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Modern pollen-vegetation-climate relationships underpin palaeovegetation and palaeoclimate reconstructions from fossil pollen records. East Siberia is an ideal area for investigating the relationships between modern pollen assemblages and near natural vegetation under cold continental climate conditions. Reliable pollen-based quantitative vegetation and climate reconstructions are still scarce due to the limited number of modern pollen datasets. Furthermore, differences in pollen representation of samples from lake sediments and soils are not well understood. Here, we present a new pollen dataset of 48 moss/soil and 24 lake surface-sediment samples collected in Chukotka and central Yakutia in East Siberia. The pollen-vegetation-climate relationships were investigated by ordination analyses. Generally, tundra and taiga vegetation types can be well distinguished in the surface pollen assemblages. Moss/soil and lake samples contain generally similar pollen assemblages as revealed by a Procrustes comparison with some exceptions. Overall, modern pollen assemblages reflect the temperature and precipitation gradients in the study areas as revealed by constrained ordination analysis. We estimate the relative pollen productivity (RPP) of major taxa and the relevant source area of pollen (RSAP) for moss/soil samples from Chukotka and central Yakutia using Extended R-Value (ERV) analysis. The RSAP of the tundra-forest transition area in Chukotka and taiga area in central Yakutia are ca. 1300 and 360 m, respectively. For Chukotka, RPPs relative to both Poaceae and Ericaceae were estimated while RPPs for central Yakutia were relative only to Ericaceae. Relative to Ericaceae (reference taxon, RPP = 1), Larix, Betula, Picea, and Pinus are overrepresented while Alnus, Cyperaceae, Poaceae, and Salix are underrepresented in the pollen spectra. Our estimates are in general agreement with previously published values and provide the basis for reliable quantitative reconstructions of East Siberian vegetation.
Uncertainty in climate change impact studies for irrigated maize cropping systems in southern Spain
(2022)
This study investigates the main drivers of uncertainties in simulated irrigated maize yield under historical conditions as well as scenarios of increased temperatures and altered irrigation water availability.
Using APSIM, MONICA, and SIMPLACE crop models, we quantified the relative contributions of three irrigation water allocation strategies, three sowing dates, and three maize cultivars to the uncertainty in simulated yields.
The water allocation strategies were derived from historical records of farmer's allocation patterns in drip-irrigation scheme of the Genil-Cabra region, Spain (2014-2017).
By considering combinations of allocation strategies, the adjusted R-2 values (showing the degree of agreement between simulated and observed yields) increased by 29% compared to unrealistic assumptions of considering only near optimal or deficit irrigation scheduling. The factor decomposition analysis based on historic climate showed that irrigation strategies was the main driver of uncertainty in simulated yields (66%).
However, under temperature increase scenarios, the contribution of crop model and cultivar choice to uncertainty in simulated yields were as important as irrigation strategy. This was partially due to different model structure in processes related to the temperature responses.
Our study calls for including information on irrigation strategies conducted by farmers to reduce the uncertainty in simulated yields at field scale.
A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component
(2022)
Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants.
One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy.
Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination.
Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown.
Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection.
Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery.
Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions.
Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species.
Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites.
For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence.
In contrast, DNA sequence information has rarely been used.
Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions.
The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far.
However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data.
Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals.
Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species.
Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research.
As the recent permafrost thawing of northern Asia proceeds due to anthropogenic climate change, precise and detailed palaeoecological records from past warm periods are essential to anticipate the extent of future permafrost variations. Here, based on the modern relationship between permafrost and vegetation (represented by pollen assemblages), we trained a Random Forest model using pollen and permafrost data and verified its reliability to reconstruct the history of permafrost in northern Asia during the Holocene. An early Holocene (12-8 cal ka BP) strong thawing trend, a middle-to-late Holocene (8-2 cal ka BP) relatively slow thawing trend, and a late Holocene freezing trend of permafrost in northern Asia are consistent with climatic proxies such as summer solar radiation and Northern Hemisphere temperature. The extensive distribution of permafrost in northern Asia inhibited the spread of evergreen coniferous trees during the early Holocene warming and might have decelerated the enhancement of the East Asian summer monsoon (EASM) by altering hydrological processes and albedo. Based on these findings, we suggest that studies of the EASM should consider more the state of permafrost and vegetation in northern Asia, which are often overlooked and may have a profound impact on climate change in this region.
Arctic coasts, which feature land-ocean transport of freshwater, sediments, and other terrestrial material, are impacted by climate change, including increased temperatures, melting glaciers, changes in precipitation and runoff.
These trends are assumed to affect productivity in fjordic estuaries.
However, the spatial extent and temporal variation of the freshwater-driven darkening of fjords remain unresolved.
The present study illustrates the spatio-temporal variability of suspended particulate matter (SPM) in the Adventfjorden estuary, Svalbard, using in-situ field campaigns and ocean colour remote sensing (OCRS) via high-resolution Sentinel-2 imagery.
To compute SPM concentration (C-SPMsat), a semi-analytical algorithm was regionally calibrated using local in-situ data, which improved the accuracy of satellite-derived SPM concentration by similar to 20% (MRD). Analysis of SPM concentration for two consecutive years (2019, 2020) revealed strong seasonality of SPM in Adventfjorden.
Highest estimated SPM concentrations and river plume extent (% of fjord with C-SPMsat > 30 mg L-1) occurred during June, July, and August.
Concurrently, we observed a strong relationship between river plume extent and average air temperature over the 24 h prior to the observation (R-2 = 0.69).
Considering predicted changes to environmental conditions in the Arctic region, this study highlights the importance of the rapidly changing environmental parameters and the significance of remote sensing in analysing fluxes in light attenuating particles, especially in the coastal Arctic Ocean.
We investigate whether the distribution of maximum seasonal streamflow is significantly affected by catchment or climate state of the season/month ahead. We fit the Generalized Extreme Value (GEV) distribution to extreme seasonal streamflow for around 600 stations across Europe by conditioning the GEV location and scale parameters on 14 indices, which represent the season-ahead climate or catchment state. The comparison of these climate-informed models with the classical GEV distribution, with time-constant parameters, suggests that there is a substantial potential for seasonal forecasting of flood probabilities. The potential varies between seasons and regions. Overall, the season-ahead catchment wetness shows the highest potential, although climate indices based on large-scale atmospheric circulation, sea surface temperature or sea ice concentration also show some skill for certain regions and seasons. Spatially coherent patterns and a substantial fraction of climate-informed models are promising signs towards early alerts to increase flood preparedness already a season ahead.
transferGWAS
(2022)
Motivation:
Medical images can provide rich information about diseases and their biology. However, investigating their association with genetic variation requires non-standard methods. We propose transferGWAS, a novel approach to perform genome-wide association studies directly on full medical images. First, we learn semantically meaningful representations of the images based on a transfer learning task, during which a deep neural network is trained on independent but similar data. Then, we perform genetic association tests with these representations.
Results:
We validate the type I error rates and power of transferGWAS in simulation studies of synthetic images. Then we apply transferGWAS in a genome-wide association study of retinal fundus images from the UK Biobank. This first-of-a-kind GWAS of full imaging data yielded 60 genomic regions associated with retinal fundus images, of which 7 are novel candidate loci for eye-related traits and diseases.
Fast Holocene slip and localized strain along the Liquiñe-Ofqui strike-slip fault system, Chile
(2021)
In active tectonic settings dominated by strike-slip kinematics, slip partitioning across subparallel faults is a common feature; therefore, assessing the degree of partitioning and strain localization is paramount for seismic hazard assessments. Here, we estimate a slip rate of 18.8 +/- 2.0 mm/year over the past 9.0 +/- 0.1 ka for a single strand of the Liquirie-Ofqui Fault System, which straddles the Main Cordillera in Southern Chile. This Holocene rate accounts for similar to 82% of the trench-parallel component of oblique plate convergence and is similar to million-year estimates integrated over the entire fault system. Our results imply that strain localizes on a single fault at millennial time scale but over longer time scales strain localization is not sustained. The fast millennial slip rate in the absence of historical Mw> 6.5 earthquakes along the Liquine-Ofqui Fault System implies either a component of aseismic slip or Mw similar to 7 earthquakes involving multi-trace ruptures and > 150-year repeat times. Our results have implications for the understanding of strike-slip fault system dynamics within volcanic arcs and seismic hazard assessments.
Rupture directivity, implying a predominant earthquake rupture propagation direction, is typically inferred upon the identification of 2D azimuthal patterns of seismic observations for weak to large earthquakes using surface-monitoring networks. However, the recent increase of 3D monitoring networks deployed in the shallow subsurface and underground laboratories toward the monitoring of microseismicity allows to extend the directivity analysis to 3D modeling, beyond the usual range of magnitudes. The high-quality full waveforms recorded for the largest, decimeter-scale acoustic emission (AE) events during a meter-scale hydraulic fracturing experiment in granites at similar to 410 m depth allow us to resolve the apparent durations observed at each AE sensor to analyze 3D-directivity effects. Unilateral and (asymmetric) bilateral ruptures are then characterized by the introduction of a parameter kappa, representing the angle between the directivity vector and the station vector. While the cloud of AE activity indicates the planes of the hydrofractures, the resolved directivity vectors show off-plane orientations, indicating that rupture planes of microfractures on a scale of centimeters have different geometries. Our results reveal a general alignment of the rupture directivity with the orientation of the minimum horizontal stress, implying that not only the slip direction but also the fracture growth produced by the fluid injections is controlled by the local stress conditions.