Population genetics assessment of two pocilloporid coral species from the northern red sea: Implications for urbanized reef sustainability.

Understanding the genetic makeup of key coral species is vital for effective coral reef management, as heightened genetic diversity directly influences long-term survival and resilience against environmental changes. This study focused on two widespread Indo-Pacific branching corals, Pocillopora damicornis (referred as Pocillopora cf. damicornis (as identified only morphologically) and Seriatopora hystrix, by genotyping 222 and 195 colonies, respectively, from 10 sites in the northern Gulf of Eilat, Red Sea, using six and five microsatellite markers, respectively. Both species exhibited low observed heterozygosity (0.47 for P. cf. damicornis, 0.32 for S. hystrix) and similar expected heterozygosity (0.576 for P. cf. damicornis, 0.578 for S. hystrix). Pocillopora cf. damicornis showed minimal deviations from Hardy-Weinberg equilibrium (HWE) and low but positive F values, indicating high gene flow, while S. hystrix exhibited higher diversion from HWE and positive F values, suggesting isolation by distance and possible non-random mating or genetic drift. As the Gulf of Eilat undergoes rapid urbanization, this study highlights the anthropogenic impacts on the population genetics of key ecosystem engineering species and emphasizes the importance of managing genetics of Marine Protected Areas while implementing active coral reef restoration. The differences in reproductive traits between the two species (S. hystrix being a brooder, while P. cf. damicornis a broadcast spawner), underscore the need for sustainable population genetics management of the coral reefs for the future and resilience of the coral reef ecosystem of the northern Red Sea region.

Historical navigation routes in European waters leave their footprint on the contemporary seascape genetics of a colonial urochordate.

Humans have intensively sailed the Mediterranean and European Atlantic waters throughout history, from the upper Paleolithic until today and centuries of human seafaring have established complex coastal and cross-seas navigation networks. Historical literature revealed three major long-lasting maritime routes (eastern, western, northern) with four commencing locations (Alexandria, Venice, Genoa, Gibraltar) and a fourth route (circum-Italian) that connected between them. Due to oceangoing and technological constraints, most voyages were coastal, lasted weeks to months, with extended resting periods, allowing the development of fouling organisms on ship hulls. One of the abiding travellers in maritime routes is the colonial ascidian Botryllus schlosseri already known since the eighteenth century in European and Mediterranean ports. This species, was almost certainly one of the common hull fouling travellers in all trade routes for centuries. Employing COI haplotypes (1008 samples) and microsatellite alleles (995 samples) on colonies sampled from 64 pan-European sites, present-day Botryllus populations in the Mediterranean Sea/European Atlantic revealed significant segregation between all four maritime routes with a conspicuous partition of the northern route. These results reveal that past anthropogenic transports of sedentary marine species throughout millennia long seafaring have left their footprint on contemporary seascape genetics of marine organisms.

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.

Developing novel microsatellite markers by NGS technology for Rhopilema nomadica, an invasive jellyfish.

Twelve microsatellite loci, obtained by whole genome sequencing approach, were developed and validated for the rhizostomatid jellyfish Rhopilema nomadica, the most pernicious invasive species in the Mediterranean Sea. A sample of 40 specimens collected at six locations along the Mediterranean coast of Israel were genotyped and all loci presented suitable outcomes to population genetic studies, revealing 5-19 alleles/locus with clean and reproducible amplifications. Observed and expected heterozygosity ranged 0.0.353 to 0.971 and 0.335 to 0.870, respectively, and the fixation index (inbreeding coefficient) and the polymorphic information content (PIC) ranged between - 0.190 and 0.240 and 0.32 to 0.858, respectively. The new set of microsatellite loci will be used to study long-term changes in the population genetic parameters of this invasive species.

Validation and redescription of the hyperiidean amphipod Brachyscelus rapacoides Stephensen, 1925 (Crustacea: Amphipoda: Hyperiidea: Brachyscelidae), a new record of association with the scyphozoan jellyfish Rhopilema nomadica Galil, 1990 (Scyphozoa: Rhizostomeae: Rhizostomatidae) in the Mediterranean Sea.

The hyperiidean amphipod Brachyscelus rapacoides Stephensen, 1925 is recorded from the scyphozoan jellyfish Rhopilema nomadica Galil, 1990, a new record of association for the genus Brachyscelus, as well as the first record of hyperiid infestation of a non-indigenous scyphozoan host. Because of some past confusion concerning the status of B. rapacoides and the closely related species B. rapax (Claus, 1871) a redescription of B. rapacoides and molecular analysis are provided in order to validate it as a species distinguished from B. rapax.

The resurrection of Charybdis (Gonioinfradens) giardi (Nobili, 1905), newly recorded from the SE Mediterranean Sea.

A single adult specimen of Gonioinfradens giardi, a portunid crab known from the Red Sea, Gulf of Oman and Arabian Gulf, was recently collected off the southern Israeli coast, in the southeastern Mediterranean Sea. Morphological characters, as well as molecular analyses based on the mitochondrial barcoding gene cytochrome oxidase sub unit I (COI), support its distinction from the widely distributed G. paucidentata. Therefore, G. giardi is reinstated as a valid species, and withdrawn from its synonymy with G. paucidentata. Previous Mediterranean records of the latter species are misidentifications and should be referred to G. giardi. The species is described, illustrated, and differentiated from its cogener.

Ambiguities in the taxonomic assignment and species delineation of botryllid ascidians from the Israeli Mediterranean and other coastlines.

Based on mtCOI sequences comparisons, recent studies reassigned the 'dwarf Botrylloides leachii' from the Levant as Botrylloides nigrum. Here we conducted a survey of the literature and of deposited mtCOI sequences of botryllid ascidians, elucidating ambiguities in their taxonomy. We found that the species, dwarf morph of Botrylloides leachii, Botrylloides nigrum, Botryllus aster and Botryllus arenaceus are grouped together on a single molecular taxon. Then, results of three additional markers (18S, 28S, H3) contradicted literature suggestions, revealing minute distances between Botrylloides leachii and the 'dwarf Botrylloides leachii'. Moreover, only Botrylloides leachii and the 'dwarf Botrylloides leachii' develop giant ampullae as an allorecognition response. Our results raise the possibility that inadequate identification, together with faults in molecular assignment, including queries regarding the efficacy of the mtCOI as the exclusive barcoding tool in botryllid ascidians, is the major culprits responsible for the emerged inconsistencies between the mtCOI sequences and traditional taxonomy. Thus, we assign the Levantine dwarf form as Botrylloides aff. leachii.

Phylogenetics, biogeography and population genetics of the ascidian Botryllus schlosseri in the Mediterranean Sea and beyond.

The wide distribution of the ascidian Botryllus schlosseri along the Mediterranean coasts has been documented since the eighteenth century. However, despite copious documentation, analyses of dispersal modes and genetic profiles were limited to local populations or restricted regions. In order to get a pan-Mediterranean overview, 288 specimens from 11 populations of B. schlosseri from the western and eastern Mediterranean basins were sampled and analyzed using five microsatellite loci and COI sequences. Both molecular markers revealed high polymorphisms, with 182 microsatellites alleles and 54 COI haplotypes. Overall, Fst, Dest, and COI Фpt values were 0.146, 0.635 and 0.322, respectively, reflecting a high genetic diversity and a significant genetic structure as compared to other B. schlosseri populations worldwide, reflected by substantially higher values for effective number of alleles (Ne) in the Mediterranean. A phylogenetic analysis of the COI sequences resulted in four distinct clades and two molecular operational taxonomic units (OTUs). We recorded a stronger genetic structure among the populations of the eastern basin compared to the western basin (microsatellites Fst=0.217 versus 0.082; COI Фpt=0.416 versus 0.171), suggesting either a restricted connectivity between the basins or a stronger genetic drift in each basin. The occurrence of two OTUs and different ecological conditions may also contribute to this finding. Mean Nei's genetic distance in the eastern Mediterranean populations was more than three times higher compared to the western basin. No correlation was observed between geographic and genetic distances (Mantel test), suggesting that maritime transport is the main dispersal vector of B. schlosseri colonies. The possibility that the Mediterranean is a center of diversity for B. schlosseri, and probably its site of origin, is further discussed.

Population genetics features for persistent, but transient, Botryllus schlosseri (Urochordata) congregations in a central Californian marina.

The colonial tunicate Botryllus schlosseri is a globally distributed, invasive ascidian that has colonized the Californian coasts of the USA during the mid-late 1940s and has, since the late 1980s, spread north to Washington. This study analyzes the population genetic characteristics of transient populations residing at the Elkhorn Yacht-Club (EYC), in central California (seven sessions, 1996-2008), which suffered periodic catastrophes caused by episodic fresh-water floods and a single sampling session (in the year 2001) of five West-Coast populations using the mtDNA COI gene and five microsatellite markers. EYC microsatellite results were further compared with the closely situated but persistent population of the Santa Cruz Harbor (SCH) to understand the impact on EYC population regeneration processes after the 2005-flood catastrophe. All microsatellites were highly polymorphic, revealing a large number of unique alleles at different sampling dates. Whereas pairwise θ did not reveal significant differences between the EYC time-series samplings, the overall θ was significant, as it was between all the 2001 West Coast populations. The most likely cluster number was 3 for the EYC samples whereas two K values were obtained (2 and 5) for the 2001 samples. Tajima's D and Fu's/Fs tests did not reject the null hypothesis for COI neutral evolution, except for in the EYC-2000, 2007 and two 2001 samplings. The wide geographical range of the analyses has indicated that following the EYC 2005-flood catastrophe, newcomers could have originated from neighboring populations, from deep-water colonies that may have escaped the 2005 low salinity event, or less expectedly, from far away West-Coast populations, while revealing that the SCH population is the most probable source for the EYC population.

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.

The involvement of three signal transduction pathways in botryllid ascidian astogeny, as revealed by expression patterns of representative genes.

The patterning of the modular body plan in colonial organisms is termed astogeny, as distinct from ontogeny, the development of an individual organism from embryo to adult. Evolutionarily conserved signaling pathways suggest shared roots and common uses for both ontogeny and astogeny. Botryllid ascidians, a widely dispersed group of colonial tunicates, exhibit an intricate modular life form, in which astogeny develops as weekly, highly synchronized growth/death cycles termed blastogenesis, abiding by a strictly regulated plan. In these organisms both astogeny and ontogeny form similar body structures. Working on Botryllus schlosseri, and choosing a representative gene from each of three key Signal Transduction Pathways (STPs: Wnt/ß-catenin; TGF-ß, MAPK/ERK), we explored and compared gene expression at different stages of ontogeny and blastogenesis. Protein expression was studied via immunohistochemistry, ELISA and Western blotting. Five specific inhibitors and an activator for the selected pathways were used and followed to assess their impact during the blastogenic cycle and the development of distinctive phenotypes. Outcomes show that STPs are activated and function (while not necessarily co-localized) during both ontogeny and astogeny. Cellular patterns in blastogenesis, such as colony architecture, are shaped by these STPs. These results are further supported by administering Wnt agonist and anatagonist, TGF-ß receptor antagonists and inhibitors of Mek1/Mek2. Independent of their expression during ontogeny, some of the spatiotemporal patterns of STPs developed within short blastogenic windows. The results support the notion that while the same molecular machinery is functioning in Botryllus schlosseri astogeny and ontogeny, astogenic development is not an ontogenic replicate.

Repeated, long-term cycling of putative stem cells between niches in a basal chordate.

The mechanisms that sustain stem cells are fundamental to tissue maintenance. Here, we identify "cell islands" (CIs) as a niche for putative germ and somatic stem cells in Botryllus schlosseri, a colonial chordate that undergoes weekly cycles of death and regeneration. Cells within CIs express markers associated with germ and somatic stem cells and gene products that implicate CIs as signaling centers for stem cells. Transplantation of CIs induced long-term germline and somatic chimerism, demonstrating self-renewal and pluripotency of CI cells. Cell labeling and in vivo time-lapse imaging of CI cells reveal waves of migrations from degrading CIs into developing buds, contributing to soma and germline development. Knockdown of cadherin, which is highly expressed within CIs, elicited the migration of CI cells to circulation. Piwi knockdown resulted in regeneration arrest. We suggest that repeated trafficking of stem cells allows them to escape constraints imposed by the niche, enabling self-preservation throughout life.

Marine invertebrates cross phyla comparisons reveal highly conserved immune machinery.

Naturally occurring histocompatibility responses, following tissue-to-tissue allogeneic contacts, are common among numerous colonial marine invertebrate taxa, including sponges, cnidarians, bryozoans and ascidians. These responses, often culminating in either tissue fusions or rejections, activate a wide array of innate immune components. By comparing two allorejection EST libraries, developed from alloincompatible challenged colonies of the stony coral Stylophora pistillata and the ascidian Botryllus schlosseri, we revealed a common basis for innate immunity in these two evolutionary distant species. Two prominent genes within this common basis were the immunophilins, Cyclophilin A (CypA) and FK506-binding protein (FKBP). In situ hybridizations revealed that mRNA expression of the coral and ascidian immunophilins was restricted to specific allorecognition effector cell populations (nematoblasts and nematocytes in the coral and morula cells in the ascidian). The expressions were limited to only some of the effector cells within a population, disclosing disparities in numbers and location between naïve colonies and their immune challenged counterparts. Administration of the immunosuppression drug Cyclosporine-A during ascidian's allogeneic assays inhibited both fusion and rejection reactions, probably through the inhibition of ascidian's immunocytes (morula cells) movement and activation. Our results, together with previous published data, depict an immunophilins-based immune mechanism, which is similarly activated in allogeneic responses of distantly related animals from sponges to humans.

The candidate Fu/HC gene in Botryllusschlosseri (Urochordata) and ascidians' historecognition--an oxymoron?

Allorecognition, distinguishing self from non-self allogeneic tissues is the underlying basis of innate immunity. In the colonial tunicate Botryllus schlosseri this historecognition is governed at a single genetic locus, Fu/HC (for fusibility/histocompatibility), with hundreds of co-dominantly expressed alleles. Several years ago, De Tomaso et al. (2005) have revolutionized the discipline of invertebrate allorecognition by describing a novel form of immune recognition in B. schlosseri, a non-vertebrate candidate histocompatibility gene (cFu/HC), revealing that allorecognition machinery in urochordates has nothing in common with the vertebrates' MHC-based histocompatibility. The authors reported absolute concordance of fusibility and cFu/HC genotype, predicted fusion/rejection outcomes in allorecognition settings from allelic polymorphism at the cFu/HC, also claiming cFu/HC gene expressions only in tissues directly engaged in histocompatibility. Here, we raise queries for the validity of the results and conclusions of De Tomaso et al. (2005) publication. Our reservations include discrepancies in the paper's results, including the perplexing absence of key sequencing material from public domains and above all, our own impugning outcomes. These include cloning efforts, in situ hybridization results, semi quantitative PCR outcomes, and the incongruence emerged between fusion/rejection profiles and cFu/HC segregated polymorphism that separately and cumulatively contradict the original publication. We conclude that Botryllus histocompatibility properties are not signaled in the claimed cFu/HC and that cFu/HC gene is unlikely the allodeterminant for Botryllus histocompatibility locus. Hence, the molecular nature of the Fu/HC locus in botryllid ascidians is still awaiting elucidation.

Maternal-larval population genetic traits in Stylophora pistillata, a hermaphroditic brooding coral species.

Aspects of maternal-planula larval genetics in the monoecious scleractinian coral Stylophora pistillata (Red Sea, Eilat) were studied by amplified fragment length polymorphism (AFLP) methodology in two successive reproductive seasons. In total, 293 planulae and 10 adult colonies were analyzed. In June 2006, 147 planulae were collected from 10 shallow water colonies. In March, April and June 2007, 146 additional planulae were sampled from five of the ten 2006 sampled colonies. All AFLP products showed unalike band profiles indicating a fully sexual production pattern. We used 181 and 210 putative AFLP loci, of which the overall level of polymorphism in 2006 was 92 and 99  % in 2007 (respectively). Differences were also observed between 2006 and 2007 reproductive seasons in terms of total average gene diversity (0.191 vs. 0.247, respectively), suggesting fast turnover of sperm donor genotypes. In addition, increased numbers of potential sperm donor colonies in the vicinity of gravid females showed no impact on genetic differentiation levels in released larvae. UPGMA tree revealed clustering of maternal genotypes and their offspring, suggesting, as expected, high relatedness between planulae and their mothers. In addition, the average heterozygosity of each group of siblings was persistently lower than heterozygosity calculated for the respective maternal colony, suggesting the possibility of partial inbreeding. This trend of reduced genetic heterogeneity in Stylophora pistillata is an alarming sign for populations residing in the northern Red Sea coral reefs.

'Rejected' vs. 'rejecting' transcriptomes in allogeneic challenged colonial urochordates.

In botryllid ascidians, allogeneic contacts between histoincompatible colonies lead to inflammatory rejection responses, which eventually separate the interacting colonies. In order to elucidate the molecular background of allogeneic rejection in the colonial ascidian Botryllus schlosseri, we performed microarray assays verified by qPCR, and employed bioinformatic analyses of the results, revealing disparate transcription profiles of the rejecting partners. While only minor expression changes were documented during rejection when both interacting genotypes were pooled together, analyses performed on each genotype separately portrayed disparate transcriptome responses. Allogeneic interacting genotypes that developed the morphological markers of rejection (points of rejection; PORs), termed 'rejected' genotypes, showed transcription inhibition of key functional gene groups, including protein biosynthesis, cell structure and motility and stress response genes. In contrast, the allogeneic partners that did not show PORs, termed 'rejecting' genotypes, showed minor expression changes that were different from those of the 'rejected' genotypes. This data demonstrates that the observed morphological changes in the 'rejected' genotypes are not due to active transcriptional response to the immune challenge but reflect transcription inhibition of response elements. Based on the morphological and molecular outcomes we suggest that the 'rejected' colony activates an injurious self-destructive mechanism in order to disconnect itself from its histoincompatible neighboring colony.

Employing of the amplified fragment length polymorphism (AFLP) methodology as an efficient population genetic tool for symbiotic cnidarians.

Although the use of molecular markers in population genetics of marine organisms is increasingly employed, methodologic limitations still hampered the research for some taxa, such as symbiotic cnidarians, including scleractinian corals. The development of molecular tools in scleractinian corals' studies is faced with a list of obstacles, such as high cost, labor, time consuming, contamination with foreign DNA, and markers with low resolution. The AFLP (amplified fragment length polymorphism) method, overcomes most of the obstacles listed above except of the difficulty of contamination by algal symbiont DNA. We compared the implication of two pre-DNA extraction treatments to obtain coral DNA free of algal contaminations, termed as CPEM, cell population enriched method, and TTEM, total tissue extraction method. The CPEM process result in pure coral DNA for all samples, but is time consuming, whereas in the TTEM process, approximately 25% to 18% of the samples are still contaminated by algal DNA. However, algal DNA contaminations in the PCR at 2.5 x 10(-1) ng level (approximately 100 algal cells) and below, did not amplify any new AFLP band or peak for neither radioactive nor florescence analyses. Therefore, even the TTEM process may be used because it is faster, easier to handle, and easily employed on a large amount of samples, with minimal contamination artifacts. When correctly employed, both methods are applicable to wide experimental manipulations.

Urochordate whole body regeneration inaugurates a diverse innate immune signaling profile.

The phenomenon of whole body regeneration (WBR) from minute soma fragments is a rare event in chordates, confined to the subfamily of botryllid ascidians and is poorly understood on the cellular and molecular levels. We assembled a list of 1326 ESTs from subtracted mRNA, at early stages of Botrylloides leachi WBR, and classified them into functional categories. Sixty-seven (15%) ESTs with roles in innate immunity signaling were classified into a broad functional group, a result supported by domain search and RT-PCR reactions. Gene ontology analysis for human homologous to the immune gene category, identified 22 significant entries, of which "peptidase activity" and "protease inhibitor activity", stood out as functioning during WBR. Analyzing expressions of serine protease Bl-TrSP, a representative candidate gene from the "peptidase activity" subgroup, revealed low transcript levels in naïve vasculature with upregulated expression during WBR. This was confirmed by in situ hybridization that further elucidated staining restricted to a circulating population of macrophage cells. Furthermore, Bl-TrSP was localized in regeneration niches within vasculature, in regenerating buds, and in buds, during blastogenesis. Functional inhibition of serine protease activity disrupts early remodeling processes of the vasculature microenvironment and hinders WBR. Comparison of genome-wide transcription of WBR with five other developmental processes in ascidians (including metamorphosis, budding and blastogenesis), revealed a broad conservation of immune signaling expressions, suggesting a ubiquitous route of harnessing immune-related genes within a broader range of tunicate developmental context. This, in turn, may have enabled the high diversity of life history traits represented by urochordate ascidians.

Identification of immune-relevant genes in histoincompatible rejecting colonies of the tunicate Botryllus schlosseri.

The colonial ascidian Botryllus schlosseri manifests a unique allorecognition system that is controlled by a single histocompatibility haplotype, the Fu/HC locus. When two allogeneic incompatible colonies come into direct contact, they develop inflammatory-like rejection lesions, called points of rejection (POR). While screening for differentially expressed genes during POR formation, we developed and analyzed a cDNA library of expressed sequence tags (ESTs) with 1693 unique ESTs that were clustered and assembled into 217 contigs and 1476 singlets. About 51% of these ESTs showed high similarity (E-value 0.005) to known database sequences, of which 123 matches were identified as immune-relevant genes encoding for stress proteins, pattern recognition receptors and complement proteins, proteases and protease inhibitors, cell adhesion and coagulation proteins, cytokine-related proteins, programmed cell death and proteasome-associated proteins. This first EST wide-screening analysis of the Botryllus allorecognition effector arm reveals a complex innate immune system, hallmarked by a whole genome response to allorecognition challenge.