Chimerism in wild adult populations of the broadcast spawning coral Acropora millepora on the Great Barrier Reef

Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics

Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). As the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection. Then, SNPs and genes variable within colonies were characterised. While most of the tested bioinformatics parameters did not significantly impact the detection of IGV, filtering on genotype depth of coverage strongly improved its detection by reducing genotyping errors. Mosaicism and chimerism, the two processes leading to IGV (the first through somatic mutations, the second through fusion of distinct organisms), were found in 7% and 12% of the colonies, respectively. Both processes led to several intra-colonial allelic differences, but most were non-coding or silent. However, 7% of the differences were non-silent and found in genes involved in a high diversity of biological processes, some of which were directly linked to responses to environmental stresses. IGV, therefore, appears as a source of genetic diversity and genetic plasticity, increasing the adaptive potential of colonies. Such benefits undoubtedly play an important role in the maintenance and the evolution of scleractinian populations and appear crucial for the future of coral reefs in the context of ongoing global changes.

Is chimerism associated with cancer across the tree of life?

Chimerism is a widespread phenomenon across the tree of life. It is defined as a multicellular organism composed of cells from other genetically distinct entities. This ability to 'tolerate' non-self cells may be linked to susceptibility to diseases like cancer. Here we test whether chimerism is associated with cancers across obligately multicellular organisms in the tree of life. We classified 12 obligately multicellular taxa from lowest to highest chimerism levels based on the existing literature on the presence of chimerism in these species. We then tested for associations of chimerism with tumour invasiveness, neoplasia (benign or malignant) prevalence and malignancy prevalence in 11 terrestrial mammalian species. We found that taxa with higher levels of chimerism have higher tumour invasiveness, though there was no association between malignancy or neoplasia and chimerism among mammals. This suggests that there may be an important biological relationship between chimerism and susceptibility to tissue invasion by cancerous cells. Studying chimerism might help us identify mechanisms underlying invasive cancers and also could provide insights into the detection and management of emerging transmissible cancers.

Inheritance of somatic mutations by animal offspring

Since 1892, it has been widely assumed that somatic mutations are evolutionarily irrelevant in animals because they cannot be inherited by offspring. However, some nonbilaterians segregate the soma and germline late in development or never, leaving the evolutionary fate of their somatic mutations unknown. By investigating uni- and biparental reproduction in the coral Acropora palmata (Cnidaria, Anthozoa), we found that uniparental, meiotic offspring harbored 50% of the 268 somatic mutations present in their parent. Thus, somatic mutations accumulated in adult coral animals, entered the germline, and were passed on to swimming larvae that grew into healthy juvenile corals. In this way, somatic mutations can increase allelic diversity and facilitate adaptation across habitats and generations in animals.

Paternal genome elimination promotes altruism in viscous populations

Population viscosity has long been thought to promote the evolution of altruism. However, in the simplest scenarios, the potential for altruism is invariant with respect to dispersal-a surprising result that holds for haploidy, diploidy, and haplodiploidy (arrhenotoky). Here, we develop a kin-selection model to investigate how population viscosity affects the potential for altruism in species with male paternal genome elimination (PGE), exploring altruism enacted by both females and males, and both juveniles and adults. We find that (1) PGE promotes altruistic behaviors relative to the other inheritance systems, and to a degree that depends on the extent of paternal genome expression. (2) Under PGE, dispersal increases the potential for altruism in juveniles and decreases it in adults. (3) The genetics of PGE can lead to striking differences in sex-specific potentials for altruism, even in the absence of any sex differences in ecology.

Settling in aggregation: Spatial planning consideration for brooding coral transplants

Aggregated larval co-settlement has been documented in myriad marine invertebrate taxa, shaping adult population structures. Still, kinship settlement patterns in brooding corals have not been studied in detail, especially under scenarios of enhanced larval assemblies. Employing two sets of ex-situ experiments, planulae staining for kinship resolution and a computer random settlement simulation, we show that larval settlement of the coral Stylophora pistillata, a brooding species in the Gulf of Aqaba/Eilat, is mostly affected by the number of larval donors, and that larvae tend to aggregate (up to 50% tissue-contacts; distances <3 mm), compared to 3% predicted in a computer simulation, all without a kinship-bias. Field surveys on juvenile colonies revealed a similar clustering pattern. Although aggregated settlement inevitably carries disadvantages such as intraspecific competition, it may be bracketed in adult colonies with benefits such as enhanced fertilization and chimerism-related ecological advantages, including augmented colony size and survivorship. These improved life-history traits of brooding coral species that aggregate could be harnessed as applied ecological engineering tools in reef restoration acts.

Spatial distribution of conspecific genotypes within chimeras of the branching coral Stylophora pistillata

Chimerism is a coalescence of conspecific genotypes. Although common in nature, fundamental knowledge, such as the spatial distribution of the genotypes within chimeras, is lacking. Hence, we investigated the spatial distribution of conspecific genotypes within the brooding coral Stylophora pistillata, a common species throughout the Indo-Pacific and Red Sea. From eight gravid colonies, we collected planula larvae that settled in aggregates, forming 2–3 partner chimeras. Coral chimeras grew in situ for up to 25 months. Nine chimeras (8 kin, 1 non-related genotypes) were sectioned into 7–17 fragments (6–26 polyps/fragment), and genotyped using eight microsatellite loci. The discrimination power of each microsatellite-locus was evaluated with 330 ‘artificial chimeras,’ made by mixing DNA from three different S. pistillata genotypes in pairwise combinations. In 68% of ‘artificial chimeras,’ the second genotype was detected if it constituted 5–30% of the chimera. Analyses of S. pistillata chimeras revealed that: (a) chimerism is a long-term state; (b) conspecifics were intermixed (not separate from one another); (c) disproportionate distribution of the conspecifics occurred; (d) cryptic chimerism (chimerism not detected via a given microsatellite) existed, alluding to the underestimation of chimerism in nature. Mixed chimerism may affect ecological/physiological outcomes for a chimera, especially in clonal organisms, and challenges the concept of individuality, affecting our understanding of the unit of selection.

Exploring Traits of Engineered Coral Entities to be Employed in Reef Restoration

Aggregated settlement of coral larvae results in a complex array of compatible (chimerism) and incompatible (rejection) allogenic responses. Each chimeric assemblage is considered as a distinct biological entity, subjected to selection, however, the literature lacks the evolutionary and ecological functions assigned to these units of selection. Here, we examined the effects of creating chimera/rejecting partners in terms of growth and survival under prolonged field conditions. Bi/multichimeras, bi/multi-rejecting entities, and genetically homogenous colonies (GHC) of the coral Stylophora pistillata were monitored under prolonged field conditions in a mid-water floating nursery in the northern Red Sea. Results revealed an increased aerial size and aeroxial ecological volume for rejected and chimeric entities compared to GHCs. At age 18 months, there were no significant differences in these parameters among the entities and traits, and rejecting partners did not differ from GHC. However, survival probabilities were significantly higher for chimeras that further revealed disparate initiation of up-growing branches and high diversity of chimeric phenotypes. These results suggest enhanced fitness for chimerism, augmenting earlier alluded chimeric benefits that trail the increased size at crucial early life-stages. Adding chimerism to the tool-box of reef restoration may enhance coral fitness in mitigating anthropogenic/climate change impacts.

Genes with evidence of positive selection as potentially related to coloniality and the evolution of morphological features among the lophophorates and entoprocts

Evolutionary mechanisms that underlie the origins of coloniality among organisms are diverse. Some animal colonies may be comprised strictly of clonal individuals formed from asexual budding or comprised of a chimera of clonal and sexually produced individuals that fuse secondarily. This investigation focuses on select members of the lophophorates and entoprocts whose evolutionary relationships remain enigmatic even in the age of genomics. Using transcriptomic data sets, two coloniality-based hypotheses are tested in a phylogenetic context to find candidate genes showing evidence of positive selection and potentially convergent molecular signatures among solitary species and taxa-forming colonies from aggregate groups or clonal budding. Approximately 22% of the 387 orthogroups tested showed evidence of positive selection in at least one of the three branch-site tests (CODEML, BUSTED, and aBSREL). Only 12 genes could be reliably associated with a developmental function related to traits linked with coloniality, neuroanatomy, or ciliary fields. Genes testing for both positive selection and convergent molecular characters include orthologues of Radial spoke head, Elongation translation initiation factors, SEC13, and Immediate early response gene5. Maximum likelihood analyses included here resulted in tree topologies typical of other phylogenetic investigations based on wider genomic information. Further genomic and experimental evidence will be needed to resolve whether a solitary ancestor with multiciliated cells that formed aggregate groups gave rise to colonial forms in bryozoans (and perhaps the entoprocts) or that the morphological differences exhibited by phoronids and brachiopods represent trait modifications from a colonial ancestor.

Full allogeneic fusion of embryos in a holothuroid echinoderm

Whole-body chimaeras (organisms composed of genetically distinct cells) have been directly observed in modular/colonial organisms (e.g. corals, sponges, ascidians); whereas in unitary deuterostosmes (including mammals) they have only been detected indirectly through molecular analysis. Here, we document for the first time the step-by-step development of whole-body chimaeras in the holothuroid Cucumaria frondosa, a unitary deuterostome belonging to the phylum Echinodermata. To the best of our knowledge, this is the most derived unitary metazoan in which direct investigation of zygote fusibility has been undertaken. Fusion occurred among hatched blastulae, never during earlier (unhatched) or later (larval) stages. The fully fused chimaeric propagules were two to five times larger than non-chimaeric embryos. Fusion was positively correlated with propagule density and facilitated by the natural tendency of early embryos to agglomerate. The discovery of natural chimaerism in a unitary deuterostome that possesses large externally fertilized eggs provides a framework to explore key aspects of evolutionary biology, histocompatibility and cell transplantation in biomedical research.

Coral chimerism as an evolutionary rescue mechanism to mitigate global climate change impacts

Climate change and anthropogenic pressures inflict a wide range of profound damages on coral reef ecosystems, reshaping coral reef communities due to their physiological and ecological intolerance to the newly developing environmental conditions. Here, I present coral chimerism as an evolutionary rescue tool for accelerating adaptive responses to global climate change impacts. The "evolutionary rescue" power is contingent on the premise that coral chimerism counters the erosion of genetic and phenotypic diversity. Further benefits are gained when flexible chimeric entities alter their somatic constituents following changes in environmental conditions, synergistically presenting the best-fitting combination of their genetic components to endure in a capricious environment, exhibiting always their environmentally matched physiological characteristics. Chimerism should be considered as an integral part of the ecological engineering toolbox being developed for active reef restoration.

Somatic Mutation Is a Function of Clone Size and Depth in Orbicella Reef-Building Corals

In modular organisms, the propagation of genetic variability within a clonal unit can alter the scale at which ecological and evolutionary processes operate. Genetic variation within an individual primarily arises through the accretion of somatic mutations over time, leading to genetic mosaicism. Here, we assess the prevalence of intraorganismal genetic variation and potential mechanisms influencing the degree of genetic mosaicism in the reef corals Orbicella franksi and Orbicella annularis. Colonies of both species, encompassing a range of coral sizes and depths, were sampled multiple times and genotyped at the same microsatellite loci to detect intraorganismal genetic variation. Genetic mosaicism was detected in 38% of corals evaluated, and mutation frequency was found to be positively related with clonal size and negatively associated with coral depth. We suggest that larger clones experience a greater number of somatic cell divisions and consequently have an elevated potential to accumulate mutations. Furthermore, corals at shallower depths may be exposed to abiotic conditions such as elevated thermal regimes, which promote increased mutation rates. The results highlight the pervasiveness of intraorganismal genetic variation in reef-building corals and emphasize potential mechanisms generating somatic mutations in modular organisms.

Intraorganismal genetic heterogeneity as a source of genetic variation in modular macroalgae

Genetic diversity is considered a key factor of population survival and evolution, especially in changing environments. Genetic diversity arises from mutations in the DNA sequence of cell lines and from there it reaches the level of organisms, populations, and regions. However, many previous studies have not considered the organism architecture or pattern of thallus construction, ignoring the potential genetic complexities that intraorganismal genetic heterogeneity could generate in modular organisms. In seaweeds, modularity and clonality exist in many species. Modular organization has been related to advantages in terms of rapid construction and recovery after the loss of individual modules, which have their own demographic properties as they generate, mature, senesce, and die. Based on recent evidence from the literature, we suggest that modules also have their own genetic properties. Specifically, modular seaweeds have two possible sources of genetic diversity at the individual level: the heterozygosity of the genotypes composing the genet, and genetic heterogeneity among the modules within a genet (i.e., intraclonal genetic variability). Both sources of genetic diversity can have ecological and evolutionary consequences, and most of them must be considered in research on modular seaweeds. Linking intraorganismal genetic diversity with clonal architecture and propagation styles may help us to understand important ecological and evolutionary processes such as speciation modes, invasive capacities, or farming potential.

Nonclonal coloniality: Genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan Ectopleura larynx

Hydrozoans typically develop colonies through asexual budding of polyps. Although colonies of Ectopleura are similar to other hydrozoans in that they consist of multiple polyps physically connected through continuous epithelia and shared gastrovascular cavity, Ectopleura larynx does not asexually bud polyps indeterminately. Instead, after an initial phase of limited budding in a young colony, E. larynx achieves its large colony size through the aggregation and fusion of sexually (nonclonally) produced polyps. The apparent chimerism within a physiologically integrated colony presents a potential source of conflict between distinct genetic lineages, which may vary in their ability to access the germline. To determine the extent to which the potential for genetic conflict exists, we characterized the types of genetic relationships between polyps within colonies, using a RAD‐Seq approach. Our results indicate that E. larynx colonies are indeed comprised of polyps that are clones and sexually reproduced siblings and offspring, consistent with their life history. In addition, we found that colonies also contain polyps that are genetically unrelated, and that estimates of genome‐wide relatedness suggests a potential for conflict within a colony. Taken together, our data suggest that there are distinct categories of relationships in colonies of E. larynx, likely achieved through a range of processes including budding, regeneration, and fusion of progeny and unrelated polyps, with the possibility for a genetic conflict resolution mechanism. Together these processes contribute to the reevolution of the ecologically important trait of coloniality in E. larynx.

On the occurrence of intracolonial genotypic variability in highly clonal populations of the hydrocoral Millepora platyphylla at Moorea (French Polynesia)

Intracolonial genotypic variability is described in many colonial organisms and arises from mosaicism (somatic mutation) and/or chimerism (allogenic fusion). Both processes provide an additional source of genotypic variation in natural populations and raise questions on the biological significance of colonies having more than one genotype. Using fifteen microsatellite markers, we screened for potential genetic heterogeneity within Millepora platyphylla colonies, a hydrocoral species known for its extensive morphological plasticity among reef habitats. We aimed to determine whether mosaicism and chimerism were related to specific reef habitats and/or colony morphologies. Our results show that intracolonial genotypic variability was common (31.4%) in M. platyphylla at Moorea, French Polynesia, with important variations in its frequency among habitats (0–60%), while no effect of morphology was observed. Mosaicism seemed responsible for most of the genetic heterogeneity (87.5%), while chimerism was rarer. Some mosaics were shared among fire coral clones indicating that mutations could be spread via colony fragmentation. Further, the genotypic variability among clones suggests that colonies produced asexually through fragmentation have the potential to accumulate their own mutations over time. Such mutation dynamics might have important implications for the adaptive potential of long-lived reef-builder populations that are predominantly sustained through asexual reproduction.

Enhanced larval supply and recruitment can replenish reef corals on degraded reefs

Reef-building corals have essential roles in reef ecosystems but are highly susceptible to disturbances. Increasing anthropogenic disturbances are eroding coral community resilience, leading to declining reef ecosystem function and status globally. Successful reproduction and recruitment are essential for restoring coral populations but recruitment-limitation can constrain recovery. We supplied ~400,000 Acropora tenuis larvae in fine-mesh enclosures on each of four larval-enhancement plots, comprising natural reef substrata and ten settlement tiles, on degraded reef areas in the northwestern Philippines. Initial mean total settlement on tiles in larval-enhancement plots was high (255.3 ± 68.6), whereas no larvae settled in natural control plots. Recruit survivorship began stabilising after five months, with juveniles becoming visible by eye at nine months. After three years a mean of 2.3 m⁻² colonies survived within each larval-enhancement plot. Most colonies grew rapidly (16.1 ± 0.7 cm mean diameter) and spawned successfully at three years, thereby quickly re-establishing a breeding population. In contrast, natural recruitment failed to produce any new visible A. tenuis colonies. These results demonstrate that mass larval settlement can rapidly enhance recruitment and coral recovery on degraded reef areas, and provides an important option for active reef restoration where larval supply and recruitment success are limiting.

Invasiveness, chimerism and genetic diversity

Adaptation for invasiveness should comprise the capability to exploit and prosper in a wide range of ecological conditions and is therefore expected to be associated with a certain level of genetic diversity. Paradoxically, however, invasive populations are established by only a few founders, resulting in low genetic diversity. As a conceivable way of attaining high genetic diversity and high variance of gene expression even when a small number of founders is involved in invasiveness, I suggest here chimerism, a fusion between different individuals-a common phenomenon found in numerous phyla. The composite entity offers the chimeric organism genetic flexibility and higher inclusive fitness that depends on the joint genomic fitness of the original partners. The ability to form a chimeric entity is also applied to subsequent generations, and consequently, the level of genetic diversity does not decline over generations of population establishment following invasion.

Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals

Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata, Acropora digitifera, and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex secondary structures and are located in untranslated regions and introns, but most abundant in intergenic DNA. These repeat families have undergone frequent duplication and degradation, suggesting a 'boom and bust' cycle of invasion and loss. We speculate that due to their surprisingly high sequence identities across deeply diverged corals, physical association with genes, and dynamic evolution, SCORs might have adaptive functions in corals that need to be explored using population genomic and function-based approaches.

Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata

We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.

Frequency of chimerism in populations of the kelp Lessonia spicata in central Chile

Chimerism occurs when two genetically distinct conspecific individuals fuse together generating a single entity. Coalescence and chimerism in red seaweeds has been positively related to an increase in body size, and the consequent reduction in susceptibility to mortality factors, thus increasing survival, reproductive potential and tolerance to stress in contrast to genetically homogeneous organisms. In addition, they showed that a particular pattern of post-fusion growth maintains higher genetic diversity and chimerism in the holdfast but homogenous axes. In Chilean kelps (brown seaweeds), intraorganismal genetic heterogeneity (IGH) and holdfast coalescence has been described in previous research, but the extent of chimerism in wild populations and the patterns of distribution of the genetically heterogeneous thallus zone have scarcely been studied. Since kelps are under continuous harvesting, with enormous social, ecological and economic importance, natural chimerism can be considered a priceless in-situ reservoir of natural genetic resources and variability. In this study, we therefore examined the frequency of IGH and chimerism in three harvested populations of Lessonia spicata. We then evaluated whether chimeric wild-type holdfasts show higher genetic diversity than erect axes (stipe and lamina) and explored the impact of this on the traditional estimation of genetic diversity at the population level. We found a high frequency of IGH (60-100%) and chimerism (33.3-86.7%), varying according to the studied population. We evidenced that chimerism occurs mostly in holdfasts, exhibiting heterogeneous tissues, whereas stipes and lamina were more homogeneous, generating a vertical gradient of allele and genotype abundance as well as divergence, constituting the first time "within- plant" genetic patterns have been reported in kelps. This is very different from the chimeric patterns described in land plants and animals. Finally, we evidenced that IGH affected genetic differentiation among populations, showed lower levels of FST index when we compared holdfast than lamina samples. In the light of this, future studies should evaluate the significance of chimeric holdfasts in their ability to increase kelps resilience, improve restoration and ecosystem service.

Coalescing red algae exhibit noninvasive, reversible chimerism

Chimerism is produced by the somatic fusion of two or more genetically distinct conspecific individuals. In animals, the main cost of fusion is competition between genetically different cell lineages and the probability of original cell line replacement by more competitive invasive lines, which limits its natural frequency (3%-5%). In red and brown seaweeds, chimerism is widespread (27%-53%), seemingly without the negative outcomes described for animals. The rigidity of cell walls in macroalgae prevents cell motility and invasions. In addition, in moving waters, most somatic fusions involve the holdfast. Histological observations in laboratory-built bicolor macroalgal chimeras indicated that upright axes emerge from the base of plants by proliferation and vertical growth of discrete cell groups that include one or just a few of the cell lineages occurring in the holdfasts. Laboratory experiments showed growth competition between cell lineages, thus explaining lineage segregation during growth along originally chimeric erect axes. Genotyping of the axes showed more heterogeneous tissues basally, but apically more homogeneous ones, generating a vertical gradient of allele abundance and diversity. The few chimeric primary branches produced, eventually became homogenous after repeated branching. Therefore, coalescing macroagae exhibit a unique pattern of post-fusion growth, with the capacity to reverse chimerism. This pattern is significantly different from those in animals and land plants, suggesting chimerism is a biologically heterogeneous concept.

Venturing in coral larval chimerism: a compact functional domain with fostered genotypic diversity

The globally distributed coral species Pocillopora damicornis is known to release either sexual or asexual derived planula-larvae in various reef locations. Using microsatellite loci as markers, we documented the release of asexually derived chimeric larvae (CL), originating from mosaicked maternal colonies that were also chimeras, at Thai and Philippines reefs. The CL, each presenting different combinations of maternal genotypic constituents, create genetically-complex sets of asexual propagules. This novel mode of inheritance in corals challenges classical postulations of sexual/asexual reproduction traits, as asexual derived CL represent an alliance between genotypes that significantly sways the recruits' absolute fitness. This type of inherited chimerism, while enhancing intra-entity genetic heterogeneity, is an evolutionary tactic used to increase genetic-heterogeneity, primarily in new areas colonized by a limited number of larvae. Chimerism may also facilitate combat global change impacts by exhibiting adjustable genomic combinations of within-chimera traits that could withstand alterable environmental pressures, helping Pocillopora become a successful cosmopolitan species.

Growing coral larger and faster: micro-colony-fusion as a strategy for accelerating coral cover

Fusion is an important life history strategy for clonal organisms to increase access to shared resources, to compete for space, and to recover from disturbance. For reef building corals, fragmentation and colony fusion are key components of resilience to disturbance. Observations of small fragments spreading tissue and fusing over artificial substrates prompted experiments aimed at further characterizing Atlantic and Pacific corals under various conditions. Small (∼1–3 cm²) fragments from the same colony spaced regularly over ceramic tiles resulted in spreading at rapid rates (e.g., tens of square centimeters per month) followed by isogenic fusion. Using this strategy, we demonstrate growth, in terms of area encrusted and covered by living tissue, of Orbicella faveolata, Pseudodiploria clivosa, and Porites lobata as high as 63, 48, and 23 cm² per month respectively. We found a relationship between starting and ending size of fragments, with larger fragments growing at a faster rate. Porites lobata showed significant tank effects on rates of tissue spreading indicating sensitivity to biotic and abiotic factors. The tendency of small coral fragments to encrust and fuse over a variety of surfaces can be exploited for a variety of applications such as coral cultivation, assays for coral growth, and reef restoration.

Estimating Trait Heritability in Highly Fecund Species

Increasingly, researchers are interested in estimating the heritability of traits for nonmodel organisms. However, estimating the heritability of these traits presents both experimental and statistical challenges, which typically arise from logistical difficulties associated with rearing large numbers of families independently in the field, a lack of known pedigree, the need to account for group or batch effects, etc. Here we develop both an empirical and computational methodology for estimating the narrow-sense heritability of traits for highly fecund species. Our experimental approach controls for undesirable culturing effects while minimizing culture numbers, increasing feasibility in the field. Our statistical approach accounts for known issues with model-selection by using a permutation test to calculate significance values and includes both fitting and power calculation methods. We further demonstrate that even with moderately high sample-sizes, the p-values derived from asymptotic properties of the likelihood ratio test are overly conservative, thus reducing statistical power. We illustrate our methodology by estimating the narrow-sense heritability for larval settlement, a key life-history trait, in the reef-building coral Orbicella faveolata. The experimental, statistical, and computational methods, along with all of the data from this study, are available in the R package multiDimBio.

Fused embryos and pre-metamorphic conjoined larvae in a broadcast spawning reef coral

Fusion of embryos or larvae prior to metamorphosis is rarely known to date in colonial marine organisms. Here, we document for the first time that the embryos of the broadcast spawning coral Platygyra daedalea could fuse during blastulation and further develop into conjoined larvae, and the settlement of conjoined larvae immediately resulted in inborn juvenile colonies. Fusion of embryos might be an adaptive strategy to form pre-metamorphic chimeric larvae and larger recruits, thereby promoting early survival. However, future studies are needed to explore whether and to what extent fusion of coral embryos occurs in the field, and fully evaluate its implications.

Self-recognition in corals facilitates deep-sea habitat engineering

The ability of coral reefs to engineer complex three-dimensional habitats is central to their success and the rich biodiversity they support. In tropical reefs, encrusting coralline algae bind together substrates and dead coral framework to make continuous reef structures, but beyond the photic zone, the cold-water coral Lophelia pertusa also forms large biogenic reefs, facilitated by skeletal fusion. Skeletal fusion in tropical corals can occur in closely related or juvenile individuals as a result of non-aggressive skeletal overgrowth or allogeneic tissue fusion, but contact reactions in many species result in mortality if there is no ‘self-recognition’ on a broad species level. This study reveals areas of ‘flawless’ skeletal fusion in Lophelia pertusa, potentially facilitated by allogeneic tissue fusion, are identified as having small aragonitic crystals or low levels of crystal organisation, and strong molecular bonding. Regardless of the mechanism, the recognition of ‘self’ between adjacent L. pertusa colonies leads to no observable mortality, facilitates ecosystem engineering and reduces aggression-related energetic expenditure in an environment where energy conservation is crucial. The potential for self-recognition at a species level, and subsequent skeletal fusion in framework-forming cold-water corals is an important first step in understanding their significance as ecological engineers in deep-seas worldwide.

The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral-algal associations

Reef-building corals owe much of their success to a symbiosis with dinoflagellate microalgae in the genus Symbiodinium. In this association, the performance of each organism is tied to that of its partner, and together the partners form a holobiont that can be subject to selection. Climate change affects coral reefs, which are declining globally as a result. Yet the extent to which coral holobionts will be able to acclimate or evolve to handle climate change and other stressors remains unclear. Selection acts on individuals and evidence from terrestrial systems demonstrates that intraspecific genetic diversity plays a significant role in symbiosis ecology and evolution. However, we have a limited understanding of the effects of such diversity in corals. As molecular methods have advanced, so too has our recognition of the taxonomic and functional diversity of holobiont partners. Resolving the major components of the holobiont to the level of the individual will help us assess the importance of intraspecific diversity and partner interactions in coral-algal symbioses. Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. Our synthesis is derived from reviewing existing evidence and presenting novel data. By incorporating the effects of holobiont extended phenotypes into predictive models, we may refine our understanding of the evolutionary trajectory of corals and reef communities responding to climate change.

Gross and microscopic pathology of hard and soft corals in New Caledonia

We surveyed the reefs of Grande Terre, New Caledonia, for coral diseases in 2010 and 2013. Lesions encountered in hard and soft corals were systematically described at the gross and microscopic level. We sampled paired and normal tissues from 101 and 65 colonies in 2010 and 2013, respectively, comprising 51 species of corals from 27 genera. Tissue loss was the most common gross lesion sampled (40%) followed by discoloration (28%), growth anomalies (13%), bleaching (10%), and flatworm infestation (1%). When grouped by gross lesions, the diversity of microscopic lesions as measured by Shannon-Wiener index was highest for tissue loss, followed by discoloration, bleaching, and growth anomaly. Our findings document an extension of the range of certain diseases such as Porites trematodiasis and endolithic hypermycosis (dark spots) to the Western Pacific as well as the presence of a putative cnidarian endosymbiont. We also expand the range of species infected by cell-associated microbial aggregates, and confirm the trend that these aggregates predominate in dominant genera of corals in the Indo-Pacific. This study highlights the importance of including histopathology as an integral component of baseline coral disease surveys, because a given gross lesion might be associated with multiple potential causative agents.

Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments

Studying the mechanisms that enable coral populations to inhabit spatially varying thermal environments can help evaluate how they will respond in time to the effects of global climate change and elucidate the evolutionary forces that enable or constrain adaptation. Inshore reefs in the Florida Keys experience higher temperatures than offshore reefs for prolonged periods during the summer. We conducted a common garden experiment with heat stress as our selective agent to test for local thermal adaptation in corals from inshore and offshore reefs. We show that inshore corals are more tolerant of a 6-week temperature stress than offshore corals. Compared with inshore corals, offshore corals in the 31 °C treatment showed significantly elevated bleaching levels concomitant with a tendency towards reduced growth. In addition, dinoflagellate symbionts (Symbiodinium sp.) of offshore corals exhibited reduced photosynthetic efficiency. We did not detect differences in the frequencies of major (>5%) haplotypes comprising Symbiodinium communities hosted by inshore and offshore corals, nor did we observe frequency shifts ('shuffling') in response to thermal stress. Instead, coral host populations showed significant genetic divergence between inshore and offshore reefs, suggesting that in Porites astreoides, the coral host might play a prominent role in holobiont thermotolerance. Our results demonstrate that coral populations inhabiting reefs <10-km apart can exhibit substantial differences in their physiological response to thermal stress, which could impact their population dynamics under climate change.

Rarity and genetic diversity in Indo-Pacific Acropora corals

Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome.

Cooperation among germinating spores facilitates the growth of the fungus, Neurospora crassa

Fusions between individuals are a common feature of organisms with modular, indeterminate life forms, including plants, marine invertebrates and fungi. The consequences of fusion for an individual fungus are poorly understood. We used wild-type and fusion mutant strains of the genetic model Neurospora crassa to chronicle the fitness in two different laboratory habitats, and in each experiment started colonies from multiple different densities of asexual spores. On round Petri dishes, fusion enabled wild-type colonies to grow larger than mutant (soft) colonies; but in linear 'race tubes', the soft mutant always grew more quickly than the wild-type. Starting a colony with more spores always provided an advantage to a wild-type colony, but was more often neutral or a cost to the soft mutant. The ability to fuse does not provide a consistent advantage to wild-type colonies; net benefits are shaped by both habitat and initial spore densities.

Neglected biological features in cnidarians self-nonself recognition

Cnidarian taxa, currently of the most morphologically simplest extant metazoans, exhibit many salient properties of innate immunity that are shared by most Animalia. One hallmark constituent of immunity exhibit by most cnidarians is histocompatibility, marked by wide spectrum of allogeneic and xenogeneic effector arms, progressing into tissue fusions or inflammatory rejections. Scientific propensity on cnidarians immunity, while discussing historecognition as the ground for immunity in these organisms, concentrates on host-parasitic and disease oriented studies, or focuses on genome approaches that search for gene homologies with the vertebrates. Above tendency for mixing up between historecognition and host-parasitic/disease, highlights a serious obstacle for the progress in our understanding of cnidarian immunobiology. Here I critically overview four 'forgotten' cnidarian immune features, namely, specificity, immunological memory, allogeneic maturation and natural chimerism, presenting insights into perspectives that are prerequisite for any discussion on cnidarian evolution. It is evident that cnidarian historecognition embraces elements that the traditional field of vertebrate immunology has never encountered (i.e., variety of cytotoxic outcomes, different types of effector mechanisms, chimerism, etc.). Also, cnidarian immune features dictating that different individuals within the same species seem to respond differently to the same immunological challenge, is far from that recorded in the vertebrates' adaptive immunity. While above features may be connected to host-parasitic and disease phenomena and effector arms, they clearly attest to their unique critical roles in shaping cnidarians historecognition, calling for improved distinction between historecognition and host-response/ disease disciplines. The research on cnidarians immunity still suffers from the lack of accepted synthesis of what historecognition is or does. Mounting of an immune response against conspecifics or xenogeneic organisms should therefore be clearly demarcated from other paths of immunity, till cnidarian innate immunity as a whole is expounded.

Inter-specific coral chimerism: genetically distinct multicellular structures associated with tissue loss in Montipora capitata

Montipora white syndrome (MWS) results in tissue-loss that is often lethal to Montipora capitata, a major reef building coral that is abundant and dominant in the Hawai'ian Archipelago. Within some MWS-affected colonies in Kane'ohe Bay, Oahu, Hawai'i, we saw unusual motile multicellular structures within gastrovascular canals (hereafter referred to as invasive gastrovascular multicellular structure-IGMS) that were associated with thinning and fragmentation of the basal body wall. IGMS were in significantly greater densities in coral fragments manifesting tissue-loss compared to paired normal fragments. Mesenterial filaments from these colonies yielded typical M. capitata mitochondrial haplotypes (CO1, CR), while IGMS from the same colony consistently yielded distinct haplotypes previously only found in a different Montipora species (Montipora flabellata). Protein profiles showed consistent differences between paired mesenterial filaments and IGMS from the same colonies as did seven microsatellite loci that also exhibited an excess of alleles per locus inconsistent with a single diploid organism. We hypothesize that IGMS are a parasitic cellular lineage resulting from the chimeric fusion between M. capitata and M. flabellata larvae followed by morphological reabsorption of M. flabellata and subsequent formation of cell-lineage parasites. We term this disease Montiporaiasis. Although intra-specific chimerism is common in colonial animals, this is the first suspected inter-specific example and the first associated with tissue loss.

High potential for formation and persistence of chimeras following aggregated larval settlement in the broadcast spawning coral, Acropora millepora

In sessile modular marine invertebrates, chimeras can originate from fusions of closely settling larvae or of colonies that come into contact through growth or movement. While it has been shown that juveniles of brooding corals fuse under experimental conditions, chimera formation in broadcast spawning corals, the most abundant group of reef corals, has not been examined. This study explores the capacity of the broadcast spawning coral Acropora millepora to form chimeras under experimental conditions and to persist as chimeras in the field. Under experimental conditions, 1.5-fold more larvae settled in aggregations than solitarily, and analyses of nine microsatellite loci revealed that 50 per cent of juveniles tested harboured different genotypes within the same colony. Significantly, some chimeric colonies persisted for 23 months post-settlement, when the study ended. Genotypes within persisting chimeric colonies all showed a high level of relatedness, whereas rejecting colonies displayed variable levels of relatedness. The nearly threefold greater sizes of chimeras compared with solitary juveniles, from settlement through to at least three months, suggest that chimerism is likely to be an important strategy for maximizing survival of vulnerable early life-history stages of corals, although longer-term studies are required to more fully explore the potential benefits of chimerism.

Internal brooding favours pre-metamorphic chimerism in a non-colonial cnidarian, the sea anemone Urticina felina

The concept of intraorganismal genetic heterogeneity resulting from allogeneic fusion (i.e. chimerism) has almost exclusively been explored in modular organisms that have the capacity to reproduce asexually, such as colonial ascidians and corals. Apart from medical conditions in mammals, the natural development of chimeras across ontogenetic stages has not been investigated in any unitary organism incapable of asexual propagation. Furthermore, chimerism was mainly studied among gregarious settlers to show that clustering of genetically similar individuals upon settlement promotes the occurrence of multi-chimeras exhibiting greater fitness. The possible occurrence of chimeric embryos and larvae prior to settlement has not received any attention. Here we document for the first time the presence of natural chimeras in brooded embryos and larvae of a unitary cnidarian, the sea anemone Urticina felina. Rates of visible bi- and multi-chimerism of up to 3.13 per cent were measured in the broods of 16 females. Apart from these sectorial chimeras, monitored fusion events also yielded homogeneous chimeric entities (mega-larvae) suggesting that the actual rates of natural chimerism in U. felina are greater than predicted by visual assessment. In support of this assumption, the broods of certain individuals comprised a dominant proportion (to 90%) of inexplicably large embryos and larvae (relative to oocyte size). Findings of fusion and chimerism in a unitary organism add a novel dimension to the framework within which the mechanisms and evolutionary significance of genetic heterogeneity in animal taxa can be explored.

Genetic heterogeneity in wild isolates of cellular slime mold social groups

This study addresses the issues of spatial distribution, dispersal, and genetic heterogeneity in social groups of the cellular slime molds (CSMs). The CSMs are soil amoebae with an unusual life cycle that consists of alternating solitary and social phases. Because the social phase involves division of labor with what appears to be an extreme form of "altruism", the CSMs raise interesting evolutionary questions regarding the origin and maintenance of sociality. Knowledge of the genetic structure of social groups in the wild is necessary for answering these questions. We confirm that CSMs are widespread in undisturbed forest soil from South India. They are dispersed over long distances via the dung of a variety of large mammals. Consistent with this mode of dispersal, most social groups in the two species examined for detailed study, Dictyostelium giganteum and Dictyostelium purpureum, are multi-clonal.