The surprisingly complex immune gene repertoire of a simple sponge, exemplified by the NLR genes: a capacity for specificity?

Most bacteria are not pathogenic to animals, and may instead serve beneficial functions. The requisite need for animals to differentiate between microbial friend and foe is likely borne from a deep evolutionary imperative to recognise self from non-self, a service ably provided by the innate immune system. Recent findings from an ancient lineage of simple animals - marine sponges - have revealed an unexpectedly large and diverse suite of genes belonging to one family of pattern recognition receptors, namely the NLR genes. Because NLRs can recognise a broad spectrum of microbial ligands, they may play a critical role in mediating the animal-bacterial crosstalk needed for sophisticated discrimination between microbes of various relationships. The building blocks for an advanced NLR-based immune specificity encoded in the genome of the coral reef sponge Amphimedon queenslandica may provide a specialisation and diversity of responses that equals, or even exceeds, that of vertebrate NLRs.

Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts

Since the origin of the animal kingdom, marine animals have lived in association with viruses, prokaryotes and unicellular eukaryotes, often as symbionts. This long and continuous interaction has provided ample opportunity not only for the evolution of intimate interactions such as sharing of metabolic pathways, but also for horizontal gene transfer (HGT) of non-metazoan genes into metazoan genomes. The number of demonstrated cases of inter-kingdom HGT is currently small, such that it is not yet widely appreciated as a significant player in animal evolution. Sessile marine invertebrates that vertically inherit bacterial symbionts, that have no dedicated germ line, or that bud or excise pluripotent somatic cells during their life history may be particularly receptive to HGT from their symbionts. Closer scrutiny of the growing number of genomes being accrued for these animals may thus reveal HGT as a regular source of novel variation that can function to extend the host phenotype metabolically, morphologically, or even behaviorally. Taxonomic identification of symbionts will help to address the intriguing question of whether past HGT events may constrain contemporary symbioses.

Analysis of the biomass composition of the demosponge Amphimedon queenslandica on Heron Island Reef, Australia

Marine sponges are a potential source of important pharmaceutical drugs, the commercialisation of which is restricted by the difficulties of obtaining a sufficient and regular supply of biomass. One way to optimize commercial cell lines for production is the in-depth characterization and target identification through genome scale metabolic modeling and flux analysis. By applying these tools to a sponge, we hope to gain insights into how biomass is formed. We chose Amphimedon queenslandica as it has an assembled and annotated genome, a prerequisite for genome scale modeling. The first stepping stone on the way to metabolic flux analysis in a sponge holobiont, is the characterization of its biomass composition. In this study we quantified the macromolecular composition and investigated the variation between and within sponges of a single population. We found lipids and protein to be the most abundant macromolecules, while carbohydrates were the most variable. We also analysed the composition and abundance of the fatty acids and amino acids, the important building blocks required to synthesise the abundant macromolecule types, lipids, and protein. These data complement the extensive genomic information available for A. queenslandica and lay the basis for genome scale modelling and flux analysis.

The characterization of sponge NLRs provides insight into the origin and evolution of this innate immune gene family in animals

The "Nucleotide-binding domain and Leucine-rich Repeat" (NLR) genes are a family of intracellular pattern recognition receptors (PRR) that are a critical component of the metazoan innate immune system, involved in both defense against pathogenic microorganisms and in beneficial interactions with symbionts. To investigate the origin and evolution of the NLR gene family, we characterized the full NACHT domain-containing gene complement in the genome of the sponge, Amphimedon queenslandica. As sister group to all animals, sponges are ideally placed to inform our understanding of the early evolution of this ancient PRR family. Amphimedon queenslandica has a large NACHT domain-containing gene complement that is dominated by bona fide NLRs (n = 135) with varied phylogenetic histories. Approximately half of these have a tripartite architecture that includes an N-terminal CARD or DEATH domain. The multiplicity of the A. queenslandica NLR genes and the high variability across the N- and C-terminal domains are consistent with involvement in immunity. We also provide new insight into the evolution of NLRs in invertebrates through comparative genomic analysis of multiple metazoan and nonmetazoan taxa. Specifically, we demonstrate that the NLR gene family appears to be a metazoan innovation, characterized by two major gene lineages that may have originated with the last common eumetazoan ancestor. Subsequent lineage-specific gene duplication, gene loss and domain shuffling all have played an important role in the highly dynamic evolutionary history of invertebrate NLRs.

Nitric oxide acts as a positive regulator to induce metamorphosis of the ascidian Herdmania momus

Marine invertebrates commonly have a biphasic life cycle in which the metamorphic transition from a pelagic larva to a benthic post-larva is mediated by the nitric oxide signalling pathway. Nitric oxide (NO) is synthesised by nitric oxide synthase (NOS), which is a client protein of the molecular chaperon heat shock protein 90 (HSP90). It is notable, then, that both NO and HSP90 have been implicated in regulating metamorphosis in marine invertebrates as diverse as urochordates, echinoderms, molluscs, annelids, and crustaceans. Specifically, the suppression of NOS activity by the application of either NOS- or HSP90-inhibiting pharmacological agents has been shown consistently to induce the initiation of metamorphosis, leading to the hypothesis that a negative regulatory role of NO is widely conserved in biphasic life cycles. Further, the induction of metamorphosis by heat-shock has been demonstrated for multiple species. Here, we investigate the regulatory role of NO in induction of metamorphosis of the solitary tropical ascidian, Herdmania momus. By coupling pharmacological treatments with analysis of HmNOS and HmHSP90 gene expression, we present compelling evidence of a positive regulatory role for NO in metamorphosis of this species, in contrast to all existing ascidian data that supports the hypothesis of NO as a conserved negative regulator of metamorphosis. The exposure of competent H. momus larvae to a NOS inhibitor or an NO donor results in an up-regulation of NOS and HSP90 genes. Heat shock of competent larvae induces metamorphosis in a temperature dependent manner, up to a thermal tolerance that approaches 35°C. Both larval/post-larval survival and the appearance of abnormal morphologies in H. momus post-larvae reflect the magnitude of up-regulation of the HSP90 gene in response to heat-shock. The demonstrated role of NO as a positive metamorphic regulator in H. momus suggests the existence of inter-specific adaptations of NO regulation in ascidian metamorphosis.

Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions

Background

The biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the Porifera (sponges), which are the earliest branching metazoans. The demosponge, Amphimedon queenslandica, undergoes metamorphosis from a free-swimming larva into a sessile adult that bears no morphological resemblance to other animals. While the genome of A. queenslandica contains an extensive repertoire of genes very similar to that of complex bilaterians, it is as yet unclear how this is drawn upon to coordinate changing morphological features and ecological demands throughout the sponge life cycle.

Results

To identify genome-wide events that accompany the pelagobenthic transition in A. queenslandica, we compared global gene expression profiles at four key developmental stages by sequencing the poly(A) transcriptome using SOLiD technology. Large-scale changes in transcription were observed as sponge larvae settled on the benthos and began metamorphosis. Although previous systematics suggest that the only clear homology between Porifera and other animals is in the embryonic and larval stages, we observed extensive use of genes involved in metazoan-associated cellular processes throughout the sponge life cycle. Sponge-specific transcripts are not over-represented in the morphologically distinct adult; rather, many genes that encode typical metazoan features, such as cell adhesion and immunity, are upregulated. Our analysis further revealed gene families with candidate roles in competence, settlement, and metamorphosis in the sponge, including transcription factors, G-protein coupled receptors and other signaling molecules.

Conclusions

This first genome-wide study of the developmental transcriptome in an early branching metazoan highlights major transcriptional events that accompany the pelagobenthic transition and point to a network of regulatory mechanisms that coordinate changes in morphology with shifting environmental demands. Metazoan developmental and structural gene orthologs are well-integrated into the expression profiles at every stage of sponge development, including the adult. The utilization of genes involved in metazoan-associated processes throughout sponge development emphasizes the potential of the genome of the last common ancestor of animals to generate phenotypic complexity.

Marked changes in neuropeptide expression accompany broadcast spawnings in the gastropod Haliotis asinina

Introduction

A huge diversity of marine species reproduce by synchronously spawning their gametes into the water column. Although this species-specific event typically occurs in a particular season, the precise time and day of spawning often can not be predicted. There is little understanding of how the environment (e.g. water temperature, day length, tidal and lunar cycle) regulates a population’s reproductive physiology to synchronise a spawning event. The Indo-Pacific tropical abalone, Haliotis asinina, has a highly predictable spawning cycle, where individuals release gametes on the evenings of spring high tides on new and full moons during the warmer half of the year. These calculable spawning events uniquely allow for the analysis of the molecular and cellular processes underlying reproduction. Here we characterise neuropeptides produced in H. asinina ganglia that are known in egg-laying molluscs to control vital aspects of reproduction.

Results

We demonstrate that genes encoding APGWamide, myomodulin, the putative proctolin homologue whitnin, FMRFamide, a schistosomin-like peptide (SLP), a molluscan insulin-related peptide (MIP) and a haliotid growth-associated peptide (HGAP) all are differentially expressed in the anterior ganglia during the two week spawning cycle in both male and female abalone. Each gene has a unique and sex-specific expression profile. Despite these differences, expression levels in most of the genes peak at or within 12 h of the spawning event. In contrast, lowest levels of transcript abundance typically occurs 36 h before and 24 h after spawning, with differences in peak and low expression levels being most pronounced in genes orthologous to known molluscan reproduction neuromodulators.

Conclusions

Exploiting the predictable semi-lunar spawning cycle of the gastropod H. asinina, we have identified a suite of evolutionarily-conserved, mollusc-specific and rapidly-evolving neuropeptides that appear to contribute to the regulation of spawning. Dramatic increases and decreases in ganglionic neuropeptide expression levels from 36 h before to 24 h after the broadcast spawning event are consistent with these peptides having a regulatory role in translating environmental signals experienced by a population into a synchronous physiological output, in this case, the release of gametes.

Variation in rates of early development in Haliotis asinina generate competent larvae of different ages

INTRODUCTION

Inter-specific comparisons of metazoan developmental mechanisms have provided a wealth of data concerning the evolution of body form and the generation of morphological novelty. Conversely, studies of intra-specific variation in developmental programs are far fewer. Variation in the rate of development may be an advantage to the many marine invertebrates that posses a biphasic life cycle, where fitness commonly requires the recruitment of planktonically dispersing larvae to patchily distributed benthic environments.

RESULTS

We have characterised differences in the rate of development between individuals originating from a synchronised fertilisation event in the tropical abalone Haliotis asinina, a broadcast spawning lecithotrophic vetigastropod. We observed significant differences in the time taken to complete early developmental events (time taken to complete third cleavage and to hatch from the vitelline envelope), mid-larval events (variation in larval shell development) and late larval events (the acquisition of competence to respond to a metamorphosis inducing cue). We also provide estimates of the variation in maternally provided energy reserves that suggest maternal provisioning is unlikely to explain the majority of the variation in developmental rate we report here.

CONCLUSIONS

Significant differences in the rates of development exist both within and between cohorts of synchronously fertilised H. asinina gametes. These differences can be detected shortly after fertilisation and generate larvae of increasingly divergent development states. We discuss the significance of our results within an ecological context, the adaptive significance of mechanisms that might maintain this variation, and potential sources of this variation.

A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function

Background

The mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS gene is favored for octocoral molecular systematics, due to its high information content. Several hypotheses concerning the origins of mtMutS have been proposed, and remain equivocal, although current weight of support is for a horizontal gene transfer from either an epsilonproteobacterium or a large DNA virus. Here we present new and compelling evidence on the evolutionary origin of mtMutS, and provide the very first data on its activity, functional capacity and stability within the octocoral mitochondrial genome.

Results

The mtMutS gene has the expected conserved amino acids, protein domains and predicted tertiary protein structure. Phylogenetic analysis indicates that mtMutS is not a member of the MSH family and therefore not of eukaryotic origin. MtMutS clusters closely with representatives of the MutS7 lineage; further support for this relationship derives from the sharing of a C-terminal endonuclease domain that confers a self-contained mismatch repair function. Gene expression analyses confirm that mtMutS is actively transcribed in octocorals. Rates of mitochondrial gene evolution in mtMutS-containing octocorals are lower than in their hexacoral sister-group, which lacks the gene, although paradoxically the mtMutS gene itself has higher rates of mutation than other octocoral mitochondrial genes.

Conclusions

The octocoral mtMutS gene is active and codes for a protein with all the necessary components for DNA mismatch repair. A lower rate of mitochondrial evolution, and the presence of a nicking endonuclease domain, both indirectly support a theory of self-sufficient DNA mismatch repair within the octocoral mitochondrion. The ancestral affinity of mtMutS to non-eukaryotic MutS7 provides compelling support for an origin by horizontal gene transfer. The immediate vector of transmission into octocorals can be attributed to either an epsilonproteobacterium in an endosymbiotic association or to a viral infection, although DNA viruses are not currently known to infect both bacteria and eukaryotes, nor mitochondria in particular. In consolidating the first known case of HGT into an animal mitochondrial genome, these findings suggest the need for reconsideration of the means by which metazoan mitochondrial genomes evolve.

Evolution of RNA-binding proteins in animals: insights from genome-wide analysis in the sponge Amphimedon queenslandica

RNA-binding proteins (RBPs) are key players in various biological processes, most notably regulation of gene expression at the posttranscriptional level. Although many RBPs have been carefully studied in model organisms, very few studies have addressed the evolution of these proteins at the scale of the animal kingdom. We identified a large set of putative RBPs encoded by the genome of the demosponge Amphimedon queenslandica, a species representing a basal animal lineage. We compared the Amphimedon RBPs with those encoded by the genomes of two bilaterians (human and Drosophila), representatives of two other basal metazoan lineages (a placozoan and a cnidarian), a choanoflagellate (probable sister group of animals), and two fungi. We established the evolutionary history of 32 families of RBPs and found that most of the diversity of RBPs present in contemporary metazoans, including humans, was already established in the last common ancestor (LCA) of animals. This includes RBPs known to be involved in key processes in bilaterians, such as development, stem and/or germ cells properties, and noncoding RNA pathways. From this analysis, we infer that a complex toolkit of RBPs was present in the LCA of animals and that it has been recruited to perform new functions during early animal evolution, in particular in relation to the acquisition of multicellularity.

Identifying the germline in an equally cleaving mollusc: Vasa and Nanos expression during embryonic and larval development of the vetigastropod Haliotis asinina

Members of the Vasa and Nanos gene families are important for the specification and development of the germline in diverse animals. Here, we determine spatial and temporal expression of Vasa and Nanos to investigate germline development in the vetigastropod Haliotis asinina. This is the first time these genes have been examined in an equally cleaving lophotrochozoan species. We find that HasVasa and HasNanos have largely overlapping, but not identical, expression patterns during embryonic and larval development, with both being maternally expressed and localized to the micromere cell lineages during cleavage. As embryonic development continues, HasVasa and HasNanos become progressively more enriched in the dorsal quadrant of the embryo. By the trochophore stage, both HasVasa and HasNanos are expressed in the putative mesodermal bands of the larva. This differs from the unequally cleaving gastropod Illyanasa obsoleta, in which IoVasa and IoNanos expression is detectable only in the early embryo and not during gastrulation and larval development. Our results suggest that the H. asinina germline arises from the 4d cell lineage and that primordial germ cells (PGCs) are not specified exclusively by maternally inherited determinants (preformation). As such, we infer that inductive signals (epigenesis) play an important role in specifying PGCs in H. asinina. We hypothesize that HasVasa is expressed in a population of undifferentiated multipotent cells, from which the PGCs are segregated later during development.

The initiation of metamorphosis as an ancient polyphenic trait and its role in metazoan life-cycle evolution

Comparative genomics of representative basal metazoans leaves little doubt that the most recent common ancestor to all modern metazoans was morphogenetically complex. Here, we support this interpretation by demonstrating that the demosponge Amphimedon queenslandica has a biphasic pelagobenthic life cycle resembling that present in a wide range of bilaterians and anthozoan cnidarians. The A. queenslandica life cycle includes a compulsory planktonic larval phase that can end only once the larva develops competence to respond to benthic signals that induce settlement and metamorphosis. The temporal onset of competence varies between individuals as revealed by idiosyncratic responses to inductive cues. Thus, the biphasic life cycle with a dispersing larval phase of variable length appears to be a metazoan synapomorphy and may be viewed as an ancestral polyphenic trait. Larvae of a particular age that are subjected to an inductive cue either maintain the larval form or metamorphose into the post-larval/juvenile form. Variance in the development of competence dictates that only a subset of a larval cohort will settle and undergo metamorphosis at a given time, which in turn leads to variation in dispersal distance and in location of settlement. Population divergence and allopatric speciation are likely outcomes of this conserved developmental polyphenic trait.

Carry-over effect of larval settlement cue on postlarval gene expression in the marine gastropod Haliotis asinina

The drastic shift from pelagic larvae to benthic adult form that occurs during marine invertebrate metamorphosis is often induced by intimate interactions between settling larvae and their benthic environment. Larval experience prior to and during metamorphosis can significantly affect adult fitness, but it is presently unknown whether the exact nature of the inductive cue is an experience that matters, or by what mechanism such carry-over effects are mediated. Here we test for carry-over effects of the specific nature of inductive cues on gene expression in metamorphosing postlarvae of the tropical abalone, Haliotis asinina. Postlarvae induced by three different species of coralline algae all successfully undergo metamorphosis, yet the expression profiles of 11 of 17 metamorphosis-related genes differ according to which species of algae the larvae settled upon. Significantly, several genes continue to be differentially expressed for at least 40 h after removal of the algae from the postlarvae, clearly demonstrating a carry-over effect of inductive cue on gene expression. We observe a carryover effect in several genes with varying functions and spatial expression patterns, indicating that each algal species impacts global gene expression in a unique manner. These data unexpectedly reveal that transcriptional modulation of metamorphosis-related genes is contingent upon the precise composition of the benthic microenvironment experienced directly at induction of settlement, and highlight transcription as a mechanism that can mediate between larval and postlarval experiences. For new recruits into an abalone population, metamorphosis clearly does not represent a new transcriptional beginning.

Settlement specifics: Effective induction of abalone settlement and metamorphosis corresponds to biomolecular composition of natural cues

Chemical signaling plays a major role in shaping life history processes that drive ecology and evolution in marine systems, notably including habitat selection by marine invertebrate larvae that must settle out of the plankton onto the benthos.1 For larvae, the identification of appropriate habitats in which to settle and undergo metamorphosis to the adult form relies heavily on the recognition of cues indicative of a favorable environment. By documenting settlement responses of larvae of the tropical abalone, Haliotis asinina, to a range of coralline algae species, we recently highlighted the species-specific nature of this interaction.2 Here, we demonstrate that this specificity is likely driven by chemical, rather than physical, properties of the algae. Our initial characterization of the surface cell biomarkers from three different algal species shows that inductive cue biomolecular composition correlates with variations in larval settlement response.

Isolation of amphimedon developmental material

INTRODUCTIONFertilization occurs internally in Amphimedon and embryos are brooded in multiple chambers throughout the adult. Each chamber contains a mixture of developmental stages, from egg to late ring stages (i.e., prehatch late embryos). At the end of embryogenesis, swimming parenchymella larvae emerge from the adult. After several hours in the water column, the larvae settle and metamorphose into juvenile sponges. This protocol details how to obtain Amphimedon larvae and post-larvae/juveniles as well as embryos. Once isolated, these biological stages can be used for a variety of molecular and cellular analyses.

Genotyping individual amphimedon embryos, larvae, and adults

INTRODUCTIONThe distribution of Amphimedon queenslandica is patchy on coral reefs in the Great Barrier Reef, with small, localized populations detected in shallow, still water reef-flat environments. A. queenslandica is a spermcast spawner, in which fertilization occurs internally. Sperm presumably originate from neighboring reproductive individuals within the population. The ability to genotype individual embryos within a single brood chamber has the potential to shed light on the fertilization biology and generation/maintenance of genetic diversity in this sessile invertebrate. Here, we describe a protocol for rapidly genotyping individuals using polymorphic microsatellite loci. The loci are amplified by PCR using a pair of primers specifically designed for the region of interest with a fluorescent dye attached to the 5'-end to enable easy detection of the amplified product. An advantage of this procedure is that fluorescently labeled PCR products can be combined (i.e., multiplexed) to reduce time and cost when using the genotyping machine. The dye label and size of the product must be taken into consideration when multiplexing. For example, three differently labeled PCR products can be multiplexed, or PCR products with the same label can be multiplexed as long as the allelic size ranges do not overlap. The amount of each cleaned, labeled PCR product added to the multiplex must be optimized depending on the dye and the PCR efficiency.

The Demosponge Amphimedon queenslandica: Reconstructing the Ancestral Metazoan Genome and Deciphering the Origin of Animal Multicellularity

INTRODUCTIONSponges are one of the earliest branching metazoans. In addition to undergoing complex development and differentiation, they can regenerate via stem cells and can discern self from nonself ("allorecognition"), making them a useful comparative model for a range of metazoan-specific processes. Molecular analyses of these processes have the potential to reveal ancient homologies shared among all living animals and critical genomic innovations that underpin metazoan multicellularity. Amphimedon queenslandica (Porifera, Demospongiae, Haplosclerida, Niphatidae) is the first poriferan representative to have its genome sequenced, assembled, and annotated. Amphimedon exemplifies many sessile and sedentary marine invertebrates (e.g., corals, ascidians, bryozoans): They disperse during a planktonic larval phase, settle in the vicinity of conspecifics, ward off potential competitors (including incompatible genotypes), and ensure that brooded eggs are fertilized by conspecific sperm. Using genomic and expressed sequence tag (EST) resources from Amphimedon, functional genomic approaches can be applied to a wide range of ecological and population genetic processes, including fertilization, dispersal, and colonization dynamics, host-symbiont interactions, and secondary metabolite production. Unlike most other sponges, Amphimedon produce hundreds of asynchronously developing embryos and larvae year-round in distinct, easily accessible brood chambers. Embryogenesis gives rise to larvae with at least a dozen cell types that are segregated into three layers and patterned along the body axis. In this article, we describe some of the methods currently available for studying A. queenslandica, focusing on the analysis of embryos, larvae, and post-larvae.

Articulated coralline algae of the genus Amphiroa are highly effective natural inducers of settlement in the tropical abalone Haliotis asinina

The initiation of metamorphosis in marine invertebrates is strongly linked to the environment. Planktonic larvae typically are induced to settle and metamorphose by external cues such as coralline algae (Corallinaceae, Rhodophyta). Although coralline algae are globally abundant, invertebrate larvae of many taxa settle in response to a very limited suite of species. This specificity impacts population structure, as only locations with the appropriate coralline species can attract new recruits. Abalone (Gastropoda, Haliotidae) are among those taxa in which closely related species are known to respond to different coralline algae. Here we identify highly inductive natural cues of the tropical abalone Haliotis asinina. In contrast to reports for other abalone, the greatest proportion of H. asinina larvae are induced to settle and metamorphose (92.8% to 100% metamorphosis by 48 h postinduction) by articulated corallines of the genus Amphiroa. Comparison with field distribution data for different corallines suggests larvae are likely to be settling on the seaward side of the reef crest. We then compare the response of six different H. asinina larval families to five different coralline species to demonstrate that induction by the best inductive cue (Amphiroa spp.) effectively extinguishes substantial intraspecific variation in the timing of settlement.

Wnt and TGF-beta expression in the sponge Amphimedon queenslandica and the origin of metazoan embryonic patterning

BACKGROUND

The origin of metazoan development and differentiation was contingent upon the evolution of cell adhesion, communication and cooperation mechanisms. While components of many of the major cell signalling pathways have been identified in a range of sponges (phylum Porifera), their roles in development have not been investigated and remain largely unknown. Here, we take the first steps toward reconstructing the developmental signalling systems used in the last common ancestor to living sponges and eumetazoans by studying the expression of genes encoding Wnt and TGF-beta signalling ligands during the embryonic development of a sponge.

METHODOLOGY/PRINCIPAL FINDINGS

Using resources generated in the recent sponge Amphimedon queenslandica (Demospongiae) genome project, we have recovered genes encoding Wnt and TGF-beta signalling ligands that are critical in patterning metazoan embryos. Both genes are expressed from the earliest stages of Amphimedon embryonic development in highly dynamic patterns. At the time when the Amphimedon embryos begin to display anterior-posterior polarity, Wnt expression becomes localised to the posterior pole and this expression continues until the swimming larva stage. In contrast, TGF-beta expression is highest at the anterior pole. As in complex animals, sponge Wnt and TGF-beta expression patterns intersect later in development during the patterning of a sub-community of cells that form a simple tissue-like structure, the pigment ring. Throughout development, Wnt and TGF-beta are expressed radially along the anterior-posterior axis.

CONCLUSIONS/SIGNIFICANCE

We infer from the expression of Wnt and TGF-beta in Amphimedon that the ancestor that gave rise to sponges, cnidarians and bilaterians had already evolved the capacity to direct the formation of relatively sophisticated body plans, with axes and tissues. The radially symmetrical expression patterns of Wnt and TGF-beta along the anterior-posterior axis of sponge embryos and larvae suggest that these signalling pathways contributed to establishing axial polarity in the very first metazoans.

The NK homeobox gene cluster predates the origin of Hox genes

Hox and other Antennapedia (ANTP)-like homeobox gene subclasses - ParaHox, EHGbox, and NK-like - contribute to key developmental events in bilaterians [1-4]. Evidence of physical clustering of ANTP genes in multiple animal genomes [4-9] suggests that all four subclasses arose via sequential cis-duplication events. Here, we show that Hox genes' origin occurred after the divergence of sponge and eumetazoan lineages and occurred concomitantly with a major evolutionary transition in animal body-plan complexity. By using whole genome information from the demosponge Amphimedon queenslandica, we provide the first conclusive evidence that the earliest metazoans possessed multiple NK-like genes but no Hox, ParaHox, or EHGbox genes. Six of the eight NK-like genes present in the Amphimedon genome are clustered within 71 kb in an order akin to bilaterian NK clusters. We infer that the NK cluster in the last common ancestor to sponges, cnidarians, and bilaterians consisted of at least five genes. It appears that the ProtoHox gene originated from within this ancestral cluster after the divergence of sponge and eumetazoan lineages. The maintenance of the NK cluster in sponges and bilaterians for greater than 550 million years is likely to reflect regulatory constraints inherent to the organization of this ancient cluster.

Pleistocene isolation and recent gene flow in Haliotis asinina, an Indo-Pacific vetigastropod with limited dispersal capacity

Haliotis asinina is a broadcast-spawning mollusc that inhabits Indo-Pacific coral reefs. This tropical abalone develops through a nonfeeding larval stage that is competent to settle on specific species of coralline algae after 3-4 days in the plankton. Failure to contact an inductive algae within 10 days of hatching usually results in death. These life cycle characteristics suggest a limited capacity for dispersal and thus gene flow. This makes H. asinina particularly suitable for elucidating phylogeographical structure throughout the Indo-Malay Archipelagoes, and eastern Indian and western Pacific Oceans, all regions of biogeographical complexity and high conservation value. We assayed 482 bp of the mitochondrial cytochrome oxidase II gene in 206 abalone collected from 16 geographically discrete sites across the Indian and Pacific Oceans and Indo-Malay Archipelagoes. DNA sequence variation was analysed via population genetics and phylogenetics, and by nested clade analyses (NCA). Our data resolved clear phylogeographical breaks among major biogeographical regions, with sequence divergences ranging from a high of 3.7% and 3.0% between Indian and Pacific sites and Pacific and Indo-Malay sites, respectively, to a low of 1.1% between Indian and Indo-Malay sites. Despite the apparent limited dispersal capacity of H. asinina, no finer scale phylogeographical structure was resolved within the respective biogeographical regions. However, amova and NCA identified several significant associations between haplotypes and geographical distribution, most notably higher gene flow among geographical populations associated with major ocean currents. Our study provides further evidence that larval dispersal capacity alone is not a good predictor of population genetic structure in marine invertebrates. We infer instead that a combination of historical events (long-term barriers followed by range expansion associated with Pleistocene sea level changes) and contemporary processes (gene flow restricted by life history and oceanography) have shaped observed patterns of H. asinina phylogeography.

Microevolution in island forms: the roles of drift and directional selection in morphological divergence of a passerine bird

Theory predicts that in small isolated populations random genetic drift can lead to phenotypic divergence; however this prediction has rarely been tested quantitatively in natural populations. Here we utilize natural repeated island colonization events by members of the avian species complex, Zosterops lateralis, to assess whether or not genetic drift alone is an adequate explanation for the observed patterns of microevolutionary divergence in morphology. Morphological and molecular genetic characteristics of island and mainland populations are compared to test three predictions of drift theory: (1) that the pattern of morphological change is idiosyncratic to each island; (2) that there is concordance between morphological and neutral genetic shifts across island populations; and (3) for populations whose time of colonization is known, that the rate of morphological change is sufficiently slow to be accounted for solely by genetic drift. Our results are not consistent with these predictions. First, the direction of size shifts was consistently towards larger size, suggesting the action of a nonrandom process. Second, patterns of morphological divergence among recently colonized populations showed little concordance with divergence in neutral genetic characters. Third, rate tests of morphological change showed that effective population sizes were not small enough for random processes alone to account for the magnitude of microevolutionary change. Altogether, these three lines of evidence suggest that drift alone is not an adequate explanation of morphological differentiation in recently colonized island Zosterops and therefore we suggest that the observed microevolutionary changes are largely a result of directional natural selection.