ALBERT

Description: Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.

Description: Among animals, genome sizes range from 20 Mb to 130 Gb, with 380-fold variation across vertebrates. Most of the largest vertebrate genomes are found in salamanders, an amphibian clade of 660 species. Thus, salamanders are an important system for studying causes and consequences of genomic gigantism. Previously, we showed that plethodontid salamander genomes accumulate higher levels of long terminal repeat (LTR) retrotransposons than do other vertebrates, although the evolutionary origins of such sequences remained unexplored. We also showed that some salamanders in the family Plethodontidae have relatively slow rates of DNA loss through small insertions and deletions. Here, we present new data from Cryptobranchus alleganiensis , the hellbender. Cryptobranchus and Plethodontidae span the basal phylogenetic split within salamanders; thus, analyses incorporating these taxa can shed light on the genome of the ancestral crown salamander lineage, which underwent expansion. We show that high levels of LTR retrotransposons likely characterize all crown salamanders, suggesting that disproportionate expansion of this transposable element (TE) class contributed to genomic expansion. Phylogenetic and age distribution analyses of salamander LTR retrotransposons indicate that salamanders’ high TE levels reflect persistence and diversification of ancestral TEs rather than horizontal transfer events. Finally, we show that relatively slow DNA loss rates through small indels likely characterize all crown salamanders, suggesting that a decreased DNA loss rate contributed to genomic expansion at the clade’s base. Our identification of shared genomic features across phylogenetically distant salamanders is a first step toward identifying the evolutionary processes underlying accumulation and persistence of high levels of repetitive sequence in salamander genomes.

Description: Evolutionary changes in genome size result from the combined effects of mutation, natural selection, and genetic drift. Insertion and deletion mutations (indels) directly impact genome size by adding or removing sequences. Most species lose more DNA through small indels (i.e., ~1–30 bp) than they gain, which can result in genome reduction over time. Because this rate of DNA loss varies across species, small indel dynamics have been suggested to contribute to genome size evolution. Species with extremely large genomes provide interesting test cases for exploring the link between small indels and genome size; however, most large genomes remain relatively unexplored. Here, we examine rates of DNA loss in the tetrapods with the largest genomes—the salamanders. We used low-coverage genomic shotgun sequence data from four salamander species to examine patterns of insertion, deletion, and substitution in neutrally evolving non-long terminal repeat (LTR) retrotransposon sequences. For comparison, we estimated genome-wide DNA loss rates in non-LTR retrotransposon sequences from five other vertebrate genomes: Anolis carolinensis , Danio rerio , Gallus gallus , Homo sapiens , and Xenopus tropicalis . Our results show that salamanders have significantly lower rates of DNA loss than do other vertebrates. More specifically, salamanders experience lower numbers of deletions relative to insertions, and both deletions and insertions are skewed toward smaller sizes. On the basis of these patterns, we conclude that slow DNA loss contributes to genomic gigantism in salamanders. We also identify candidate molecular mechanisms underlying these differences and suggest that natural variation in indel dynamics provides a unique opportunity to study the basis of genome stability.

Description: Airborne in-situ observations of ClO in the tropics were made during the TROCCINOX (Aracatuba, Brazil, February 2005) and SCOUT-O3 (Darwin, Australia, November/December 2005) field campaigns. While during most flights significant amounts of ClO (≈10–20 parts per trillion, ppt) were present only in aged stratospheric air, instances of enhanced ClO mixing ratios of up to 40 ppt – significantly exceeding those expected from gas phase chemistry – were observed in air masses of a more tropospheric character. Most of these observations are associated with low temperatures or with the presence of cirrus clouds (often both), suggesting that cirrus ice particles and/or liquid aerosol at low temperatures may promote significant heterogeneous chlorine activation in the tropical upper troposphere lower stratosphere (UTLS). In two case studies, particularly high levels of ClO observed were reproduced by chemistry simulations only under the assumption that significant denoxification had occurred in the observed air. However, to reproduce the ClO observations in these simulations, O3 mixing ratios higher than observed had to be assumed, and at least for one of these flights, a significant denoxification is in contrast to the observed NO levels, suggesting that the coupling of chlorine and nitrogen compounds in the tropical UTLS may not be completely understood.

Description: Multi-annual simulations with the Chemical Lagrangian Model of the Stratosphere (CLaMS) were conducted to study the seasonality of O3 within the stratospheric part of the tropical tropopause layer (TTL), i.e. above θ=360 K potential temperature level. In agreement with satellite (HALOE) and in-situ observations (SHADOZ), CLaMS simulations show a pronounced annual cycle in O3, at and above θ=380 K, with the highest mixing ratios in the late boreal summer. Within the model, this cycle is driven by the seasonality of both upwelling and in-mixing. The latter process occurs through enhanced horizontal transport from the extratropics into the TTL that is mainly driven by the meridional, isentropic winds. The strongest in-mixing occurs during the late boreal summer from the Northern Hemisphere in the potential temperature range between 370 and 420 K. Complementary, the strongest upwelling occurs in winter reducing O3 to the lowest values in early spring. Both CLaMS simulations and Aura MLS O3 observations consistently show that enhanced in-mixing in summer is mainly driven by the Asian monsoon anticyclone.

Description: Using a combination of ozonesonde data and numerical simulations of the Chemical Lagrangian Model of the Stratosphere (CLaMS), the trend of tropospheric ozone (O3) during 2002–2010 over Beijing was investigated. Tropospheric ozone over Beijing shows a winter minimum and a broad summer maximum with a clear positive trend in the maximum summer ozone concentration over the last decade. The observed significant trend of tropospheric column ozone is mainly caused by photochemical production (3.1% yr−1 for a mean level of 52 DU). This trend is close to the significant trend of partial column ozone in the lower troposphere (0–3 km) resulting from the enhanced photochemical production during summer (3.0% yr−1 for a mean level of 23 DU). Analysis of the CLaMS simulation shows that transport rather than chemistry drives most of the seasonality of tropospheric ozone. However, dynamical processes alone cannot explain the trend of tropospheric ozone in the observational data. Clearly enhanced ozone values and a negative vertical ozone gradient in the lower troposphere in the observational data emphasize the importance of photochemistry within the troposphere during spring and summer, and suggest that the photochemistry within the troposphere significantly contributes to the tropospheric ozone trend over Beijing during the last decade.

Description: A modified form of tracer–tracer correlations of N2O and O3 has been used as a tool for the evaluation of atmospheric photochemical models. Applying this method, monthly averages of N2O and O3 are derived for both hemispheres by partitioning the data into altitude (or potential temperature) bins and then averaging over a fixed interval of N2O. In a previous study, the method has been successfully applied to the evaluation of two chemical transport models (CTMs) and one chemistry–climate model (CCM) using a 1 yr climatology derived from the Odin Sub-Millimetre Radiometer (Odin/SMR). However, the applicability of a 1 yr climatology of monthly averages of N2O and O3 has been questioned due to the inability of some CCMs to simulate a specific year for the evaluation of CCMs. In this study, satellite measurements from Odin/SMR, the Aura Microwave Limb Sounder (Aura/MLS), the Michelson Interferometer for Passive Atmospheric Sounding on ENVISAT (ENVISAT/MIPAS), and the Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere (CRISTA-1 and CRISTA-2) as well as model simulations from the Whole Atmosphere Community Climate Model (WACCM) are considered. By using seven to eight years of satellite measurements derived between 2003 and 2010 from Odin/SMR, Aura/MLS, ENVISAT/MIPAS and six years of model simulations from WACCM, the interannual variability of lower stratospheric monthly averages of N2O and O3 is assessed. It is shown that the interannual variability of the monthly averages of N2O and O3 is low, and thus can be easily distinguished from model deficiencies. Furthermore, it is investigated why large differences are found between Odin/SMR observations and model simulations from the Karlsruhe Simulation Model of the Middle Atmosphere (KASIMA) and the atmospheric general circulation model ECHAM5/Messy1 for the Northern and Southern Hemisphere tropics (0° to 30° N and 0° to −30° S, respectively). The differences between model simulations and observations are most likely caused by an underestimation of the quasi-biennial oscillation and tropical upwelling by the models as well as due to biases and/or instrument noise from the satellite instruments. A realistic consideration of the QBO in the model reduces the differences between model simulation and observations significantly. Finally, an intercomparison between Odin/SMR, Aura/MLS, ENVISAT/MIPAS and WACCM was performed. The comparison shows that these data sets are generally in good agreement, although some known biases of the data sets are clearly visible in the monthly averages. Nevertheless, the differences caused by the uncertainties of the satellite data sets are sufficiently small and can be clearly distinguished from model deficiencies. Thus, the method applied in this study is not only a valuable tool for model evaluation, but also for satellite data intercomparisons.

Description: We explore the potential of ozone observations to constrain transport processes in the tropical tropopause layer (TTL), and contrast it with insights that can be obtained from water vapour. Global fields from Halogen Occultation Experiment (HALOE) and in-situ observations are predicted using a backtrajectory approach that captures advection, instantaneous freeze-drying and photolytical ozone production. Two different representations of transport (kinematic and diabatic 3-month backtrajectories based on ERA-Interim data) are used to evaluate the sensitivity to differences in transport. Results show that mean profiles and seasonality of both tracers can be reasonably reconstructed. Water vapour predictions are similar for both transport representations, but predictions for ozone are systematically higher for kinematic transport. Compared to global HALOE observations, the diabatic model prediction underestimates the vertical ozone gradient. Comparison of the kinematic prediction with observations obtained during the tropical SCOUT-O3 campaign shows a large high bias above 390 K potential temperature. We show that ozone predictions and vertical dispersion of the trajectories are highly correlated, rendering ozone an interesting tracer for aspects of transport to which water vapour is not sensitive. We show that dispersion and mean upwelling have similar effects on ozone profiles, with slower upwelling and larger dispersion both leading to higher ozone concentrations. Analyses of tropical upwelling based on mean transport characteristics, and model validation have to take into account this ambiguity between tropical ozone production and in-mixing from the stratosphere. In turn, ozone provides constraints on transport in the TTL and lower stratosphere that cannot be obtained from water vapour.

Description: In January 2010 and December 2011, synoptic-scale polar stratospheric cloud (PSC) fields were probed during seven flights of the high-altitude research aircraft M-55 Geophysica within the RECONCILE (Reconciliation of essential process parameters for an enhanced predictability of Arctic stratospheric ozone loss and its climate interaction) and the ESSenCe (ESSenCe: ESA Sounder Campaign) projects. Particle size distributions in a diameter range between 0.46 and 40μm were recorded by four different optical in situ instruments. Three of these particle instruments are based on the detection of forward-scattered light by single particles. The fourth instrument is a grayscale optical array imaging probe. Optical particle diameters of up to 35μm were detected with particle number densities and total particle volumes exceeding previous Arctic measurements. Also, gas-phase and particle-bound NOy was measured, as well as water vapor concentrations. The optical characteristics of the clouds were measured by the remote sensing lidar MAL (Miniature Aerosol Lidar) and by the in situ backscatter sonde MAS (Multiwavelength Aerosol Scatterometer), showing the synoptic scale of the encountered PSCs. The particle mode below 2μm in size diameter has been identified as supercooled ternary solution (STS) droplets. The PSC particles in the size range above 2μm in diameter are considered to consist of nitric acid hydrates, and the particles' high HNO3 content was confirmed by the NOy instrument. Assuming a particle composition of nitric acid trihydrate (NAT), the optically measured size distributions result in particle-phase HNO3 mixing ratios exceeding available stratospheric values. Therefore the measurement uncertainties concerning probable overestimations of measured particle sizes and volumes are discussed in detail. We hypothesize that either a strong asphericity or an alternate particle composition (e.g., water ice coated with NAT) could explain our observations. In particular, with respect to the denitrification by sedimentation of large HNO3-containing particles, generally considered to be NAT, our new measurements raise questions concerning composition, shape and nucleation pathways. Answering these would improve the numerical simulation of PSC microphysical processes like cloud particle formation, growth and denitrification, which is necessary for better predictions of future polar ozone losses, especially under changing global climate conditions. Generally, it seems that the occurrence of large NAT particles – sometimes termed "NAT rocks" – are a regular feature of synoptic-scale PSCs in the Arctic.