Phylogenetic inference and evaluating support for inferred relationships is at the core of many studies testing evolutionary hypotheses. Despite the popularity of nonparametric bootstrap frequencies and Bayesian posterior probabilities, the interpretation of these measures of tree branch support remains a source of discussion. Furthermore, both methods are computationally expensive and become prohibitive for large data sets. Recent fast approximate likelihood-based measures of branch supports (approximate likelihood ratio test [aLRT] and Shimodaira–Hasegawa [SH]-aLRT) provide a compelling alternative to these slower conventional methods, offering not only speed advantages but also excellent levels of accuracy and power. Here we propose an additional method: a Bayesian-like transformation of aLRT (aBayes). Considering both probabilistic and frequentist frameworks, we compare the performance of the three fast likelihood-based methods with the standard bootstrap (SBS), the Bayesian approach, and the recently introduced rapid bootstrap. Our simulations and real data analyses show that with moderate model violations, all tests are sufficiently accurate, but aLRT and aBayes offer the highest statistical power and are very fast. With severe model violations aLRT, aBayes and Bayesian posteriors can produce elevated false-positive rates. With data sets for which such violation can be detected, we recommend using SH-aLRT, the nonparametric version of aLRT based on a procedure similar to the Shimodaira–Hasegawa tree selection. In general, the SBS seems to be excessively conservative and is much slower than our approximate likelihood-based methods.

This work investigated the roles of b-amylases in the breakdown of leaf starch. Of the nine b-amylase (BAM)-like proteins encoded in the Arabidopsis thaliana genome, at least four (BAM1, -2, -3, and -4) are chloroplastic. When expressed as recombinant proteins in Escherichia coli, BAM1, BAM2, and BAM3 had measurable b-amylase activity but BAM4 did not. BAM4 has multiple amino acid substitutions relative to characterized b-amylases, including one of the two catalytic residues. Modeling predicts major differences between the glucan binding site of BAM4 and those of active b-amylases. Thus, BAM4 probably lost its catalytic capacity during evolution. Total b-amylase activity was reduced in leaves of bam1 and bam3 mutants but not in bam2 and bam4 mutants. The bam3 mutant had elevated starch levels and lower nighttime maltose levels than the wild type, whereas bam1 did not. However, the bam1 bam3 double mutant had a more severe phenotype than bam3, suggesting functional overlap between the two proteins. Surprisingly, bam4 mutants had elevated starch levels. Introduction of the bam4 mutation into the bam3 and bam1 bam3 backgrounds further elevated the starch levels in both cases. These data suggest that BAM4 facilitates or regulates starch breakdown and operates independently of BAM1 and BAM3. Together, our findings are consistent with the proposal that b-amylase is a major enzyme of starch breakdown in leaves, but they reveal unexpected complexity in terms of the specialization of protein function.

Abstract. A Lagrangian approach has been used to assess the degree of chemically induced ozone loss in the Arctic lower stratosphere in winter 1991/1992. Trajectory calculations are used to identify air parcels probed by two ozonesondes at different points along the trajectories. A statistical analysis of the measured differences in ozone mixing ratio and the time the air parcel spent in sunlight between the measurements provides the chemical ozone loss. Initial results were first described by von der Gathen et al. [1995]. Here we present a more detailed description of the technique and a more comprehensive discussion of the results. Ozone loss rates of up to 10 ppbv per sunlit hour (or 54 ppbv per day) were found inside the polar vortex on the 475 K potential temperature surface (about 19.5 km in altitude) at the end of January. The period of rapid ozone loss coincides and slightly lags a period when temperatures were cold enough for type I polar stratospheric clouds to form. It is shown that the ozone loss occurs exclusively during the sunlit portions of the trajectories. The time evolution and vertical distribution of the ozone loss rates are discussed.

Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently introduced phylogenetic tests of alignment accuracy on a large number of gene families and contrast the performance of unfiltered versus filtered alignments in the context of single-gene phylogeny reconstruction. Based on multiple genome-wide empirical and simulated data sets, we show that the trees obtained from filtered MSAs are on average worse than those obtained from unfiltered MSAs. Furthermore, alignment filtering often leads to an increase in the proportion of well-supported branches that are actually wrong. We confirm that our findings hold for a wide range of parameters and methods. Although our results suggest that light filtering (up to 20% of alignment positions) has little impact on tree accuracy and may save some computation time, contrary to widespread practice, we do not generally recommend the use of current alignment filtering methods for phylogenetic inference. By providing a way to rigorously and systematically measure the impact of filtering on alignments, the methodology set forth here will guide the development of better filtering algorithms.

Hierarchical orthologous groups are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest. Identifying such groups is useful in a wide range of contexts, including inference of gene function, study of gene evolution dynamics and comparative genomics. Hierarchical orthologous groups can be derived from reconciled gene/species trees but, this being a computationally costly procedure, many phylogenomic databases work on the basis of pairwise gene comparisons instead (“graph-based” approach). To our knowledge, there is only one published algorithm for graph-based hierarchical group inference, but both its theoretical justification and performance in practice are as of yet largely uncharacterised. We establish a formal correspondence between the orthology graph and hierarchical orthologous groups. Based on that, we devise GETHOGs (“Graph-based Efficient Technique for Hierarchical Orthologous Groups”), a novel algorithm to infer hierarchical groups directly from the orthology graph, thus without needing gene tree inference nor gene/species tree reconciliation. GETHOGs is shown to correctly reconstruct hierarchical orthologous groups when applied to perfect input, and several extensions with stringency parameters are provided to deal with imperfect input data. We demonstrate its competitiveness using both simulated and empirical data. GETHOGs is implemented as a part of the freely-available OMA standalone package (http://omabrowser.org/standalone). Furthermore, hierarchical groups inferred by GETHOGs (“OMA HOGs”) on >1,000 genomes can be interactively queried via the OMA browser (http://omabrowser.org).

Abstract. Accurate long-term monitoring of total ozone is one of the most important requirements for identifying possible natural or anthropogenic changes in the composition of the stratosphere. For this purpose, the NDACC (Network for the Detection of Atmospheric Composition Change) UV-visible Working Group has made recommendations for improving and homogenizing the retrieval of total ozone columns from twilight zenith-sky visible spectrometers. These instruments, deployed all over the world in about 35 stations, allow measuring total ozone twice daily with limited sensitivity to stratospheric temperature and cloud cover. The NDACC recommendations address both the DOAS spectral parameters and the calculation of air mass factors (AMF) needed for the conversion of O 3 slant column densities into vertical column amounts. The most important improvement is the use of O 3 AMF lookup tables calculated using the TOMS V8 (TV8) O 3 profile climatology, that allows accounting for the dependence of the O 3 AMF on the seasonal and latitudinal variations of the O 3 vertical distribution. To investigate their imCorrespondence to: F. Hendrick (franch@oma.be) pact on the retrieved ozone columns, the recommendations have been applied to measurements from the NDACC/SAOZ (Système d'Analyse par Observation Zénithale) network. The revised SAOZ ozone data from eight stations deployed at all latitudes have been compared to TOMS, GOME-GDP4, SCIAMACHY-TOSOMI, SCIAMACHY-OL3, OMI-TOMS, and OMI-DOAS satellite overpass observations, as well as to those of collocated Dobson and Brewer instruments at Observatoire de Haute Provence (44 • N, 5.5 • E) and Sodankyla (67 • N, 27 • E), respectively. A significantly better agreement is obtained between SAOZ and correlative reference ground-based measurements after applying the new O 3 AMFs. However, systematic seasonal differences between SAOZ and satellite instruments remain. These are shown to mainly originate from (i) a possible problem in the satellite retrieval algorithms in dealing with the temperature dependence of the ozone cross-sections in the UV and the solar zenith angle (SZA) dependence, (ii) zonal modulations and seasonal variations of tropospheric ozone columns not accounted for in the TV8 profile climatology, and (iii) uncertainty on the stratospheric ozone profiles at high latitude in the winter in the TV8 climatology. For those measurements mostly sensitive to stratospheric temperature like TOMS, OMI-TOMS, Dobson and Brewer, or to SZA like Published by Copernicus Publications on behalf of the European Geosciences Union. 5976 F. Hendrick et al.: NDACC/SAOZ UV-visible total ozone measurements SCIAMACHY-TOSOMI, the application of temperature and SZA corrections results in the almost complete removal of the seasonal difference with SAOZ, improving significantly the consistency between all ground-based and satellite total ozone observations.

Tree-based tests of alignment methods enable the evaluation of the effect of gap placement on the inference of phylogenetic relationships.

[1] This paper describes the validation of ozone profiles from the Polar Ozone and Aerosol Measurement (POAM) III instrument. POAM III O 3 is measured with 1-km vertical resolution throughout most of the stratosphere and random errors of $5%. It is shown that sunspots do not significantly affect the POAM O 3 retrievals, nor do polar stratospheric clouds, except under rarely encountered, extreme conditions of very low O 3 and exceptionally high aerosol extinction. A statistical analysis is presented of comparisons between coincident measurements from POAM III and ozonesondes, the Halogen Occultation Experiment (HALOE) and the Stratospheric Aerosol and Gas Experiment (SAGE) II. On average, POAM III O 3 profiles agree to within ±5% with these correlative data from 13 to 60 km. There is a suggestion that from 30 to 60 km POAM III sunrise data might be biased slightly low (<5%) relative to POAM sunset data. There is evidence that POAM III has a high bias of up to $0.1 ppmv from 10 to 12 km, and that this bias might stem, in part, from errors in the retrieval of aerosol extinction at 0.6 mm, the primary O 3 absorption wavelength in the POAM retrievals. Below 10 km the POAM III data agree with coincident sonde measurements to better than 0.05 ppmv on average, which can correspond to large relative differences of more than +30% at 8-9 km and À100% at 5 km. We conclude that the POAM III profiles are highly accurate and adequate for quantitative scientific studies.