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: Chemical ozone loss in the Arctic stratosphere was investigated for the twelve years between 1991 and 2003 employing the ozone-tracer correlation method. For this method, the change in the relation between ozone and a long-lived tracer is considered for all twelve years over the lifetime of the polar vortex to calculate chemical ozone loss. Both the accumulated local ozone loss in the lower stratosphere and the column ozone loss were derived consistently, mainly on the basis of HALOE satellite observations. HALOE measurements do not cover the polar region homogeneously over the course of the winter. Thus, to derive an early winter reference function for each of the twelve years, all available measurements were additionally used; for two winters climatological considerations were necessary. Moreover, a detailed quantification of uncertainties was performed. This study further demonstrates the interaction between meteorology and ozone loss. The connection between temperature conditions and chlorine activation, and in turn, the connection between chlorine activation and ozone loss, becomes obvious in the HALOE HCl measurements. Additionally, the degree of homogeneity of ozone loss within the vortex was shown to depend on the meteorological conditions. Results derived here are in general agreement with the results obtained by other methods for deducing polar ozone loss. Differences occur mainly owing to different time periods considered in deriving accumulated ozone loss. However, very strong ozone losses as deduced from SAOZ for January in winters 1993-1994 and 1995-1996 cannot be identified using available HALOE observations in the early winter. In general, strong accumulated ozone loss was found to occur in conjunction with a strong cold vortex containing a large volume of possible PSC existence (VPSC), whereas moderate ozone loss was found if the vortex was less strong and moderately warm. Hardly any ozone loss was calculated for very warm winters with small amounts of VPSC during the entire winter. This study supports the linear relationship between VPSC and the accumulated ozone loss reported by Rex et al. (2004) if VPSC was averaged over the entire winter period. Here, further meteorological factors controlling ozone loss were additionally identified if VPSC was averaged over the same time interval as that for which the accumulated ozone loss was deduced. A significant difference in ozone loss (of ≈36DU) was found due to the different duration of solar illumination of the polar vortex of at maximum 4 hours per day in the observed years. Further, the increased burden of aerosols in the atmosphere after the Pinatubo volcanic eruption in 1991 significantly increased the extent of chemical ozone loss.

Description: Current stratospheric chemical model simulations underestimate substantially the large ozone loss rates that are derived for the Arctic from ozone sondes for January of some years. Until now, no explanation for this discrepancy has been found. Here, we examine the influence of intrusions of mid-latitude air into the polar vortex on these ozone loss estimates. This study focuses on the winter 1991/92, because during this winter the discrepancy between simulated and experimentally derived ozone loss rates is reported to be the largest. Also during the considered period the vortex was disturbed by a strong warming event with large-scale intrusions of mid-latitude air into the polar vortex, which is quite unusual for this time of the year. The study is based on simulations performed with the Chemical Lagrangian Model of the Stratosphere (CLaMS). Two methods for determination the ozone loss are investigated, the so-called vortex average approach and the Match method. The simulations for January 1992 show that the intrusions induce a reduction of vortex average ozone mixing ratio corresponding to a systematic offset of the ozone loss rate of about 12 ppb per day. This should be corrected for in the vortex average method. The simulations further suggest, that these intrusions do not cause a significant bias for the Match method due to effective quality control measures in the Match technique.

Description: High-resolution simulations of the chemical composition of the Arctic stratosphere during late spring 1997 and 2000 were performed with the Chemical Lagrangian Model of the Stratosphere (CLaMS). The simulations were performed for the entire northern hemisphere on two isentropic levels 450 K (~18 km) and 585 K (~24 km). The spatial distribution and the lifetime of the vortex remnants formed after the vortex breakup in May 1997 display different behavior above and below 20 km. Above 20 km, vortex remnants propagate southward (up to 40°N) and are "frozen in'' in the summer circulation without significant mixing. Below 20 km the southward propagation of the remnants is bounded by the subtropical jet. Their lifetime is shorter by a factor of 2 than that above 20 km, owing to significant stirring below this altitude. The behavior of vortex remnants formed in March 2000 is similar but, due to an earlier vortex breakup, dominated during the first 6 weeks after the vortex breakup by westerly winds, even above 20 km. Vortex remnants formed in May 1997 are characterized by large mixing ratios of HCl indicating negligible, halogen-induced ozone loss. In contrast, mid-latitude ozone loss in late boreal spring 2000 is dominated, until mid-April, by halogen-induced ozone destruction within the vortex remnants, and subsequent transport of the ozone-depleted polar air masses (dilution) into the mid-latitudes. By varying the intensity of mixing in CLaMS, the impact of mixing on the formation of ClONO2 and ozone depletion is investigated. We find that the photochemical decomposition of HNO3 and not mixing with NOx-rich mid-latitude air is the main source of NOx within the vortex remnants in March and April 2000. Ozone depletion in the remnants is driven by ClOx photolytically formed from ClONO2. At the end of May 1997, the halogen-induced ozone deficit at 450 K poleward of 30°N amounts to ~12% with ~10% in the polar vortex and ~2% in well-isolated vortex remnants after the vortex breakup.

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.