Research Interests

  • Gene Regulatory Networks 
  • Evolutionary Developmental Biology
  • Development of Marine Invertebrates, esp. molluscs, annelids and echinoderms

Education

  • Mount Holyoke College, MA, B.A. Biology
  • U.C. Berkeley, CA, PhD, Molecular and Cell Biology

Recent Publications

Martik, ML, Lyons DC, McClay DR.  2016.  Developmental gene regulatory networks in sea urchins and what we can learn from them.. F1000 Faculty Rev. 203
Henry, JQ, Lyons DC.  2016.  Molluscan models: Crepidula fornicata. Current Opinion in Genetics & Development. 39:138-148. AbstractWebsite

Gastropod snails in the genus Crepidula have emerged as model systems for studying a metazoan super clade, the Spiralia. Recent work on one species in particular, Crepidula fornicata, has produced high-resolution cell lineage fate maps, details of morphogenetic events during gastrulation, key insights into the molecular underpinnings of early development, and the first demonstration of CRISPR/Cas9 genome editing in the Spiralia. Furthermore, invasive species of Crepidula are a significant ecological threat, while one of these, C. fornicata, is also being harvested for food. This review highlights progress towards developing these animals as models for evolutionary, developmental, and ecological studies. Such studies have contributed greatly to our understanding of biology in a major clade of bilaterians. This information may also help us to control and cultivate these snails.

Perry, KJ, Lyons DC, Truchado-Garcia M, Fischer AHL, Helfrich LW, Johansson KB, Diamond JC, Grande C, Henry JQ.  2015.  Deployment of regulatory genes during gastrulation and germ layer specification in a model spiralian mollusc Crepidula. Developmental Dynamics. 244:1215-1248. AbstractWebsite

During gastrulation, endoderm and mesoderm are specified from a bipotential precursor (endomesoderm) that is argued to be homologous across bilaterians. Spiralians also generate mesoderm from ectodermal precursors (ectomesoderm), which arises near the blastopore. While a conserved gene regulatory network controls specification of endomesoderm in deuterostomes and ecdysozoans, little is known about genes controlling specification or behavior of either source of spiralian mesoderm or the digestive tract.: Using the mollusc Crepidula, we examined conserved regulatory factors and compared their expression to fate maps to score expression in the germ layers, blastopore lip, and digestive tract. Many genes were expressed in both ecto- and endomesoderm, but only five were expressed in ectomesoderm exclusively. The latter may contribute to epithelial-to-mesenchymal transition seen in ectomesoderm. : We present the first comparison of genes expressed during spiralian gastrulation in the context of high-resolution fate maps. We found variation of genes expressed in the blastopore lip, mouth, and cells that will form the anus. Shared expression of many genes in both mesodermal sources suggests that components of the conserved endomesoderm program were either co-opted for ectomesoderm formation or that ecto- and endomesoderm are derived from a common mesodermal precursor that became subdivided into distinct domains during evolution. Developmental Dynamics 244:1215-1248, 2015. (c) 2015 Wiley Periodicals, Inc.

Moczek, AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, De Tomaso AW, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG.  2015.  The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evolution & Development. 17:198-219. AbstractWebsite

Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplinesfrom Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itselfand discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.

Lyons, DC, Perry KJ, Henry JQ.  2015.  Spiralian gastrulation: germ layer formation, morphogenesis, and fate of the blastopore in the slipper snail Crepidula fornicata. Evodevo. 6 AbstractWebsite

Background: Gastrulation is a critical step in bilaterian development, directly linked to the segregation of germ layers, establishment of axes, and emergence of the through-gut. Theories about the evolution of gastrulation often concern the fate of the blastopore (site of endomesoderm internalization), which varies widely in a major branch of bilaterians, the Spiralia. In this group, the blastopore has been said to become the mouth, the anus, both, or neither. Different developmental explanations for this variation exist, yet no modern lineage tracing study has ever correlated the position of cells surrounding the blastopore with their contribution to tissues of the mouth, foregut, and anus in a spiralian. This is the first study to do so, using the gastropod Crepidula fornicata. Results: Crepidula gastrulation occurs by epiboly: the first through third quartet micromeres form an epithelial animal cap that expands to cover vegetal endomesodermal precursors. Initially, descendants of the second and third quartet micromeres (2a-2d, 3a-3d) occupy a portion of the blastopore lip. As the blastopore narrows, the micromeres' progeny exhibit lineage-specific behaviors that result in certain sublineages leaving the lip's edge. Anteriorly, cells derived from 3a(2) and 3b(2) undergo a unique epithelial-to-mesenchymal transition involving proliferation and a collective movement of cells into the archenteron. These cells make a novel spiralian germ layer, the ectomesoderm. Posteriorly, cells derived from 3c(2) and 3d(2) undergo a form of convergence and extension that involves zippering of cells and their intercalation across the ventral midline. During this process, several of these cells, as well as the 2d clone, become displaced posteriorly, away from the blastopore. Progeny of 2a-2c and 3a-3d make the mouth and foregut, and the blastopore becomes the opening to the mouth. The anus forms days later, as a secondary opening within the 2d(2) clone, and not from the classically described "anal cells", which we identify as the 3c(221) and 3d(221) cells. Conclusions: Our analysis of Crepidula gastrulation constitutes the first description of blastopore lip morphogenesis and fates using lineage tracing and live imaging. These data have profound implications for hypotheses about the evolution of the bilaterian gut and help explain observed variation in blastopore morphogenesis among spiralians.

McIntyre, DC, Lyons DC, Martik M, McClay DR.  2014.  Branching out: Origins of the sea urchin larval skeleton in development and evolution. Genesis. 52:173-185. AbstractWebsite

It is a challenge to understand how the information encoded in DNA is used to build a three-dimensional structure. To explore how this works the assembly of a relatively simple skeleton has been examined at multiple control levels. The skeleton of the sea urchin embryo consists of a number of calcite rods produced by 64 skeletogenic cells. The ectoderm supplies spatial cues for patterning, essentially telling the skeletogenic cells where to position themselves and providing the factors for skeletal growth. Here, we describe the information known about how this works. First the ectoderm must be patterned so that the signaling cues are released from precise positions. The skeletogenic cells respond by initiating skeletogenesis immediately beneath two regions (one on the right and the other on the left side). Growth of the skeletal rods requires additional signaling from defined ectodermal locations, and the skeletogenic cells respond to produce a membrane-bound template in which the calcite crystal grows. Important in this process are three signals, fibroblast growth factor, vascular endothelial growth factor, and Wnt5. Each is necessary for explicit tasks in skeleton production. genesis 52:173-185. (c) 2014 Wiley Periodicals, Inc.

Lyons, DC, Martindale MQ, Srivastava M.  2014.  The cell's view of animal body-plan evolution. Integrative and Comparative Biology. 54:658-666. AbstractWebsite

An adult animal's form is shaped by the collective behavior of cells during embryonic development. To understand the forces that drove the divergence of animal body-plans, evolutionary developmental biology has focused largely on studying genetic networks operating during development. However, it is less well understood how these networks modulate characteristics at the cellular level, such as the shape, polarity, or migration of cells. We organized the "Cell's view of animal body plan evolution" symposium for the 2014 The Society for Integrative and Comparative Biology meeting with the explicit goal of bringing together researchers studying the cell biology of embryonic development in diverse animal taxa. Using a broad range of established and emerging technologies, including live imaging, single-cell analysis, and mathematical modeling, symposium participants revealed mechanisms underlying cells' behavior, a few of which we highlight here. Shape, adhesion, and movements of cells can be modulated over the course of evolution to alter adult body-plans and a major theme explored during the symposium was the role of actomyosin in coordinating diverse behaviors of cells underlying morphogenesis in a myriad of contexts. Uncovering whether conserved or divergent genetic mechanisms guide the contractility of actomyosin in these systems will be crucial to understanding the evolution of the body-plans of animals from a cellular perspective. Many speakers presented research describing developmental phenomena in which cell division and tissue growth can control the form of the adult, and other presenters shared work on studying cell-fate specification, an important source of novelty in animal body-plans. Participants also presented studies of regeneration in annelids, flatworms, acoels, and cnidarians, and provided a unifying view of the regulation of cellular behavior during different life-history stages. Additionally, several presentations highlighted technological advances that glean mechanistic insights from new and emerging model systems, thereby providing the phylogenetic breadth so essential for studying animal evolution. Thus, we propose that an explicit study of cellular phenomena is now possible for a wide range of taxa, and that it will be highly informative for understanding the evolution of animal body-plans.

Lyons, DC, Martik ML, Saunders LR, McClay DR.  2014.  Specification to biomineralization: Following a single cell type as it constructs a skeleton. Integrative and Comparative Biology. 54:723-733. AbstractWebsite

The sea urchin larva is shaped by a calcite endoskeleton. That skeleton is built by 64 primary mesenchyme cells (PMCs) in Lytechinus variegatus. The PMCs originate as micromeres due to an unequal fourth cleavage in the embryo. Micromeres are specified in a well-described molecular sequence and enter the blastocoel at a precise time using a classic epithelial-mesenchymal transition. To make the skeleton, the PMCs receive signaling inputs from the overlying ectoderm, which provides positional information as well as control of the growth of initial skeletal tri-radiates. The patterning of the skeleton is the result both of autonomous inputs from PMCs, including production of proteins that are included in the skeletal matrix, and of non-autonomous dynamic information from the ectoderm. Here, we summarize the wealth of information known about how a PMC contributes to the skeletal structure. The larval skeleton is a model for understanding how information encoded in DNA is translated into a three-dimensional crystalline structure.

Lyons, DC, Henry JQ.  2014.  Ins and outs of Spiralian gastrulation. International Journal of Developmental Biology. 58:413-428. AbstractWebsite

Gastrulation is a critical stage of metazoan development during which endodermal and mesodermal tissues are internalized, and morphogenesis transforms the early embryo into each animal's unique body-plan. While gastrulation has been studied extensively in classic model systems such as flies, worms, and vertebrates, less is known about gastrulation at a mechanistic level in other taxa. Surprisingly, one particularly neglected group constitutes a major branch of animals: the Spiralia. A unique feature of spiralian development is that taxa with diverse adult body-plans, such as annelids, molluscs, nemerteans and platyhelminths all share a highly stereotyped suite of characters during embryogenesis called spiral cleavage.The spiral cleavage program makes it possible to compare distantly related embryos using not only morphological features, and gene expression patterns, but also homologous cell lineages. Having all three criteria available for comparison is especially critical for understanding the evolution of a complex process like gastrulation.Thus studying gastrulation in spiralians is likely to lead to novel insights about the evolution of body-plans, and the evolution of morphogenesis itself. Here we review relevant literature about gastrulation in spiralians and frame questions for future studies. We describe the internalization of the endoderm, endomesoderm and ectomesoderm; where known, we review data on the cellular and molecular control of those processes. We also discuss several morphogenetic events that are tied to gastrulation including: axial elongation, origins of the mouth and anus, and the fate of the blastopore. Since spiral cleavage is ancestral for a major branch of bilaterians, understanding gastrulation in spiralians will contribute more broadly to ongoing debates about animal body-plan divergence, such as: the origin of the through-gut, the emergence of indirect versus direct development, and the evolution of gene-regulatory networks that specify endomesoderm. We emphasize the fact that spiralian gastrulation provides the unique opportunity to connect well-defined embryonic cell lineages to variation in cell fate and cell behavior, making it an exceptional case study for evo-devo.

Cheng, XR, Lyons DC, Socolar JES, McClay DR.  2014.  Delayed transition to new cell fates during cellular reprogramming. Developmental Biology. 391:147-157. AbstractWebsite

In many embryos specification toward one cell fate can be diverted to a different cell fate through a reprogramming process. Understanding how that process works will reveal insights into the developmental regulatory logic that emerged from evolution. In the sea urchin embryo, cells at gastrulation were found to reprogram and replace missing cell types after surgical dissections of the embryo. Non-skeletogenic mesoderm (NSM) cells reprogrammed to replace missing skeletogenic mesoderm cells and animal caps reprogrammed to replace all endomesoderm. In both cases evidence of reprogramming onset was first observed at the early gastrula stage, even if the cells to be replaced were removed earlier in development Once started however, the reprogramming occurred with compressed gene expression dynamics. The NSM did not require early contact with the skeletogenic cells to reprogram, but the animal cap cells gained the ability to reprogram early in gastrulation only after extended contact with the vegetal halves prior to that time. If the entire vegetal half was removed at early gastrula, the animal caps reprogrammed and replaced the vegetal half endomesoderm. If the animal caps carried morpholinos to either hox11/13b or foxA (endomesoderm specification genes), the isolated animal caps failed to reprogram. Together these data reveal that the emergence of a reprogramming capability occurs at early gastrulation in the sea urchin embryo and requires activation of early specification components of the target tissues. (C) 2014 Elsevier Inc. All rights reserved.