A systematic review and meta-analysis of the direct effects of nutrients on corals

Chronic exposure of coral reefs to elevated nutrient conditions can modify the performance of the coral holobiont and shift the competitive interactions of reef organisms. Many studies have nowquantified the links between nutrients and coral performance, but fewhave translated these studies to directly address coastal water quality standards. To address this management need, we conducted a systematic review of peer-reviewed studies, public reports, and gray literature that examined the impacts of dissolved inorganic nitrogen (DIN: nitrate, nitrite, and ammonium) and dissolved inorganic phosphorus (DIP: phosphate) on scleractinian corals. The systematic review resulted in 47 studies with comparable data on coral holobiont responses to nutrients: symbiont density, chlorophyll α (chl-α) concentration, photosynthesis, photosynthetic efficiency, growth, calcification, adult survival, juvenile survival, and fertilization. Mixed-effects meta-regression meta-analyses were used to determine the magnitude of the positive or negative effects of DIN and DIP on coral responses. Zooxanthellae density (DIN & DIP), chl-α concentration (DIN), photosynthetic rate (DIN), and growth (DIP) all exhibited positive responses to nutrient addition; maximum quantum yield (DIP), growth (DIN), larval survival (DIN), and fertilization (DIN) exhibited negative responses. In lieu of developing specific thresholds for the management of nutrients as a stressor on coral reefs, we highlight important inflection points in the magnitude and direction of the effects of inorganic nutrients and identify trends among coral responses. The responses of corals to nutrients are complex, warranting conservative guidelines for elevated nutrient concentrations on coral reefs

Widespread horizontal transfer of mitochondrial genes in flowering plants

Horizontal gene transfer - the exchange of genes across mating barriers - is recognized as a major force in bacterial evolution(1,2). However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes(3-5). Although the human genome was initially reported(6) to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted(7,8). Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements(9-12). Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62688/1/nature01743.pd

Identification and Characterization of RcMADS1, an AGL24 Ortholog from the Holoparasitic Plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae)

10.1371/journal.pone.0067243PLoS ONE86-POLN

Factors influencing epiphytic bryophyte and lichen species richness at different spatial scales in managed temperate forests

The effect of management related factors on species richness of epiphytic bryophytes and lichens was studied in managed deciduous-coniferous mixed forests in Western-Hungary. At the stand level, the potential explanatory variables were tree species composition, stand structure, microclimate and light conditions, landscape and historical variables; while at tree level host tree species, tree size and light were studied. Species richness of the two epiphyte groups was positively correlated. Both for lichen and bryophyte plot level richness, the composition and diversity of tree species and the abundance of shrub layer were the most influential positive factors. Besides, for bryophytes the presence of large trees, while for lichens amount and heterogeneity of light were important. Tree level richness was mainly determined by host tree species for both groups. For bryophytes oaks, while for lichens oaks and hornbeam turned out the most favourable hosts. Tree size generally increased tree level species richness, except on pine for bryophytes and on hornbeam for lichens. The key variables for epiphytic diversity of the region were directly influenced by recent forest management; historical and landscape variables were not influential. Forest management oriented to the conservation of epiphyte s should focus on: (i) the maintenance of tree species diversity in mixed stands; (ii) increment the proportion of deciduous trees (mainly oaks); (iii) conserving large trees within the stands; (iv) providing the presence of shrub and regeneration layer; (v) creating heterogeneous light conditions. For these purposes tree selection and selective cutting management seem more appropriate than shelterwood system

Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147147/1/tax25065680.pd

Development of Secondary Woodland in Oak Wood Pastures Reduces the Richness of Rare Epiphytic Lichens

Wooded pastures with ancient trees were formerly abundant throughout Europe, but during the last century, grazing has largely been abandoned often resulting in dense forests. Ancient trees constitute habitat for many declining and threatened species, but the effects of secondary woodland on the biodiversity associated with these trees are largely unknown. We tested for difference in species richness, occurrence, and abundance of a set of nationally and regionally red-listed epiphytic lichens between ancient oaks located in secondary woodland and ancient oaks located in open conditions. We refined the test of the effect of secondary woodland by also including other explanatory variables. Species occurrence and abundance were modelled jointly using overdispersed zero-inflated Poisson models. The richness of the red-listed lichens on ancient oaks in secondary woodland was half of that compared with oaks growing in open conditions. The species-level analyses revealed that this was mainly the result of lower occupancy of two of the study species. The tree-level abundance of one species was also lower in secondary woodland. Potential explanations for this pattern are that the study lichens are adapted to desiccating conditions enhancing their population persistence by low competition or that open, windy conditions enhance their colonisation rate. This means that the development of secondary woodland is a threat to red-listed epiphytic lichens. We therefore suggest that woody vegetation is cleared and grazing resumed in abandoned oak pastures. Importantly, this will also benefit the vitality of the oaks

On plexus representation of dissimilarities

Correspondence analysis has found widespread application in analysing vegetation gradients. However, it is not clear how it is robust to situations where structures other than a simple gradient exist. The introduction of instrumental variables in canonical correspondence analysis does not avoid these difficulties. In this paper I propose to examine some simple methods based on the notion of the plexus (sensu McIntosh) where graphs or networks are used to display some of the structure of the data so that an informed choice of models is possible. I showthat two different classes of plexus model are available. These classes are distinguished by the use in one case of a global Euclidean model to obtain well-separated pair decomposition (WSPD) of a set of points which implicitly involves all dissimilarities, while in the other a Riemannian view is taken and emphasis is placed locally, i.e., on small dissimilarities. I showan example of each of these classes applied to vegetation data

First Results from HERA Phase I: Upper Limits on the Epoch of Reionization 21 cm Power Spectrum

We report upper limits on the Epoch of Reionization 21 cm power spectrum at redshifts 7.9 and 10.4 with 18 nights of data (∼36 hr of integration) from Phase I of the Hydrogen Epoch of Reionization Array (HERA). The Phase I data show evidence for systematics that can be largely suppressed with systematic models down to a dynamic range of ∼109 with respect to the peak foreground power. This yields a 95% confidence upper limit on the 21 cm power spectrum of 212≤(30.76)2mK2 at k = 0.192 h Mpc-1 at z = 7.9, and also 212≤(95.74)2mK2 at k = 0.256 h Mpc-1 at z = 10.4. At z = 7.9, these limits are the most sensitive to date by over an order of magnitude. While we find evidence for residual systematics at low line-of-sight Fourier k π modes, at high k π modes we find our data to be largely consistent with thermal noise, an indicator that the system could benefit from deeper integrations. The observed systematics could be due to radio frequency interference, cable subreflections, or residual instrumental cross-coupling, and warrant further study. This analysis emphasizes algorithms that have minimal inherent signal loss, although we do perform a careful accounting in a companion paper of the small forms of loss or bias associated with the pipeline. Overall, these results are a promising first step in the development of a tuned, instrument-specific analysis pipeline for HERA, particularly as Phase II construction is completed en route to reaching the full sensitivity of the experiment

The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades – Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes