Evaluation of soil carbon simulation in CMIP6 Earth system models

The response of soil carbon represents one of the key uncertainties in future climate change. The ability of Earth system models (ESMs) to simulate present-day soil carbon is therefore vital for reliably estimating global carbon budgets required for Paris Agreement targets. In this study CMIP6 ESMs are evaluated against empirical datasets to assess the ability of each model to simulate soil carbon and related controls: net primary productivity (NPP) and soil carbon turnover time (τs). Comparing CMIP6 with the previous generation of models (CMIP5), a lack of consistency in modelled soil carbon remains, particularly the underestimation of northern high-latitude soil carbon stocks. There is a robust improvement in the simulation of NPP in CMIP6 compared with CMIP5; however, an unrealistically high correlation with soil carbon stocks remains, suggesting the potential for an overestimation of the long-term terrestrial carbon sink. Additionally, the same improvements are not seen in the simulation of τs. These results suggest that much of the uncertainty associated with modelled soil carbon stocks can be attributed to the simulation of below-ground processes, and greater emphasis is required on improving the representation of below-ground soil processes in future developments of models. These improvements would help to reduce the uncertainty in projected carbon release from global soils under climate change and to increase confidence in the carbon budgets associated with different levels of global warming.</p

Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

Background Heterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the “lower heterobranchs”. Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia. Results To assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of “lower heterobranchs”. Maximum likelihood analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades. Conclusions Analysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT + GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.publishedVersio

Long-term forest soil warming alters microbial communities in temperate forest soils

Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming

A rapid application emissions-to-impacts tool for scenario assessment: Probabilistic Regional Impacts from Model patterns and Emissions (PRIME)

Climate policies evolve quickly, and new scenarios designed around these policies are used to illustrate how they impact global mean temperatures using simple climate models (or climate emulators). Simple climate models are extremely efficient although limited to showing only the global picture. Within the Intergovernmental Panel on Climate Change (IPCC) framework, there is a need to understand the regional impacts of scenarios that include the most recent science and policy decisions quickly to support government in negotiations. To address this, we present PRIME (Probabilistic Regional Impacts from Model patterns and Emissions), a new flexible probabilistic framework which aims to provide an efficient means to run new scenarios without the significant overheads of larger more complex Earth system models (ESMs). PRIME provides the capability to include the most recent models, science and scenarios to run ensemble simulations on multi-centennial timescales and include analysis of many variables that are relevant and important for impacts assessments. We use a simple climate model to provide the global temperatures to scale the patterns from a large number of the CMIP6 ESMs. These provide the inputs to a weather generator and a land-surface model, which generates an estimate of the land-surface impacts from the emissions scenarios. Here we test PRIME using known scenarios in the form of the Shared Socioeconomic Pathways (SSPs) to demonstrate that PRIME reproduces the climate response to a range of emissions scenarios, as shown in the IPCC reports. We show results for a range of scenarios including the SSP5-8.5 high emissions scenario, which was used to define the patterns; SSP1-2.6, a mitigation scenario with low emissions and SSP5-3.4-OS, an overshoot scenario. PRIME correctly represents the climate response for these known scenarios, which gives us confidence that PRIME will be useful for rapidly providing probabilistic spatially resolved information for novel climate scenarios; substantially reducing the time between the scenarios being released and being used in impacts assessments

HLA genotyping in the international Type 1 Diabetes Genetics Consortium

Background Although human leukocyte antigen (HLA) DQ and DR loci appear to confer the strongest genetic risk for type 1 diabetes, more detailed information is required for other loci within the HLA region to understand causality and stratify additional risk factors. The Type 1 Diabetes Genetics Consortium (T1DGC) study design included high-resolution genotyping of HLA-A, B, C, DRB1, DQ, and DP loci in all affected sibling pair and trio families, and cases and controls, recruited from four networks worldwide, for analysis with clinical phenotypes and immunological markers

The iron-responsive genome of the Chiton <i>Acanthopleura granulata</i>

Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization

Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

Background Heterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the “lower heterobranchs”. Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia. Results To assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of “lower heterobranchs”. Maximum likelihood analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades. Conclusions Analysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT + GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade