Regulatory punctuated equilibrium and convergence in the evolution of developmental pathways in direct-developing sea urchins

A transitional fossil mite (Astigmata: Levantoglyphidae fam. n.) from the early Cretaceous suggests gradual evolution of phoresy-related metamorphosis

Metamorphosis is a key innovation allowing the same species to inhabit different environments and accomplish different functions, leading to evolutionary success in many animal groups. Astigmata is a megadiverse lineage of mites that expanded into a great number of habitats via associations with invertebrate and vertebrate hosts (human associates include stored food mites, house dust mites, and scabies). The evolutionary success of Astigmata is linked to phoresy-related metamorphosis, namely the origin of the heteromorphic deutonymph, which is highly specialized for phoresy (dispersal on hosts). The origin of this instar is enigmatic since it is morphologically divergent and no intermediate forms are known. Here we describe the heteromorphic deutonymph of Levantoglyphus sidorchukae n. gen. and sp. (Levantoglyphidae fam. n.) from early Cretaceous amber of Lebanon (129 Ma), which displays a transitional morphology. It is similar to extant phoretic deutonymphs in its modifications for phoresy but has the masticatory system and other parts of the gnathosoma well-developed. These aspects point to a gradual evolution of the astigmatid heteromorphic morphology and metamorphosis. The presence of well-developed presumably host-seeking sensory elements on the gnathosoma suggests that the deutonymph was not feeding either during phoretic or pre- or postphoretic periods.

The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements

Theories of the genetics underlying punctuated equilibrium (PE) have been vague to date. Here the developmental gene hypothesis is proposed, which states that: 1) developmental regulatory (DevReg) genes are responsible for the orchestration of metazoan morphogenesis and their extreme conservation and mutation intolerance generates the equilibrium or stasis present throughout much of the fossil record and 2) the accumulation of regulatory elements and recombination within these same genes-often derived from transposable elements-drives punctuated bursts of morphological divergence and speciation across metazoa. This two-part hypothesis helps to explain the features that characterize PE, providing a theoretical genetic basis for the once-controversial theory. Also see the video abstract here https://youtu.be/C-fu-ks5yDs.

Procuring animals and culturing of eggs and embryos

Echinoderms and especially echinoids have a rich history as model systems for the study of oogenesis, fertilization, and early embryogenesis. The ease of collecting and maintaining adults, as well as in obtaining gametes and culturing large quantities of synchronous embryos, is complemented by the ability to do biochemistry, reverse genetics, embryo manipulations and study gene regulatory networks. The diversity of species and developmental modes as well as unparalleled transparency in early developmental stages also makes echinoderms an excellent system in which to study evolutionary aspects of developmental biology. This chapter provides a practical guide to experimental methods for procuring adults and gametes, achieving synchronous in vitro fertilization, and culturing embryos through early larval stages for several echinoderm species representing four classes (Echinoidea, Asteroidea, Ophiuroidea, and Holothuroidea). We provide specific examples of protocols for obtaining adults and gametes and for culturing embryos of a selected number of species for experimental analysis of their development. The species were chosen to provide breadth across the phylum Echinodermata, as well as to provide practical guidelines for handling some of the more commonly studied species. For each species, we highlight specific advantages, and special note is made of key issues to consider when handling adults, collecting gametes, or setting and maintaining embryo cultures. Finally, information regarding interspecific crosses is provided.

The developmental transcriptomes of two sea biscuit species with differing larval types

BACKGROUND

Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a rare, intermediate larval type-facultative feeding- and can develop through metamorphosis entirely based on egg provisioning in under one week.

RESULTS

Overall, the two transcriptomes are highly similar, containing largely orthologous contigs with similar functional annotation. However, we found distinct differences in gene expression patterns between the two species. Larvae from C. rosaceus, the facultative planktotroph, turned genes on at earlier stages and had less differentiation in gene expression between larval stages, whereas, C. subdepressus showed a higher degree of stage-specific gene expression.

CONCLUSION

This study is the first genetic analysis of a species with facultatively feeding larvae. Our results are consistent with known developmental differences between the larval types and raise the question of whether earlier onset of developmental genes is a key step in the evolution of a reduced larval period. By publishing a transcriptome for this rare, intermediate, larval type, this study adds developmental breadth to the current genetic resources, which will provide a valuable tool for future research on echinoderm development as well as studies on the evolution of development in general.

Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod

Population-level consequences of dispersal ability remain poorly understood, especially for marine animals in which dispersal is typically considered a species-level trait governed by oceanographic transport of microscopic larvae. Transitions from dispersive (planktotrophic) to nondispersive, aplanktonic larvae are predicted to reduce connectivity, genetic diversity within populations, and the spatial scale at which reproductive isolation evolves. However, larval dimorphism within a species is rare, precluding population-level tests. We show the sea slug Costasiella ocellifera expresses both larval morphs in Florida and the Caribbean, regions with divergent mitochondrial lineages. Planktotrophy predominated at 11 sites, 10 of which formed a highly connected and genetically diverse Caribbean metapopulation. Four populations expressed mainly aplanktonic development and had markedly reduced connectivity, and lower genetic diversity at one mitochondrial and six nuclear loci. Aplanktonic dams showed partial postzygotic isolation in most interpopulation crosses, regardless of genetic or geographic distance to the sire's source, suggesting that outbreeding depression affects fragmented populations. Dams from genetically isolated and neighboring populations also exhibited premating isolation, consistent with reinforcement contingent on historical interaction. By increasing self-recruitment and genetic drift, the loss of dispersal may thus initiate a feedback loop resulting in the evolution of reproductive isolation over small spatial scales in the sea.

Species Selection Favors Dispersive Life Histories in Sea Slugs, but Higher Per-Offspring Investment Drives Shifts to Short-Lived Larvae

For 40 years, paleontological studies of marine gastropods have suggested that species selection favors lineages with short-lived (lecithotrophic) larvae, which are less dispersive than long-lived (planktotrophic) larvae. Although lecithotrophs appeared to speciate more often and accumulate over time in some groups, lecithotrophy also increased extinction rates, and tests for state-dependent diversification were never performed. Molecular phylogenies of diverse groups instead suggested lecithotrophs accumulate without diversifying due to frequent, unidirectional character change. Although lecithotrophy has repeatedly originated in most phyla, no adult trait has been correlated with shifts in larval type. Thus, both the evolutionary origins of lecithotrophy and its consequences for patterns of species richness remain poorly understood. Here, we test hypothesized links between development mode and evolutionary rates using likelihood-based methods and a phylogeny of 202 species of gastropod molluscs in Sacoglossa, a clade of herbivorous sea slugs. Evolutionary quantitative genetics modeling and stochastic character mapping supported 27 origins of lecithotrophy. Tests for correlated evolution revealed lecithotrophy evolved more often in lineages investing in extra-embryonic yolk, the first adult trait associated with shifts in development mode across a group. However, contrary to predictions from paleontological studies, species selection actually favored planktotrophy; most extant lecithotrophs originated through recent character change, and did not subsequently diversify. Increased offspring provisioning in planktotrophs thus favored shifts to short-lived larvae, which led to short-lived lineages over macroevolutionary time scales. These findings challenge long-standing assumptions about the effects of alternative life histories in the sea. Species selection can explain the long-term persistence of planktotrophy, the ancestral state in most clades, despite frequent transitions to lecithotrophy.

The evolution of larval developmental mode: insights from hybrids between species with obligately and facultatively planktotrophic larvae

Life history characteristics play a pervasive role in the ecology and evolution of species. Transitions between feeding and non-feeding larval development have occurred many times in both terrestrial and marine phyla, however we lack a comprehensive understanding of how such shifts occur. The sea biscuits Clypeaster rosaceus and Clypeaster subdepressus employ different life history strategies (facultatively feeding larvae and obligately feeding larvae, respectively) but can hybridize. In this study, we examined the development of hybrid larvae between these two species in order to investigate the inheritance of larval developmental mode. Our results show that both reciprocal hybrid crosses developed via the feeding mode of their maternal species. However, as feeding larvae can obtain both energy and hormones from algal food, we tested how hormones alone affected development by setting up a treatment where we added exogenous thyroid hormone, but no food. In this treatment the offspring of all four crosses (two homospecific and two heterospecific crosses) were able to metamorphose without algal food. Therefore we hypothesize that although hybrid developmental mode was inherited from the maternal species, this result was not solely due to energetic constraints of egg size.

Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea?

BACKGROUND

Two theories for the origin of animal life cycles with planktotrophic larvae are now discussed seriously: The terminal addition theory proposes a holopelagic, planktotrophic gastraea as the ancestor of the eumetazoans with addition of benthic adult stages and retention of the planktotrophic stages as larvae, i.e. the ancestral life cycles were indirect. The intercalation theory now proposes a benthic, deposit-feeding gastraea as the bilaterian ancestor with a direct development, and with planktotrophic larvae evolving independently in numerous lineages through specializations of juveniles.

RESULTS

Information from the fossil record, from mapping of developmental types onto known phylogenies, from occurrence of apical organs, and from genetics gives no direct information about the ancestral eumetazoan life cycle; however, there are plenty of examples of evolution from an indirect development to direct development, and no unequivocal example of evolution in the opposite direction. Analyses of scenarios for the two types of evolution are highly informative. The evolution of the indirect spiralian life cycle with a trochophora larva from a planktotrophic gastraea is explained by the trochophora theory as a continuous series of ancestors, where each evolutionary step had an adaptational advantage. The loss of ciliated larvae in the ecdysozoans is associated with the loss of outer ciliated epithelia. A scenario for the intercalation theory shows the origin of the planktotrophic larvae of the spiralians through a series of specializations of the general ciliation of the juvenile. The early steps associated with the enhancement of swimming seem probable, but the following steps which should lead to the complicated downstream-collecting ciliary system are without any advantage, or even seem disadvantageous, until the whole structure is functional. None of the theories account for the origin of the ancestral deuterostome (ambulacrarian) life cycle.

CONCLUSIONS

All the available information is strongly in favor of multiple evolution of non-planktotrophic development, and only the terminal addition theory is in accordance with the Darwinian theory by explaining the evolution through continuous series of adaptational changes. This implies that the ancestor of the eumetazoans was a holopelagic, planktotrophic gastraea, and that the adult stages of cnidarians (sessile) and bilaterians (creeping) were later additions to the life cycle. It further implies that the various larval types are of considerable phylogenetic value.

How did indirect development with planktotrophic larvae evolve?

The two main types of theories for the evolution of the biphasic life cycles in marine invertebrates are discussed. The "intercalation" theories propose that the larval stages (planktotrophic or lecithotrophic) have evolved as specializations from the ancestral, direct life cycle. The opposing "terminal addition" theories propose that the ancestor was holopelagic and that the adult stage was added to the life cycle with the pelagic stage retained as a planktotrophic larva. It is emphasized that theories based on hypothetical ancestors that were unable to feed must be rejected. This applies to planula theories based on a compact planula. Various arguments against the theories that consider the feeding larvae as ancestral in the major eumetazoan lineages and in particular against the trochaea theory are discussed and found untenable. It is suggested that the "Cambrian explosion" was actually a rapid Ediacaran radiation of the eubilaterians that was made possible by the evolution of a tubular gut with all the resulting possibilities for new body plans.

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).

Major regulatory factors in the evolution of development: the roles of goosecoid and Msx in the evolution of the direct-developing sea urchin Heliocidaris erythrogramma

The transcription factors Gsc and Msx are expressed in the oral ectoderm of the indirect-developing sea urchin Heliocidaris tuberculata. Their patterns of expression are highly modified in the direct developer Heliocidaris erythrogramma, which lacks an oral ectoderm. We here test the hypothesis that they are large effect genes responsible for the loss of the oral ectoderm module in the direct-developing larva of H. erythrogramma as well as for the restoration of an overt oral ectoderm in H.e. xH.t. hybrids. We undertook misexpression/overexpression and knockdown assays in the two species and in hybrids by mRNA injection. The results indicate that dramatic changes of function of these transcription factors has occurred. One of these genes, Gsc, has the ability when misexpressed to partially restore oral ectoderm in H. erythrogramma. On the other hand, Msx has lost any oral function and instead has a role in mesoderm proliferation and patterning. In addition, we found that the H. tuberculataGsc is up regulated in H.e. xH.t. hybrids, showing a preferential use of the indirect developing parental gene in the development of the hybrid. We suggest that Gsc qualifies as a gene of large evolutionary effect and is partially responsible for the evolution of direct development of H. erythrogramma. We discuss these results in light of modularity and genetic networks in development, as well as in their implications for the rapid evolution of large morphological changes in development.

Trochophora larvae: cell-lineages, ciliary bands and body regions. 2. Other groups and general discussion

The embryology of sipunculans, entoprocts, nemertines, platyhelminths (excluding acoelomorphs), rotifers, ectoprocts, phoronids, brachiopods, echinoderms and enteropneusts is reviewed with special emphasis on cell-lineage and differentiation of ectodermal structures. A group Spiralia comprising the four first-mentioned phyla plus annelids and molluscs seems well defined through the presence of spiral cleavage with early blastomere specification, prototroch with characteristic cell-lineage, cerebral ganglia developing from cells of the first micromere quartet (i.e., the episphere) and a ventral nervous system developing from the hyposphere. The planktotrophic trochophore was probably the larval type of the ancestor of this group. Another group comprising phoronids, brachiopods, echinoderms and enteropneusts appears equally well delimited. It is characterized by radial cleavage with late blastomere specification, possibly by the presence of a neotroch consisting of monociliate cells, by the absence of cerebral ganglia and of a well-defined brain and paired longitudinal nerve cords developing in connection with the blastopore, and by coelomic organization. Its ancestral larval type was probably a dipleurula. Several characters link rotifers with the spiralians, although they do not show the spiral pattern in the cleavage. Ectoprocts are still a problematic group, but some characters indicate spiralian affinities.

Evolution of OTP-independent larval skeleton patterning in the direct-developing sea urchin, Heliocidaris erythrogramma

Heliocidaris erythrogramma is a direct-developing sea urchin that has evolved a modified ontogeny, a reduced larval skeleton, and accelerated development of the adult skeleton. The Orthopedia gene (Otp) encodes a homeodomain transcription factor crucial in patterning the larval skeleton of indirect-developing sea urchins. We compare the role of Otp in larvae of the indirect-developing sea urchin Heliocidaris tuberculata and its direct-developing congener H. erythrogramma. Otp is a single-copy gene with an identical protein sequence in these species. Expression of Otp is initiated by the late gastrula, initially in two cells of the oral ectoderm in H. tuberculata. These cells are restricted to oral ectoderm and exhibit left-right symmetry. There are about 266 copies of Otp mRNA per Otp- expressing cell in H. tuberculata. We tested OTP function in H. tuberculata and H. erythrogramma embryos by microinjection of Otp mRNA. Mis-expression of Otp mRNA in H. tuberculata radialized the embryos and caused defects during larval skeletogenesis. Mis-expression of Otp mRNA in H. erythrogramma embryos did not affect skeleton formation. This is consistent with the observation by in situ hybridization of no concentration of Otp transcript in any particular cells or region of the H. erythrogramma larva, and measurement of a level of less than one copy of endogenous Otp mRNA per cell in H. erythrogramma. OTP plays an important role in patterning the larval skeleton of H. tuberculata, but this role apparently has been lost in the evolution of the H. erythrogramma larva, and replaced by a new patterning mechanism.

Morphological evolution in sea urchin development: hybrids provide insights into the pace of evolution

Hybridisations between related species with divergent ontogenies can provide insights into the bases for evolutionary change in development. One example of such hybridisations involves sea urchin species that exhibit either standard larval (pluteal) stages or those that develop directly from embryo to adult without an intervening feeding larval stage. In such crosses, pluteal features were found to be restored in fertilisations of the eggs of some direct developing sea urchins (Heliocidaris erythrogramma) with the sperm of closely (Heliocidaris tuberculata) and distantly (Pseudoboletia maculata) related species with feeding larvae. Such results can be argued to support the punctuated equilibrium model-conservation in pluteal regulatory systems and a comparatively rapid switch to direct development in evolution.1,2 Generation of hybrids between distantly related direct developers may, however, indicate evolutionary convergence. The 'rescue' of pluteal features by paternal genomes may require maternal factors from H. erythrogramma because the larva of this species has pluteal features. In contrast, pluteal features were not restored in hybridisations with the eggs of Holopneustes purpurescens, which lacks pluteal features. How much of pluteal development can be lost before it cannot be rescued in such crosses? The answer awaits hybridisations among indirect and direct developing sea urchins differing in developmental phenotype, in parallel with investigations of the genetic programs involved.

Kowalevsky, comparative evolutionary embryology, and the intellectual lineage of evo-devo

Alexander Kowalevsky was one of the most significant 19th century biologists working at the intersection of evolution and embryology. The reinstatement of the Alexander Kowalevsky Medal by the St. Petersburg Society of Naturalists for outstanding contributions to understanding evolutionary relationships in the animal kingdom, evolutionary developmental biology, and comparative zoology is timely now that Evo-devo has emerged as a major research discipline in contemporary biology. Consideration of the intellectual lineage of comparative evolutionary embryology explicitly forces a reconsideration of some current conceptions of the modern emergence of Evo-devo, which has tended to exist in the shadow of experimental embryology throughout the 20th century, especially with respect to the recent success of developmental biology and developmental genetics. In particular we advocate a sharper distinction between the heritage of problems and the heritage of tools for contemporary Evo-devo. We provide brief overviews of the work of N. J. Berrill and D. T. Anderson to illustrate comparative evolutionary embryology in the 20th century, which provides an appropriate contextualization for a conceptual review of our research on the sea urchin genus Heliocidaris over the past two decades. We conclude that keeping research questions rather than experimental capabilities at the forefront of Evo-devo may be an antidote to any repeat of the stagnation experienced by the first group of evolutionary developmental biologists over one hundred years ago and acknowledges Kowalevsky's legacy in evolutionary embryology.

Patterning mechanisms in the evolution of derived developmental life histories: the role of Wnt signaling in axis formation of the direct-developing sea urchin Heliocidaris erythrogramma

A number of echinoderm species have replaced indirect development with highly modified direct-developmental modes, and provide models for the study of the evolution of early embryonic development. These divergent early ontogenies may differ significantly in life history, oogenesis, cleavage pattern, cell lineage, and timing of cell fate specification compared with those of indirect-developing species. No direct-developing echinoderm species has been studied at the level of molecular specification of embryonic axes. Here we report the first functional analysis of Wnt pathway components in Heliocidaris erythrogramma, a direct-developing sea urchin. We show by misexpression and dominant negative knockout construct expression that Wnt8 and TCF are functionally conserved in the generation of the primary (animal/vegetal) axis in two independently evolved direct-developing sea urchins. Thus, Wnt pathway signaling is an overall deeply conserved mechanism for axis formation that transcends radical changes to early developmental ontogenies. However, the timing of expression and linkages between Wnt8, TCF, and components of the PMC-specification pathway have changed. These changes correlate with the transition from an indirect- to a direct-developing larval life history.