Simulations with the sea ice model CICE investigating the impact of sea ice floe size distribution on seasonal Arctic sea ice retreat.

This dataset has been generated by implementing a power law derived sea ice floe size distribution model within the CICE sea ice model. We use this dataset within the associated paper (Bateson et al., 2019) to investigate the impact of floe size on the seasonal fragmentation and melt of Arctic sea ice. We document several findings including that the floe size distribution model has a spatially and temporally dependent impact on the sea ice cover, in particular enhancing the role of the marginal ice zone in sea ice loss. We also show a strong model sensitivity to floe size distribution parameters within limits constrained by observations. We furthermore find that the impact of waves on floe size and the sea ice cover is strongly moderated by the wave attenuation rate

Simulations of the Arctic sea ice comparing different approaches to modelling the floe size distribution and their respective impacts on the sea ice cover

This dataset has been produced by implementing either a power law derived or prognostic sea ice floe size distribution model within the CICE sea ice model. This dataset is used within the thesis ‘Fragmentation and melting of the seasonal sea ice cover’ (Bateson, 2021) to investigate the impact of the sea ice floe size distribution on the evolution of the Arctic sea ice cover and to compare different approaches to modelling floe size. Results are presented to show how variable floe size changes the seasonal retreat of the Arctic sea ice cover via changes to lateral melt volume and momentum exchange between the sea ice, ocean, and atmosphere. Winter floe formation and growth processes are found to strongly influence FSD impacts on the seasonal retreat of the sea ice, and the need to include brittle fracture processes in floe size distribution models is also demonstrated. A high sensitivity is found to poorly constrained FSD parameters, highlighting the need for further observations of floe size

Fragmentation and melting of the seasonal sea ice cover

The Arctic sea ice cover is in retreat. Accurate representation of the marginal ice zone (MIZ), the region of the sea ice cover that separates open ocean from the pack ice, is important to capture this retreat in models. The MIZ is associated with complex interactions of the atmosphere, sea ice, and oceans, and a highly heterogenous sea ice cover. Several important sea ice properties and processes that determine the evolution of the MIZ, including lateral melting, momentum exchange, and sea ice rheology, are dependent on floe size. Climate models have historically treated floe size as a fixed parameter, if at all. Observations have shown that floes adopt sizes from scales of metres to kilometres. Here I investigate two alternative models of the floe size distribution (FSD). The first approach assumes the FSD follows a power law with a fixed exponent and the second approach is a prognostic floe size-thickness distribution model where the shape of the FSD freely evolves. These models are used to understand how variable floe size in the MIZ changes the seasonal retreat of the Arctic sea ice cover, both through the impact on lateral melt volume and on momentum exchange coefficients. I discuss the advantages and disadvantages of each approach, including an assessment of whether either model improves sea ice model performance compared to observations. I find a high sensitivity to poorly constrained FSD parameters and parameterisations, highlighting the need to better characterise the FSD with observations. I show that winter floe formation and growth processes strongly influence FSD impacts on the sea ice over the melt season. I also demonstrate the need to incorporate brittle fracture in FSD models. I conclude that simple representations of floe size are sufficient to project future sea ice trends, but FSD models are important to capture the spatial distribution of the sea ice

Impact of sea ice floe size distribution on seasonal fragmentation and melt of Arctic sea ice

Recent years have seen a rapid reduction in the summer Arctic sea ice extent. To both understand this trend and project the future evolution of the summer Arctic sea ice, a better understanding of the physical processes that drive the seasonal loss of sea ice is required. The marginal ice zone, here defined as regions with between 15 % and 80 % sea ice cover, is the region separating pack ice from the open ocean. Accurate modelling of this region is important to understand the dominant mechanisms involved in seasonal sea ice loss. Evolution of the marginal ice zone is determined by complex interactions between the atmosphere, sea ice, ocean, and ocean surface waves. Therefore, this region presents a significant modelling challenge. Sea ice floes span a range of sizes but sea ice models within climate models assume they adopt a constant size. Floe size influences the lateral melt rate of sea ice and momentum transfer between atmosphere, sea ice, and ocean, all important processes within the marginal ice zone. In this study, the floe size distribution is represented as a power law defined by an upper floe size cut-off, lower floe size cut-off, and power-law exponent. This distribution is also defined by a new tracer that varies in response to lateral melting, wave-induced break-up, freezing conditions, and advection. This distribution is implemented within a sea ice model coupled to a prognostic ocean mixed-layer model. We present results to show that the use of a power-law floe size distribution has a spatially and temporally dependent impact on the sea ice, in particular increasing the role of the marginal ice zone in seasonal sea ice loss. This feature is important in correcting existing biases within sea ice models. In addition, we show a much stronger model sensitivity to floe size distribution parameters than other parameters used to calculate lateral melt, justifying the focus on floe size distribution in model development. We also find that the attenuation rate of waves propagating under the sea ice cover modulates the impact of wave break-up on the floe size distribution. It is finally concluded that the model approach presented here is a flexible tool for assessing the importance of a floe size distribution in the evolution of sea ice and is a useful stepping stone for future development of floe size modelling

Baseline and acquired resistance to bedaquiline, linezolid and pretomanid, and impact on treatment outcomes in four tuberculosis clinical trials containing pretomanid

Bedaquiline (B), pretomanid (Pa) and linezolid (L) are key components of new regimens for treating rifampicin-resistant tuberculosis (TB). However, there is limited information on the global prevalence of resistance to these drugs and the impact of resistance on treatment outcomes. Mycobacterium tuberculosis (MTB) phenotypic drug susceptibility and whole-genome sequence (WGS) data, as well as patient profiles from 4 pretomanid-containing trials–STAND, Nix-TB, ZeNix and SimpliciTB–were used to investigate the rates of baseline resistance (BR) and acquired resistance (AR) to BPaL drugs, as well as their genetic basis, risk factors and impact on treatment outcomes. Data from >1,000 TB patients enrolled from 2015 to 2020 in 12 countries was assessed. We identified 2 (0.3%) participants with linezolid BR. Pretomanid BR was also rare, with similar rates across TB drug resistance types (0–2.1%). In contrast, bedaquiline BR was more prevalent among participants with highly resistant TB or longer prior treatment histories than those with newly diagnosed disease (5.2–6.3% vs. 0–0.3%). Bedaquiline BR was a risk factor for bacteriological failure or relapse in Nix-TB/ZeNix; 3/12 (25%, 95% CI 5–57%) participants with vs. 6/185 (3.2%, 1.2–6.9%) without bedaquiline BR. Across trials, we observed no linezolid AR, and only 3 cases of bedaquiline AR, including 2 participants with poor adherence. Overall, pretomanid AR was also rare, except in ZeNix patients with bedaquiline BR. WGS analyses revealed novel mutations in canonical resistant genes and, in 7 MTB isolates, the genetic determinants could not be identified. The overall low rates of BR to linezolid and pretomanid, and to a lesser extent to bedaquiline, observed in the pretomanid trials are in support of the worldwide implementation of BPaL-based regimens. Similarly, the overall low AR rates observed suggest BPaL drugs are better protected in the regimens trialed here than in other regimens combining bedaquiline with more, but less effective drugs

Sea ice fragmentation and its role in the evolution of the arctic sea ice cover

The Arctic sea ice cover is not a continuous expanse of ice but is instead composed of individual sea ice floes. These floes can range in size from just a few metres to tens of kilometres. Floe size can influence a variety of processes, including lateral melt rates, momentum transfer within the sea ice-ocean-atmosphere system, surface moisture flux, and sea ice rheology. Sea ice models have traditionally defined floe size using a single parameter, if floe size is explicitly treated at all. There have been several recent efforts to incorporate models of the Floe Size Distribution (FSD) into sea ice models in order to explore both how the shape of the FSD emerges and evolves and its impact on the sea ice cover, including the seasonal retreat. Existing models have generally focused on ocean surface wave-floe interactions and thermodynamic melting and growth processes. However, in-situ observations have indicated the presence of mechanisms other than wave fracture involved in the fragmentation of floes, including brittle failure and melt-induced break up. In this study we consider two alternative FSD models within the CICE sea ice model: the first assumes the FSD follows a power law with a fixed exponent, with parameterisations of individual processes characterised using a variable FSD tracer; the second uses a prognostic approach, with the shape of the FSD an emergent characteristic of the model rather than imposed. We firstly use case studies to understand how similarities and differences in the impacts of the two FSD models on the sea ice emerge, including the different spatial and temporal variability of these impacts. We also consider whether the inclusion of FSD processes in sea ice models can enhance seasonal predictability. We will also demonstrate the need to include in-plane brittle fracture processes in FSD models and discuss the requirements needed within any parameterisation of the brittle failure mechanism

The Carbon-Sulfur Link in the Remineralization of Organic Carbon in Surface Sediments

Here we present the carbon isotopic composition of dissolved inorganic carbon (DIC) and the sulfur isotopic composition of sulfate, along with changes in sulfate concentrations, of the pore fluid collected from a series of sediment cores located along a depth transect on the Iberian Margin. We use these data to explore the coupling of microbial sulfate reduction (MSR) to organic carbon oxidation in the uppermost (up to nine meters) sediment. We argue that the combined use of the carbon and sulfur isotopic composition, of DIC and sulfate respectively, in sedimentary pore fluids, viewed through a δ13CDIC vs. δ34SSO4 cross plot, reveals significant insight into the nature of carbon-sulfur coupling in marine sedimentary pore fluids on continental margins. Our data show systemic changes in the carbon and sulfur isotopic composition of DIC and sulfate (respectively) where, at all sites, the carbon isotopic composition of the DIC decreases before the sulfur isotopic composition of sulfate increases. We compare our results to global data and show that this behavior persists over a range of sediment types, locations and water depths. We use a reactive-transport model to show how changes in the amount of DIC in seawater, the carbon isotopic composition of organic matter, the amount of organic carbon oxidation by early diagenetic reactions, and the presence and source of methane influence the carbon and sulfur isotopic composition of sedimentary pore fluids and the shape of the δ13CDIC vs. δ34SSO4 cross plot. The δ13C of the DIC released during sulfate reduction and sulfate-driven anaerobic oxidation of methane is a major control on the minimum δ13CDIC value in the δ13CDIC vs. δ34SSO4 cross plot, with the δ13C of the organic carbon being important during both MSR and combined sulfate reduction, sulfate-driven AOM and methanogenesis

Evolutionary connectionism: algorithmic principles underlying the evolution of biological organisation in evo-devo, evo-eco and evolutionary transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions

Ancient and recent differences in the intrinsic susceptibility of Mycobacterium tuberculosis complex to pretomanid

OBJECTIVES: To develop a robust phenotypic antimicrobial susceptibility testing (AST) method with a correctly set breakpoint for pretomanid (Pa), the most recently approved anti-tuberculosis drug. METHODS: The Becton Dickinson Mycobacterial Growth Indicator Tube™ (MGIT) system was used at six laboratories to determine the MICs of a phylogenetically diverse collection of 356 Mycobacterium tuberculosis complex (MTBC) strains to establish the epidemiological cut-off value for pretomanid. MICs were correlated with WGS data to study the genetic basis of differences in the susceptibility to pretomanid. RESULTS: We observed ancient differences in the susceptibility to pretomanid among various members of MTBC. Most notably, lineage 1 of M. tuberculosis, which is estimated to account for 28% of tuberculosis cases globally, was less susceptible than lineages 2, 3, 4 and 7 of M. tuberculosis, resulting in a 99th percentile of 2 mg/L for lineage 1 compared with 0.5 mg/L for the remaining M. tuberculosis lineages. Moreover, we observed that higher MICs (≥8 mg/L), which probably confer resistance, had recently evolved independently in six different M. tuberculosis strains. Unlike the aforementioned ancient differences in susceptibility, these recent differences were likely caused by mutations in the known pretomanid resistance genes. CONCLUSIONS: In light of these findings, the provisional critical concentration of 1 mg/L for MGIT set by EMA must be re-evaluated. More broadly, these findings underline the importance of considering the global diversity of MTBC during clinical development of drugs and when defining breakpoints for AST

Paternal attractiveness and the effects of differential allocation of parental investment

The differential allocation hypothesis (DAH) predicts that an individual should vary its reproductive investment according to the attractiveness of its mate. A recently revised version of the DAH makes explicit that investment can be positive, i.e. higher for the offspring of attractive males which should be of higher quality, or negative, i.e. higher for offspring of unattractive males, for example compensating for inheriting poor paternal genes. Moreover, investment can be made by the father and the mother. Here, we tested whether experimental manipulation of male attractiveness affected parental investment at different reproductive stages and thus influenced fitness-related traits in offspring. In two aviaries, all male zebra finches, Taeniopygia guttata, were given red leg rings to increase attractiveness and in two aviaries all males received green leg rings to decrease attractiveness. This controlled for assortative mating between treatments. Ring colour was merely an experimental manipulation of male attractiveness, not paternal quality, so we might expect additional investment to elevate offspring quality. Eggs were cross-fostered between and within treatments to allow differentiation of effects of investment in eggs and nestlings. Clutch and brood sizes were standardized. Both positive and negative investment were observed: Eggs from red-ringed fathers had higher yolk to albumen ratios than eggs from green-ringed fathers. Nestlings from eggs laid and incubated by parents in the red-ringed group had higher hatching masses than those in the green-ringed group. Both parents in the green-ringed group fed nestlings more frequently than red-ringed parents. Offspring performance was influenced by the treatment of both foster and biological parents, but combined effects of these different investment patterns on fitness-related traits were ambiguous. Male attractiveness appeared to affect patterns of reproductive investment but not consistently across all forms of reproductive investment suggesting that the costs and benefits of differential allocation vary among individuals and across contexts