• European Marine Science
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We used previously published datasets of growth rates of, and mutations in, mutation accumulation lines in Saccharomyces cerevisiae and Chlamydomonas reinhardtii. We computed the mutated proteins and ran the protein variant, as compared to the laboratory ancestor, through PROVEAN. We ran PROVEAN on the ComputeCanada cluster. As the program failed to run with the recent BLAST software (version 2.9.0), we configured PROVEAN to run with PSI-BLAST and BLASTDBCMD (Altschul et al. 1997)from BLAST version 2.4.0. We used version 4.8.1 of CD-HIT. We ran our variants with the NCBI nr database from 12/11/2019, which holds 142 GB of non-redundant sequences (229,636,095 sequences). We ran a subset of variants using the 2012 database, on which PROVEAN was developed (the first 5 GB), without radical changes to the PROVEAN scores of variants. The supporting sequence sets used to compute the alignment scores for all proteins were saved. Sc1 We used the mutations reported in Sharp et al. (2018; Dataset_S2.xlsx). There were 1474 genic mutations in the dataset, occurring in 1219 unique genes across 218 MA lines. We extracted the nucleotide and protein sequence of the genes affected using YeastMine (Balakrishnan et al. 2012). From the same database, we downloaded the location of introns in these genes. The reference nucleotide sequence was then mutated in silicoto represent the mutant sequence, which was then transcribed and translated, using the seqinr package (Charif and Lobry 2007)in R (R Core Team 2019). Additionally, we analyzed VCF files to obtain a table of mutations in the ancestral line as compared to the yeast reference genome (version R64-2-1). In cases where the ancestor and reference strain differed for a mutated gene (126 genes) we separately computed the ancestral protein and used it for comparison to the MA lines. We wrote a script to produce protein variants in the format PROVEAN requires. From 1474 genic mutations, 1126 protein variants were computed (in 961 unique proteins). Two samples (lines 113 and 206) had no nonsynonymous mutations. When an MA line had more than one nonsynonymous mutation in a particular gene both mutations were considered when altering the protein and the number of mutant proteins is reported once. Out of 961 altered proteins, 126 already differed between the S288C reference genome and the laboratory ancestor, in which case the latter was used as the query sequence. Sc2 We used the mutations reported in Liu and Zhang (2019; Data_S1.xlsx). Additionally, the authors supplied us with a table of mutations in their ancestral line relative to the S288C reference genome. We used the same method as described above for dataset Sc1. There were 1147 genic mutations, occurring in 968 unique genes, across 165 MA lines. From 1147 genic mutations, 877 protein variants were computed (in 754 unique proteins). Out of 754 altered proteins, 16 already differed between the S288C reference genome and the laboratory ancestor, in which case the latter was used as the query sequence. Cr We received an annotated table of the mutations reported in Ness et al. (2015)as well as VCF files containing the mutations in their six ancestral lines compared to the reference genome. We downloaded an annotated table for all transcripts in the Chlamydomonasreference genome from Dicots PLAZA 4.0 (version 5.5, Van Bel et al., 2018)to identify mutations in coding sequences. Out of the original 6843 mutations, 3889 affected protein sequence, representing 1439 mutated proteins after combining mutations. We found that the majority of transcripts that were mutated during mutation accumulation already had existing variants in the ancestral strain, relative to the reference (table 1). 1397 out of the originally predicted 1439 protein variants remained once ancestral variation had been considered (table 1). As in the other datasets, we use the ancestral protein as the query protein. We found 2 cases in the C. reinhardtiidataset where the reported reference nucleotide deviated from that found in the Dicots PLAZA 4.0 sequence; in each case, the differences between the two reference sequences were synonymous. This discrepancy was likely due to the two different reference genomes used (Ness et al. used v5.3; Van Bel et al. used v5.5). To test the accuracy of our sequence-mutating code, we mutated the coding sequence to the reference nucleotide given by the C. reinhardtiidataset and verified that this produced the reference transcript. We converted the protein variants into the format PROVEAN requires. In cases with alternative transcripts, we treat these as separate proteins in PROVEAN and then report the minimum score given to any protein variant of a gene. This occurred in 42 unique cases, involving all genetic backgrounds. While the difference in scores between transcripts in general was small, we found two cases where the score for one affected transcript was below the default threshold of –2.5 while the other was above it, and six cases where the scores fell above and below zero. Six out of the total 1397 protein variants failed to receive a score from PROVEAN, likely because the changes to the protein were too large to compute alignment scores between the clusters gathered and the mutant protein and were ignored in the analysis (these occurred in six different samples across five ancestral backgrounds). Predicting fitness in natural populations is a major challenge in biology. It may be possible to leverage fast-accumulating genomic datasets to infer the fitness effects of mutant alleles, allowing evolutionary questions to be addressed in any organism. In this paper, we investigate the utility of one such tool, called PROVEAN. This program compares a query sequence with existing data to provide an alignment-based score for any protein variant, with scores categorized as neutral or deleterious based on a preset threshold. PROVEAN has been used widely in evolutionary studies, e.g., to estimate mutation load in natural populations, but has not been formally tested as a predictor of aggregate mutational effects on fitness. Using three large, published datasets on the genome sequences of laboratory mutation accumulation lines, we assessed how well PROVEAN predicted the actual fitness patterns observed, relative to other metrics. In most cases, we find that a simple count of the total number of mutant proteins is a better predictor of fitness than the number of variants scored as deleterious by PROVEAN. We also find that the sum of all mutant protein scores explains variation in fitness better than the number of mutant proteins in one of the datasets. We discuss the implications of these results for studies of populations in the wild. Details and usage notes can be found in Sandell_provean_project_README.txt.

As part of the Model Intercomparison Project on the climatic response to Volcanic forcing (VolMIP), several climate modeling centers performed a coordinated pre-study experiment with interactive stratospheric aerosol models simulating the volcanic aerosol cloud from an eruption resembling the 1815 Mt. Tambora eruption (VolMIP-Tambora ISA ensemble). The pre-study provided the ancillary ability to assess intermodel diversity in the radiative forcing for a large stratospheric-injecting equatorial eruption when the volcanic aerosol cloud is simulated interactively. An initial analysis of the VolMIP-Tambora ISA ensemble showed large disparities between models in the stratospheric global mean aerosol optical depth (AOD). In this study, we now show that stratospheric global mean AOD differences among the participating models are primarily due to differences in aerosol size, which we track here by effective radius. We identify specific physical and chemical processes that are missing in some models and/or parameterized differently between models, which are together causing the differences in effective radius. In particular, our analysis indicates that interactively tracking hydroxyl radical (OH) chemistry following a large volcanic injection of sulfur dioxide (SO2) is an important factor in allowing for the timescale for sulfate formation to be properly simulated. In addition, depending on the timescale of sulfate formation, there can be a large difference in effective radius and subsequently AOD that results from whether the SO2 is injected in a single model grid cell near the location of the volcanic eruption, or whether it is injected as a longitudinally averaged band around the Earth.

The mid-Pliocene is a valuable time interval for investigating equilibrium climate at current atmospheric CO2 concentrations because atmospheric CO2 concentrations are thought to have been comparable to the current day and yet the climate and distribution of ecosystems were quite different. One intriguing, but not fully understood, feature of the early to mid-Pliocene climate is the amplified Arctic temperature response and its impact on Arctic ecosystems. Only the most recent models appear to correctly estimate the degree of warming in the Pliocene Arctic and validation of the currently proposed feedbacks is limited by scarce terrestrial records of climate and environment. Here we reconstruct the summer temperature and fire regime from a subfossil fen-peat deposit on west–central Ellesmere Island, Canada, that has been chronologically constrained using cosmogenic nuclide burial dating to 3.9+1.5/-0.5 Ma. The estimate for average mean summer temperature is 15.4±0.8 ∘C using specific bacterial membrane lipids, i.e., branched glycerol dialkyl glycerol tetraethers. This is above the proposed threshold that predicts a substantial increase in wildfire in the modern high latitudes. Macro-charcoal was present in all samples from this Pliocene section with notably higher charcoal concentration in the upper part of the sequence. This change in charcoal was synchronous with a change in vegetation that included an increase in abundance of fire-promoting Pinus and Picea. Paleo-vegetation reconstructions are consistent with warm summer temperatures, relatively low summer precipitation and an incidence of fire comparable to fire-adapted boreal forests of North America and central Siberia. To our knowledge, this site provides the northernmost evidence of fire during the Pliocene. It suggests that ecosystem productivity was greater than in the present day, providing fuel for wildfires, and that the climate was conducive to the ignition of fire during this period. The results reveal that interactions between paleo-vegetation and paleoclimate were mediated by fire in the High Arctic during the Pliocene, even though CO2 concentrations were similar to modern values.

Enhanced release of alkalinity from the seafloor, principally driven by anaerobic degradation of organic matter under low-oxygen conditions and associated secondary redox reactions, can increase the carbon dioxide (CO2) buffering capacity of seawater and therefore oceanic CO2 uptake. The Baltic Sea has undergone severe changes in oxygenation state and total alkalinity (TA) over the past decades. The link between these concurrent changes has not yet been investigated in detail. A recent system-wide TA budget constructed for the past 50 years using BALTSEM, a coupled physical–biogeochemical model for the whole Baltic Sea area revealed an unknown TA source. Here we use BALTSEM in combination with observational data and one-dimensional reactive-transport modeling of sedimentary processes in the Fårö Deep, a deep Baltic Sea basin, to test whether sulfate (SO42-) reduction coupled to iron (Fe) sulfide burial can explain the missing TA source in the Baltic Proper. We calculated that this burial can account for up to 26 % of the missing source in this basin, with the remaining TA possibly originating from unknown river inputs or submarine groundwater discharge. We also show that temporal variability in the input of Fe to the sediments since the 1970s drives changes in sulfur (S) burial in the Fårö Deep, suggesting that Fe availability is the ultimate limiting factor for TA generation under anoxic conditions. The implementation of projected climate change and two nutrient load scenarios for the 21st century in BALTSEM shows that reducing nutrient loads will improve deep water oxygen conditions, but at the expense of lower surface water TA concentrations, CO2 buffering capacities and faster acidification. When these changes additionally lead to a decrease in Fe inputs to the sediment of the deep basins, anaerobic TA generation will be reduced even further, thus exacerbating acidification. This work highlights that Fe dynamics plays a key role in the release of TA from sediments where Fe sulfide formation is limited by Fe availability, as exemplified by the Baltic Sea. Moreover, it demonstrates that burial of Fe sulfides should be included in TA budgets of low-oxygen basins.

Diatoms account for a large proportion of primary productivity in Antarctic coastal and continental shelf zones. Diatoms, which have been used for a long time to infer past sea surface conditions in the Southern Ocean, have recently been associated with diatom-specific biomarkers (highly branched isoprenoids, HBI). Our study is one of the few sedimentary research projects on diatom ecology and associated biomarkers in the Antarctic seasonal sea ice zone. To date, the Adélie Land region has received little attention, despite evidence for the presence of high accumulation of laminated sediment, allowing for finer climate reconstructions and sedimentary process studies. Here we provide a sequence of seasonally to annually laminated diatomaceous sediment from a 72.5 cm interface core retrieved on the continental shelf off Adélie Land, covering the 1970–2010 CE period. Investigations through statistical analyses of diatom communities, diatom-specific biomarkers and major element abundances document the relationships between these proxies at an unprecedented resolution. Additionally, comparison of sedimentary records to meteorological data monitored by automatic weather station and satellite derived sea ice concentrations help to refine the relationships between our proxies and environmental conditions over the last decades. Our results suggest a coupled interaction of the atmospheric and sea surface variability on sea ice seasonality, which acts as the proximal forcing of siliceous productivity at that scale.

Dansgaard–Oeschger oscillations constitute one of the most enigmatic features of the last glacial cycle. Their cold atmospheric phases have been commonly associated with cold sea-surface temperatures and expansion of sea ice in the North Atlantic and adjacent seas. Here, based on dinocyst analyses from the 48–30 ka interval of four sediment cores from the northern Northeast Atlantic and southern Norwegian Sea, we provide direct and quantitative evidence of a regional paradoxical seesaw pattern: cold Greenland and North Atlantic phases coincide with warmer sea-surface conditions and shorter seasonal sea-ice cover durations in the Norwegian Sea as compared to warm phases. Combined with additional palaeorecords and multi-model hosing simulations, our results suggest that during cold Greenland phases, reduced Atlantic meridional overturning circulation and cold North Atlantic sea-surface conditions were accompanied by the subsurface propagation of warm Atlantic waters that re-emerged in the Nordic Seas and provided moisture towards Greenland summit.

This work aims at characterising the seamount physiography and biology in the OSPAR Convention limits (north-east Atlantic Ocean) and Mediterranean Sea. We first inferred potential abundance, location and morphological characteristics of seamounts, and secondly, summarized the existing biological, geological and oceanographic in situ research, identifying examples of well-studied seamounts. Our study showed that the seamount population in the OSPAR area (north-east Atlantic) and in the Mediterranean Sea is large with around 557 and 101 seamount-like features, respectively. Similarly, seamounts occupy large areas of about 616 000 km2 in the OSPAR region and of about 89 500 km2 in the Mediterranean Sea. The presence of seamounts in the north-east Atlantic has been known since the late 19th century, but overall knowledge regarding seamount ecology and geology is still relatively poor. Only 37 seamounts in the OSPAR area (3.5% of all seamounts in the region), 22 in the Mediterranean Sea (9.2% of all seamounts in the region) and 25 in the north-east Atlantic south of the OSPAR area have in situ information. Seamounts mapped in both areas are in general very heterogeneous, showing diverse geophysical characteristics. These differences will likely affect the biological diversity and production of resident and associated organisms.

We reconstruct the geometry and strength of the Atlantic meridional overturning circulation during the Heinrich stadial 2 and three Greenland interstadials of the 20–50 ka period based on the comparison of new and published sedimentary 231Pa / 230Th data with simulated sedimentary 231Pa / 230Th. We show that the deep Atlantic circulation during these interstadials was very different from that of the Holocene. Northern-sourced waters likely circulated above 2500 m depth, with a flow rate lower than that of the present-day North Atlantic deep water (NADW). Southern-sourced deep waters most probably flowed northwards below 4000 m depth into the North Atlantic basin and then southwards as a return flow between 2500 and 4000 m depth. The flow rate of this southern-sourced deep water was likely larger than that of the modern Antarctic bottom water (AABW). Our results further show that during Heinrich stadial 2, the deep Atlantic was probably directly affected by a southern-sourced water mass below 2500 m depth, while a slow, southward-flowing water mass originating from the North Atlantic likely influenced depths between 1500 and 2500 m down to the equator.

In June 2009, 22 spectrometers from 14 institutes measured tropospheric and stratospheric NO2 from the ground for more than 11 days during the Cabauw Intercomparison Campaign of Nitrogen Dioxide measuring Instruments (CINDI), at Cabauw, NL (51.97° N, 4.93° E). All visible instruments used a common wavelength range and set of cross sections for the spectral analysis. Most of the instruments were of the multi-axis design with analysis by differential spectroscopy software (MAX-DOAS), whose non-zenith slant columns were compared by examining slopes of their least-squares straight line fits to mean values of a selection of instruments, after taking 30-min averages. Zenith slant columns near twilight were compared by fits to interpolated values of a reference instrument, then normalised by the mean of the slopes of the best instruments. For visible MAX-DOAS instruments, the means of the fitted slopes for NO2 and O4 of all except one instrument were within 10% of unity at almost all non-zenith elevations, and most were within 5%. Values for UV MAX-DOAS instruments were almost as good, being 12% and 7%, respectively. For visible instruments at zenith near twilight, the means of the fitted slopes of all instruments were within 5% of unity. This level of agreement is as good as that of previous intercomparisons, despite the site not being ideal for zenith twilight measurements. It bodes well for the future of measurements of tropospheric NO2, as previous intercomparisons were only for zenith instruments focussing on stratospheric NO2, with their longer heritage.