bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of active hot-spring analogues of Rhynie: environments, habitats and ecosystems
Authors: Channing Alan 
Published: December 2017

The Lower Devonian Rhynie chert formed as silica sinter entombed an early terrestrial ecosystem. Silica sinter precipitates only from water flowing from alkali-chloride hot springs and geysers, the surface expression of crustal-scale geothermal systems that form low-sulfidation mineral deposits in the shallow subsurface. Active alkali-chloride hot springs at Yellowstone National Park create a suite of geothermally influenced environments; vent pools, sinter aprons, run-off streams, supra-apron terrace pools and geothermal wetlands that are habitats for modern hot-spring ecosystems. The plant-rich chert, which makes Rhynie internationally famous, probably formed in low-temperature environments at the margins of a sinter apron where frequent flooding by geothermal water and less frequent flooding by river waters created ephemeral to permanent wetland conditions. Here, the plants and associated microbes and animals would be immersed in waters with elevated temperature, brackish salinity, high pH and a cocktail of phytotoxic elements which created stresses that the fossil ecosystem must have tolerated. The environment excluded coeval mesophytic plants, creating a low-diversity hot-spring flora. Comparison with Yellowstone suggests the Rhynie plants were preadapted to their environment by life in more common and widespread environments with elevated salinity and pH such as coastal marshes, salt lakes, estuaries and saline seeps.
This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Palaeoecology and palaeophytogeography of the Rhynie chert plants: further evidence from integrated analysis ofin situand dispersed spores
Authors: Wellman Charles H. 
Published: December 2017

The remarkably preserved Rhynie chert plants remain pivotal to our understanding of early land plants. The extraordinary anatomical detail they preserve is a consequence of exceptional preservation, by silicification, in the hot-springs environment they inhabited. However, this has prompted questions as to just how typical of early land plants the Rhynie chert plants really are. Some have suggested that they were highly adapted to the unusual hot-springs environment and are unrepresentative of ‘normal’ plants of the regional flora. New quantitative analysis of dispersed spore assemblages from the stratigraphical sequence of the Rhynie outlier, coupled with characterization of thein situspores of the Rhynie chert plants, permits investigation of their palaeoecology and palaeophytogeography. It is shown that the Rhynie inland intermontane basin harboured a relatively diverse flora with only a small proportion of these plants actually inhabiting the hot-springs environment. However, the flora of the Rhynie basin differed from coeval lowland floodplain deposits on the same continent, as it was less diverse, lacked some important spore groups and contained some unique elements. At least some of the Rhynie plants (e.g.Horneophyton lignieri) existed outside the hot-springs environment, inhabiting the wider basin, and were indeed palaeogeographically widespread. They probably existed in the hot-springs environment because they were preadapted to this unstable and harsh setting.This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
The origin and early evolution of vascular plant shoots and leaves
Authors: Harrison C. Jill , Morris Jennifer L. 
Published: December 2017

The morphology of plant fossils from the Rhynie chert has generated longstanding questions about vascular plant shoot and leaf evolution, for instance, which morphologies were ancestral within land plants, when did vascular plants first arise and did leaves have multiple evolutionary origins? Recent advances combining insights from molecular phylogeny, palaeobotany and evo–devo research address these questions and suggest the sequence of morphological innovation during vascular plant shoot and leaf evolution. The evidence pinpoints testable developmental and genetic hypotheses relating to the origin of branching and indeterminate shoot architectures prior to the evolution of leaves, and demonstrates underestimation of polyphyly in the evolution of leaves from branching forms in ‘telome theory’ hypotheses of leaf evolution. This review discusses fossil, developmental and genetic evidence relating to the evolution of vascular plant shoots and leaves in a phylogenetic framework.This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Bilaterally symmetric axes with rhizoids composed the rooting structure of the common ancestor of vascular plants
Authors: Hetherington Alexander J. , Dolan Liam 
Published: December 2017

There are two general types of rooting systems in extant land plants: gametophyte rhizoids and sporophyte root axes. These structures carry out the rooting function in the free-living stage of almost all land plant gametophytes and sporophytes, respectively. Extant vascular plants develop a dominant, free-living sporophyte on which roots form, with the exception of a small number of taxa that have secondarily lost roots. However, fossil evidence indicates that early vascular plants did not develop sporophyte roots. We propose that the common ancestor of vascular plants developed a unique rooting system—rhizoidal sporophyte axes. Here we present a synthesis and reinterpretation of the rootless sporophytes ofHorneophyton lignieri,Aglaophyton majus,Rhynia gwynne-vaughaniiandNothia aphyllapreserved in the Rhynie chert. We show that the sporophyte rooting structures of all four plants comprised regions of plagiotropic (horizontal) axes that developed unicellular rhizoids on their underside. These regions of axes with rhizoids developed bilateral symmetry making them distinct from the other regions which were radially symmetrical. We hypothesize that rhizoidal sporophyte axes constituted the rooting structures in the common ancestor of vascular plants because the phylogenetic positions of these plants span the origin of the vascular lineage.This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
FertilePrototaxites taiti: a basal ascomycete with inoperculate, polysporous asci lacking croziers
Authors: Honegger Rosmarie , Edwards Dianne , Axe Lindsey , Strullu-Derrien Christine 
Published: December 2017

The affinities ofPrototaxiteshave been debated ever since its fossils, some attaining tree-trunk proportions, were discovered in Canadian Lower Devonian rocks in 1859. Putative assignations include conifers, red and brown algae, liverworts and fungi (some lichenised). Detailed anatomical investigation led to the reconstruction of the type species,P. logani, as a giant sporophore (basidioma) of an agaricomycete (= holobasidiomycete), but evidence for its reproduction remained elusive. Tissues associated withP. taitiin the Rhynie chert plus charcoalified fragments from southern Britain are investigated here to describe the reproductive characters and hence affinities ofPrototaxites. Thin sections and peels (Pragian Rhynie chert, Aberdeenshire) were examined using light and confocal microscopy; Přídolí and Lochkovian charcoalified samples (Welsh Borderland) were liberated from the rock and examined with scanning electron microscopy.Prototaxites taitipossessed a superficial hymenium comprising an epihymenial layer, delicate septate paraphyses, inoperculate polysporic asci lacking croziers and a subhymenial layer composed predominantly of thin-walled hyphae and occasional larger hyphae.Prototaxites taiticombines features of extant Taphrinomycotina (Neolectomycetes lacking croziers) and Pezizomycotina (epihymenial layer secreted by paraphyses) but is not an ancestor of the latter. Brief consideration is given to its nutrition and potential position in the phylogeny of the Ascomycota.This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Changing expressions: a hypothesis for the origin of the vascular plant life cycle
Authors: Kenrick Paul 
Published: December 2017

Plant life cycles underwent fundamental changes during the initial colonization of the land in the Early Palaeozoic, shaping the direction of evolution. Fossils reveal unanticipated diversity, including new variants of meiotic cell division and leafless gametophytes with mycorrhizal-like symbioses, rhizoids, vascular tissues and stomata. Exceptional fossils from the 407-Ma Rhynie chert (Scotland) play a key role in unlocking this diversity. These fossils are reviewed against progress in our understanding of the plant tree of life and recent advances in developmental genetics. Combining data from different sources sheds light on a switch in life cycle that gave rise to the vascular plants. One crucial step was the establishment of a free-living sporophyte from one that was an obligate matrotroph borne on the gametophyte. It is proposed that this difficult evolutionary transition was achieved through expansion of gene expression primarily from the gametophyte to the sporophyte, establishing a now extinct life cycle variant that was more isomorphic than heteromorphic. These changes also linked for the first time in one developmental system rhizoids, vascular tissues and stomata, putting in place the critical components that regulate transpiration and forming a physiological platform of primary importance to the diversification of vascular plants.
This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection
Authors: Gorjanc Gregor , Gaynor R. Chris , Hickey John M. 
Published: December 2017

AbstractThis study evaluates optimal cross selection for balancing selection and maintenance of genetic diversity in two-part plant breeding programs with rapid recurrent genomic selection. The two-part program reorganizes a conventional breeding program into population improvement component with recurrent genomic selection to increase the mean of germplasm and product development component with standard methods to develop new lines. Rapid recurrent genomic selection has a large potential, but is challenging due to genotyping costs or genetic drift. Here we simulate a wheat breeding program for 20 years and compare optimal cross selection against truncation selection in the population improvement with one to six cycles per year. With truncation selection we crossed a small or a large number of parents. With optimal cross selection we jointly optimised selection, maintenance of genetic diversity, and cross allocation with AlphaMate program. The results show that the two-part program with optimal cross selection delivered the largest genetic gain that increased with the increasing number of cycles. With four cycles per year optimal cross selection had 78% (15%) higher long-term genetic gain than truncation selection with a small (large) number of parents. Higher genetic gain was achieved through higher efficiency of converting genetic diversity into genetic gain; optimal cross selection quadrupled (doubled) efficiency of truncation selection with a small (large) number of parents. Optimal cross selection also reduced the drop of genomic selection accuracy due to the drift between training and prediction populations. In conclusion, optimal cross-selection enables optimal management and exploitation of population improvement germplasm in two-part programs.Key messageOptimal cross selection increases long-term genetic gain of two-part programs with rapid recurrent genomic selection. It achieves this by optimising efficiency of converting genetic diversity into genetic gain through reducing the loss of genetic diversity and reducing the drop of genomic prediction accuracy with rapid cycling.
Sex-specific genome-wide association study in glioma identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21
Authors: Ostrom Quinn T. , Kinnersley Ben , Wrensch Margaret R. , Eckel-Passow Jeanette E. , Armstrong Georgina , Rice Terri , Chen Yanwen , Wiencke John K. , McCoy Lucie S. , Hansen Helen M. , Amos Christopher I. , Bernstein Jonine L. , Claus Elizabeth B. , Il’yasova Dora , Johansen Christoffer , Lachance Daniel H. , Lai Rose K. , Merrell Ryan T. , Olson Sara H. , Sadetzki Siegel , Schildkraut Joellen M. , Shete Sanjay , Rubin Joshua B. , Lathia Justin D. , Berens Michael E. , Andersson Ulrika , Rajaraman Preetha , Chanock Stephen J. , Linet Martha S. , Wang Zhaoming , Linet Martha S. , Wang Zhaoming , Yeager Meredith ,   on behalf of the GliomaScan consortium, Houlston Richard S. , Jenkins Robert B. , Melin Beatrice , Bondy Melissa L. , Barnholtz-Sloan Jill. S. 
Published: December 2017

AbstractIncidence of glioma is approximately 50% higher in males. Previous analyses have examined exposures related to sex hormones in women as potential protective factors for these tumors, with inconsistent results. Previous glioma genome-wide association studies (GWAS) have not stratified by sex. Potential sex-specific genetic effects were assessed in autosomal SNPs and sex chromosome variants for all glioma, GBM and non-GBM patients using data from four previous glioma GWAS. Datasets were analyzed using sex-stratified logistic regression models and combined using meta-analysis. There were 4,831 male cases, 5,216 male controls, 3,206 female cases and 5,470 female controls. A significant association was detected at rs11979158 (7p11.2) in males only. Association at rs55705857 (8q24.21) was stronger in females than in males. A large region on 3p21.31 was identified with significant association in females only. The identified differences in effect of risk variants do not fully explain the observed incidence difference in glioma by sex.
Long-read sequencing of nascent RNA reveals coupling among RNA processing events
Authors: Herzel Lydia , Straube Korinna , Neugebauer Karla M. 
Published: December 2017

AbstractPre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur co-transcriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe. Most multi-intron transcripts were fully spliced, consistent with rapid co-transcriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in Prp2, the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded co-transcriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of co-transcriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3’ end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation.
Molecular data from Orthonectid worms show they are highly degenerate members of phylum Annelida not phylum Mesozoa
Authors: Schiffer Philipp H. , Robertson Helen E. , Telford Maximilian J. 
Published: December 2017

Summary:The Mesozoa are a group of tiny, extremely simple, vermiform endoparasites of various marine animals (Fig. 1). There are two recognised groups within the Mesozoa: the Orthonectida (Fig. 1a,b; with a few hundred cells including a nervous system made up of just 10 cells [1]) and the Dicyemids (Fig. 1c; with at most 42 cells [2]). They are classic ‘Problematica’ [3] - the name Mesozoa suggests an evolutionary position intermediate between Protozoa and Metazoa (animals) [4] and implies their simplicity is a primitive state, but molecular data have shown they are members of Lophotrochozoa within Bilateria [5-8] which would mean they derive from a more complex ancestor. Their precise phylogenetic affinities remain uncertain, however, and ascertaining this is complicated by the very fast evolution observed in genes from both groups, leading to the common systematic error of Long Branch Attraction (LBA) [9]. Here we use mitochondrial and nuclear gene sequence data, and show beyond doubt that both dicyemids and orthonectids are members of the Lophotrochozoa. Carefully addressing the effects of systematic errors due to unequal rates of evolution, we show that the phylum Mesozoa is polyphyletic. While the precise position of dicyemids remains unresolved within Lophotrochozoa, we unequivocally identify orthonectids as members of the phylum Annelida. This result reveals one of the most extreme cases of body plan simplification in the animal kingdom; our finding makes sense of an annelid-like cuticle in orthonectids [1] and suggests the circular muscle cells repeated along their body [10] may be segmental in origin.
Deep generative models of genetic variation capture mutation effects
Authors: Riesselman Adam J. , Ingraham John B. , Marks Debora S. 
Published: December 2017

AbstractThe functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise interactions, these approaches do not provide a tractable path towards modeling higher-order dependencies. Here, we show how latent variable models with nonlinear dependencies can be applied to capture beyond-pairwise constraints in biomolecules. We present a new probabilistic model for sequence families, DeepSequence, that can predict the effects of mutations across a variety of deep mutational scanning experiments significantly better than site independent or pairwise models that are based on the same evolutionary data. The model, learned in an unsupervised manner solely from sequence information, is grounded with biologically motivated priors, reveals latent organization of sequence families, and can be used to extrapolate to new parts of sequence space.
Biodiversity loss under future global socio-economic and climate scenarios
Authors: Chaudhary Abhishek , Mooers Arne O. 
Published: December 2017

ABSTRACTEfficient forward-looking mitigation measures are needed to halt the global biodiversity decline. These require spatially explicit scenarios of expected changes in multiple indicators of biodiversity under future socio-economic and environmental conditions. Here we link five future (2050 and 2100) global gridded maps (0.25° × 0.25° resolution) available from the land use harmonization (LUH) database that represent alternative representative concentration and shared socio-economic pathways (RCP-SSP) with the countryside species-area relationship model to project the future land use change driven rates of species extinctions and phylogenetic diversity loss (in million years) for mammals, birds and amphibians in each of the 804 terrestrial ecoregions and 176 countries and compare them to the current (1900-2015) and past (850-1900) rates of biodiversity loss. Future land-use changes are projected to commit an additional 209-818 endemic species and 1190-4402 million years of evolutionary history to extinction by 2100 depending upon the scenario, equivalent to 20–80% of the number committed to extinction under current (2015) land use extent. Results show that hotspots of future biodiversity loss differ depending upon the scenario, taxon and metric considered. The most aggressive climate mitigation scenario (RCP2.6 SSP-1), representing a world shifting towards a radically more sustainable path including increasing crop yields, reduced meat production and reduced tropical deforestation coupled with high trade, projects the lowest land use change driven global biodiversity loss followed by RCP8.5 SSP-5, RCP6.0 SSP-4 and RCP7.0 SSP-3. Interestingly, the scenario with the second most aggressive climate target (RCP3.4 SSP-4) projected the highest biodiversity loss among the five scenarios tested. This is because it represents a world with continued high consumption in rich countries and increased land clearing for crop production in species rich, low-income countries such as Indonesia, Madagascar, Tanzania, Philippines and DR Congo. These contrasting results illustrate that the strategies to prevent climate change could simultaneously contribute to reduction in current high rates of biodiversity loss, but only if habitat preservation is incorporated into national and global sustainable development plans.
Multivariate genotypic analyses that identify specific genotypes to characterize disease and control groups in ADNI
Authors: Beaton Derek , Rieck Jenny R. , Alhazmi Fahd ,   ADNI, Abdi Hervé 
Published: December 2017

AbstractINTRODUCTIONGenetic contributions to Alzheimer’s Disease (AD) are likely polygenic and not necessarily explained by uniformly applied linear and additive effects. In order to better understand the genetics of AD, we require statistical techniques to address both polygenic and possible non-additive effects.METHODSWe used partial least squares-correspondence analysis (PLS-CA)—a method designed to detect multivariate genotypic effects. We used ADNI-1 (N = 756) as a discovery sample with two forms of PLS-CA: diagnosis-based and ApoE-based. We used ADNI-2 (N= 791) as a validation sample with a diagnosis-based PLS-CA.RESULTSWith PLS-CA we identified some expected genotypic effects (e.g., APOE/TOMM40, and APP) and a number of new effects that include, for examples, risk-associated genotypes in RBFOX1 and GPC6 and control-associated genotypes in PTPN14 and CPNE5.DISCUSSIONThrough the use of PLS-CA, we were able to detect complex (multivariate, genotypic) genetic contributions to AD, which included many non-additive and non-linear risk and possibly protective effects.