bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applications of Codon and Rate Variation Models in Molecular Phylogeny
Authors: Schadt Eric E. , Sinsheimer Janet S. , Lange Kenneth 
Published: January 2012

Abstract
The current article illustrates the practical advantages of some new models and statistical algorithms for codon substitution and spatial rate variation in molecular phylogeny. Our companion paper in this issue discusses at length the mathematical properties of these models for nucleotide and codon substitution, for site-to-site and branch-to-branch heterogeneity in rates of evolution, and for spatial correlation in the assignment of rates. In this study we summarize the theoretical background and apply the models and algorithms to data on β-globin, the complete HIV genome, and the mitochondrial genome. Our complex but realistic models enhance biological interpretation of sequence data and show substantial improvements in model fit over existing models. All the new statistical algorithms applied are incorporated in our phylogeny software LINNAEUS, which is tuned for performance and modeling flexibility.
A Strong Effect of AT Mutational Bias on Amino Acid Usage in Buchnera is Mitigated at High-Expression Genes
Authors: Palacios Carmen , Wernegreen Jennifer J. 
Published: January 2012

Abstract
The advent of full genome sequences provides exceptionally rich data sets to explore molecular and evolutionary mechanisms that shape divergence among and within genomes. In this study, we use multivariate analysis to determine the processes driving genome-wide patterns of amino usage in the obligate endosymbiont Buchnera and its close free-living relative Escherichia coli. In the AT-rich Buchnera genome, the primary source of variation in amino acid usage differentiates high- and low-expression genes. Amino acids of high-expression Buchnera genes are generally less aromatic and use relatively GC-rich codons, suggesting that selection against aromatic amino acids and against amino acids with AT-rich codons is stronger in high-expression genes. Selection to maintain hydrophobic amino acids in integral membrane proteins is a primary factor driving protein evolution in E. coli but is a secondary factor in Buchnera. In E. coli, gene expression is a secondary force driving amino acid usage, and a correlation with tRNA abundance suggests that translational selection contributes to this effect. Although this and previous studies demonstrate that AT mutational bias and genetic drift influence amino acid usage in Buchnera, this genome-wide analysis argues that selection is sufficient to affect the amino acid content of proteins with different expression and hydropathy levels.
The Plastid Chromosome of Atropa belladonna and its Comparison with that of Nicotiana tabacum: The Role of RNA Editing in Generating Divergence in the Process of Plant Speciation
Authors: Schmitz-Linneweber Christian , Regel Ralph , Du Tung Gia , Hupfer Holger , Herrmann Reinhold G. , Maier Rainer M. 
Published: January 2012

Abstract
The nuclear and plastid genomes of the plant cell form a coevolving unit which in interspecific combinations can lead to genetic incompatibility of compartments even between closely related taxa. This phenomenon has been observed for instance in Atropa-Nicotiana cybrids. We have sequenced the plastid chromosome of Atropa belladonna (deadly nightshade), a circular DNA molecule of 156,688 bp, and compared it with the corresponding published sequence of its relative Nicotiana tabacum (tobacco) to understand how divergence at the level of this genome can contribute to nuclear-plastid incompatibilities and to speciation. It appears that (1) regulatory elements, i.e., promoters as well as translational and replicational signal elements, are well conserved between the two species; (2) genes—including introns—are even more highly conserved, with differences residing predominantly in regions of low functional importance; and (3) RNA editotypes differ between the two species, which makes this process an intriguing candidate for causing rapid reproductive isolation of populations.
The 5′ Leader of Plant PgiC has an Intron: The Leader Shows Both the Loss and Maintenance of Constraints Compared with Introns and Exons in the Coding Region
Authors: Gottlieb L. D. , Ford V. S. 
Published: January 2012

Abstract
PgiC, a complex gene with 23 coding exons and 22 intervening introns, encodes the cytosolic isozyme of phosphoglucose isomerase (EC 5.3.1.9) in higher plants. Here, we report RNA ligase–mediated rapid amplification of cDNA ends experiments that showed that PgiC in Clarkia (Onagraceae) and Arabidopsis thaliana has an intron in the 5′ leader. Comparison of the EMBL accessions of the cDNA and genomic sequences showed that this is also the case in rice (Oryza sativa), suggesting that a leader intron is generally present in higher plant PgiC. The intron is bounded by consensus 5′-GT and AG-3′ splice sites but showed alternative splicing in Clarkia, resulting in mature transcripts that differ by 8–19 nt in length. The intron is located 18 or 10 nt upstream of the start codon in Clarkia, 2 nt upstream in Arabidopsis, and 9 nt in rice. PgiC in Clarkia was duplicated before the divergence of the extant species, many of which have two expressed genes PgiC1 and PgiC2. Full-length transcripts of both genes identified the transcription start and made it possible to identify the leader intron and leader exon (between the transcription start and leader intron) from previously obtained genomic sequences of both genes in other Clarkia species. These data permit the comparison of evolution in the leader exon and intron with the exons and introns of the coding region, a topic that has not been studied previously. Both the leader exon and the leader intron resemble introns of the coding region in base substitution rate and accumulation of gaps. But the leader intron splice junctions are not strictly conserved in position as are those of the coding region introns. Also, in base composition, the leader intron resembles the other introns, whereas the leader exon more nearly resembles the coding exons. A difference in base composition between coding exons and flanking introns is known to be important for the recognition of splice sites. Thus, the marked difference in base composition between the leader exon and leader intron is probably maintained by selection despite a high rate of sequence divergence.
Indoor radon levels in buildings in the autonomous community of Extremadura (Spain)
Authors: Baeza A. , Navarro E. , Roldán C. , L. Ferrero J. , Juanes D. , A. Corbacho J. , J. Guillén F. 
Published: January 2012

Abstract
Indoor air samples taken in buildings throughout the provinces of Cáceres and Badajoz in the Autonomous Community of Extremadura, Spain, were analysed for airborne radon concentrations using charcoal canisters. Measurements were made during the years 1998-2000. The geometrical mean indoor concentration was 90 Bq m-3. An estimated annual effective dose of 1.6 mSv y-1 was calculated for residents, assuming an equilibrium factor of 0.4 and an occupancy factor of 0.8. the relative importance of the principal variables that condition radon concentrations inside buildings was also delimited experimentally. These were soil type, construction materials used, the height of the room above ground level, and the degree of ventilation. The temporal evolution of the radon concentration was analysed, as this aspect could be particularly important in a Continental-Mediterranean climate such as that of the two provinces of the study.
Percutaneous mitral valve repair in a ventilator‐dependant patient
Authors: Davis C. 
Published: January 2012

SummaryI report the case of a 57‐year‐old patient admitted to the intensive care unit with severe community‐acquired pneumonia, complicated by prolonged mechanical ventilation of the lungs and intractable cardiac failure. He underwent percutaneous coronary angioplasty of the right coronary artery, but this did not improve his clinical condition. He was subsequently found to be suffering from mitral valve prolapse, that was felt to be the cause of recurrent episodes of severe pulmonary oedema. As open surgery was felt to be not feasible, the patient underwent percutaneous repair of his mitral valve using the MitraClip® device, and, after months of ventilatory support, was then weaned from the ventilator in a matter of days. While the procedure itself and the technology employed are still under evaluation, I conclude that the technique of percutaneous mitral valve repair may be considered for similar patients for whom open repair is contraindicated.
A comparison of Rapydan® patch and Ametop® gel for venous cannulation*
Authors: Ravishankar N. , Elliot S. C. , Beardow Z. , Mallick A. 
Published: January 2012

SummaryAmetop® gel (4% tetracaine) is used to provide topical anaesthesia for venous cannulation. Rapydan® patch (7% lidocaine and 7% tetracaine) has been developed to provide topical anaesthesia by a different mechanism, that of heat assisted delivery. We compared the topical anaesthetic effect of these agents for venous cannulation. One hundred healthy adults undergoing day‐case surgery were randomly assigned to receive either Rapydan (n = 50) or Ametop (n = 50) before venous cannulation. Pain on insertion was scored on a visual analogue scale between 0 and 100 (where 100 = unbearable pain). Median(IQR[range]) pain scores were not different between groups with 11 (5–20 [0–72]) for Rapydan and 10 (5–24 [0–95]) for Ametop (p = 0.63). Adequate topical anaesthesia was achieved in over 90% of patients in both groups. Rapydan produces topical anaesthesia comparable with Ametop for venous cannulation.
The projected effects of climatic and vegetation changes on the distribution and diversity of Southeast Asian bats
Authors: Hughes Alice C. , Satasook Chutamas , Bates Paul J. J. , Bumrungsri Sara , Jones Gareth 
Published: January 2012

AbstractSoutheast‐Asia (SEA) constitutes a global biodiversity hotspot, but is exposed to extensive deforestation and faces numerous threats to its biodiversity. Climate change represents a major challenge to the survival and viability of species, and the potential consequences must be assessed to allow for mitigation. We project the effects of several climate change scenarios on bat diversity, and predict changes in range size for 171 bat species throughout SEA. We predict decreases in species richness in all areas with high species richness (>80 species) at 2050–2080, using bioclimatic IPCC scenarios A2 (a severe scenario, continuously increasing human population size, regional changes in economic growth) and B1 (the ‘greenest’ scenario, global population peaking mid‐century). We also predicted changes in species richness in scenarios that project vegetation changes in addition to climate change up to 2050. At 2050 and 2080, A2 and B1 scenarios incorporating changes in climatic factors predicted that 3–9% species would lose all currently suitable niche space. When considering total extents of species distribution in SEA (including possible range expansions), 2–6% of species may have no suitable niche space in 2050–2080. When potential vegetation and climate changes were combined only 1% of species showed no changes in their predicted ranges by 2050. Although some species are projected to expand ranges, this may be ecologically impossible due to potential barriers to dispersal, especially for species with poor dispersal ability. Only 1–13% of species showed no projected reductions in their current range under bioclimatic scenarios. An effective way to facilitate range shift for dispersal‐limited species is to improve landscape connectivity. If current trends in environmental change continue and species cannot expand their ranges into new areas, then the majority of bat species in SEA may show decreases in range size and increased extinction risk within the next century.
Consequences of declining snow accumulation for water balance of mid‐latitude dry regions
Authors: Schlaepfer Daniel R. , Lauenroth William K. , Bradford John B. 
Published: January 2012

AbstractWidespread documentation of positive winter temperature anomalies, declining snowpack and earlier snow melt in the Northern Hemisphere have raised concerns about the consequences for regional water resources as well as wildfire. A topic that has not been addressed with respect to declining snowpack is effects on ecosystem water balance. Changes in water balance dynamics will be particularly pronounced at low elevations of mid‐latitude dry regions because these areas will be the first to be affected by declining snow as a result of rising temperatures. As a model system, we used simulation experiments to investigate big sagebrush ecosystems that dominate a large fraction of the semiarid western United States. Our results suggest that effects on future ecosystem water balance will increase along a climatic gradient from dry, warm and snow‐poor to wet, cold and snow‐rich. Beyond a threshold within this climatic gradient, predicted consequences for vegetation switched from no change to increasing transpiration. Responses were sensitive to uncertainties in climatic prediction; particularly, a shift of precipitation to the colder season could reduce impacts of a warmer and snow‐poorer future, depending on the degree to which ecosystem phenology tracks precipitation changes. Our results suggest that big sagebrush and other similar semiarid ecosystems could decrease in viability or disappear in dry to medium areas and likely increase only in the snow‐richest areas, i.e. higher elevations and higher latitudes. Unlike cold locations at high elevations or in the arctic, ecosystems at low elevations respond in a different and complex way to future conditions because of opposing effects of increasing water‐limitation and a longer snow‐free season. Outcomes of such nonlinear interactions for future ecosystems will likely include changes in plant composition and productivity, dynamics of water balance, and availability of water resources.
Size increase in high elevation ground squirrels over the last century
Authors: Eastman Lindsey M. , Morelli Toni Lyn , Rowe Kevin C. , Conroy Chris J. , Moritz Craig 
Published: January 2012

AbstractThere is increasing evidence for morphological change in response to recent environmental change, but how this relates to fluctuations in geographic range remains unclear. We measured museum specimens from two time periods (1902–1950 and 2000–2008) that vary significantly in climate to assess if and how two high elevation contracting species of ground squirrels in the Sierra Nevada of California, Belding's ground squirrel (Urocitellus beldingi) and the golden‐mantled ground squirrel (Callospermophilus lateralis), and one lower elevation, stable species, the California ground squirrel (Otospermophilus beecheyi), have responded morphologically to changes over the last century. We measured skull length (condylobasal length), an ontogenetically more labile trait highly correlated with body size, and maxillary toothrow length, a more developmentally constrained trait predictive of skull shape. C. lateralis and U. beldingi, both obligate hibernators, have increased in body size, but have not changed in shape. In contrast, O. beecheyi, which only hibernates in parts of its range, has shown no significant change in either morphometric trait. The increase in body size in the higher elevation species, hypothesized to be a plastic effect due to a longer growing season and thus prolonged food availability, opposes the expected direction of selection for decreased body size under chronic warming. Our study supports that population contraction is related to physiological rather than nutritional constraints.
Simulating devil facial tumour disease outbreaks across empirically derived contact networks
Authors: Hamede Rodrigo , Bashford Jim , Jones Menna , McCallum Hamish 
Published: January 2012

Summary1. Understanding the nature and characteristics of contact heterogeneities is crucial for predicting the epidemic behaviour of infectious diseases. Nonetheless, few studies include contact heterogeneities when modelling disease outbreaks in wildlife, which differ in their population impact from human diseases.2. We use empirical estimates of contact heterogeneities and network metrics to simulate outbreaks of devil facial tumour disease (DFTD), an extinction‐threatening infectious cancer. We incorporate tuneable algorithms, with a range of transmission rates and latent periods of DFTD, to grow devil population networks capable of reproducing observed aspects of devil ecology, demographic and seasonal‐based mixing preferences. The outputs of the network model are compared with a stochastic mean‐field model, in which every individual is equally likely to pass or acquire infection through time.3. Our network model predicts a lower epidemic threshold for DFTD compared with the stochastic mean‐field model. While host extinction probabilities are similar in both models, the network model predicts faster devil extinction and higher DFTD extinction probabilities, particularly for intermediate levels of transmissibility.4. While the time taken to devil extinction increases with the longer estimate of latent period, probabilities of both, disease and devil extinction, are greater with the shorter latent period. Host–pathogen coexistence is strictly subject to the longest plausible estimate of latent period and low transmissibility.5.
Synthesis and applications. In the particular case of DFTD, incorporating observed host network structure has only a modest effect on the outcome of the host pathogen interaction. In general, however, non‐random network structure may have major implications for the management of wildlife diseases. Our results suggest that this is particularly likely for pathogens in which the probability of transmission given a contact is intermediate. Our approach provides a template for using empirically obtained data on contact networks to develop models to explore the extent to which network structure influences R0, the probability of extinction and the mean time until extinction.
Assessing the role of competition and stress: a critique of importance indices and the development of a new approach
Authors: Rees Mark , Childs Dylan Z. , Freckleton Robert P. 
Published: January 2012

Summary1. Many studies have explored how plant interactions vary along environmental gradients, and these relationships are fundamental to the many ideas in vegetation dynamics.2. It has been argued that studies should differentiate between the intensity (absolute effect) and importance (relative effect) of a process, and several important indices have been presented in the literature.3. We explore the mathematical properties of one of the most popular of these indices (Cimp) and demonstrate that it is (i) insensitive to the underlying ecology, (ii) highly constrained, so making statistical analysis difficult and (iii) can have more complex behaviour than the processes it seeks to summarise.4. We demonstrate that the positive relationship between Cimp and productivity, which has been used to support the ideas of Grime, is entirely predictable without any information on competition and how it affects plant performance.5. The properties of three other competition indices (ACI, RCI and lnRR) in relation to habitat productivity are briefly presented. ACI is closely related to Cimp and so shares many of its properties, see Summary point 3 above.6. An alternative method of analysing variation in plant performance on environmental gradients is then presented. This approach, which is based on a variance decomposition, is easy to implement and has a simple biological interpretation.7. Synthesis. We strongly discourage the use of heuristic indices in ecological research. The majority of the 50 or so indices that have been used in competition studies have been developed with little or no regard to underlying theory or models. However, it is possible to make predictions about how competition varies along gradients from models that translate into both qualitative and quantitative conditions and metrics, and we encourage authors to do this.
Relationships between spatio‐temporal environmental and genetic variation reveal an important influence of exogenous selection in a pupfish hybrid zone
Authors: CARSON EVAN W. , TOBLER MICHAEL , MINCKLEY W. L. , AINSWORTH RYAN J. , DOWLING THOMAS E. 
Published: January 2012

AbstractThe importance of exogenous selection in a natural hybrid zone between the pupfishesCyprinodon atrorusandCyprinodon bifasciatuswas tested via spatio‐temporal analyses of environmental and genetic change over winter, spring and summer for three consecutive years. A critical influence of exogenous selection on hybrid zone regulation was demonstrated by a significant relationship between environmental (salinity and temperature) and genetic (three diagnostic nuDNA loci) variation over space and time (seasons) in the Rio Churince system, Cuatro Ciénegas, Mexico. At sites environmentally more similar to parental habitats, the genetic composition of hybrids was stable and similar to the resident parental species, whereas complex admixtures of parental and hybrid genotypic classes characterized intermediate environments, as did the greatest change in allelic and genotypic frequencies across seasons. Within hybrids across the entire Rio Churince system, seasonal changes in allelic and genotypic frequencies were consistent with results from previous reciprocal transplant experiments, which showedC. bifasciatusto suffer high mortality (75%) when exposed to the habitat ofC. atrorusin winter (extreme temperature lows and variability) and summer (abrupt salinity change and extreme temperature highs and variability). Although unconfirmed, the distributional limits ofC. atrorusandC. atrorus‐like hybrids appear to be governed by similar constraints (predation or competition). The argument favouring evolutionary significance of hybridization in animals is bolstered by the results of this study, which links the importance of exogenous selection in a contemporary hybrid zone betweenC. atrorusandC. bifasciatusto previous demonstration of the long‐term evolutionary significance of environmental variation and introgression on the phenotypic diversification Cuatro CiénegasCyprinodon.