Sea ice trends in climate models only accurate in runs with biased global warming

Observations indicate that the Arctic sea ice cover is rapidly retreating while the Antarctic sea ice cover is steadily expanding. State-of-the-art climate models, by contrast, typically simulate a moderate decrease in both the Arctic and Antarctic sea ice covers. However, in each hemisphere there is a small subset of model simulations that have sea ice trends similar to the observations. Based on this, a number of recent studies have suggested that the models are consistent with the observations in each hemisphere when simulated internal climate variability is taken into account. Here we examine sea ice changes during 1979-2013 in simulations from the most recent Coupled Model Intercomparison Project (CMIP5) as well as the Community Earth System Model Large Ensemble (CESM-LE), drawing on previous work that found a close relationship in climate models between global-mean surface temperature and sea ice extent. We find that all of the simulations with 1979-2013 Arctic sea ice retreat as fast as observed have considerably more global warming than observations during this time period. Using two separate methods to estimate the sea ice retreat that would occur under the observed level of global warming in each simulation in both ensembles, we find that simulated Arctic sea ice retreat as fast as observed would occur less than 1% of the time. This implies that the models are not consistent with the observations. In the Antarctic, we find that simulated sea ice expansion as fast as observed typically corresponds with too little global warming, although these results are more equivocal. We show that because of this, the simulations do not capture the observed asymmetry between Arctic and Antarctic sea ice trends. This suggests that the models may be getting the right sea ice trends for the wrong reasons in both polar regions

Faster Arctic sea ice retreat in CMIP5 than in CMIP3 due to volcanoes

The downward trend in Arctic sea ice extent is one of the most dramatic signals of climate change during recent decades. Comprehensive climate models have struggled to reproduce this, typically simulating a slower rate of sea ice retreat than has been observed. However, this bias has been widely noted to have decreased in models participating in the most recent phase of the Coupled Model Intercomparison Project (CMIP5) compared with the previous generation of models (CMIP3). Here we examine simulations from both CMIP3 and CMIP5. We find that simulated historical sea ice trends are influenced by volcanic forcing, which was included in all of the CMIP5 models but in only about half of the CMIP3 models. The volcanic forcing causes temporary simulated cooling in the 1980s and 1990s, which contributes to raising the simulated 1979-2013 global-mean surface temperature trends to values substantially larger than observed. We show that this warming bias is accompanied by an enhanced rate of Arctic sea ice retreat and hence a simulated sea ice trend that is closer to the observed value, which is consistent with previous findings of an approximately linear relationship between sea ice extent and global-mean surface temperature. We find that both generations of climate models simulate Arctic sea ice that is substantially less sensitive to global warming than has been observed. The results imply that the much of the difference in Arctic sea ice trends between CMIP3 and CMIP5 occurred due to the inclusion of volcanic forcing, rather than improved sea ice physics or model resolution.Comment: revised submission to Journal of Climat

Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

Emerging infectious diseasespose a significant threat to global health, but predicting disease outcomes for particular species can be complicated when pathogen virulence varies across space, time, or hosts. The pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd) has caused worldwide declines in frog populations. Not only do Bd isolates from wild populations vary in virulence, but virulence shifts can occur over short timescales when Bd is maintained in the laboratory. We leveraged changes in Bd virulence over multiple generations of passage to better understand mechanisms of pathogen virulence. We conducted whole-genome resequencing of two samples of the same Bd isolate, differing only in passage history, to identify genomic processes associated with virulence attenuation. The isolate with shorter passage history (and greater virulence) had greater chromosome copy numbers than the isolate maintained in culture for longer, suggesting that virulence attenuation may be associated with loss of chromosome copies. Our results suggest that genomic processes proposed as mechanisms for rapid evolution in Bd are correlated with virulence attenuation in laboratory culture within a single lineage of Bd. Moreover, these genomic processes can occur over extremely short timescales. On a practical level, our results underscore the importance of immediately cryo-archiving new Bd isolates and using fresh isolates, rather than samples cultured in the laboratory for long periods, for laboratory infection experiments. Finally, when attempting to predict disease outcomes for this ecologically important pathogen, it is critical to consider existing variation in virulence among isolates and the potential for shifts in virulence over short timescales

Turbulent Mixing and Layer Formation in Double-Diffusive Convection: 3D Numerical Simulations and Theory

Double-diffusive convection, often referred to as semi-convection in astrophysics, occurs in thermally and compositionally stratified systems which are stable according to the Ledoux criterion but unstable according to the Schwarzschild criterion. This process has been given relatively little attention so far, and its properties remain poorly constrained. In this paper, we present and analyze a set of three-dimensional simulations of this phenomenon in a Cartesian domain under the Boussinesq approximation. We find that in some cases the double-diffusive convection saturates into a state of homogeneous turbulence, but with turbulent fluxes several orders of magnitude smaller than those expected from direct overturning convection. In other cases, the system rapidly and spontaneously develops closely packed thermo-compositional layers, which later successively merge until a single layer is left. We compare the output of our simulations with an existing theory of layer formation in the oceanographic context and find very good agreement between the model and our results. The thermal and compositional mixing rates increase significantly during layer formation and increase even further with each merger. We find that the heat flux through the staircase is a simple function of the layer height. We conclude by proposing a new approach to studying transport by double-diffusive convection in astrophysics

GLI3 Repressor Controls Nephron Number via Regulation of Wnt11 and Ret in Ureteric Tip Cells

Truncating GLI3 mutations in Pallister-Hall Syndrome with renal malformation suggests a requirement for Hedgehog signaling during renal development. HH-dependent signaling increases levels of GLI transcriptional activators and decreases processing of GLI3 to a shorter transcriptional repressor. Previously, we showed that Shh-deficiency interrupts early inductive events during renal development in a manner dependent on GLI3 repressor. Here we identify a novel function for GLI3 repressor in controlling nephron number. During renal morphogenesis, HH signaling activity, assayed by expression of Ptc1-lacZ, is localized to ureteric cells of the medulla, but is undetectable in the cortex. Targeted inactivation of Smo, the HH effector, in the ureteric cell lineage causes no detectable abnormality in renal morphogenesis. The functional significance of absent HH signaling activity in cortical ureteric cells was determined by targeted deletion of Ptc1, the SMO inhibitor, in the ureteric cell lineage. Ptc1−/−UB mice demonstrate ectopic Ptc1-lacZ expression in ureteric branch tips and renal hypoplasia characterized by reduced kidney size and a paucity of mature and intermediate nephrogenic structures. Ureteric tip cells are remarkable for abnormal morphology and impaired expression of Ret and Wnt11, markers of tip cell differentiation. A finding of renal hypoplasia in Gli3−/− mice suggests a pathogenic role for reduced GLI3 repressor in the Ptc1−/−UB mice. Indeed, constitutive expression of GLI3 repressor via the Gli3Δ699 allele in Ptc1−/−UB mice restores the normal pattern of HH signaling, and expression of Ret and Wnt11 and rescued the renal phenotype. Thus, GLI3 repressor controls nephron number by regulating ureteric tip cell expression of Wnt11 and Ret

Thermal Performance Curves of Multiple Isolates of Batrachochytrium dendrobatidis, a Lethal Pathogen of Amphibians

Emerging infectious disease is a key factor in the loss of amphibian diversity. In particular, the disease chytridiomycosis has caused severe declines around the world. The lethal fungal pathogen that causes chytridiomycosis, Batrachochytrium dendrobatidis (Bd), has affected amphibians in many different environments. One primary question for researchers grappling with disease-induced losses of amphibian biodiversity is what abiotic factors drive Bd pathogenicity in different environments. To study environmental influences on Bd pathogenicity, we quantified responses of Bd phenotypic traits (e.g., viability, zoospore densities, growth rates, and carrying capacities) over a range of environmental temperatures to generate thermal performance curves. We selected multiple Bd isolates that belong to a single genetic lineage but that were collected across a latitudinal gradient. For the population viability, we found that the isolates had similar thermal optima at 21°C, but there was considerable variation among the isolates in maximum viability at that temperature. Additionally, we found the densities of infectious zoospores varied among isolates across all temperatures. Our results suggest that temperatures across geographic point of origin (latitude) may explain some of the variation in Bd viability through vertical shifts in maximal performance. However, the same pattern was not evident for other reproductive parameters (zoospore densities, growth rates, fecundity), underscoring the importance of measuring multiple traits to understand variation in pathogen responses to environmental conditions. We suggest that variation among Bd genetic variants due to environmental factors may be an important determinant of disease dynamics for amphibians across a range of diverse environments

Repeated evolution of blanched coloration in a lizard across independent white-sand habitats

The White Sands lizards of New Mexico are a rare and classic example of convergent evolution where three species have evolved blanched coloration on the white gypsum dunes. Until now, no geological replicate of the pattern had been described. However, one of the White Sands species, the lesser earless lizard (Holbrookia maculata), has been discovered to also inhabit the Salt Basin Dunes of Texas, where it has also evolved a blanched morph. We here present a first phenotypic and genetic description of the Salt Basin Dunes population of H. maculata. Phylogenetic inference based on a housekeeping gene (ND4) and a classic candidate gene in the melanin-synthesis pathway (Melanocortin 1 Receptor; Mc1r) shows the newly discovered population as an independent lineage, with no evidence of genetic parallelism in the coding region of Mc1r. Initial morphological data suggest that while this population displays convergent evolution in blanched coloration, there are divergent patterns in limb length and habitat use behavior between the gypsum environments. Our findings present the White Sands/Salt Basin Dunes as an exceptionally promising comparative model for studies of adaptation and convergent evolution

Sources of seasonal sea-ice bias for CMIP6 models in the Hudson Bay Complex

The seasonal ice-free period in the Hudson Bay Complex (HBC) has grown longer in recent decades in response to warming, both from progressively earlier sea-ice retreat in summer and later sea-ice advance in fall. Such changes disrupt the HBC ecosystem and ice-based human activities. In this study, we compare 102 simulations from 37 models participating in phase 6 of the Coupled Model Intercomparison Project to the satellite passive microwave record and atmospheric reanalyses. We show that, throughout the HBC, models simulate an ice-free period that averages 30 d longer than in satellite observations. This occurs because seasonal sea-ice advance is unrealistically late and seasonal sea-ice retreat is unrealistically early. We find that much of the ice-season bias can be linked to a warm bias in the atmosphere that is associated with a southerly wind bias, especially in summer. Many models also exhibit an easterly wind bias during winter and spring, which reduces sea-ice convergence on the east side of Hudson Bay and impacts the spatial patterns of summer sea-ice retreat. These results suggest that, for many models, more realistic simulation of atmospheric circulation would improve their simulation of HBC sea ice

Invasive Vegetation Affects Amphibian Skin Microbiota and Body Condition

Invasive plants are major drivers of habitat modification and the scale of their impact is increasing globally as anthropogenic activities facilitate their spread. In California, an invasive plant genus of great concern is Eucalyptus. Eucalyptus leaves can alter soil chemistry and negatively affect underground macro- and microbial communities. Amphibians serve as excellent models to evaluate the effect of Eucalyptus invasion on ground-dwelling species as they predate on soil arthropods and incorporate soil microbes into their microbiotas. The skin microbiota is particularly important to amphibian health, suggesting that invasive plant species could ultimately affect amphibian populations. To investigate the potential for invasive vegetation to induce changes in microbial communities, we sampled microbial communities in the soil and on the skin of local amphibians. Specifically, we compared Batrachoseps attenuatus skin microbiomes in both Eucalyptus globulus (Myrtaceae) and native Quercus agriflolia (Fagaceae) dominated forests in the San Francisco Bay Area. We determined whether changes in microbial diversity and composition in both soil and Batrachoseps attenuatus skin were associated with dominant vegetation type. To evaluate animal health across vegetation types, we compared Batrachoseps attenuatus body condition and the presence/absence of the amphibian skin pathogen Batrachochytrium dendrobatidis. We found that Eucalyptus invasion had no measurable effect on soil microbial community diversity and a relatively small effect (compared to the effect of site identity) on community structure in the microhabitats sampled. In contrast, our results show that Batrachoseps attenuatus skin microbiota diversity was greater in Quercus dominated habitats. One amplicon sequence variant identified in the family Chlamydiaceae was observed in higher relative abundance among salamanders sampled in Eucalyptus dominated habitats. We also observed that Batrachoseps attenuatus body condition was higher in Quercus dominated habitats. Incidence of Batrachochytrium dendrobatidis across all individuals was very low (only one Batrachochytrium dendrobatidis positive individual). The effect on body condition demonstrates that although Eucalyptus may not always decrease amphibian abundance or diversity, it can potentially have cryptic negative effects. Our findings prompt further work to determine the mechanisms that lead to changes in the health and microbiome of native species post-plant invasion

Phase II Trial of IL-12 Plasmid Transfection and PD-1 Blockade in Immunologically Quiescent Melanoma.

PurposeTumors with low frequencies of checkpoint positive tumor-infiltrating lymphocytes (cpTIL) have a low likelihood of response to PD-1 blockade. We conducted a prospective multicenter phase II trial of intratumoral plasmid IL-12 (tavokinogene telseplasmid; "tavo") electroporation combined with pembrolizumab in patients with advanced melanoma with low frequencies of checkpoint positive cytotoxic lymphocytes (cpCTL).Patients and methodsTavo was administered intratumorally days 1, 5, and 8 every 6 weeks while pembrolizumab (200 mg, i.v.) was administered every 3 weeks. The primary endpoint was objective response rate (ORR) by RECIST, secondary endpoints included duration of response, overall survival and progression-free survival. Toxicity was evaluated by the CTCAE v4. Extensive correlative analysis was done.ResultsThe combination of tavo and pembrolizumab was well tolerated with adverse events similar to those previously reported with pembrolizumab alone. Patients had a 41% ORR (n = 22, RECIST 1.1) with 36% complete responses. Correlative analysis showed that the combination enhanced immune infiltration and sustained the IL-12/IFNγ feed-forward cycle, driving intratumoral cross-presenting dendritic cell subsets with increased TILs, emerging T cell receptor clones and, ultimately, systemic cellular immune responses.ConclusionsThe combination of tavo and pembrolizumab was associated with a higher than expected response rate in this poorly immunogenic population. No new or unexpected toxicities were observed. Correlative analysis showed T cell infiltration with enhanced immunity paralleling the clinical activity in low cpCTL tumors