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

Micro-to multi-chimerism: the multiple facets of a singular phenomenon

Natural chimeras are prevalent in nature (> 10 phyla of protists, plants, invertebrates, and vertebrates), disrupting the conventional believe that genetically homogeneous entities are selected to prevent conflicts within an organism. Chimerism emerges as a significant ecological/evolutionary mechanism, shaping the life history characteristics of metazoans, and it develops in various forms, one of which is called 'microchimerism'. Furthermore, chimerism is a pivotal phenomenon, presenting complex biological and ecological expressions akin to a "double-edged sword", bypassing both innate and adaptive immune responses. Considering the proportionate contribution of chimeric partners and their spatial arrangements within chimeras, unveils six somatic states of chimerism (purged-chimerism, sectorial-chimerism, mosaic-chimerism, mixed-chimerism, microchimerism and multi-chimerism) and three states of germline chimerism (mixed-chimerism, male/female chimerism and parasitic germline chimerism). These diverse chimeric states are categorized into two distinct series of continua, namely 'somatic cell chimerism' and 'germline chimerism' scenarios where dynamic chimeric states transit into other states, and vice versa, within a specific continuum that relies on the concept of an endless 'Escherian stairwell' of chimerism states. Also, the same chimera may portray simultaneously, different chimeric states in various parts/organs. We further reviewed the evolutionary perspectives for chimerism, raising five commonly shared features of chimerism (multichimerism, ontogenic windows, reproductive chimerism, transmissible chimerism, germline hitchhiking) and 'costs' and 'benefits' accrued to chimerism, shared between invertebrates and vertebrates, including humans. We contest that 'microchimerism' lacks any quantitative definition, represents just a single facet in the multi-facet panorama of chimeric phenomena that demonstrate transitions over time into other states. All of the above carry evolutionary and clinical implications.

Making Neurobots and Chimerical Ctenophores

Making living machines using biological materials (cells, tissues, and organs) is one of the challenges in developmental biology and modern biomedicine. Constraints in regeneration potential and immune self-defense mechanisms limit the progress in the field. Here, we present unanticipated features related to self-recognition and ancestral neuro-immune architectures of new emerging reference species - ctenophores or comb jellies. These are descendants of the earliest survival metazoan lineage with unique tissues, organs and independent origins of major animal traits such as neurons, muscles, mesoderm, and through-gut. Thus, ctenophores convergently evolved complex organization, compared to bilaterians. Nevertheless, their neural and immune systems are likely functionally coupled, enabling designs and experimental construction of hybrid neural systems and even entire animals. This report illustrates impressive opportunities to build both chimeric animals and neurobots using ctenophores as models for bioengineering. The obtained neurobots and chimeric animals from three ctenophore species (Bolinopsis, Mnemiopsis, and Pleurobrachia) were able to be autonomous and survive for days. In sum, the unification of biodiversity, cell biology, and neuroscience opens unprecedented opportunities for experimental synthetic biology.

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.

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.

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.

From the individual to the colony: Marine invertebrates as models to understand levels of biological organization

The developmental and evolutionary principles of coloniality in marine animals remain largely unexplored. Although many common traits have evolved independently in different groups of colonial animals, questions about their significance for colonial life histories remain unanswered. In 2018 (Nov. 25 - Dec. 8), the inaugural course on the Evolution of Coloniality and Modularity took place at the Center for Marine Biology of the University of São Paulo (CEBIMAR-USP), Brazil. During the intensive two-week graduate-level course, we addressed some of the historical ideas about animal coloniality by focal studies in bryozoans, tunicates, cnidarians, and sponges. We discussed many historical hypotheses and ways to test these using both extant and paleontological data, and we carried direct observations of animal colonies in the different phyla to address questions about coloniality. We covered topics related to multi-level selection theory and studied colonial traits, including modular miniaturization, polymorphism, brooding, and allorecognition. Course participants carried out short research projects using local species of animals to address questions on allorecognition and regeneration in ascidians and sponges, fusion and chimerism in anthoathecate hydrozoans, and evolution of polymorphism in bryozoans. Although many questions remain unanswered, this course served as a foundation to continue to develop a developmental and evolutionary synthesis of clonal and modular development in colonial marine organisms.

Phenotypic plasticity rather than genotype drives reproductive choices in Hydra populations

Facultative clonality is associated with complex life cycles where sexual and asexual forms can be exposed to contrasting selection pressures. Facultatively clonal animals often have distinct developmental capabilities that depend on reproductive mode (e.g., negligible senescence and exceptional regeneration ability in asexual individuals, which are lacking in sexual individuals). Understanding how these differences in life history strategies evolved is hampered by limited knowledge of the population structure underlying sexual and asexual forms in nature. Here we studied genetic differentiation of coexisting sexual and asexual Hydra oligactis polyps, a freshwater cnidarian where reproductive mode-dependent life history patterns are observed. We collected asexual and sexual polyps from 13 Central European water bodies and used restriction-site associated DNA sequencing to infer population structure. We detected high relatedness among populations and signs that hydras might spread with resting eggs through zoochory. We found no genetic structure with respect to mode of reproduction (asexual vs. sexual). On the other hand, clear evidence was found for phenotypic plasticity in mode of reproduction, as polyps inferred to be clones differed in reproductive mode. Moreover, we detected two cases of apparent sex change (males and females found within the same clonal lineages) in this species with supposedly stable sexes. Our study describes population genetic structure in Hydra for the first time, highlights the role of phenotypic plasticity in generating patterns of life history variation, and contributes to understanding the evolution of reproductive mode-dependent life history variation in coexisting asexual and sexual forms.

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.

The evolution and development of coloniality in hydrozoans

Hydrozoan colonies display a variety of shapes and sizes including encrusting, upright, and pelagic forms. Phylogenetic patterns reveal a complex evolutionary history of these distinct colony forms, as well as colony loss. Within a species, phenotypic variation in colonies as a response to changing environmental cues and resources has been documented. The patterns of branching of colony specific tissue, called stolons in encrusting colonies and stalks in upright colonies, are likely under the control of signaling mechanisms whose changing expression in evolution and development are responsible for the diversity of hydrozoan colony forms. Although mechanisms of polyp development have been well studied, little research has focused on colony development and patterning. In the few studies that investigated mechanisms governing colony patterning, the Wnt signaling pathway has been implicated. The diversity of colony form, evolutionary patterns, and mechanisms of colony variation in Hydrozoa are reviewed here.

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.

Frizzled3 expression and colony development in hydractiniid hydrozoans

Hydractiniid hydrozoan colonies are comprised of individual polyps connected by tube-like stolons or a sheet-like mat. Mat and stolons function to integrate the colony through continuous epithelia and shared gastrovascular cavity. Although mechanisms of hydrozoan polyp development have been well studied, little is known about the signaling processes governing the patterning of colonies. Here we investigate the Wnt receptor family Frizzled. Phylogenetic analysis reveals that hydrozoans possess four Frizzled orthologs. We find that one of these genes, Frizzled3, shows a spatially restricted expression pattern in colony-specific tissue in two hydractiniid hydrozoans, Hydractinia symbiolongicarpus and Podocoryna carnea, in a manner that corresponds to their distinct colony forms (stolonal mat in Hydractinia and free stolons in Podocoryna). Interestingly, Frizzled3 was lost in the genome of Hydra, which is a solitary polyp and thus lacks colony-specific tissue. Current evidence suggests that the Wnt signaling pathway plays a key role in the evolution of colony diversity and colony loss in Hydrozoa.

Enforcing Cooperation in the Social Amoebae

Cooperation has been essential to the evolution of biological complexity, but many societies struggle to overcome internal conflicts and divisions. Dictyostelium discoideum, or the social amoeba, has been a useful model system for exploring these conflicts and how they can be resolved. When starved, these cells communicate, gather into groups, and build themselves into a multicellular fruiting body. Some cells altruistically die to form the rigid stalk, while the remainder sit atop the stalk, become spores, and disperse. Evolutionary theory predicts that conflict will arise over which cells die to form the stalk and which cells become spores and survive. The power of the social amoeba lies in the ability to explore how cooperation and conflict work across multiple levels, ranging from proximate mechanisms (how does it work?) to ultimate evolutionary answers (why does it work?). Recent studies point to solutions to the problem of ensuring fairness, such as the ability to suppress selfishness and to recognize and avoid unrelated individuals. This work confirms a central role for kin selection, but also suggests new explanations for how social amoebae might enforce cooperation. New approaches based on genomics are also enabling researchers to decipher for the first time the evolutionary history of cooperation and conflict and to determine its role in shaping the biology of multicellular organisms.

Together stronger: Intracolonial genetic variability occurrence in Pocillopora corals suggests potential benefits

We investigated the occurrence of intracolonial genetic variability (IGV) in Pocillopora corals in the southwestern Indian Ocean. Ninety-six colonies were threefold-sampled from three sites in Reunion Island. Nubbins were genotyped using 13 microsatellite loci, and their multilocus genotypes compared. Over 50% of the colonies presented at least two different genotypes among their three nubbins, and IGV was found abundant in all sites (from 36.7% to 58.1%). To define the threshold distinguishing mosaicism from chimerism, we developed a new method based on different evolution models by computing the number of different alleles for the infinite allele model (IAM) and the Bruvo's distance for the stepwise mutation model (SMM). Colonies were considered as chimeras if their nubbins differed from more than four alleles and if the pairwise Bruvo's distance was higher than 0.12. Thus 80% of the IGV colonies were mosaics and 20% chimeras (representing almost 10% of the total sampling). IGV seems widespread in scleractinians and beyond the disabilities of this phenomenon reported in several studies, it should also bring benefits. Next steps are to identify these benefits and to understand processes leading to IGV, as well as factors influencing them.

Coloniality, clonality, and modularity in animals: The elephant in the room

Nearly half of the animal phyla contain species that propagate asexually via agametic reproduction, often forming colonies of genetically identical modules, that is, ramets, zooids, or polyps. Clonal reproduction, colony formation, and modular organization have important consequences for many aspects of organismal biology. Theories in ecology, evolution, and development are often based on unitary and, mainly, strictly sexually reproducing organisms, and though colonial animals dominate many marine ecosystems and habitats, recognized concepts for the study of clonal species are often lacking. In this review, we present an overview of the study of colonial and clonal animals, from the historic interests in this subject to modern research in a range of topics, including immunology, stem cell biology, aging, biogeography, and ecology. We attempt to portray the fundamental questions lying behind the biology of colonial animals, focusing on how colonial animals challenge several dogmas in biology as well as the remaining puzzles still to be answered, of which there are many.

Evolutionary conflict and coloniality in animals

Despite considerable interest in the effects of evolutionary conflict in colonies of social insects, relatively little attention has been paid to this issue in clonal animals with modular construction, such as colonial ascidians, bryozoans, and cnidarians. These colonial animals are structural individuals, subdivided into repeated morphological modules, which can individually acquire, process, and share resources. While size-related selection favors colony formation, evolutionary conflicts remain a potent obstacle to such cooperation. These conflicts can occur at several levels and must be mediated for cooperation to emerge. Module-level conflicts potentially result in coalitions of genetically similar modules failing to share resources or monopolizing reproduction. Mediation occurs by a number of mechanisms including: (a) a single-module bottleneck at the initiation of colony formation, (b) allorecognition that limits colony fusion to close kin, (c) development of new modules from connective tissue, (d) synchronization of module budding, (e) programmed module death, (f) terminal differentiation of reproductive modules, and (g) architectural constraints. Effective mediation of module-level conflicts, however, may in some cases contribute to cell-level conflicts. Animal colonies typically have multipotent stem cells, and genetically variant stem cells can potentially monopolize gamete formation. Limiting colony fusion to close kin may not eliminate such conflict. Finally, in at least some taxa an association between photosymbiosis and coloniality is found. Allocation of photosynthate can lead to host-symbiont conflicts that can be mediated by housing symbionts intracellularly and using chemiosmotic mechanisms to detect defectors. Colonial animals thus serve as a living laboratory of evolutionary conflict and its mediation.