, but in some cases the bacteria generate stabilizing biofilms on recipient tissue that preserve its shape. We isolated, cultured, and identified phylogenetically diverse bacterial strains from the endogenous microbiotas of brine shrimp larvae (Artemia sinica) and sea urchin embryos (Heliocidaris erythrogramma) that had been killed anaerobically and then incubated aerobically to allow proliferation of endogenous bacteria in the dead tissue. We found that one Artemia-derived isolate, Marinobacter sp., is a potent generator of stabilizing biofilms and that other isolates can participate in biofilm formation or cause destruction. These results show the relative frequency of stabilizing bacteria in the endogenous microbiotas of newly dead organisms. Their ease of transmission reveals the potential for generation of a shared microbiology among groups of dead organisms, a possible contributor to uniform preservation in fossil assemblages such as Neoproterozoic and Cambrian fossil embryos.