Some Rare Indo-Pacific Coral Species Are Probable Hybrids

Background: coral reefs worldwide face a variety of threats and many coral species are increasingly endangered. It is often assumed that rare coral species face higher risks of extinction because they have very small effective population sizes, a predicted consequence of which is decreased genetic diversity and adaptive potential.\ud \ud Methodology/Principal Findings: here we show that some Indo-Pacific members of the coral genus Acropora have very small global population sizes and are likely to be unidirectional hybrids. Whether this reflects hybrid origins or secondary hybridization following speciation is unclear.\ud \ud Conclusions/Significance: the interspecific gene flow demonstrated here implies increased genetic diversity and adaptive potential in these coral species. Rare Acropora species may therefore be less vulnerable to extinction than has often been assumed because of their propensity for hybridization and introgression, which may increase their adaptive potential

The Young Lady in Pink. New Light on the Life and Afterlife of an Ancient Portrait

A Roman-Egyptian mummy portrait of a young woman in a pink tunic is part of the Allard Pierson collection in Amsterdam. The portrait is well-known and a key piece of the collection, but has received little scholarly attention so far. The life and the afterlife of the portrait are therefore poorly understood. The authors approach the portrait from different perspectives: its provenance and acquisition, the artist’s materials and techniques, the dating conventions surrounding mummy portraits and their cultural context. The authors advocate for this in-depth multidisciplinary approach primarily because it spotlights specific areas in mummy portraits (in this case, the pearl earrings) where iconography, materials and techniques and ancient socio-economic developments converge. Provenance research proved important not only for securing the object’s bona fide acquisition, but also for tracing its second-life biography. These converging perspectives effectively cast light on research areas where more work remains desirable. In lieu of secure documentation of the archaeological findspot (which is the case with most mummy portraits) this approach is a powerful tool to nonetheless compose histories that help to understand the meaning of mummy portraits in the past and in the present and provide a durable framework for future research

Berry phase and persistent current in disordered mesoscopic rings

A novel quantum interference effect in disordered quasi-one-dimensional rings in the inhomogeneous magnetic field is reported. We calculate the canonical disorder averaged persistent current using the diagrammatic perturbation theory. It is shown that within the adiabatic regime the average current oscillates as a function of the geometric flux which is related to the Berry phase and the period becomes half the value of the case of a single one-dimensional ring. We also discuss the magnetic dephasing effect on the averaged current.Comment: 6 pages, RevTeX, 2 figures. To appear in Phys. Rev. B Rapid Communications Vol.60 No.12 (1999

CRISPR-Cas defense system and potential prophages in cyanobacteria associated with the coral black band disease

Understanding how pathogens maintain their virulence is critical to developing tools to mitigate disease in animal populations. We sequenced and assembled the first draft genome of Roseofilum reptotaenium AO1, the dominant cyanobacterium underlying pathogenicity of the virulent coral black band disease (BBD), and analyzed parts of the BBD-associated Geitlerinema sp. BBD_1991 genome in silico. Both cyanobacteria are equipped with an adaptive, heritable clustered regularly interspaced short palindromic repeats (CRISPR)-Cas defense system type I-D and have potential virulence genes located within several prophage regions. The defense system helps to prevent infection by viruses and mobile genetic elements via identification of short fingerprints of the intruding DNA, which are stored as templates in the bacterial genome, in so-called CRISPRs. Analysis of CRISPR target sequences (protospacers) revealed an unusually high number of self-targeting spacers in R. reptotaenium AO1 and extraordinary long CRIPSR arrays of up to 260 spacers in Geitlerinema sp. BBD_1991. The self-targeting spacers are unlikely to be a form of autoimmunity; instead these target an incomplete lysogenic bacteriophage. Lysogenic virus induction experiments with mitomycin C and UV light did not reveal an actively replicating virus population in R. reptotaenium AO1 cultures, suggesting that phage functionality is compromised or excision could be blocked by the CRISPR-Cas system. Potential prophages were identified in three regions of R. reptotaenium AO1 and five regions of Geitlerinema sp. BBD_1991, containing putative BBD relevant virulence genes, such as an NAD-dependent epimerase/dehydratase (a homolog in terms of functionality to the third and fourth most expressed gene in BBD), lysozyme/metalloendopeptidases and other lipopolysaccharide modification genes. To date, viruses have not been considered to be a component of the BBD consortium or a contributor to the virulence of R. reptotaenium AO1 and Geitlerinema sp. BBD_(1)991. We suggest that the presence of virulence genes in potential prophage regions, and the CRISPR-Cas defense systems are evidence of an arms race between the respective cyanobacteria and their bacteriophage predators. The presence of such a defense system likely reduces the number of successful bacteriophage infections and mortality in the cyanobacteria, facilitating the progress of BBD

Real-time PCR reveals a high incidence of Symbiodinium clade D at low levels in four scleractinian corals across the Great Barrier Reef:Implications for symbiont shuffling

Reef corals form associations with an array of genetically and physiologically distinct endosymbionts from the genus Symbiodinium. Some corals harbor different clades of symbionts simultaneously, and over time the relative abundances of these clades may change through a process called symbiont shuffling. It is hypothesized that this process provides a mechanism for corals to respond to environmental threats such as global warming. However, only a minority of coral species have been found to harbor more than one symbiont clade simultaneously and the current view is that the potential for symbiont shuffling is limited. Using a newly developed real-time PCR assay, this paper demonstrates that previous studies have underestimated the presence of background symbionts because of the low sensitivity of the techniques used. The assay used here targets the multi-copy rDNA ITS1 region and is able to detect Symbiodinium clades C and D with > 100-fold higher sensitivity compared to conventional techniques. Technical considerations relating to intragenomic variation, estimating copy number and non-symbiotic contamination are discussed. Eighty-two colonies from four common scleractinian species (Acropora millepora, Acropora tenuis, Stylophora pistillata and Turbinaria reniformis) and 11 locations on the Great Barrier Reef were tested for background Symbiodinium clades. Although these colonies had been previously identified as harboring only a single clade based on SSCP analyses, background clades were detected in 78% of the samples, indicating that the potential for symbiont shuffling may be much larger than currently thought

Foraging by the stoplight parrotfish Sparisoma viride. I.:Food selection in different, socially determined habitats

Food selection by the Caribbean stoplight parrotfish Sparisoma viride was investigated on a fringing coral reef of Bonaire, Netherlands Antilles. For different reef zones, the diet composition for each life phase was determined by description of randomly selected bites, and compared to the availability of food resources, as determined with the aid of chain-link transects. S. viride employs an excavating grazing mode, and feeds almost exclusively on algae associated with dead coral substrates. Preferred food types are large and sparse turfs growing on carbonate substrates inhabited by endolithic algae. Crustose corallines, with or without algal turfs, are not preferred. Feeding forays were longer on the preferred food types. Foraging preferences are related to nutritional quality of the food types and their yield, i.e. the amounts of biomass, protein and energy that can be ingested per bite, as calculated from the size of grazing scars and the biochemical composition of the algae. In spite of selective foraging, a large proportion of bites is taken on inferior food types. Endolithic algae constitute an important food resource for scraping herbivores, such as S. viride, These algae have relatively high energetic value, and allow a high yield as a result of weakening the carbonate matrix by their boring filaments. The yield of algal resources also depends on the skeletal density of the limestone substrates. On deeper reef parts (> 3.5 m depth), low-density substrates predominate, resulting in higher yields of algae per bite than are attained from high-density substrates that predominate on shallower reef parts. The increased availability of high-yield food and substrate types coincides with the occurrence of haremic territorial behaviour in S. viride males on the deeper reef parts. Territories are defended against conspecifics and have an important function as spawning sites. It is argued that the access to superior food resources on the deeper reef makes territorial defence feasible for S. viride

Coulomb-assisted braiding of Majorana fermions in a Josephson junction array

We show how to exchange (braid) Majorana fermions in a network of superconducting nanowires by control over Coulomb interactions rather than tunneling. Even though Majorana fermions are charge-neutral quasiparticles (equal to their own antiparticle), they have an effective long-range interaction through the even-odd electron number dependence of the superconducting ground state. The flux through a split Josephson junction controls this interaction via the ratio of Josephson and charging energies, with exponential sensitivity. By switching the interaction on and off in neighboring segments of a Josephson junction array, the non-Abelian braiding statistics can be realized without the need to control tunnel couplings by gate electrodes. This is a solution to the problem how to operate on topological qubits when gate voltages are screened by the superconductor

Estimating the Potential for Adaptation of Corals to Climate Warming

The persistence of tropical coral reefs is threatened by rapidly increasing climate warming, causing a functional breakdown of the obligate symbiosis between corals and their algal photosymbionts (Symbiodinium) through a process known as coral bleaching. Yet the potential of the coral-algal symbiosis to genetically adapt in an evolutionary sense to warming oceans is unknown. Using a quantitative genetics approach, we estimated the proportion of the variance in thermal tolerance traits that has a genetic basis (i.e. heritability) as a proxy for their adaptive potential in the widespread Indo-Pacific reef-building coral Acropora millepora. We chose two physiologically different populations that associate respectively with one thermo-tolerant (Symbiodinium clade D) and one less tolerant symbiont type (Symbiodinium C2). In both symbiont types, pulse amplitude modulated (PAM) fluorometry and high performance liquid chromatography (HPLC) analysis revealed significant heritabilities for traits related to both photosynthesis and photoprotective pigment profile. However, quantitative real-time polymerase chain reaction (qRT-PCR) assays showed a lack of heritability in both coral host populations for their own expression of fundamental stress genes. Coral colony growth, contributed to by both symbiotic partners, displayed heritability. High heritabilities for functional key traits of algal symbionts, along with their short clonal generation time and high population sizes allow for their rapid thermal adaptation. However, the low overall heritability of coral host traits, along with the corals' long generation time, raise concern about the timely adaptation of the coral-algal symbiosis in the face of continued rapid climate warming

Die Agitpropbewegung als Teil der Arbeiterkultur der Weimarer Republik

The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources. Results: Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the "peaks" method, which can be applied to large numbers of SNPs, and the "curves" method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the "peaks" method can be rapidly scaled to screen several hundred SNPs at once, whereas the "curves" method is better suited for smaller numbers of SNPs. Conclusions: Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies.Australian Institute of Marine ScienceNational Science Foundation DEB-1054766Cellular and Molecular Biolog

Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium

Background: Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection.\ud \ud Methodology/Principal Findings: Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a ~30 m depth range) at three locations on the Great Barrier Reef (n = 336). The populations were assessed for genetic structure using a combination of mitochondrial (putative control region) and nuclear (three microsatellites) markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium). Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location.\ud \ud Conclusions/Significance: This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix