Expression of engrailed proteins in arthropods, annelids, and chordates

engrailed is a homeobox gene that has an important role in Drosophila segmentation. Genes homologous to engrailed have been identified in several other organisms. Here we describe a monoclonal antibody that recognizes a conserved epitope in the homeodomain of engrailed proteins of a number of different arthropods, annelids, and chordates; we use this antibody to isolate the grasshopper engrailed gene. In Drosophila embryos, the antibody reveals engrailed protein in the posterior portion of each segment during segmentation, and in a segmentally reiterated subset of neuronal cells during neurogenesis. Other arthropods, including grasshopper and two crustaceans, have similar patterns of engrailed expression. However, these patterns of expression are not shared by the annelids or chordates we examined. Our results provide the most comprehensive view that has been obtained of how expression patterns of a regulatory gene vary during evolution. On the basis of these patterns, we suggest that engrailed is a gene whose ancestral function was in neurogenesis and whose function was co-opted during the evolution of segmentation in the arthropods, but not in the annelids and chordates.     

The expression of an engrailed protein during embryonic shell formation of the tusk-shell, Antalis entalis (Mollusca, Scaphopoda)

SUMMARY This study presents the first detailed account of the larval and early post-metamorphic development of a scaphopod species, Antalis entalis , since 1883. Special reference is given to the expression pattern of an engrailed protein during the formation of the embryonic (protoconch) and adult shell (teleoconch). We found that in the trochophore-like larva the engrailed protein is expressed in shell-secreting cells at the margin of the protoconch close to the mantle edge. During metamorphosis the growth of the protoconch and expression of the engrailed protein along its margin stop and the teleoconch starts to form. These data suggest a different genetic background regarding protoconch and teleoconch formation in the Scaphopoda and possibly all Conchifera, thus inferring a different evolutionary origin of both organs. The single anlage of the scaphopod protoconch contradicts earlier hypotheses of a monophyletic taxon Diasoma (Scaphopoda + Bivalvia), which has been mainly based on the assumption of a primarily bilobed shell in both taxa. Comparative data on engrailed expression patterns suggest nervous system patterning as the basic function of engrailed in the Bilateria. However, there are several independent gain-of-function events, namely segment compartmentation in the Annelida and Arthropoda, protoconch formation in the Mollusca, skeletogenesis in the Echinodermata, and limb formation in vertebrates. These findings provide further evidence that homologous genes may act in very different pathways of bilaterian body plan formation in various animal phyla.     

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Many eukaryotes form multinucleated cells during their development. Some cells persist as such during their lifetime, others choose to cleave each nucleus individually using a specialized cytokinetic process known as cellularization. What is cellularization and how is it achieved across the eukaryotic tree of life? Are there common pathways among all species supporting a shared ancestry, or are there key differences, suggesting independent evolutionary paths? In this review, we discuss common strategies and key mechanistic differences in how cellularization is executed across vastly divergent eukaryotic species. We present a number of novel methods and non-model organisms that may provide important insight into the evolutionary origins of cellularization.     

Functional conservation of the wingless-engrailed interaction as shown by a widely applicable baculovirus misexpression system

BACKGROUND: The expression patterns of the segment polarity genes wingless and engrailed are conserved during segmentation in a variety of arthropods, suggesting that the regulatory interactions between these two genes are also evolutionarily conserved. Hypotheses derived from such comparisons of gene expression patterns are difficult to test experimentally as genetic manipulation is currently possible for only a few model organisms. RESULTS: We have developed a system, using recombinant baculoviruses, that can be applied to a wide variety of organisms to study the effects of ectopic expression of genes. As a first step, we studied the range and type of infection of several reporter viruses in the embryos of two arthropod and one vertebrate species. Using this system to express wingless, we were able to induce expression of engrailed in the anterior half of each parasegment in embryos of the fruit fly Drosophila melanogaster. Virus-mediated wingless expression also caused ectopic naked ventral cuticle formation in wild-type Drosophila larvae. In the flour beetle, Tribolium castaneum, ectopic wingless also induced engrailed expression. As in Drosophila, this expression was only detectable in the anterior half of the parasegment. CONCLUSIONS: The functional interaction between wingless and engrailed, and the establishment of cells competent to express engrailed, appears to be conserved between Drosophila and Tribolium. The data on the establishment of an engrailed-competent domain also support the idea that prepatterning by pair-rule genes is conserved between these two insects. The recombinant baculovirus technology reported here may help answer other long-standing comparative evolutionary questions.     

Embryonic expression of engrailed in sea urchins

Neural patterning genes that are expressed along the anterior-posterior axis of deuterostomes are expressed late in larval development in echinoderms and are thought to function in establishing the highly-derived, adult body plan. We have used genomic resources to clone an engrailed gene (SpEn) from Strongylocentrotus purpuratus, and with this we have developed an antibody specific for SpEn. SpEn is expressed late in embryogenesis in the developing larval nervous system. At the prism stage, a small number of neuroblasts in the oral ectoderm on the edge of the larval mouth begin expressing SpEn. The cells are in bilaterally symmetric positions. The expression of SpEn precedes the expression of the neural markers, synaptotagmin and serotonin in the SpEn immunoreactive cells. The SpEn cells are located on the margin of the domain of cells expressing SpNK2.1, but they do not have nuclear SpNK2.1. Expression of engrailed in a pair of bilateral neural structures in early development appears to be a shared feature of bilaterians.     

The state of engrailed expression is not clonally transmitted during early Drosophila development.

In Drosophila embryos, boundaries of lineage restriction separate groups of cells, or compartments. Engrailed is essential for specification of the posterior compartment of each segment, and its expression is thought to mark this compartment. Using a new photo-activatable lineage tracer, we followed the progeny of single embryonic cells marked at the blastoderm stage. No clones straddled the anterior edges of engrailed stripes (the parasegment border). However, posterior cells of each stripe lose engrailed expression, producing mixed clones. We suggest that stable expression of engrailed by cells at the anterior edge of the stripe reflects, not cell-intrinsic mechanisms, but proximity to cells that produce Wingless, an extracellular signal needed for maintenance of engrailed expression. If control of posterior cell fate parallels control of engrailed expression, cell fate is initially responsive to cell environment and cell fate determination is a later event.     

Engrailed gene expression in Drosophila imaginal discs.

Genetic and molecular analyses indicate that the Drosophila engrailed gene is required to distinguish posterior from anterior compartments in each segment of the developing animal. Here, the patterns of engrailed expression in the imaginal discs and ventral ganglion of Drosophila larvae are examined, using an antiserum against the engrailed protein and a novel image processing method to reduce non-specific background. As expected, engrailed expression generally is restricted to cells in the posterior compartment of the discs, and the patterns of expression allow refinements in the fate maps of the discs to be made. More significant is the finding that expression of the gene is highly variable in different regions of posterior compartments, suggesting that engrailed may do more than simply specify 'posteriorness'. In the ventral ganglion engrailed appears to be expressed by a subset of cells, primarily in the posterior regions of each segment. In wing discs from animals that are homozygous for the en1 mutation, the pattern of expression of the gene is altered, as opposed to being simply reduced uniformly in the posterior cells.     

The need to incorporate human variation and evolutionary theory in forensic anthropology: A call for reform

In 1992, Norm Sauer called for a language shift in which practitioners would move away from the socially loaded term “race” and replace it with the less provocative term “ancestry.” While many heeded the call and moved towards ancestry in their research and reports, the actual approach to research and analysis did not change. In response to this change, there was a large growth in ancestry estimation method development in the early decade of the 2000s. However, the practice of ancestry estimation did not adequately incorporate evolutionary theory in interpretation or trait selection and continued with little critical reflection. In the past decade, there has been an increase in ancestry validation methods with little critique of the “race” concept or discussion of modern human variation or reference samples. To advance, forensic anthropologists need to reckon with the practice of ancestry estimation as it is currently practiced. We are calling for another reform in the axiom focusing on evolutionary theory, population history, trait selection, and population-level reference samples. The practice needs to abandon the terms ancestry and race completely and recalibrate to an analysis of population affinity. Population affinity is a statistical approach based on the underlying population structure that would allow the understanding of how microevolutionary forces act in concert with historical events (e.g., colonization, the Transatlantic Slave Trade, etc.) to shape modern human variation. This is not to be confused with geographic ancestry that all too often can be perceived as interchangeable with social race and as an affirmation of the biological concept of race. It is time to critically evaluate the social and scientific implications of the current practice of ancestry estimation, and re-frame our approach to studying and analyzing modern human variation through a population structure approach.     

Toward a Rosetta stone for the stem cell genome: Stochastic gene expression, network architecture, and external influences

We review literature relating to three types of factors known to influence stem cell behavior. These factors are stochastic gene expression, regulatory network architecture, and the influence of external signals, such as those emanating from the niche. Although these factors are considered separately, their shared evolutionary history necessitates integration. Stochastic gene expression pervades network components; network architecture controls, modulates, or exploits this noise while performing additional computation; and such complexity also interplays with factors external to cells. Adequate understanding of each of these components, and how they interact, will lead to a conceptual model of the stem cell regulatory system that can be used to drive hypothesis-driven research and facilitate interpretation of experimental data.     

Segmentation gene expression in the housefly Musca domestica.

Drosophila and Musca both belong to the group of higher dipteran flies and show morphologically a very similar early development. However, these two species are evolutionary separated by at least 100 million years. This presents the opportunity for a comparative analysis of segmentation gene expression across a large evolutionary distance in a very similar embryonic background. We have analysed in detail the early expression of the maternal gene bicoid, the gap genes hunchback, Krüppel, knirps and tailless, the pair-rule gene hairy, the segment-polarity gene engrailed and the homoeotic gene Ultrabithorax. We show that the primary expression domains of these genes are conserved, while some secondary expression aspects have diverged. Most notable is the finding of hunchback expression in 11-13 stripes shortly before gastrulation, as well as a delayed expression of terminal domains of various genes. We conclude that the early developmental gene hierarchy, as it has been defined in Drosophila, is evolutionary conserved in Musca domestica.     

Establishment of rostrocaudal polarity in tectal primordium: engrailed expression and subsequent tectal polarity.

In the E4 (embryonic day 4) chick tectal primordium, engrailed expression is strong at the caudal end and gradually weakens toward the rostral end. We used quail-chick chimeric tecta to investigate how the caudorostral gradient of engrailed expression is established and whether it is correlated with the subsequent rostrocaudal polarity of tectal development. To examine the positional value of the tectal primordium, we produced ectopic tecta in the diencephalon by transplanting a part of the mesencephalic alar plate heterotopically. In the ectopic tectum, the gradient of the engrailed expression reversed and the strength of the expression was dependent on the distance from the mes-diencephalon junction; the nearer the ectopic tectum was to the junction, the weaker the expression was. Consequently, the pattern of the engrailed expression in the host and ectopic tecta was nearly a mirror image, suggesting the existence of a repressive influence around the mes-diencephalon junction on the engrailed expression. We examined cytoarchitectonic development in the ectopic tecta, which normally proceeds in a gradient along the rostrocaudal axis; the rostral shows more advanced lamination than the caudal. In contrast, the caudal part of the ectopic tecta (near to the mes-diencephalon junction) showed more advanced lamination than the rostral. In both the host and ectopic tecta, advanced lamination was observed where the engrailed expression was repressed, and vice versa. Next we studied the correlation between engrailed expression and retinotectal projection from a view of plasticity and rigidity of rostrocaudal polarity in the tectum. We produced ectopic tecta by anisochronal transplantations between E3 host and E2 donor, and showed that there is little repressive influence at E3 around the mes-diencephalon junction. We then made chimeric double-rostral tectum (caudal half of it was replaced by rostral half of the donor tectum) or double-caudal tectum at E3. The transplants kept their original staining pattern in hosts. Consequently, the chimeric tecta showed wholly negative or positive staining of engrailed protein on the grafted side. In such tecta retinotectal projection pattern was disturbed as if the transplants retained their original position-specific characters. We propose from these heterotopic and anisochronal experiments that the engrailed expression can be a marker for subsequent rostrocaudal polarity in the tectum, both as regards cytoarchitectonic development and retinotectal projection.     

Arthropod-like expression patterns of engrailed and wingless in the annelid Platynereis dumerilii suggest a role in segment formation

The origin of animal segmentation, the periodic repetition of anatomical structures along the anteroposterior axis, is a long-standing issue that has been recently revived by comparative developmental genetics. In particular, a similar extensive morphological segmentation (or metamerism) is commonly recognized in annelids and arthropods. Mostly based on this supposedly homologous segmentation, these phyla have been united for a long time into the clade Articulata. However, recent phylogenetic analysis dismissed the Articulata and thus challenged the segmentation homology hypothesis. Here, we report the expression patterns of genes orthologous to the arthropod segmentation genes engrailed and wingless in the annelid Platynereis dumerilii. In Platynereis, engrailed and wingless are expressed in continuous ectodermal stripes on either side of the segmental boundary before, during, and after its formation; this expression pattern suggests that these genes are involved in segment formation. The striking similarities of engrailed and wingless expressions in Platynereis and arthropods may be due to evolutionary convergence or common heritage. In agreement with similarities in segment ontogeny and morphological organization in arthropods and annelids, we interpret our results as molecular evidence of a segmented ancestor of protostomes.     

The caudal gene of the barnacle Sacculina carcini is not expressed in its vestigial abdomen

We report the characterization of a caudal gene from the rhizocephalan cirripede Sacculina carcini and its embryonic and larval expression patterns. Cirripedes are maxillopodan crustaceans that are devoid of any complete abdominal segment at the adult stage. We currently explore the genetic basis of this peculiar body plan. In a previous study we have shown that they probably lack the abdominalA gene, while possessing the other Hox genes shared by arthropods. However, at least a part of the genetic program might be conserved, since the engrailed.a and engrailed.b genes are expressed in a posterior region that we interpret as a relic of an ancestral abdomen. Here we show first that the Sacculina caudal gene is expressed early in embryogenesis, which makes it the earliest genetic marker evidenced in the development of Sacculina and of any other crustacean species. It is expressed later in the embryo in the caudal papilla, a posterior proliferating zone of cells. During the larval stages, the caudal gene is first expressed in the whole thoracic region; then its expression regresses to the posterior end of the larva. Surprisingly, it is never expressed in the vestigial abdomen. This lack of expression of the Sacculina caudal gene in a posterior region, at odds with what is known in all other studied metazoan species, might be correlated with the defective development of the abdomen.     

Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer

It has become clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference methods. Due to the diverse effects of admixture, this interest is shared across disparate fields, from human genetics to research in ecology and evolutionary biology. However, local ancestry inference methods are sensitive to a range of biological and technical parameters which can impact accuracy. Here we present paired simulation and ancestry inference pipelines, mixnmatch and ancestryinfer, to help researchers plan and execute local ancestry inference studies. mixnmatch can simulate arbitrarily complex demographic histories in the parental and hybrid populations, selection on hybrids, and technical variables such as coverage and contamination. ancestryinfer takes as input sequencing reads from simulated or real individuals, and implements an efficient local ancestry inference pipeline. We perform a series of simulations with mixnmatch to pinpoint factors that influence accuracy in local ancestry inference and highlight useful features of the two pipelines. mixnmatch is a powerful tool for simulations of hybridization while ancestryinfer facilitates local ancestry inference on real or simulated data.     

Parasegmental organization of the spider embryo implies that the parasegment is an evolutionary conserved entity in arthropod embryogenesis

Spiders belong to the chelicerates, which is a basal arthropod group. To shed more light on the evolution of the segmentation process, orthologs of the Drosophila segment polarity genes engrailed, wingless/Wnt and cubitus interruptus have been recovered from the spider Cupiennius salei. The spider has two engrailed genes. The expression of Cs-engrailed-1 is reminiscent of engrailed expression in insects and crustaceans, suggesting that this gene is regulated in a similar way. This is different for the second spider engrailed gene, Cs-engrailed-2, which is expressed at the posterior cap of the embryo from which stripes split off, suggesting a different mode of regulation. Nevertheless, the Cs-engrailed-2 stripes eventually define the same border as the Cs-engrailed-1 stripes. The spider wingless/Wnt genes are expressed in different patterns from their orthologs in insects and crustaceans. The Cs-wingless gene is expressed in iterated stripes just anterior to the engrailed stripes, but is not expressed in the most ventral region of the germ band. However, Cs-Wnt5-1 appears to act in this ventral region. Cs-wingless and Cs-Wnt5-1 together seem to perform the role of insect wingless. Although there are differences, the wingless/Wnt-expressing cells and en-expressing cells seem to define an important boundary that is conserved among arthropods. This boundary may match the parasegmental compartment boundary and is even visible morphologically in the spider embryo. An additional piece of evidence for a parasegmental organization comes from the expression domains of the Hox genes that are confined to the boundaries, as molecularly defined by the engrailed and wingless/Wnt genes. Parasegments, therefore, are presumably important functional units and conserved entities in arthropod development and form an ancestral character of arthropods. The lack of by engrailed and wingless/Wnt-defined boundaries in other segmented phyla does not support a common origin of segmentation.     

The consequences of ubiquitous expression of the wingless gene in the Drosophila embryo.

The segment polarity gene wingless has an essential function in cell-to-cell communication during various stages of Drosophila development. The wingless gene encodes a secreted protein that affects gene expression in surrounding cells but does not spread far from the cells where it is made. In larvae, wingless is necessary to generate naked cuticle in a restricted part of each segment. To test whether the local accumulation of wingless is essential for its function, we made transgenic flies that express wingless under the control of a hsp70 promoter (HS-wg flies). Uniform wingless expression results in a complete naked cuticle, uniform armadillo accumulation and broadening of the engrailed domain. The expression patterns of patched, cubitus interruptus Dominant and Ultrabithorax follow the change in engrailed. The phenotype of heatshocked HS-wg embryos resembles the segment polarity mutant naked, suggesting that embryos that overexpress wingless or lack the naked gene enter similar developmental pathways. The ubiquitous effects of ectopic wingless expression may indicate that most cells in the embryo can receive and interpret the wingless signal. For the development of the wild-type pattern, it is required that wingless is expressed in a subset of these cells.     

Engrailed expression in the anterior lineage compartment of the developing wing blade of Drosophila.

The developing wing of Drosophila melanogaster was examined at larval and pupal stages of development to determine whether the anterior-posterior lineage boundary, as identified by lineage restrictions, was congruent with the boundaries defined by the expression of posterior-specific (engrailed, invected), and anterior-specific (cubitus interruptus-D) genes. The lineage boundary was identified by marking mitotic recombinant clones, using an enhancer trap line with ubiquitous beta-gal expression in imaginal tissues; clones of +/+ cells were identified by their lack of beta-gal expression. Domains of gene expression were localized using antibodies and gene specific lacZ constructs. Surprisingly, it was found that engrailed expression extended a small distance into the anterior lineage compartment of the wing blade, as identified with anti-en/inv mAb, anti-en polyclonal antiserum, or an en-promoter-lacZ insert, ryxho25. This anterior expression was not present in early third instar discs, but appeared during subsequent larval and pupal development. In contrast, the expression of cubitus interruptus-D, as identified using the ci-Dplac insert, appeared to be limited to the anterior lineage compartment. Thus, en expression is not limited to cells from the posterior lineage compartment, and en and ci-D activities can overlap in a region just anterior to the lineage compartment boundary in the developing wing. The lineage boundary could also be identified by a line of aligned cells in the prospective wing blade region of wandering third instar discs. A decapentaplegic-lacZ construct was expressed in a stripe several cells anterior to the lineage boundary, and did not define or overlap into the posterior lineage compartment.