Multiple origins of anural development in ascidians inferred from rDNA sequences

Women in tunicate research: Pioneers of the past and their present legacy

The search for female scientists who pioneered the research on tunicates is hindered by the tradition of reporting only the first initials of authors' names on scientific publications using only the initials of their first names. While this practice has the theoretical merit of broadening the readership by preventing the possible bias that could be caused by the gender of the author(s) in some of the readers, it rendered the identification of female researchers active in, or before, the first half of the 20th century quite challenging. Sifting through several dozen electronic records, and with the help of references and/or quotes found online, we have stitched together the information that we were able to retrieve on the life of female scientists who authored some of the earliest publications on tunicates, and we have organized them in (approximate) chronological order. We have also compiled brief synopses of the findings of scientists active in the field of tunicate biology in more recent times, and organized them by subdiscipline.

A cis-regulatory change underlying the motor neuron-specific loss of Ebf expression in immotile tunicate larvae

Many species in the tunicate family Molgulidae have independently lost their swimming larval form and instead develop as tailless, immotile larvae. These larvae do not develop structures that are essential for swimming such as the notochord, otolith, and tail muscles. However, little is known about neural development in these nonswimming larvae. Here, we studied the patterning of the Motor Ganglion (MG) of Molgula occulta, a nonswimming species. We found that spatial patterns of MG neuron regulators in this species are conserved, compared with species with swimming larvae, suggesting that the gene networks regulating their expression are intact despite the loss of swimming. However, expression of the key motor neuron regulatory gene Ebf (Collier/Olf/EBF) was reduced in the developing MG of M. occulta when compared with molgulid species with swimming larvae. This was corroborated by measuring allele-specific expression of Ebf in hybrid embryos from crosses of M. occulta with the swimming species M. oculata. Heterologous reporter construct assays in the model tunicate species Ciona robusta revealed a specific cis-regulatory sequence change that reduces expression of Ebf in the MG, but not in other cells. Taken together, these data suggest that MG neurons are still specified in M. occulta larvae, but their differentiation might be impaired due to reduction of Ebf expression levels.

Regulation and evolution of muscle development in tunicates

For more than a century, studies on tunicate muscle formation have revealed many principles of cell fate specification, gene regulation, morphogenesis, and evolution. Here, we review the key studies that have probed the development of all the various muscle cell types in a wide variety of tunicate species. We seize this occasion to explore the implications and questions raised by these findings in the broader context of muscle evolution in chordates.

EVOLUTION OF ALLORECOGNITION IN BOTRYLLID ASCIDIANS INFERRED FROM A MOLECULAR PHYLOGENY

Despite the functional and phyletic ubiquity of highly polymorphic genetic recognition systems, the evolution and maintenance of these remarkable loci remain an empirical and theoretical puzzle. Many clonal invertebrates use polymorphic genetic recognition systems to discriminate kin from unrelated individuals during behavioral interactions that mediate competition for space. Space competition may have been a selective force promoting the evolution of highly polymorphic recognition systems, or preexisting polymorphic loci may have been coopted for the purpose of mediating space competition. Ascidian species in the family Botryllidae have an allorecognition system in which fusion or rejection between neighboring colonies is controlled by allele-sharing at a single, highly polymorphic locus. The behavioral sequence involved in allorecognition varies in a species-specific fashion with some species requiring extensive intercolony tissue integration prior to the allorecognition response, while other species contact opposing colonies at only a few points on the outer surface before resolving space conflicts. Due to an apparent species-specific continuum of behavioral variation in the degree of intercolony tissue integration required for allorecognition, this system lends itself to a phylogenetic analysis of the evolution of an allorecognition system. We constructed a molecular phylogeny of the botryllids based on 18S rDNA sequence and mapped allorecognition behavioral variation onto the phylogeny. Our phylogeny shows the basal allorecognition condition for the group is the most internal form of the recognition reaction. More derived species show progressively more external allorecognition responses, and in some cases loss of some features of internal function. We suggest that external allorecognition appears to be a secondary function of a polymorphic discriminatory system that was already in place due to other selective pressures such as gamete, pathogen, or developmental cell lineage recognition.

Molecular phylogeny of four ascidian species inferred from mitochondrial Cytochrome Oxidase subunit I (COI) sequence

Ascidians is a crucial group for the studies of deuterostome evolution and the origin of chordates, yet little molecular work has been done to determine the evolutionary relationships and largely unexplored beyond a few species. The phylogenetic analysis are presented for four different species of solitary ascidians, Ascidia virginea, Ascidiella aspersa, Clavelina oblonga and Aplidium fuscum, obtained from Great Nicobar Biosphere reserve (GNBR). Mitochondrial Cytochrome Oxidase subunit 1(COI) gene was amplified and the genetic diversity at the phylogenic level was measured. Bar-coded sequences were extracted with BLAST format from NCBI and the genetic diversity of the submitted sequences were compared with the related ascidian species. Maximum divergences measured among the four species were as follows: Ascidia virginea (96%), Ascidiella aspersa (96%), Clavelina oblonga (94%) and Aplidium fuscum (97%). This is the first report of molecular phylogeny of ascidians from Great Nicobar Biosphere Reserve, Andaman and Nicobar Islands. From this study, we found some stable clades on the evolutionary relationships among these ascidian species that may prompt a reevaluation of some morphological characters.

Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley

This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult anatomy and life cycle of thaliaceans and appendicularians, the pelagic relatives of ascidians. In the first part of this review, we discuss the novel anatomical observations and evolutionary hypotheses made by Huxley, which would have a lasting influence on tunicate biology. We also briefly comment on the more philosophical reflections of Huxley on individuality. In the second part, we stress the originality and relevance of past and future studies of tunicates in the resolution of major biological issues. In particular, we focus on the complex relationship between genotype and phenotype and the phenomenon of developmental system drift. We propose that more than 150 years after Huxley's papers, tunicate embryos are still worth studying in their own right, independently of their evolutionary proximity to vertebrates, as they provide original and crucial insights into the process of animal evolution. Tunicates are still at the forefront of biological research.

The Comparative Organismal Approach in Evolutionary Developmental Biology: Insights from Ascidians and Cavefish

Important contributions to evolutionary developmental biology have been made using the comparative organismal approach. As examples, I describe insights obtained from studies of Molgula ascidians and Astyanax cavefish.

Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians

Ascidians present a striking dichotomy between conserved phenotypes and divergent genomes: embryonic cell lineages and gene expression patterns are conserved between distantly related species. Much research has focused on Ciona or Halocynthia spp. but development in other ascidians remains poorly characterized. In this study, we surveyed the multipotent myogenic B7.5 lineage in Molgula spp. Comparisons to the homologous lineage in Ciona revealed identical cell division and fate specification events that result in segregation of larval, cardiac, and pharyngeal muscle progenitors. Moreover, the expression patterns of key regulators are conserved, but cross-species transgenic assays uncovered incompatibility, or ‘unintelligibility’, of orthologous cis-regulatory sequences between Molgula and Ciona. These sequences drive identical expression patterns that are not recapitulated in cross-species assays. We show that this unintelligibility is likely due to changes in both cis- and trans-acting elements, hinting at widespread and frequent turnover of regulatory mechanisms underlying otherwise conserved aspects of ascidian embryogenesis.

DOI:http://dx.doi.org/10.7554/eLife.03728.001

When two species have features that look similar, this may be because the features arise by the same processes during development. Other features may look similar yet develop by different mechanisms. ‘Developmental system drift’ refers to the process where a physical feature remains unaltered during evolution, but the underlying pathway that controls its development is changed. However, to date, there have been only a few experimental studies that support this idea.

Ascidians—also commonly known as sea squirts—are vase-like marine creatures, which start off as tadpole-like larvae that swim around until they find a place to settle down and attach themselves. Once attached, the sea squirts lose the ability to swim and start feeding, typically by filtering material out of the seawater. Sea squirts and their close relatives are the invertebrates (animals without backbones) that are most closely related to all vertebrates (animals with backbones), including humans. Furthermore, although different species of sea squirt have almost identical embryos, their genomes are very different.

Stolfi et al. have now studied whether developmental system drift may have occurred during the evolution of ascidians, by analyzing different species of sea squirt named Molgula and Ciona. Stolfi et al. compared the genomes of Molgula and Ciona and studied the expression of genes in the cells that give rise to the heart and the muscles of the head. As an embryo develops, specific genes are switched on or off, and these patterns of gene activation were broadly identical in the two species of sea squirt examined.

Enhancers are sequences of DNA that control when and how a gene is switched on. Given the similarities between the development of heart and head muscle cells in the different sea squirts, Stolfi et al. looked to see if the mechanisms of gene expression, and therefore the enhancers, were also conserved. Unexpectedly, this was not the case. When enhancers from Molgula were introduced into Ciona (and vice versa), these sequences were unable to switch on gene expression—thus enhancers from one sea squirt species could not function in the other.

Stolfi et al. conclude that the developmental systems may have drifted considerably during evolution of the sea squirts, in spite of their nearly identical embryos. This reinforces the view that different paths can lead to the formation of similar physical features.

DOI:http://dx.doi.org/10.7554/eLife.03728.002

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.

Life history evolution of marine invertebrates: New views from phylogenetic systematics

Established theories on the evolution of the diverse life histories of marine metazoans, specifically invertebrates, were developed in the absence of rigorous phylogenetic methods. With improved estimates of evolutionary relationships for various marine invertebrate groups, based on phylogenetic systematics, we can now critically evaluate the assumptions upon which these theories are based. Several studies emphasizing a phylogenetic systematics approach have recently examined the evolutionary transitions among reproductive traits and challenge us to reconsider the generality of the assumptions made about life history evolution. The results point towards exciting possibilities for a better understanding of the great diversity of reproductive and developmental modes we observe in marine invertebrates today.

A molecular phylogeny of bryozoans

We present the most comprehensive molecular phylogeny of bryozoans to date. Our concatenated alignment of two nuclear ribosomal and five mitochondrial genes includes 95 taxa and 13,292 nucleotide sites, of which 8297 were included. The number of new sequences generated during this project are for each gene:ssrDNA (32), lsrDNA (22), rrnL (38), rrnS (35), cox1 (37), cox3 (34), and cytb (44). Our multi-gene analysis provides a largely stable topology across the phylum. The major groups were unambiguously resolved as (Phylactolaemata (Cyclostomata (Ctenostomata, Cheilostomata))), with Ctenostomata paraphyletic. Within Phylactolaemata, (Stephanellidae, Lophopodidae) form the earliest divergent clade. Fredericellidae is not resolved as a monophyletic family and forms a clade together with Plumatellidae, Cristatellidae and Pectinatellidae, with the latter two as sister taxa. Hyalinella and Gelatinella nest within the genus Plumatella. Cyclostome taxa fall into three major clades: i. (Favosipora (Plagioecia, Rectangulata)); ii. (Entalophoroecia ((Diplosolen, Cardioecia) (Frondipora, Cancellata))); and iii. (Articulata ((Annectocyma, Heteroporidae) (Tubulipora (Tennysonia, Idmidronea)))), with suborders Tubuliporina and Cerioporina, and family Plagioeciidae each being polyphyletic. Ctenostomata is composed of three paraphyletic clades to the inclusion of Cheilostomata: ((Alcyonidium, Flustrellidra) (Paludicella (Anguinella, Triticella)) (Hislopia (Bowerbankia, Amathia)) Cheilostomata); Flustrellidra nests within the genus Alcyonidium, and Amathia nests within the genus Bowerbankia. Suborders Carnosa and Stolonifera are not monophyletic. Within the cheilostomes, Malacostega is paraphyletic to the inclusion of all other cheilostomes. Conopeum is the most early divergent cheilostome, forming the sister group to ((Malacostega, Scrupariina, Inovicellina) ((Hippothoomorpha, Flustrina) (Lepraliomorpha, Umbonulomorpha))); Flustrina is paraphyletic to the inclusion of the hippothoomorphs; neither Lepraliomorpha nor Umbonulomorpha is monophyletic. Ascophorans are polyphyletic, with hippothoomorphs grouping separately from lepraliomorphs and umbonulomorphs; no cribrimorphs were included in the analysis. Results are discussed in the light of molecular and morphological evidence. Ancestral state reconstruction of larval strategy in Gymnolaemata revealed planktotrophy and lecithotrophy as equally parsimonious solutions for the ancestral condition. More comprehensive taxon sampling is expected to clarify this result. We discuss the extent of non-bryozoan contaminant sequences deposited in GenBank and their impact on the reconstruction of metazoan phylogenies and those of bryozoan interrelationships.

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.

Analysis of large scale expression sequenced tags (ESTs) from the anural ascidian, Molgula tectiformis

Anural ascidians show embryogenesis during which tail formation does not take place. This mode of development is a derived character acquired several times independently in ascidian evolution. We identified approximately 20,000 each ESTs (i. e. 10,000 clones each were sequenced from both 5' and 3' ends) of adult gonads, cleaving-embryos, gastrulae/neurulae, embryos before hatching, and hatched larvae of the anural ascidian Molgula tectiformis, in order to comprehensively investigate the molecular mechanism of tailless evolution. Analyses of these ESTs showed that in this species, (1) the expression of embryonic/larval muscle structural genes which are expressed abundantly during embryogenesis of the urodele ascidian Ciona intestinalis, is suppressed; (2) genes that encode proteins with no similarity to known proteins of other organisms are abundantly expressed; (3) genes that show similarity with those up-regulated at metamorphosis in urodele ascidians are up-regulated within several hours after hatching; and (4) 15 of 35 putative orthologues of the downstream components of Brachyury, a key transcription factor for ascidian notochord formation, were found in the ESTs, even though differentiation of notochord is suppressed in this species. We discuss these remarkable results that allow insight into the molecular mechanism(s) responsible for the anural mode of ascidian development.

Expression of a muscle determinant gene, macho-1, in the anural ascidian Molgula tectiformis

In anural (tailless) ascidian species, functional embryonic muscle is not formed. In urodele (tailed) ascidians, macho-1 functions as a maternally supplied factor for embryonic muscle formation. The failure of embryonic muscle development in anural ascidians may be due to the suppression of macho-1 expression. In this paper, however, we report the expression of macho-1 in embryos of an anural ascidian, Molgula tectiformis. Although M. tectiformis has lost the developmental potential to form functional embryonic muscle, macho-1 was expressed in a very similar manner as in urodele ascidians. This result, together with those of previous studies, strongly suggests that in M. tectiformis the upstream genetic cascade responsible for muscle formation is intact, while the downstream cascade including the expression of muscle structural genes is severely affected.

Decoding cis-regulatory systems in ascidians

Ascidians, or sea squirts, are lower chordates, and share basic gene repertoires and many characteristics, both developmental and physiological, with vertebrates. Therefore, decoding cis-regulatory systems in ascidians will contribute toward elucidating the genetic regulatory systems underlying the developmental and physiological processes of vertebrates. cis-Regulatory DNAs can also be used for tissue-specific genetic manipulation, a powerful tool for studying ascidian development and physiology. Because the ascidian genome is compact compared with vertebrate genomes, both intergenic regions and introns are relatively small in ascidians. Short upstream intergenic regions contain a complete set of cis-regulatory elements for spatially regulated expression of a majority of ascidian genes. These features of the ascidian genome are a great advantage in identifying cis-regulatory sequences and in analyzing their functions. Function of cis-regulatory DNAs has been analyzed for a number of tissue-specific and developmentally regulated genes of ascidians by introducing promoter-reporter fusion constructs into ascidian embryos. The availability of the whole genome sequences of the two Ciona species, Ciona intestinalis and Ciona savignyi, facilitates comparative genomics approaches to identify cis-regulatory DNAs. Recent studies demonstrate that computational methods can help identify cis-regulatory elements in the ascidian genome. This review presents a comprehensive list of ascidian genes whose cis-regulatory regions have been subjected to functional analysis, and highlights the recent advances in bioinformatics and comparative genomics approaches to cis-regulatory systems in ascidians.

Ascidian molecular phylogeny inferred from mtDNA data with emphasis on the Aplousobranchiata

We explored the usefulness of mtDNA data in assessing phylogenetic relationships within the Ascidiacea. Although ascidians are a crucial group in studies of deuterostome evolution and the origin of chordates, little molecular work has been done to ascertain the evolutionary relationships within the class, and in the studies performed to date the key group Aplousobranchiata has not been adequately represented. We present a phylogenetic analysis based on mitochondrial cytochrome c oxidase subunit I (COI) sequences of 37 ascidian species, mainly Aplousobranchiata (26 species). Our data retrieve the main groups of ascidians, although Phlebobranchiata appeared paraphyletic in some analyses. Aplousobranch ascidians consistently appeared as a derived group, suggesting that their simple branchial structure is not a pleisiomorphic feature. Relationships between the main groups of ascidians were not conclusively determined, the sister group of Aplousobranchiata was the Stolidobranchiata or the Phlebobranchiata, depending on the analysis. Therefore, our data could not confirm an Enterogona clade (Aplousobranchiata+Phlebobranchiata). All of the tree topologies confirmed previous ideas, based on morphological and biochemical characters, suggesting that Cionidae and Diazonidae are members of the clade Aplousobranchiata, with Cionidae occupying a basal position within them in our analyses. Within the Aplousobranchiata, we found some stable clades that provide new data on the evolutionary relationships within this large group of ascidians, and that may prompt a re-evaluation of some morphological characters.

Mitochondrial DNA phylogeny and rates of larval evolution in Macrophiothrix brittlestars

Phylogenetic analysis has led to significant insights into the evolution of early life-history stages of marine invertebrates. Although echinoderms have been a major focus, developmental and phylogenetic information are relatively poor for ophiuroids, the most species-rich echinoderm class. We used DNA sequences from two mitochondrial genes to develop a phylogenetic hypothesis for 14 brittlestar species in the genus Macrophiothrix (Family Ophiotrichidae). Species are similar in adult form and ecology, but have diverse egg sizes and modes of larval development. In particular, two species have rare larval forms with characteristics that are intermediate between more common modes of feeding and non-feeding development. We use the phylogeny to address whether intermediate larval forms are rare because the evolution of a simplified morphology is rapid once food is no longer required for development. In support of this hypothesis, branch lengths for intermediate forms were short relative to those for species with highly derived non-feeding forms. The absolute rarity of such forms makes robust tests of the hypothesis difficult.

A phylogeny of the hemichordates based on morphological characters

A comprehensive review of literature on all 15 genera constituting the phylum Hemichordata resulted in a morphological matrix of 105 characters. The echinoderms, tunicates, cephalochordates, and vertebrates were included in the analysis, and the cnidarians, polychaetes, and sipunculids were employed as outgroup taxa. The consensus tree supported the traditional view of a monophyletic Hemichordata, Echinodermata, Ambulacraria, and Chordata. The enteropneust families Spengelidae and Ptychoderidae were each monophyletic and sister-taxa, but there was no resolution among the family Harrimaniidae. A detailed sensitivity analysis provided (i) tree lengths of competing evolutionary hypothesis and (ii) a test of monophyly of groups under a variety of evolutionary models. It is argued that the ancestral deuterostome was a benthic vermiform organism with a terminal mouth and anus, well-developed circular and longitudinal muscles, a simple nerve plexus with little sign of regionalization, a pharynx with gill slits and collagenous gill bars, a cluster of vacuolated cells with myofilaments, produced iodotyrosine, and displayed direct development. The pterobranchs have lost many of these features as a consequence of evolving a small body size and living in tubes, but these features exist in present-day enteropneusts, suggesting that they are a plausible model for the proximate ancestor of deuterostomes.

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.

Molecular phylogeny of the protochordates: chordate evolution

The deuterostomes are a monophyletic group of multicellular animals that include the Chordata, a phylum that exhibits a unique body plan within the metazoans. Deuterostomes classically contained three phyla, Echinodermata, Hemichordata, and Chordata. Protochordata describes two invertebrate chordate subphyla, the Tunicata (Urochordata) and the Cephalochordata. Tunicate species are key to understanding chordate origins, as they have tadpole larvae with a chordate body plan. However, molecular phylogenies show only weak support for the Tunicata as the sister-group to the rest of the chordates, suggesting that they are highly divergent from the Cephalochordata and Vertebrata. We believe that members of the Tunicata exhibit a unique adult body plan and should be considered a separate phylum rather than a subphylum of Chordata. The molecular phylogeny of the deuterostomes is reviewed and discussed in the context of likely morphological evolutionary scenarios and the possibility is raised that the ancestor of the Tunicata was colonial. In this scenario, the colonial tadpole larva would more resemble an ancestral chordate than the solitary tadpole larva. In contrast, the true chordates (vertebrates and cephalochordates) would have evolved from filter-feeding benthic worms with cartilaginous gill slits, similar to extant enteropneust hemichordates.

Invertebrate species with nonpelagic larvae have elevated levels of nonsynonymous substitutions and reduced nucleotide diversities

Under a nearly neutral model in which most amino acid substitutions are slightly deleterious, variation in demography, population structure, and other ecological factors among closely related species can potentially modify the effective population size or the selective regime, leading to differences in the rate of nonsynonymous substitution. Ratios of nonsynonymous to synonymous substitutions (d(N)/d(S)) between species were analyzed in a sea star genus (Patiriella) and a molluscan genus (Littorina), each with diverse modes of reproduction, including multiple lineages with pelagic and nonpelagic larvae. In both genera, lineages with nonpelagic larvae had significantly higher d(N)/d(S) ratios than lineages with pelagic larvae. The hypothesis that the elevated d(N)/d(S) ratios in species with nonpelagic larvae was due to reduced effective population size was tested by comparing nucleotide diversities in three genera of gastropod mollusks (Littorina, Crepidula, and Hydrobia), each with several modes of reproduction. Overall, there was a significant (p < 0.05) reduction in nucleotide diversity in species with nonpelagic larvae compared to species with pelagic larvae.

Evolution and development of brain sensory organs in molgulid ascidians

The ascidian tadpole larva has two brain sensory organs containing melanocytes: the otolith, a gravity receptor, and the ocellus, part of a photoreceptor. One or both of these sensory organs are absent in molgulid ascidians. We show here that developmental changes leading to the loss of sensory pigment cells occur by different mechanisms in closely related molgulid species. Sensory pigment cells are formed through a bilateral determination pathway in which two or more precursor cells are specified as an equivalence group on each side of the embryo. The precursor cells subsequently converge at the midline after neurulation and undergo cell interactions that decide the fates of the otolith and ocellus. Molgula occidentalis and M. oculata, which exhibit a tadpole larva with an otolith but lacking an ocellus, have conserved the bilateral pigment cell determination pathway. Programmed cell death (PCD) is superimposed on this pathway late in development to eliminate the ocellus precursor and supernumerary pigment cells, which do not differentiate into either an otolith or ocellus. In contrast to molgulids with tadpole larvae, no pigment cell precursors are specified on either side of the M. occulta embryo, which forms a tailless (anural) larva lacking both sensory organs, suggesting that the bilateral pigment cell determination pathway has been lost. The bilateral pigment cell determination pathway and superimposed PCD can be restored in hybrids obtained by fertilizing M. occulta eggs with M. oculata sperm, indicating control by a zygotic process. We conclude that PCD plays an important role in the evolution and development of brain sensory organs in molgulid ascidians.

Phylogeny and evolution of developmental mode in temnopleurid echinoids

The phylogenetic relationships of 24 nominal species of temnopleurid echinoid were established using molecular and morphological data sets. The analysis combined sequence data from mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes and the nuclear 18S-like small subunit rRNA gene with morphological data concerning coronal, lantern, spine, and pedicellarial traits. All four data sets contain similar phylogenetic information, although each provides support at a different taxonomic level. Two data congruence tests (Templeton's test and the incongruence length difference test) suggested no significant heterogeneity between the data sets, and all data were combined in a total evidence analysis. The resulting well-resolved phylogeny suggests that Microcyphus, Amblypneustes, and Holopneustes are not monophyletic genera, and that Temnopleurus (Temnopleurus) and Temnopleurus (Toreumatica) are not closely related and should not be regarded as subgenera. In contrast to previous morphological analyses, Mespilia is found to be more closely related to Temnotrema and Toreumatica than it is to Microcyphus. The phylogeny was used to test a series of hypotheses about the evolution of developmental patterns. All species of Amblypneustes, Holopneustes, and Microcyphus are lecithotrophic, and many of these taxa are restricted to southern Australia. Planktotrophy is the ancestral condition for the temnopleurids, and the 11 instances of lecithotrophic nonplanktotrophy in this clade can be accounted for by a single developmental transition that occurred an estimated 4.4-7.4 million years ago, apparently before the migration of Microcyphus to southern Australia. The switch to a nonplanktotrophic mode of development is unidirectional with no evidence of reversals.

Defining phyla: morphological and molecular clues to metazoan evolution

None of the supraspecific taxonomic categories can be defined objectively. Each taxon should of course be monophyletic, but there is no morphological or molecular character that identifies, for example, the phylum level. This has led some authors to abandon the Linnaean categories, but they appear to be practical "handles" in daily communication. It has been proposed that each phylum exhibits a characteristic Bauplan, but the identification of such "types" have in practice proved difficult or impossible for several phyla. Monophyly of some of the approximately 30 morphology-based phyla has been put in question by molecular studies, but recent reports clearly show that the 18S rRNA molecule, which has been used extensively in phylogenetic analyses, cannot be used alone in identifying phyla (or other higher taxonomic groups). Some higher taxa, for example Chordata, Vertebrata, and Echinodermata, consistently show up as monophyletic in the analyses, whereas molluscan and annelidan subgroups just as consistently are mixed with each other and with a number of other protostomian phyla in varying patterns.

Macroevolutionary consequences of developmental mode in temnopleurid echinoids from the Tertiary of southern Australia

Taxonomic revision and cladistic analysis of a morphological dataset for Australian Tertiary temnopleurids resolve the phylogeny of the group and allow the testing of a series of hypotheses about the evolution of larval development and consequences of changes in development. Australian Tertiary temnopleurids encompass all three major developmental types found in marine invertebrates (planktotrophy, lecithotrophy, and brooding). Planktotrophy is plesiomorphic for this clade, and nonplanktotrophic larval development evolved independently at least three times during the Tertiary. The change to a nonplanktotrophic mode of larval development is unidirectional with no evidence of reversal. In addition, there is no evidence of an ordered transformation series from planktotrophy through planktonic lecithotrophy to brooding. In common with previous studies of other invertebrate groups, analysis of the raw data suggests that nonplanktotrophic taxa within this clade have significantly shorter species longevities, more restricted geographic ranges and higher speciation rates than taxa with planktotrophic development. However, analysis using phylogenetically independent contrasts is unable to confirm that the stratigraphic and geographic patterns are unbiased by the phylogenetic relationships of the included taxa.

Programmed cell death in the ascidian embryo: modulation by FoxA5 and Manx and roles in the evolution of larval development

Programmed cell death (PCD) has been discounted in the ascidian embryo because the descendants of every embryonic cell appear to be present in the tadpole larva. Here we show that apoptotic PCD is initiated in the epidermis and central nervous system (CNS) but not in the endoderm, mesenchyme, muscle, and notochord cells during embryogenesis in molgulid ascidians. However, the affected cells do not actually die until the beginning of metamorphosis. Although specific patterns of PCD were different in distantly related ascidian species, the results suggest that removal of CNS cells by apoptosis is a urchordate feature predating the origin of the vertebrates. Certain molgulid ascidian species have evolved an anural (tailless) larva in which notochord cells fail to undergo the morphogenetic movements culminating in tail development. These anural species include Molgula occulta, the sister species of the urodele (tailed) species Molgula oculata. We show that PCD in the notochord cell lineage precedes the arrest of tail development in M. occulta and other independently evolved anural species. The notochord cells are rescued from PCD and a tail develops in hybrid embryos produced by fertilizing M. occulta eggs with M. oculata sperm, implying that apoptosis is controlled zygotically. Antisense inhibition experiments show that zygotic expression of the FoxA5 and Manx genes is required to prevent notochord PCD in urodele species and hybrids with restored tails. The results provide the first indication of PCD in the ascidian embryo and suggest that apoptosis modulated by FoxA5 and Manx is involved in notochord and tail regression during anural development. Differences in PCD that occur between ascidian species suggest that diversity in programming apoptosis may explain differences in larval form.

Brachyury expression in tailless Molgulid ascidian embryos

The T-box transcription factor gene Brachyury is important for the differentiation of notochord in all chordates, including the ascidians Halocynthia roretzi and Ciona intestinalis. We isolated Brachyury from molgulid ascidians, which have evolved tailless larvae multiple times independently, and found the genes appear functional by cDNA sequence analyses. We then compared the expression of Mocu-Bra in tailed Molgula oculata embryos to two tailless species, Molgula occulta (Mocc-Bra) and Molgula tectiformis (Mt-Bra). Here we show that both tailless species express Brachyury in the notochord lineage during embryogenesis. Initial expression of Mocu-Bra is normal in tailed M. oculata embryos; 10 precursor notochord cells divide twice to result in 40 notochord cells that converge and extend to make a notochord down the center of the tail. In contrast, in tailless Molgula occulta, Mocc-Bra expression disappears prematurely, and there is only one round of division, resulting in 20 cells in the final notochord lineage that never converge or extend. In M. occulta x M. oculata hybrid embryos, expression of Mocu-Bra is prolonged, and the embryos form a tail with 20 notochord cells that converge and extend normally. However, in Molgula tectiformis, a different tailless ascidian, Mt-Bra was expressed only in the 10 notochord precursor cells, which never divide, converge, or extend. In summary, neither Brachyury function nor the early establishment of the notochord lineage appears to be impaired in tailless embryos. In light of these results, we are continuing to investigate how and why notochord development is lost in tailless molgulid ascidian embryos.

Breaking up and getting together: evolution of symbiosis and cloning by fission in sea anemones (Genus Anthopleura)

Clonal growth and symbiosis with photosynthetic zooxanthellae typify many genera of marine organisms, suggesting that these traits are usually conserved. However, some, such as Anthopleura, a genus of sea anemones, contain members lacking one or both of these traits. The evolutionary origins of these traits in 13 species of Anthopleura were inferred from a molecular phylogeny derived from 395 bp of the mitochondrial 16S rRNA gene and 410 bp of the mitochondrial cytochrome oxidase subunit III gene. Sequences from these genes were combined and analyzed by maximum-parsimony, maximum-likelihood, and neighbor-joining methods. Best trees from each method indicated a minimum of four changes in growth mode and that symbiosis with zooxanthellae has arisen independently in eastern and western Pacific species. Alternative trees in which species sharing growth modes or the symbiotic condition were constrained to be monophyletic were significantly worse than best trees. Although clade composition was mostly consistent with geographic sympatry, A. artemisia from California was included in the western Pacific clade. Likewise, A. midori from Japan was not placed in a clade containing only other Asian congeners. The history of Anthopleura includes repeated shifts between clonality and solitariness, repeated attainment of symbiosis with zooxanthellae, and intercontinental dispersal.

Determinants of cell and positional fate in ascidian embryos

Ascidians have played a major role in studies to understand the function of cytoplasmic determinants in animal development. Special qualities, including eggs with colored cytoplasmic regions, an invariant cleavage pattern and cell lineage, embryos with low cell numbers, larvae with typical chordate features and only six different tissues, rapid development, and a small genome, combine to make these animals a unique system for studying cytoplasmic determinants. There is evidence for determinants that specify the cleavage pattern; the differentiation of epidermal, endodermal, and muscle cells; and cell movements associated with gastrulation. The muscle determinants appear to be modified in concert with tail and muscle regression in species that have evolved an anural, or tailless, larva. Several lines of evidence suggest that determinants may be localized maternal mRNAs, which encode transcription factors or signal transduction components responsible for initiating differential gene activity. Different approaches and strategies are being used to isolate and characterize the function of these localized maternal mRNAs.

Phylogenetic analyses of mode of larval development

Phylogenies based on morphological or molecular characters have been used to provide an evolutionary context for analysis of larval evolution. Studies of gastropods, bivalves, tunicates, sea stars, sea urchins, and polychaetes have revealed massive parallel evolution of similar larval forms. Some of these studies were designed to test, and have rejected, the species selection hypothesis for evolutionary trends in the frequency of derived larvae or life history traits. However, the lack of well supported models of larval character evolution leave some doubt about the quality of inferences of larval evolution from phylogenies of living taxa. Better models based on maximum likelihood methods and known prior probabilities of larval character state changes will improve our understanding of the history of larval evolution.

The evolution of anural larvae in molgulid ascidians

Ascidians are urochordates, marine invertebrates with non-feeding motile chordate tadpole larvae, except in the family Molgulidae. Urodele, or tailed, Molgulids have typical ascidian chordate tadpole larvae possessing tails with muscle cells, a notochord, and a dorsal hollow nerve cord. In contrast, anural (or tail-less) Molgulids lack a tail and defining chordate features. Molecular phylogenies generated with 18S and 28S ribosomal sequences indicate that Molgulid species fall into at least four distinct clades, three of which have multiple anural members. This refined and expanded phylogeny allows careful examination of the factors that may have influenced the evolution of tail-less ascidians.

Functional design in the evolution of embryos and larvae

A function of development is to put the right kind of cells in the right place at the right time. Other functional analyses help define what is right. As examples, functional analyses offer explanations for the unicellular bottleneck in life histories that necessitates embryos, evolutionary divergences in embryonic cell cycles, conditions permissive of loss of larval structures and consequent change in embryonic development, and the decoupled development of larval bodies and juvenile rudiments. Functional analyses also reveal the specifications required of morphogenesis, hence defining developmental phenomena to be explained.

p68, a DEAD-box RNA helicase, is expressed in chordate embryo neural and mesodermal tissues

The p68 DEAD-box RNA helicases have been identified in diverse organisms, including yeast, invertebrates, and mammals. DEAD-box RNA helicases are thought to unwind duplexed RNAs, and the p68 family may participate in initiating nucleolar assembly. Recent evidence also suggests that they are developmentally regulated in chordate embryos. bobcat, a newly described member of this gene family, has been found in eggs and developing embryos of the ascidian urochordate, Molgula oculata. Antisense RNA experiments have implicated this gene in establishing basic chordate features, including the notochord and neural tube in ascidians (Swalla et al. 1999). We have isolated p68 homologs from chick and Xenopus in order to investigate their possible role in vertebrate development. We show that embryonic expression of p68 in chick, frog, and ascidian embryos is high in the developing brain and spinal cord as well as in the sensory vesicles. In frog embryos, p68 expression also marks the streams of migrating cranial neural crest cells throughout neural tube development and in tailbud stages, but neural crest expression is faint in chick embryos. Ascidian embryos also show mesodermal p68 expression during gastrulation and neurulation, and we document some p68 mesodermal expression in both chick and frog. Thus, as shown in these studies, p68 is expressed in early neural development and in various mesodermal tissues in a variety of chordate embryos, including chick, frog, and ascidian. Further functional experiments will be necessary to understand the role(s) p68 may play in vertebrate development.

Evolution of parental care and ovulation behavior in oysters

Approximately half of all living oysters brood offspring in the inhalant chamber of their mantle cavities; the remainder are broadcast spawners which do not engage in parental care of young. Ostreid ovulation involves a complex behavioral sequence that results in the countercurrent passage of newly spawned eggs through the gills (ctenidia) and into the inhalant chamber. We constructed molecular and combined-evidence phylogenetic trees to test hypotheses concerning the directionality of parental care evolution, and the evolutionary significance of the trans-ctenidial ovulation pathway, in the Ostreidae. Representatives of all three ostreid subfamilies, together with gryphaeid and nonostreoidean pterioid outgroups, were sequenced for a 941-nucleotide fragment of the 28S ribosomal gene. Our phylogenetic analyses indicate that (1) the Ostreidae are robustly monophyletic, (2) broadcast spawning and larval planktotrophy are ancestral ostreid traits, (3) trans-ctenidial ovulation predates the evolution of parental care in ostreid lineages, and (4) brooding originated once in the common ancestor of the Ostreinae/Lophinae, involved a modification of the final behavioral step in the ancestral ovulation pathway, and has been retained in all descendent lineages. Our data permit an independent test of fossil-based ostreid phylogenetic hypotheses and provide novel insights into oyster evolution and systematics.